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Benning S, Pritsch K, Radl V, Siani R, Wang Z, Schloter M. (Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation. Microbiol Spectr 2024; 12:e0378323. [PMID: 38376357 DOI: 10.1128/spectrum.03783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
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Affiliation(s)
- Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Zhongjie Wang
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University Munich, Munich, Germany
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Broadbent AAD, Newbold LK, Pritchard WJ, Michas A, Goodall T, Cordero I, Giunta A, Snell HSK, Pepper VVLH, Grant HK, Soto DX, Kaufmann R, Schloter M, Griffiths RI, Bahn M, Bardgett RD. Climate change disrupts the seasonal coupling of plant and soil microbial nutrient cycling in an alpine ecosystem. Glob Chang Biol 2024; 30:e17245. [PMID: 38511487 DOI: 10.1111/gcb.17245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
The seasonal coupling of plant and soil microbial nutrient demands is crucial for efficient ecosystem nutrient cycling and plant production, especially in strongly seasonal alpine ecosystems. Yet, how these seasonal nutrient cycling processes are modified by climate change and what the consequences are for nutrient loss and retention in alpine ecosystems remain unclear. Here, we explored how two pervasive climate change factors, reduced snow cover and shrub expansion, interactively modify the seasonal coupling of plant and soil microbial nitrogen (N) cycling in alpine grasslands, which are warming at double the rate of the global average. We found that the combination of reduced snow cover and shrub expansion disrupted the seasonal coupling of plant and soil N-cycling, with pronounced effects in spring (shortly after snow melt) and autumn (at the onset of plant senescence). In combination, both climate change factors decreased plant organic N-uptake by 70% and 82%, soil microbial biomass N by 19% and 38% and increased soil denitrifier abundances by 253% and 136% in spring and autumn, respectively. Shrub expansion also individually modified the seasonality of soil microbial community composition and stoichiometry towards more N-limited conditions and slower nutrient cycling in spring and autumn. In winter, snow removal markedly reduced the fungal:bacterial biomass ratio, soil N pools and shifted bacterial community composition. Taken together, our findings suggest that interactions between climate change factors can disrupt the temporal coupling of plant and soil microbial N-cycling processes in alpine grasslands. This could diminish the capacity of these globally widespread alpine ecosystems to retain N and support plant productivity under future climate change.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Biological & Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | | | - William J Pritchard
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Tim Goodall
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
- Swiss Federal Institute for Forest, Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Andrew Giunta
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | | | - Helen K Grant
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - David X Soto
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | | | - Michael Bahn
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
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Neyret M, Le Provost G, Boesing AL, Schneider FD, Baulechner D, Bergmann J, de Vries FT, Fiore-Donno AM, Geisen S, Goldmann K, Merges A, Saifutdinov RA, Simons NK, Tobias JA, Zaitsev AS, Gossner MM, Jung K, Kandeler E, Krauss J, Penone C, Schloter M, Schulz S, Staab M, Wolters V, Apostolakis A, Birkhofer K, Boch S, Boeddinghaus RS, Bolliger R, Bonkowski M, Buscot F, Dumack K, Fischer M, Gan HY, Heinze J, Hölzel N, John K, Klaus VH, Kleinebecker T, Marhan S, Müller J, Renner SC, Rillig MC, Schenk NV, Schöning I, Schrumpf M, Seibold S, Socher SA, Solly EF, Teuscher M, van Kleunen M, Wubet T, Manning P. A slow-fast trait continuum at the whole community level in relation to land-use intensification. Nat Commun 2024; 15:1251. [PMID: 38341437 PMCID: PMC10858939 DOI: 10.1038/s41467-024-45113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
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Affiliation(s)
- Margot Neyret
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Laboratoire d'Écologie Alpine, Université Grenoble Alpes - CNRS - Université Savoie Mont Blanc, Grenoble, France.
| | | | | | - Florian D Schneider
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- ISOE - Institute for social-ecological research, Frankfurt am Main, Germany
| | - Dennis Baulechner
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Joana Bergmann
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Stefan Geisen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, The Netherlands
| | - Kezia Goldmann
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
| | - Anna Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Ruslan A Saifutdinov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Nadja K Simons
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
- Applied Biodiversity Sciences, University of Würzburg, Würzburg, Germany
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Andrey S Zaitsev
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- Senckenberg Museum for Natural History Görlitz, Görlitz, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
| | - Kirsten Jung
- Institut of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Schloter
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
- Chair of Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum Muenchen, Research Unit for Comparative Microbiome Analysis, Oberschleissheim, Germany
| | - Michael Staab
- Ecological Networks, Technical University Darmstadt, Darmstadt, Germany
| | - Volkmar Wolters
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Antonios Apostolakis
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Steffen Boch
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Runa S Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
- Department Plant Production and Production Related Environmental Protection, Center for Agricultural Technology Augustenberg (LTZ), Karlsruhe, Germany
| | - Ralph Bolliger
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research (UFZ), Soil Ecology Department, Halle/Saale, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Huei Ying Gan
- Senckenberg Centre for Human Evolution and Palaeoenvironments Tübingen (SHEP), Tübingen, Germany
| | - Johannes Heinze
- Department of Biodiversity, Heinz Sielmann Foundation, Wustermark, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Katharina John
- Justus Liebig University, Department of Animal Ecology, Giessen, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Till Kleinebecker
- Institute for Landscape Ecology and Resources Management (ILR), Research Centre for BioSystems, Land Use and Nutrition (iFZ), Justus Liebig University Giessen, Giessen, Germany
- Centre for International Development and Environmental Research (ZEU), Justus Liebig University Giessen, Giessen, Germany
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Jörg Müller
- Department of Nature Conservation, Heinz Sielmann Foundation, Wustermark, Germany
| | - Swen C Renner
- Ornithology, Natural History Museum Vienna, Vienna, Autria, Germany
| | | | - Noëlle V Schenk
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department of Biogeochemical Processes, Max-Planck-Institute for Biogeochemistry, Jena, Germany
| | - Sebastian Seibold
- Technical University of Munich, TUM School of Life Sciences, Freising, Germany
- TUD Dresden University of Technology, Forest Zoology, Tharandt, Germany
| | - Stephanie A Socher
- Paris Lodron University Salzburg, Department Environment and Biodiversity, Salzburg, Austria
| | - Emily F Solly
- Helmholtz Centre for Environmental Research (UFZ), Computation Hydrosystems Department, Leipzig, Germany
| | - Miriam Teuscher
- University of Göttingen, Centre of Biodiversity and Sustainable Land Use, Göttingen, Germany
| | - Mark van Kleunen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena-, Leipzig, Germany
- Helmholtz Centre for Environmental Research (UFZ), Community Ecology Department, Halle/Saale, Germany
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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de Souza YPA, Schloter M, Weisser W, Huang Y, Schulz S. The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient. Environ Microbiome 2024; 19:11. [PMID: 38308354 PMCID: PMC10835927 DOI: 10.1186/s40793-024-00552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes are unknown. To investigate the effects of increasing plant species richness on the diversity and composition of the seed microbiome, we made use of a well-established long-term biodiversity experiment in Germany (The Jena Experiment). We sampled seeds from different Plantago lanceolata blossoms in a plant diversity gradient ranging from monoculture to 16 species mixtures. The seeds were surface sterilized to remove seed surface-associated bacteria and subjected to a metabarcoding approach to assess bacterial community structure. RESULTS Our data indicate a very stable core microbiome, which accounted for more than 90% of the reads and was present in all seeds independent of the plant richness level the seeds originated from. It consisted mainly of reads linked to Pseudomonas rhizosphaerae, Sphingomonas faeni and Pirellulla spp. 9% of the obtained reads were not part of the core microbiome and were only present in plots of specific diversity levels. The number of unique ASVs was positively correlated with plant richness. Interestingly, most reads described as non-core members belonged to the same genera described as the core microbiome, indicating the presence of different strains or species with possibly different functional properties important for seed performance. CONCLUSION Our data indicate that Plantago lanceolata maintains a large seeds core microbiome across the plant richness gradient. However, the number of unique ASVs increases alongside the plant community richness, indicating that ecosystem biodiversity also mitigates diversity loss in seed endophytes.
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Affiliation(s)
- Yuri Pinheiro Alves de Souza
- TUM School of Life Science, Chair of Environmental Microbiology, Technische Universität München, Neuherberg, Germany
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- TUM School of Life Science, Chair of Environmental Microbiology, Technische Universität München, Neuherberg, Germany.
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Wolfgang Weisser
- TUM School of Life Science, Chair of Terrestrial Ecology, Technische Universität München, Freising, Germany
| | - Yuanyuan Huang
- German Centre of Integrative Bioaffiliationersity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Experimental Interaction Ecology, Leipzig University, Leipzig, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
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Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M. Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms 2024; 12:255. [PMID: 38399658 PMCID: PMC10892684 DOI: 10.3390/microorganisms12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
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Affiliation(s)
- Oluwaseun A. Ishola
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Abilash Chakravarthy Durai Raj
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Caspar Ohnmacht
- Mucosal Immunology Group, Center of Allery and Environment (ZAUM), Technical University of Munich, Helmholtz Zentrum München, 85764 München, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Bärbel U. Foesel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
- Central Institute for Nutrition and Health, Technical University of Munich, 85354 Freising, Germany
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Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
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Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Narges Moradtalab
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis
(COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Saskia Windisch
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Lorrie Maccario
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Michael Rothballer
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Uwe Ludewig
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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Heinen R, Sanchez-Mahecha O, Martijn Bezemer T, Dominoni DM, Knappe C, Kollmann J, Kopatsch A, Pfeiffer ZA, Schloter M, Sturm S, Schnitzler JP, Corina Vlot A, Weisser WW. Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220357. [PMID: 37899021 PMCID: PMC10613545 DOI: 10.1098/rstb.2022.0357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/23/2023] [Indexed: 10/31/2023] Open
Abstract
Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant-insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to 'full' or 'part' nights of 15-20 lux ALAN, or no ALAN 'control' nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores. This article is part of the theme issue 'Light pollution in complex ecological systems'.
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Affiliation(s)
- Robin Heinen
- Terrestrial Ecology Research Group, Department for Life Science Systems, Technical University of Munich School of Life Sciences, 85354 Freising, Germany
| | - Oriana Sanchez-Mahecha
- Terrestrial Ecology Research Group, Department for Life Science Systems, Technical University of Munich School of Life Sciences, 85354 Freising, Germany
| | - T. Martijn Bezemer
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, 2333 BE Leiden, The Netherlands
| | - Davide M. Dominoni
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Claudia Knappe
- Institute of Biochemical Plant Pathology, Institute of Biochemical Plant Pathology, D-85764, Neuherberg, Germany
| | - Johannes Kollmann
- Chair of Restoration Ecology, Department for Life Science Systems, Technical University of Munich, 8534 Freising, Germany
| | - Anton Kopatsch
- Research Unit Environmental Simulation, Helmhotz, Munich, D-85764, Neuherberg, Germany
| | - Zoë A. Pfeiffer
- Terrestrial Ecology Research Group, Department for Life Science Systems, Technical University of Munich School of Life Sciences, 85354 Freising, Germany
| | - Michael Schloter
- Chair of Soil Science, Department for Life Science Systems, Technical University of Munich, 85354 Freising, Germany
- Research Unit Comparative Microbiome Analysis, Helmhotz, Munich, D-85764, Neuherberg, Germany
| | - Sarah Sturm
- Terrestrial Ecology Research Group, Department for Life Science Systems, Technical University of Munich School of Life Sciences, 85354 Freising, Germany
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation, Helmhotz, Munich, D-85764, Neuherberg, Germany
| | - A. Corina Vlot
- Institute of Biochemical Plant Pathology, Institute of Biochemical Plant Pathology, D-85764, Neuherberg, Germany
- Chair of Crop Plant Genetics, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, D-95447, Kulmbach, Germany
| | - Wolfgang W. Weisser
- Terrestrial Ecology Research Group, Department for Life Science Systems, Technical University of Munich School of Life Sciences, 85354 Freising, Germany
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8
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Bender SF, Schulz S, Martínez-Cuesta R, Laughlin RJ, Kublik S, Pfeiffer-Zakharova K, Vestergaard G, Hartman K, Parladé E, Römbke J, Watson CJ, Schloter M, van der Heijden MGA. Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses. New Phytol 2023; 240:2020-2034. [PMID: 37700504 DOI: 10.1111/nph.19252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.
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Affiliation(s)
- S Franz Bender
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Rubén Martínez-Cuesta
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ronald J Laughlin
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Kristina Pfeiffer-Zakharova
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kyle Hartman
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jörg Römbke
- ECT Ökotoxikologie GmbH, Böttgerstr. 2-14, D-65439, Flörsheim, Germany
| | - Catherine J Watson
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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9
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Shintani M, Vestergaard G, Milaković M, Kublik S, Smalla K, Schloter M, Udiković-Kolić N. Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. Environ Microbiol 2023; 25:3035-3051. [PMID: 37655671 DOI: 10.1111/1462-2920.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | | | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Croatia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
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10
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Martins BR, Siani R, Treder K, Michałowska D, Radl V, Pritsch K, Schloter M. Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars. BMC Microbiol 2023; 23:377. [PMID: 38036970 PMCID: PMC10691024 DOI: 10.1186/s12866-023-03120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). RESULTS Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil. CONCLUSIONS Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.
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Affiliation(s)
- Benoit Renaud Martins
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
| | - Krzysztof Treder
- Plant Breeding and Acclimatization Institute - National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, 76-009, Bonin, Bonin Str 3, Poland
| | - Dorota Michałowska
- Plant Breeding and Acclimatization Institute - National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, 76-009, Bonin, Bonin Str 3, Poland
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair for Environmental Microbiology, Technical University of Munich, Freising, Germany
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11
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Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
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Affiliation(s)
- René Kallies
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Die Hu
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Nafi’u Abdulkadir
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Michael Schloter
- Department of Environmental Health, Helmholtz Munich, Ingolstaedter Landstr. 1, D-85758 Neuherberg, Germany;
| | - Ulisses Rocha
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
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12
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Pinheiro Alves de Souza Y, Schloter M, Weisser W, Schulz S. Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum. Microb Ecol 2023; 86:2882-2893. [PMID: 37624441 PMCID: PMC10640511 DOI: 10.1007/s00248-023-02285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
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Affiliation(s)
- Yuri Pinheiro Alves de Souza
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Wolfgang Weisser
- Technische Universität München, TUM School of Life Science, Chair of Terrestrial Ecology, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany.
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13
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Staude B, Gschwendtner S, Frodermann T, Oehmke F, Kohl T, Kublik S, Schloter M, Ehrhardt H. Microbial signatures in amniotic fluid at preterm birth and association with bronchopulmonary dysplasia. Respir Res 2023; 24:248. [PMID: 37845700 PMCID: PMC10577941 DOI: 10.1186/s12931-023-02560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. METHODS AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. RESULTS The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. CONCLUSIONS Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD.
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Affiliation(s)
- Birte Staude
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tina Frodermann
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Frank Oehmke
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
| | - Thomas Kohl
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
- German Center for Fetal Surgery and Minimally Invasive Therapy (DZFT), University of Mannheim (UMM), Mannheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Ehrhardt
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
- Division of Neonatology and Pediatric Intensive Care Medicine, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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14
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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15
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Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Correction: Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. Microbiome 2023; 11:206. [PMID: 37705089 PMCID: PMC10500857 DOI: 10.1186/s40168-023-01665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Danielle Rogner
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, Technical University of Munich, 85354, Freising, Germany
| | - Susanne A Steimle-Grauer
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Jenny Thomas
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie Eyerich
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Dermato‑Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Kilian Eyerich
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
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Marques Dos Santos M, Pivniouk V, Rankl B, Walker A, Pagani G, Hertkorn N, Schmitt-Kopplin P, Müller C, Bracher F, Merl-Pham J, Hauck SM, Schloter M, Michael AN, Anderson D, Honeker L, Gozdz J, Pivniouk O, Ober C, Holbreich M, Martinez FD, Snyder SA, von Mutius E, Vercelli D. Asthma-protective agents in dust from traditional farm environments. J Allergy Clin Immunol 2023; 152:610-621. [PMID: 37271318 PMCID: PMC10680491 DOI: 10.1016/j.jaci.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice. OBJECTIVES This study sought to begin identifying farm-derived asthma-protective agents. METHODS Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry. RESULTS Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi. CONCLUSIONS Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.
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Affiliation(s)
| | - Vadim Pivniouk
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Ariz; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Bettina Rankl
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany
| | - Alesia Walker
- Research Unit Analytical Biogeochemistry, BGC, Helmholtz Center Munich, Munich, Germany
| | - Giulia Pagani
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany
| | - Norbert Hertkorn
- Research Unit Analytical Biogeochemistry, BGC, Helmholtz Center Munich, Munich, Germany
| | | | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, Munich, Germany
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Center Munich, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Center Munich, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Munich, Germany; ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Ashley N Michael
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Dayna Anderson
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Linnea Honeker
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz; Biosphere2, The University of Arizona, Tucson, Ariz
| | - Justyna Gozdz
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Oksana Pivniouk
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | | | - Fernando D Martinez
- Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz
| | - Shane A Snyder
- Department of Chemical & Environmental Engineering, The University of Arizona, Tucson, Ariz; The BIO5 Institute, The University of Arizona, Tucson, Ariz.
| | - Erika von Mutius
- Institute for Asthma and Allergy Prevention, IAP, Helmholtz Center Munich, Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Comprehensive Pneumology Center-Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany.
| | - Donata Vercelli
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Ariz; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, Ariz; The BIO5 Institute, The University of Arizona, Tucson, Ariz; Arizona Center for the Biology of Complex Diseases, The University of Arizona, Tucson, Ariz.
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17
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Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. Microbiome 2023; 11:162. [PMID: 37496039 PMCID: PMC10369845 DOI: 10.1186/s40168-023-01587-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/01/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Darier's disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD indicate a role for microbial dysbiosis. Here, for the first time, we investigated the DD skin microbiome using a metabarcoding approach of 115 skin swabs from 14 patients and 14 healthy volunteers. Furthermore, we analyzed its changes in the context of DD malodour and the cutaneous DD transcriptome. RESULTS We identified a disease-specific cutaneous microbiome with a loss of microbial diversity and of potentially beneficial commensals. Expansion of inflammation-associated microbes such as Staphylococcus aureus and Staphylococcus warneri strongly correlated with disease severity. DD dysbiosis was further characterized by abundant species belonging to Corynebacteria, Staphylococci and Streptococci groups displaying strong associations with malodour intensity. Transcriptome analyses showed marked upregulation of epidermal repair, inflammatory and immune defence pathways reflecting epithelial and immune response mechanisms to DD dysbiotic microbiome. In contrast, barrier genes including claudin-4 and cadherin-4 were downregulated. CONCLUSIONS These findings allow a better understanding of Darier exacerbations, highlighting the role of cutaneous dysbiosis in DD inflammation and associated malodour. Our data also suggest potential biomarkers and targets of intervention for DD. Video Abstract.
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Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Danielle Rogner
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, Technical University of Munich, 85354, Freising, Germany
| | - Susanne A Steimle-Grauer
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Jenny Thomas
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie Eyerich
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Kilian Eyerich
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
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Ohan JA, Siani R, Kurth JK, Sommer V, Glaser K, Karsten U, Schloter M, Schulz S. Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps. FEMS Microbiol Ecol 2023:fiad081. [PMID: 37463797 DOI: 10.1093/femsec/fiad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota.
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Affiliation(s)
- Juliette A Ohan
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Julia K Kurth
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Veronika Sommer
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
- upi Umweltprojektingenieurgesellschaft, Stendal, Germany
| | - Karin Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
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19
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Kurth JK, Albrecht M, Glaser K, Karsten U, Vestergaard G, Armbruster M, Kublik S, Schmid CAO, Schloter M, Schulz S. Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention. Front Microbiol 2023; 14:1169958. [PMID: 37520365 PMCID: PMC10382179 DOI: 10.3389/fmicb.2023.1169958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes. Methods We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality. Results and Discussion Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.
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Affiliation(s)
- Julia Katharina Kurth
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Martin Albrecht
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Karin Glaser
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Gisle Vestergaard
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Armbruster
- Agricultural Analytical and Research Institute Speyer (LUFA Speyer), Speyer, Germany
| | - Susanne Kublik
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Christoph A. O. Schmid
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Michael Schloter
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Stefanie Schulz
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
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20
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Angstmann H, Pfeiffer S, Kublik S, Ehrhardt B, Uliczka K, Rabe KF, Roeder T, Wagner C, Schloter M, Krauss-Etschmann S. The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats. Environ Microbiome 2023; 18:55. [PMID: 37370177 DOI: 10.1186/s40793-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. RESULTS The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish-/- compared to w1118 and wild-caught fly airways. CONCLUSIONS Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.
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Affiliation(s)
- Hanna Angstmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Stefan Pfeiffer
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Birte Ehrhardt
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Karin Uliczka
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Klaus F Rabe
- Department of Pneumology, Lungen Clinic, Grosshansdorf, Germany
- Department of Medicine, Christian Albrechts University, Germany Member of the German Center for Lung Research, Kiel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, Christian-Albrechts University, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | - Christina Wagner
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Michael Schloter
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Krauss-Etschmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany.
- Department of Medicine, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany.
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21
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Mahmoud FM, Kusari S, Kublik S, Benning S, Siani R, Zühlke S, Radl V, Mahnkopp-Dirks F, Schloter M. Draft Genome Sequence of the Bacterial Endophyte Priestia megaterium B1, Isolated from Roots of Apple ( Malus domestica). Microbiol Resour Announc 2023:e0117222. [PMID: 37199619 DOI: 10.1128/mra.01172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Over the past years, a number of important traits supporting plant growth have been shown for different strains of Priestia megaterium (formerly known as Bacillus megaterium). Here, we report the draft genome sequence of the endophytic bacterial strain Priestia megaterium B1, which was isolated from surface-sterilized roots of apple plants.
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Affiliation(s)
- Fatma M Mahmoud
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Souvik Kusari
- Faculty of Chemistry and Chemical Biology, Center for Mass Spectrometry (CMS), TU Dortmund University, Dortmund, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sebastian Zühlke
- Faculty of Chemistry and Chemical Biology, Center for Mass Spectrometry (CMS), TU Dortmund University, Dortmund, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Felix Mahnkopp-Dirks
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz University Hannover, Hanover, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Soil Science, Technical University of Munich, Freising, Germany
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22
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Escher BI, Altenburger R, Blüher M, Colbourne JK, Ebinghaus R, Fantke P, Hein M, Köck W, Kümmerer K, Leipold S, Li X, Scheringer M, Scholz S, Schloter M, Schweizer PJ, Tal T, Tetko I, Traidl-Hoffmann C, Wick LY, Fenner K. Modernizing persistence-bioaccumulation-toxicity (PBT) assessment with high throughput animal-free methods. Arch Toxicol 2023; 97:1267-1283. [PMID: 36952002 PMCID: PMC10110678 DOI: 10.1007/s00204-023-03485-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
The assessment of persistence (P), bioaccumulation (B), and toxicity (T) of a chemical is a crucial first step at ensuring chemical safety and is a cornerstone of the European Union's chemicals regulation REACH (Registration, Evaluation, Authorization, and Restriction of Chemicals). Existing methods for PBT assessment are overly complex and cumbersome, have produced incorrect conclusions, and rely heavily on animal-intensive testing. We explore how new-approach methodologies (NAMs) can overcome the limitations of current PBT assessment. We propose two innovative hazard indicators, termed cumulative toxicity equivalents (CTE) and persistent toxicity equivalents (PTE). Together they are intended to replace existing PBT indicators and can also accommodate the emerging concept of PMT (where M stands for mobility). The proposed "toxicity equivalents" can be measured with high throughput in vitro bioassays. CTE refers to the toxic effects measured directly in any given sample, including single chemicals, substitution products, or mixtures. PTE is the equivalent measure of cumulative toxicity equivalents measured after simulated environmental degradation of the sample. With an appropriate panel of animal-free or alternative in vitro bioassays, CTE and PTE comprise key environmental and human health hazard indicators. CTE and PTE do not require analytical identification of transformation products and mixture components but instead prompt two key questions: is the chemical or mixture toxic, and is this toxicity persistent or can it be attenuated by environmental degradation? Taken together, the proposed hazard indicators CTE and PTE have the potential to integrate P, B/M and T assessment into one high-throughput experimental workflow that sidesteps the need for analytical measurements and will support the Chemicals Strategy for Sustainability of the European Union.
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Affiliation(s)
- Beate I Escher
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany.
- Environmental Toxicology, Department of Geosciences, Eberhard Karls University Tübingen, Schnarrenbergstr. 94-96, E72076, Tübingen, Germany.
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Munich-German Research Centre for Environmental Health (GmbH) at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ralf Ebinghaus
- Institute of Coastal Environmental Chemistry, Helmholtz Zentrum Hereon, Max-Planck-Straße 1, 21502, Geesthacht, Germany
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Produktionstorvet 424, 2800, Kgs. Lyngby, Denmark
| | - Michaela Hein
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Wolfgang Köck
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Klaus Kümmerer
- Institute of Sustainable and Environmental Chemistry, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany
- International Sustainable Chemistry Collaboration Centre (ISC3), Friedrich-Ebert-Allee 32 + 36, D-53113, Bonn, Germany
| | - Sina Leipold
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
- Department for Political Science, Friedrich-Schiller-University Jena, Bachstr. 18k, 07743, Jena, Germany
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Martin Scheringer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092, Zurich, Switzerland
| | - Stefan Scholz
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Michael Schloter
- Comparative Microbiome Analysis, Environmental Health Centre, Helmholtz Munich - German Research Centre for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Pia-Johanna Schweizer
- Research Institute for Sustainability-Helmholtz Centre Potsdam, Berliner Strasse 130, 14467, Potsdam, Germany
| | - Tamara Tal
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Igor Tetko
- Institute of Structural Biology, Molecular Targets and Therapeutics Centre, Helmholtz Munich - German Research Centre for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Claudia Traidl-Hoffmann
- Environmental Medicine Faculty of Medicine, University of Augsburg, Stenglinstrasse 2, 86156, Augsburg, Germany
- Institute of Environmental Medicine, Environmental Health Centre, Helmholtz Munich - German Research Centre for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, E04318, Leipzig, Germany
| | - Kathrin Fenner
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Department of Chemistry, University of Zürich, 8057, Zurich, Switzerland
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23
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Ferrocino I, Rantsiou K, McClure R, Kostic T, de Souza RSC, Lange L, FitzGerald J, Kriaa A, Cotter P, Maguin E, Schelkle B, Schloter M, Berg G, Sessitsch A, Cocolin L. The need for an integrated multi-OMICs approach in microbiome science in the food system. Compr Rev Food Sci Food Saf 2023; 22:1082-1103. [PMID: 36636774 DOI: 10.1111/1541-4337.13103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023]
Abstract
Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.
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Affiliation(s)
- Ilario Ferrocino
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lene Lange
- BioEconomy, Research & Advisory, Valby, Denmark
| | - Jamie FitzGerald
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Aicha Kriaa
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Paul Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Emmanuelle Maguin
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Tulln, Austria
| | - Luca Cocolin
- Department of Agriculture, Forest and Food Science, University of Turin, Grugliasco, Italy
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24
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Bertić M, Orgel F, Gschwendtner S, Schloter M, Moritz F, Schmitt‐Kopplin P, Zimmer I, Fladung M, Schnitzler J, Schroeder H, Ghirardo A. European oak metabolites shape digestion and fitness of the herbivore
Tortrix viridana. Funct Ecol 2023. [DOI: 10.1111/1365-2435.14299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- Marko Bertić
- Research Unit Environmental Simulation (EUS) Institute of Biochemical Plant Pathology Helmholtz Zentrum München, Ingolstädter Landstr. 1 Neuherberg Germany
| | - Franziska Orgel
- Thünen‐Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85764 Neuherberg Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg Germany
| | | | - Ina Zimmer
- Research Unit Environmental Simulation (EUS) Institute of Biochemical Plant Pathology Helmholtz Zentrum München, Ingolstädter Landstr. 1 Neuherberg Germany
| | - Matthias Fladung
- Thünen‐Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf Germany
| | - Jörg‐Peter Schnitzler
- Research Unit Environmental Simulation (EUS) Institute of Biochemical Plant Pathology Helmholtz Zentrum München, Ingolstädter Landstr. 1 Neuherberg Germany
| | - Hilke Schroeder
- Thünen‐Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation (EUS) Institute of Biochemical Plant Pathology Helmholtz Zentrum München, Ingolstädter Landstr. 1 Neuherberg Germany
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25
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Weisser WW, Hensel M, Barath S, Culshaw V, Grobman YJ, Hauck TE, Joschinski J, Ludwig F, Mimet A, Perini K, Roccotiello E, Schloter M, Shwartz A, Hensel DS, Vogler V. Creating ecologically sound buildings by integrating ecology, architecture and computational design. People and Nature 2022. [DOI: 10.1002/pan3.10411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wolfgang W. Weisser
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Michael Hensel
- Department for Digital Architecture and Planning Technical University Vienna Vienna Austria
| | - Shany Barath
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Victoria Culshaw
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Yasha J. Grobman
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Thomas E. Hauck
- Department for Landscape Architecture and Landscape Planning Technical University Vienna Vienna Austria
| | | | - Ferdinand Ludwig
- Green Technologies in Landscape Architecture, School of Engineering and Design Technical University of Munich Munich Germany
| | - Anne Mimet
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Katia Perini
- Architecture and design Department University of Genoa Genoa Italy
| | - Enrica Roccotiello
- Department of Earth, Environment and Life Sciences (DISTAV) University of Genoa Genoa Italy
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich Oberschleissheim Germany
| | - Assaf Shwartz
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Defne Sunguroğlu Hensel
- Green Technologies in Landscape Architecture, School of Engineering and Design Technical University of Munich Munich Germany
| | - Verena Vogler
- Research and Development Department, McNeel Europe S.L. Barcelona Spain
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26
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Zadel U, Cruzeiro C, Raj Durai AC, Nesme J, May R, Balázs H, Michalke B, Płaza G, Schröder P, Schloter M, Radl V. Exudates from Miscanthus x giganteus change the response of a root-associated Pseudomonas putida strain towards heavy metals. Environ Pollut 2022; 313:119989. [PMID: 36028079 DOI: 10.1016/j.envpol.2022.119989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
The composition of root exudates is modulated by several environmental factors, and it remains unclear how that affects beneficial rhizosphere or inoculated microorganisms under heavy metal (HM) contamination. Therefore, we evaluated the transcriptional response of Pseudomonas putida E36 (a Miscanthus x giganteus isolate with plant growth promotion-related properties) to Cd, Pb and Zn in an in vitro study implementing root exudates from M. x giganteus. To collect root exudates and analyse their composition plants were grown in a pot experiment under HM and control conditions. Our results indicated higher exudation rate for plants challenged with HM. Further, out of 29 organic acids identified and quantified in the root exudates, 8 of them were significantly influenced by HM (e.g., salicylic and terephthalic acid). The transcriptional response of P. putida E36 was significantly affected by the HM addition to the growth medium, increasing the expression of several efflux pumps and stress response-related functional units. The additional supplementation of the growth medium with root exudates from HM-challenged plants resulted in a downregulation of 29% of the functional units upregulated in P. putida E36 as a result of HM addition to the growth medium. Surprisingly, root exudates + HM downregulated the expression of P. putida E36 functional units related to plant colonization (e.g., chemotaxis, motility, biofilm formation) but upregulated its antibiotic and biocide resistance compared to the control treatment without HM. Our findings suggest that HM-induced changes in root exudation pattern may attract beneficial bacteria that are in turn awarded with organic nutrients, helping them cope with HM stress. However, it might affect the ability of these bacteria to colonize plants growing in HM polluted areas. Those findings may offer an insight for future in vivo studies contributing to improvements in phytoremediation measures.
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Affiliation(s)
- Urška Zadel
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Catarina Cruzeiro
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Abilash Chakravarthy Raj Durai
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section for Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Robert May
- Labor Dr. Spranger & Partner, Lindberghstraße 9-13, 85051, Ingolstadt, Germany.
| | - Helga Balázs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical BioGeoChemistry, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Grażyna Płaza
- Silesian University of Technology, Faculty of Organization and Management, 26 Roosevelt street, 41-800 Zabrze, Poland.
| | - Peter Schröder
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
| | - Viviane Radl
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Ingolstädter Street 1, 85764, Neuherberg, Germany.
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27
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Timsy T, Behrendt U, Ulrich A, Foesel BU, Spanner T, Neumann-Schaal M, Wolf J, Schloter M, Horn MA, Kolb S. Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Affiliation(s)
- Timsy Timsy
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Bärbel U Foesel
- Research Unit Molecular Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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28
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Lange L, Berg G, Cernava T, Champomier-Vergès MC, Charles T, Cocolin L, Cotter P, D’Hondt K, Kostic T, Maguin E, Makhalanyane T, Meisner A, Ryan M, Kiran GS, de Souza RS, Sanz Y, Schloter M, Smidt H, Wakelin S, Sessitsch A. Microbiome ethics, guiding principles for microbiome research, use and knowledge management. Environ Microbiome 2022; 17:50. [PMID: 36180931 PMCID: PMC9526347 DOI: 10.1186/s40793-022-00444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don't Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops.
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Affiliation(s)
- Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | | | | | | | | | - Paul Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | - Kathleen D’Hondt
- Department of Economy, Science and Innovation, Flemish Government, Brussels, Belgium
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Emmanuelle Maguin
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Annelein Meisner
- Wageningen Research, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology- Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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29
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Pfeiffer S, Jatzlauk G, Lund JV, Boateng E, Kovacevic D, N. Hylkema M, Bartel S, Schloter M, Krauss‐Etschmann S. Oral application of vancomycin alters murine lung microbiome and pulmonary immune responses. Immun Inflamm Dis 2022; 10:e675. [PMID: 35894712 PMCID: PMC9281482 DOI: 10.1002/iid3.675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
Early life exposures to antibiotics negatively impact respiratory health and are associated with an increased risk of childhood asthma. It is explained that the lung is inclined to develop chronic inflammatory phenotypes due to early antibiotic alteration in the gut microbiome. We investigated whether a gut‐targeted antibiotic has an impact on the lung microbiome and on pulmonary immunity. Fourteen‐day old C57BL/6 mice were administered with vancomycin via oral gavage for 3 days (1 time/day). Control groups were treated with clarithromycin and phosphate‐buffered saline (PBS), respectively. Five days after treatment, the cecum and lung microbiome, and pulmonary immune response were analyzed. Vancomycin treatment decreased the relative abundance of the genera Clostridium XIVa and Alistipes and the family Lachnospiraceae in the cecum. Furthermore, the relative abundance of the family Parabacteroidetes and the genus Lactobacillus were increased, whereas the abundance of the phylum Firmicutes was decreased. In the lung, vancomycin treatment reduced bacteria belonging to Clostridium XIVa and the family Lachnospiraceae as compared to those in the clarithromycin treated group. Lung cells from the vancomycin‐treated mice released higher levels of interleukin (IL)‐4 and IL‐13 compared to those from the PBS group, and increased levels of IL‐6, IFN‐γ, and TNFα compared to lung cells from the clarithromycin and PBS treated mice. Our pilot study suggests that alteration in the gut microbiome could affect bacterial composition and immunity of the lung hence proposes a gut–lung microbiome axis in early life.
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Affiliation(s)
- Stefan Pfeiffer
- ZIEL—Institute for Food and Health Technical University of Munich Freising Germany
- Department for Environmental Health Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München Neuherberg Germany
| | - Gregor Jatzlauk
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
| | - Joni V. Lund
- DZL Laboratory for Experimental Microbiome Research, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
| | - Eistine Boateng
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
| | - Draginja Kovacevic
- DZL Laboratory for Experimental Microbiome Research, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
| | - Machteld N. Hylkema
- Department of Pathology and Medical Biology University of Groningen, University Medical Center Groningen Groningen The Netherlands
- GRIAC Research Institute University of Groningen, University Medical Center Groningen Groningen The Netherlands
| | - Sabine Bartel
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
- Department of Pathology and Medical Biology University of Groningen, University Medical Center Groningen Groningen The Netherlands
- GRIAC Research Institute University of Groningen, University Medical Center Groningen Groningen The Netherlands
| | - Michael Schloter
- ZIEL—Institute for Food and Health Technical University of Munich Freising Germany
- Department for Environmental Health Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München Neuherberg Germany
| | - Susanne Krauss‐Etschmann
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
- Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel Germany
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Kämpfer P, Glaeser SP, Blom J, Wolf J, Benning S, Schloter M, Neumann-Schaal M. Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks. Arch Microbiol 2022; 204:505. [PMID: 35857201 PMCID: PMC9300504 DOI: 10.1007/s00203-022-03079-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/01/2022]
Abstract
The Gram-positive strain R79T, isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79T and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79T was 67.24% mol. Predominant fatty acids were C16:0, C15:0 and C17:1ω8c. The strain contained MK8-H2 as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79T (= DSM 113102T = LMG 32444T = CCM 9183T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany.
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Giessen, 35392, Giessen, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124, Brunswick, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum Muenchen - National Research Center for Environmental Health, Oberschleissheim, 85758, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum Muenchen - National Research Center for Environmental Health, Oberschleissheim, 85758, Munich, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124, Brunswick, Germany
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Olmo R, Wetzels SU, Armanhi JSL, Arruda P, Berg G, Cernava T, Cotter PD, Araujo SC, de Souza RSC, Ferrocino I, Frisvad JC, Georgalaki M, Hansen HH, Kazou M, Kiran GS, Kostic T, Krauss-Etschmann S, Kriaa A, Lange L, Maguin E, Mitter B, Nielsen MO, Olivares M, Quijada NM, Romaní-Pérez M, Sanz Y, Schloter M, Schmitt-Kopplin P, Seaton SC, Selvin J, Sessitsch A, Wang M, Zwirzitz B, Selberherr E, Wagner M. Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies. Front Microbiol 2022; 13:834622. [PMID: 35903477 PMCID: PMC9315449 DOI: 10.3389/fmicb.2022.834622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.
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Affiliation(s)
- Rocío Olmo
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- *Correspondence: Rocío Olmo,
| | - Stefanie Urimare Wetzels
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Jaderson Silveira Leite Armanhi
- Symbiomics Microbiome Solutions, Florianópolis, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Paul D. Cotter
- Food Bioscience, Teagasc Food Research Centre Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | - Solon Cordeiro Araujo
- SCA, Consultoria em Microbiologia Agrícola, Campinas, Brazil
- Brazil National Association of Inoculant Producers and Importers (ANPII), Campinas, Brazil
| | - Rafael Soares Correa de Souza
- Symbiomics Microbiome Solutions, Florianópolis, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science, University of Torino, Torino, Italy
| | - Jens C. Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marina Georgalaki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Hanne Helene Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | | | - Tanja Kostic
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Susanne Krauss-Etschmann
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
- Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Aicha Kriaa
- Microbiota Interaction With Human and Animal Team (MIHA), Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Lene Lange
- BioEconomy, Research & Advisory, Copenhagen, Denmark
| | - Emmanuelle Maguin
- Microbiota Interaction With Human and Animal Team (MIHA), Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Birgit Mitter
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Mette Olaf Nielsen
- Department of Animal Science, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
| | - Marta Olivares
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Narciso Martín Quijada
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Marina Romaní-Pérez
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Center Munich, Neuherberg, Germany
| | | | | | - Joseph Selvin
- School of Life Sciences, Pondicherry University, Puducherry, India
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Benjamin Zwirzitz
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Muster C, Leiva D, Morales C, Grafe M, Schloter M, Carú M, Orlando J. Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria. Front Microbiol 2022; 13:843490. [PMID: 35836424 PMCID: PMC9275751 DOI: 10.3389/fmicb.2022.843490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.
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Affiliation(s)
- Cecilia Muster
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Leiva
- Institute of Biology, University of Graz, Graz, Austria
| | - Camila Morales
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Martin Grafe
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Margarita Carú
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- *Correspondence: Julieta Orlando,
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Kuhl-Nagel T, Rodriguez PA, Gantner I, Chowdhury SP, Schwehn P, Rosenkranz M, Weber B, Schnitzler JP, Kublik S, Schloter M, Rothballer M, Falter-Braun P. Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana. Front Microbiol 2022; 13:923515. [PMID: 35875540 PMCID: PMC9297469 DOI: 10.3389/fmicb.2022.923515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.
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Affiliation(s)
- Theresa Kuhl-Nagel
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patricia Antonia Rodriguez
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Isabella Gantner
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patrick Schwehn
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Maaria Rosenkranz
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Baris Weber
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
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Cernava T, Rybakova D, Buscot F, Clavel T, McHardy AC, Meyer F, Meyer F, Overmann J, Stecher B, Sessitsch A, Schloter M, Berg G. Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis. Environ Microbiome 2022; 17:33. [PMID: 35751093 PMCID: PMC9233336 DOI: 10.1186/s40793-022-00425-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. RESULTS In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community. CONCLUSIONS The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - François Buscot
- 2Soil Ecology Department, Helmholtz Centre for Environmental Research (UFZ), Halle (Saale), Germany
- 3German Centre for Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig site, Hannover, Germany
- Cluster of Excellence RESIST (EXC2155), Hannover Medical School, Hannover, Germany
| | - Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Technical University of Braunschweig, Braunschweig, Germany
| | - Bärbel Stecher
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz-Institute for Agricultural Engineering Potsdam (ATB), Potsdam, Germany
- University of Potsdam, Potsdam, Germany
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Wang Z, Jimenez-Fernandez O, Osenbrück K, Schwientek M, Schloter M, Fleckenstein JH, Lueders T. Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange. Water Res 2022; 217:118334. [PMID: 35397370 DOI: 10.1016/j.watres.2022.118334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.
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Affiliation(s)
- Zhe Wang
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany; Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany; School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Oscar Jimenez-Fernandez
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany; Department of Hydrogeology, Helmholtz-Zentrum für Umweltforschung GmbH - UFZ, Leipzig, Germany
| | - Karsten Osenbrück
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Marc Schwientek
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Michael Schloter
- Chair of Soil Science, Technical University of Munich, Freising, Germany; Research Unit for Comparative Microbiome Analyses, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Jan H Fleckenstein
- Department of Hydrogeology, Helmholtz-Zentrum für Umweltforschung GmbH - UFZ, Leipzig, Germany; Hydrologic Modelling Unit, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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36
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Sachs C, Kanaparthi D, Kublik S, Szalay AR, Schloter M, Damgaard LR, Schramm A, Lueders T. Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns. FEMS Microbiol Ecol 2022; 98:6567839. [PMID: 35416241 DOI: 10.1093/femsec/fiac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.
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Affiliation(s)
- Corinna Sachs
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Dheeraj Kanaparthi
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Anna Roza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Lars Riis Damgaard
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
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Crosbie DB, Mahmoudi M, Radl V, Brachmann A, Schloter M, Kemen E, Marín M. Microbiome profiling reveals that Pseudomonas antagonises parasitic nodule colonisation of cheater rhizobia in Lotus. New Phytol 2022; 234:242-255. [PMID: 35067935 DOI: 10.1111/nph.17988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Nodule microbiota are dominated by symbiotic nitrogen-fixing rhizobia, however, other non-rhizobial bacteria also colonise this niche. Although many of these bacteria harbour plant-growth-promoting functions, it is not clear whether these less abundant nodule colonisers impact root-nodule symbiosis. We assessed the relationship between the nodule microbiome and nodulation as influenced by the soil microbiome, by using a metabarcoding approach to characterise the communities inside nodules of healthy and starved Lotus species. A machine learning algorithm and network analyses were used to identify nodule bacteria of interest, which were re-inoculated onto plants in controlled conditions to observe their potential functionality. The nodule microbiome of all tested species differed according to inoculum, but only that of Lotus burttii varied with plant health. Amplicon sequence variants representative of Pseudomonas species were the most indicative non-rhizobial signatures inside healthy L. burttii nodules and negatively correlated with Rhizobium sequences. A representative Pseudomonas isolate co-colonised nodules infected with a beneficial Mesorhizobium, but not with an ineffective Rhizobium isolate and another even reduced the number of ineffective nodules induced on Lotus japonicus. Our results show that nodule endophytes influence the overall outcome of the root-nodule symbiosis, albeit in a plant host-specific manner.
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Affiliation(s)
| | - Maryam Mahmoudi
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Viviane Radl
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
| | | | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
- Chair for Soil Science, Technical University of Munich, Freising, 85354, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Macarena Marín
- Genetics, Biocentre, LMU Munich, Martinsried, 82152, Germany
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Mahnkopp-Dirks F, Radl V, Kublik S, Gschwendtner S, Schloter M, Winkelmann T. Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease. Front Microbiol 2022; 13:841558. [PMID: 35401446 PMCID: PMC8993231 DOI: 10.3389/fmicb.2022.841558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
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Affiliation(s)
- Felix Mahnkopp-Dirks
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
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Duffner C, Kublik S, Fösel B, Frostegård Å, Schloter M, Bakken L, Schulz S. Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers. Environ Microbiol 2022; 24:1887-1901. [PMID: 35106904 DOI: 10.1111/1462-2920.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel Fösel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lars Bakken
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
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Schloter M, Kruck D, Hintzsche H. Aktuell. Biospektrum 2022; 28:58-59. [PMID: 35194335 PMCID: PMC8852933 DOI: 10.1007/s12268-022-1709-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Karlina R, Flexeder C, Musiol S, Bhattacharyya M, Schneider E, Altun I, Gschwendtner S, Neumann AU, Nano J, Schloter M, Peters A, Schulz H, Schmidt‐Weber CB, Standl M, Traidl‐Hoffmann C, Alessandrini F, Ussar S. Differential effects of lung inflammation on insulin resistance in humans and mice. Allergy 2022; 77:2482-2497. [PMID: 35060125 DOI: 10.1111/all.15226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/07/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND The rates of obesity, its associated diseases, and allergies are raising at alarming rates in most countries. House dust mites (HDM) are highly allergenic and exposure often associates with an urban sedentary indoor lifestyle, also resulting in obesity. The aim of this study was to investigate the epidemiological association and physiological impact of lung inflammation on obesity and glucose homeostasis. METHODS Epidemiological data from 2207 adults of the population-based KORA FF4 cohort were used to test associations between asthma and rhinitis with metrics of body weight and insulin sensitivity. To obtain functional insights, C57BL/6J mice were intranasally sensitized and challenged with HDM and simultaneously fed with either low-fat or high-fat diet for 12 weeks followed by a detailed metabolic and biochemical phenotyping of the lung, liver, and adipose tissues. RESULTS We found a direct association of asthma with insulin resistance but not body weight in humans. In mice, co-development of obesity and HDM-induced lung inflammation attenuated inflammation in lung and perigonadal fat, with little impact on body weight, but small shifts in the composition of gut microbiota. Exposure to HDM improved glucose tolerance, reduced hepatosteatosis, and increased energy expenditure and basal metabolic rate. These effects associate with increased activity of thermogenic adipose tissues independent of uncoupling protein 1. CONCLUSIONS Asthma associates with insulin resistance in humans, but HDM challenge results in opposing effects on glucose homeostasis in mice due to increased energy expenditure, reduced adipose inflammation, and hepatosteatosis.
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Affiliation(s)
- Ruth Karlina
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity Helmholtz Zentrum München Munich Germany
- German Center for Diabetes Research (DZD) Munich Germany
| | - Claudia Flexeder
- Institute of Epidemiology Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
- Institute and Clinic for Occupational, Social and Environmental Medicine University Hospital, LMU Munich Munich Germany
- German Center for Lung Research (DZL) Munich Germany
| | - Stephanie Musiol
- German Center for Lung Research (DZL) Munich Germany
- Center of Allergy & Environment (ZAUM) Technical University of Munich and Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Madhumita Bhattacharyya
- Department of Environmental Medicine, Faculty of Medicine University of Augsburg Augsburg Germany
| | - Evelyn Schneider
- German Center for Lung Research (DZL) Munich Germany
- Center of Allergy & Environment (ZAUM) Technical University of Munich and Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Irem Altun
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity Helmholtz Zentrum München Munich Germany
- German Center for Diabetes Research (DZD) Munich Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
| | - Avidan U. Neumann
- Department of Environmental Medicine, Faculty of Medicine University of Augsburg Augsburg Germany
- Institute of Environmental Medicine Helmholtz Zentrum München, German Research Center for Environmental Health Augsburg Germany
| | - Jana Nano
- German Center for Diabetes Research (DZD) Munich Germany
- Institute of Epidemiology Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD) Munich Germany
- Institute of Epidemiology Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Holger Schulz
- Institute of Epidemiology Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
- German Center for Lung Research (DZL) Munich Germany
| | - Carsten B. Schmidt‐Weber
- German Center for Lung Research (DZL) Munich Germany
- Center of Allergy & Environment (ZAUM) Technical University of Munich and Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Marie Standl
- Institute of Epidemiology Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
- German Center for Lung Research (DZL) Munich Germany
| | - Claudia Traidl‐Hoffmann
- Department of Environmental Medicine, Faculty of Medicine University of Augsburg Augsburg Germany
- Institute of Environmental Medicine Helmholtz Zentrum München, German Research Center for Environmental Health Augsburg Germany
- Environmental Medicine Technical University Munich Munich Germany
| | - Francesca Alessandrini
- German Center for Lung Research (DZL) Munich Germany
- Center of Allergy & Environment (ZAUM) Technical University of Munich and Helmholtz Zentrum München, German Research Center for Environmental Health Munich Germany
| | - Siegfried Ussar
- RG Adipocytes & Metabolism, Institute for Diabetes & Obesity Helmholtz Zentrum München Munich Germany
- German Center for Diabetes Research (DZD) Munich Germany
- Department of Medicine Technical University of Munich Munich Germany
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Schröder P, Mench M, Povilaitis V, Rineau F, Rutkowska B, Schloter M, Szulc W, Žydelis R, Loit E. Relaunch cropping on marginal soils by incorporating amendments and beneficial trace elements in an interdisciplinary approach. Sci Total Environ 2022; 803:149844. [PMID: 34525739 DOI: 10.1016/j.scitotenv.2021.149844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
In the EU and world-wide, agriculture is in transition. Whilst we just converted conventional farming imprinted by the post-war food demand and heavy agrochemical usage into integrated and sustainable farming with optimized production, we now have to focus on even smarter agricultural management. Enhanced nutrient efficiency and resistance to pests/pathogens combined with a greener footprint will be crucial for future sustainable farming and its wider environment. Future land use must embrace efficient production and utilization of biomass for improved economic, environmental, and social outcomes, as subsumed under the EU Green Deal, including also sites that have so far been considered as marginal and excluded from production. Another frontier is to supply high-quality food and feed to increase the nutrient density of staple crops. In diets of over two-thirds of the world's population, more than one micronutrient (Fe, Zn, I or Se) is lacking. To improve nutritious values of crops, it will be necessary to combine integrated, systems-based approaches of land management with sustainable redevelopment of agriculture, including central ecosystem services, on so far neglected sites: neglected grassland, set aside land, and marginal lands, paying attention to their connectivity with natural areas. Here we need new integrative approaches which allow the application of different instruments to provide us not only with biomass of sufficient quality and quantity in a site specific manner, but also to improve soil ecological services, e.g. soil C sequestration, water quality, habitat and soil resistance to erosion, while keeping fertilization as low as possible. Such instruments may include the application of different forms of high carbon amendments, the application of macro- and microelements to improve crop performance and quality as well as a targeted manipulation of the soil microbiome. Under certain caveats, the potential of such sites can be unlocked by innovative production systems, ready for the sustainable production of crops enriched in micronutrients and providing services within a circular economy.
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Affiliation(s)
- Peter Schröder
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Research Unit for Comparative Microiome Analysis, D-85764 Neuherberg, Germany.
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, UMR 1202, F-33615 Pessac, France
| | - Virmantas Povilaitis
- Lithuanian Research Centre for Agriculture and Forestry, Akademija LT-58344, Kedainiai distr. Lithuania
| | - Francois Rineau
- Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Beata Rutkowska
- Warsaw University of Life Sciences - SGGW, 02-787 Warsaw, Poland
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Research Unit for Comparative Microiome Analysis, D-85764 Neuherberg, Germany
| | - Wieslaw Szulc
- Warsaw University of Life Sciences - SGGW, 02-787 Warsaw, Poland
| | - Renaldas Žydelis
- Lithuanian Research Centre for Agriculture and Forestry, Akademija LT-58344, Kedainiai distr. Lithuania
| | - Evelin Loit
- Estonian University of Life Sciences, Chair of Field Crops and Plant Biology, 51006 Tartu, Estonia.
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Siani R, Stabl G, Gutjahr C, Schloter M, Radl V. Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. Microb Genom 2021; 7. [PMID: 34889729 PMCID: PMC8767351 DOI: 10.1099/mgen.0.000666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax, isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.
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Affiliation(s)
- Roberto Siani
- Helmholtz Center for Environmental Health, Institute for Comparative Microbiome Analysis, Ingolstaedter Landstr, Oberschleissheim, Germany.,Technical University of Munich, School of Life Sciences, Chair for Soil Science, Freising, Germany
| | - Georg Stabl
- Technical University of Munich, School of Life Sciences, Plant Genetics, Freising, Germany
| | - Caroline Gutjahr
- Technical University of Munich, School of Life Sciences, Plant Genetics, Freising, Germany
| | - Michael Schloter
- Helmholtz Center for Environmental Health, Institute for Comparative Microbiome Analysis, Ingolstaedter Landstr, Oberschleissheim, Germany.,Technical University of Munich, School of Life Sciences, Chair for Soil Science, Freising, Germany
| | - Viviane Radl
- Helmholtz Center for Environmental Health, Institute for Comparative Microbiome Analysis, Ingolstaedter Landstr, Oberschleissheim, Germany
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Hwang Y, Schulze-Makuch D, Arens FL, Saenz JS, Adam PS, Sager C, Bornemann TLV, Zhao W, Zhang Y, Airo A, Schloter M, Probst AJ. Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. Microbiome 2021; 9:234. [PMID: 34836555 PMCID: PMC8627038 DOI: 10.1186/s40168-021-01177-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. RESULTS Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. CONCLUSION We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.
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Affiliation(s)
- Yunha Hwang
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dirk Schulze-Makuch
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany.
- Section Geomicrobiology, German Research Centre for Geosciences (GFZ), 14473, Potsdam, Germany.
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Stechlin, Germany.
- School of the Environment, Washington State University, Pullman, WA, 99164, USA.
| | - Felix L Arens
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Johan S Saenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Christof Sager
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Till L V Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Weishu Zhao
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Alessandro Airo
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 , Essen, Germany.
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Broadbent AAD, Bahn M, Pritchard WJ, Newbold LK, Goodall T, Guinta A, Snell HSK, Cordero I, Michas A, Grant HK, Soto DX, Kaufmann R, Schloter M, Griffiths RI, Bardgett RD. Shrub expansion modulates belowground impacts of changing snow conditions in alpine grasslands. Ecol Lett 2021; 25:52-64. [PMID: 34708508 DOI: 10.1111/ele.13903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022]
Abstract
Climate change is disproportionately impacting mountain ecosystems, leading to large reductions in winter snow cover, earlier spring snowmelt and widespread shrub expansion into alpine grasslands. Yet, the combined effects of shrub expansion and changing snow conditions on abiotic and biotic soil properties remains poorly understood. We used complementary field experiments to show that reduced snow cover and earlier snowmelt have effects on soil microbial communities and functioning that persist into summer. However, ericaceous shrub expansion modulates a number of these impacts and has stronger belowground effects than changing snow conditions. Ericaceous shrub expansion did not alter snow depth or snowmelt timing but did increase the abundance of ericoid mycorrhizal fungi and oligotrophic bacteria, which was linked to decreased soil respiration and nitrogen availability. Our findings suggest that changing winter snow conditions have cross-seasonal impacts on soil properties, but shifts in vegetation can modulate belowground effects of future alpine climate change.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Michael Bahn
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - William J Pritchard
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | | | - Tim Goodall
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Andrew Guinta
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Freising, Germany
| | - Helen K Grant
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - David X Soto
- National Environmental Isotope Facility, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, UK
| | - Rüdiger Kaufmann
- Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Freising, Germany
| | - Robert I Griffiths
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Gwynedd, UK
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, UK
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46
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Pinart M, Nimptsch K, Forslund SK, Schlicht K, Gueimonde M, Brigidi P, Turroni S, Ahrens W, Hebestreit A, Wolters M, Dötsch A, Nöthlings U, Oluwagbemigun K, Cuadrat RRC, Schulze MB, Standl M, Schloter M, De Angelis M, Iozzo P, Guzzardi MA, Vlaemynck G, Penders J, Jonkers DMAE, Stemmer M, Chiesa G, Cavalieri D, De Filippo C, Ercolini D, De Filippis F, Ribet D, Achamrah N, Tavolacci MP, Déchelotte P, Bouwman J, Laudes M, Pischon T. Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis. Nutrients 2021; 13:nu13093292. [PMID: 34579168 PMCID: PMC8466729 DOI: 10.3390/nu13093292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 01/16/2023] Open
Abstract
In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.
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Affiliation(s)
- Mariona Pinart
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
| | - Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Correspondence: ; Tel.: +49-30-9046-4573
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany;
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany
- Host-Microbiome Factors in Cardiovascular Disease Lab, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany; (K.S.); (M.L.)
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain;
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy;
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
- Institute of Statistics, Bremen University, 28359 Bremen, Germany
| | - Antje Hebestreit
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - Maike Wolters
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Ute Nöthlings
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany; (U.N.); (K.O.)
| | - Kolade Oluwagbemigun
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany; (U.N.); (K.O.)
| | - Rafael R. C. Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
- Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy;
| | - Patricia Iozzo
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy; (P.I.); (M.A.G.)
| | - Maria Angela Guzzardi
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy; (P.I.); (M.A.G.)
| | - Geertrui Vlaemynck
- Department Technology and Food, Flanders Research Institute for Agriculture, Fisheries and Food, 9090 Melle, Belgium;
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
| | - Daisy M. A. E. Jonkers
- Department of Internal Medicine, Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
| | - Maya Stemmer
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva P.O. Box 653, Israel;
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Florence, Italy;
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy;
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - David Ribet
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
| | - Najate Achamrah
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 76000 Rouen, France
| | - Marie-Pierre Tavolacci
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- INSERM CIC-CRB 1404, CHU Rouen, 76000 Rouen, France
| | - Pierre Déchelotte
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 76000 Rouen, France
| | - Jildau Bouwman
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany; (K.S.); (M.L.)
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
- Biobank Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Biobank Core Facility, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10178 Berlin, Germany
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47
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Pfeiffer S, Herzmann C, Gaede KI, Kovacevic D, Krauss-Etschmann S, Schloter M. Different responses of the oral, nasal and lung microbiomes to cigarette smoke. Thorax 2021; 77:191-195. [PMID: 34389656 PMCID: PMC8762037 DOI: 10.1136/thoraxjnl-2020-216153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/19/2021] [Indexed: 11/17/2022]
Abstract
To examine the role of smoking on the bacterial community composition of the upper and the lower respiratory tract, a monocentric, controlled prospective study was performed, including healthy smokers, ex-smokers and never-smokers. Smokers were further grouped according to their smoking history. Bacterial diversity was analysed using a molecular barcoding approach based on directly extracted DNA. Our study shows for the first time distinct bacterial response patterns in the upper and lower respiratory tract to cigarette smoking leading to a higher abundance of opportunistic pathogens. The clinical significance of these dysbioses for health needs to be further explored.
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Affiliation(s)
- Stefan Pfeiffer
- Technical University of Munich ZIEL - Institute for Food and Health, Freising, Germany.,Research Unit of Comparative Microbiome Analysis, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Herzmann
- Center for Clinical Studies, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,Clinical Trials Unit, German Center for Infection Research (DZIF), Borstel, Germany
| | - Karoline I Gaede
- BioMaterialBank North, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Draginja Kovacevic
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany.,Early Life Origins of Chronic Lung Disease, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Susanne Krauss-Etschmann
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany .,Early Life Origins of Chronic Lung Disease, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.,Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Michael Schloter
- Technical University of Munich ZIEL - Institute for Food and Health, Freising, Germany.,Research Unit of Comparative Microbiome Analysis, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
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48
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Andrade-Linares DR, Zistl-Schlingmann M, Foesel B, Dannenmann M, Schulz S, Schloter M. Short term effects of climate change and intensification of management on the abundance of microbes driving nitrogen turnover in montane grassland soils. Sci Total Environ 2021; 780:146672. [PMID: 34030328 DOI: 10.1016/j.scitotenv.2021.146672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/09/2023]
Abstract
Montane grasslands in Europe are exposed to increasing temperatures twice as fast as the global average. Changes in climatic conditions are possibly accompanied by an increase in land use intensity, caused by a prolongation of the vegetation period and the need to improve productivity. Therefore, the investigation of combined effects of climate change and land use intensity is needed to further implement agricultural management strategies. Here we present results from a study performed in the pre-alpine region of southern Germany, where intact plant-soil mesocosms from grasslands, were translocated along an altitudinal gradient, resulting in an increase in soil temperature (moderate treatment: +0.5 K; strong treatment: +1.9 K warming) during the experimental period. Additionally, we applied an extensive or intensive agricultural management (two vs. five times of mowing and slurry application) on the transplanted mesocosms. After an exposure of one year, we measured plant growth and soil properties and quantified abundances of soil microorganisms catalyzing key steps in the nitrogen (N) cycle. Our data indicate, significant interactions between climate change and management. For example, microbial biomass was significantly reduced (-47.7% and -49.8% for Cmic and Nmic respectively), which was further accompanied by lower abundances of N2-fixing bacteria (up to -89,3%), as well as ammonia oxidizing bacteria (-81.4%) under intensive management, whereas N-mineralizing bacteria increased in abundance (up to +139.8%) under extensive management. Surprisingly, the abundances of denitrifying bacteria as well as mean N2O emissions were not affected by the treatments. Overall, our data suggest pronounced shifts in the abundance of microbes driving the N cycle in soil as a result of combined climate change and land use intensification already after a short simulation period of one year.
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Affiliation(s)
- Diana R Andrade-Linares
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Marcus Zistl-Schlingmann
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Baerbel Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Dannenmann
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Soil Science, Technical University of Munich, Freising, Germany.
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49
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Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, Schöler A, Niedermeier S, Bleuel R, Zink A, Neuhaus K, Schloter M, Biedermann T, Köberle M. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome 2021; 9:123. [PMID: 34039428 PMCID: PMC8157445 DOI: 10.1186/s40168-021-01067-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/01/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. RESULTS We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias. CONCLUSIONS The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.
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Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Ilias Lagkouvardos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), HCMR, Heraklion, Greece
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Oluwaseun Ayodeji Ishola
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- DKFZ German Cancer Research Center, Berlin, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rachela Bleuel
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Alexander Zink
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany.
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
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50
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Schulze-Makuch D, Lipus D, Arens FL, Baqué M, Bornemann TLV, de Vera JP, Flury M, Frösler J, Heinz J, Hwang Y, Kounaves SP, Mangelsdorf K, Meckenstock RU, Pannekens M, Probst AJ, Sáenz JS, Schirmack J, Schloter M, Schmitt-Kopplin P, Schneider B, Uhl J, Vestergaard G, Valenzuela B, Zamorano P, Wagner D. Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. Microorganisms 2021; 9:microorganisms9051038. [PMID: 34065975 PMCID: PMC8151210 DOI: 10.3390/microorganisms9051038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
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Affiliation(s)
- Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
| | - Felix L. Arens
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Mickael Baqué
- German Aerospace Center (DLR), Institute of Planetary Research, 12489 Berlin, Germany;
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Microgravity User Support Center (MUSC), 51147 Cologne, Germany;
| | - Markus Flury
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
- Department of Crop and Soil Science, Washington State University, Puyallup, WA 98371, USA
| | - Jan Frösler
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jacob Heinz
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Yunha Hwang
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Samuel P. Kounaves
- Department of Chemistry, Tufts University, Boston, MA 02155, USA;
- Department of Earth Science & Engineering, Imperial College London, London SW7 2AZ, UK
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, 14473 Potsdam, Germany;
| | - Rainer U. Meckenstock
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Johan S. Sáenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Janosch Schirmack
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Beate Schneider
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Jenny Uhl
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
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