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Yang T, Wang Y, Zhou T, Yang J, Liu M, Shang Y, Zhang Y, Hei P. Modeling microbial impact on macrophyte debris decomposition in macrophyte-dominated eutrophic lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174442. [PMID: 38964387 DOI: 10.1016/j.scitotenv.2024.174442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The decomposition of macrophytes plays a crucial role in the nutrient cycles of macrophyte-dominated eutrophication lakes. While research on plant decomposition mechanisms and microbial influences has rapid developed, it is curious that plant decomposition models have remained stagnant at the single-stage model from 50 years ago, without endeavor to consider any important factors. Our research conducted in-situ experiments and identified the optimal metrics for decomposition-related microbes, thereby establishing models for microbial impacts on decomposition rates (k_RDR). Using backward elimination in stepwise regression, we found that the optimal subset of independent variables-specifically Gammaproteobacteria-Q-L, Actinobacteriota-Q-L, and Ascomycota-Q-L-increased the adjusted R-squared (Ra2) to 0.93, providing the best modeling for decomposition rate (p = 0.002). Additionally, k_RDR can be modeled by synergic parameters of ACHB-Q-L, LDB-Q-L, and AB-Q-L for bacteria, and SFQ for fungi, albeit with a slightly lower Ra2 of 0.7-0.9 (p < 0.01). The primary contribution of our research lies in two key aspects. Firstly, we introduced optimal metrics for modeling microbes, opting for debris surface microbes over sediment microbes, and prioritizing absolute abundance over relative abundance. Secondly, our model represents a noteworthy advancement in debris modeling. Alongside elucidating the focus and innovative aspects of our work, we also addressed existing limitations and proposed directions for future research. SYNOPSIS: This study explores optimum metrics for decomposition-related microbes, offering precise microbial models for enhanced lake nutrient cycle simulation.
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Affiliation(s)
- Tingting Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yaqin Wang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Tong Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Jing Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Manman Liu
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yizi Shang
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yingyuan Zhang
- Guizhou Academy of Testing and Analysis, Guiyang 550000, China
| | - Pengfei Hei
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China.
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2
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Papale M, Fazi S, Severini M, Scarinci R, Dell'Acqua O, Azzaro M, Venuti V, Fazio B, Fazio E, Crupi V, Irrera A, Rizzo C, Giudice AL, Caruso G. Structural properties and microbial diversity of the biofilm colonizing plastic substrates in Terra Nova Bay (Antarctica). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173773. [PMID: 38844237 DOI: 10.1016/j.scitotenv.2024.173773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization on plastic polymers has been extensively explored, however the temporal dynamics of biofilm community in Antarctic environments are almost unknown. As a contribute to fill this knowledge gap, the structural characteristics and microbial diversity of the biofilm associated with polyvinyl chloride (PVC) and polyethylene (PE) panels submerged at 5 m of depth and collected after 3, 9 and 12 months were investigated in four coastal sites of the Ross Sea. Additional panels placed at 5 and 20 m were retrieved after 12 months. Chemical characterization was performed by FTIR-ATR and Raman (through Surface-Enhanced Raman Scattering, SERS) spectroscopy. Bacterial community composition was quantified at a single cell level by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and Confocal Laser Scanning Microscopy (CLSM); microbial diversity was assessed by 16S rRNA gene sequencing. This multidisciplinary approach has provided new insights into microbial community dynamics during biofouling process, shedding light on the biofilm diversity and temporal succession on plastic substrates in the Ross Sea. Significant differences between free-living and microbial biofilm communities were found, with a more consolidated and structured community composition on PVC compared to PE. Spectral features ascribable to tyrosine, polysaccharides, nucleic acids and lipids characterized the PVC-associated biofilms. Pseudomonadota (among Gamma-proteobacteria) and Alpha-proteobacteria dominated the microbial biofilm community. Interestingly, in Road Bay, close to the Italian "Mario Zucchelli" research station, the biofilm growth - already observed during summer season, after 3 months of submersion - continued afterwards leading to a massive microbial abundance at the end of winter (after 12 months). After 3 months, higher percentages of Gamma-proteobacteria in Road Bay than in the not-impacted site were found. These observations lead us to hypothesize that in this site microbial fouling developed during the first 3 months could serve as a starter pioneering community stimulating the successive growth during winter.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Stefano Fazi
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy; National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Maila Severini
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy
| | - Roberta Scarinci
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300 CP10, 00015 Monterotondo, Rome, Italy
| | - Ombretta Dell'Acqua
- DISTAV, Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa, 26, 16132 Genoa, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Valentina Venuti
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Barbara Fazio
- URT "LabSens of Beyond Nano" of the Department of Physical Sciences and Technologies of Matter, National Research Council (CNR- DSFTM-ME), Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy; Institute for Chemical and Physical Processes, National Research Council (CNR-IPCF), Viale Ferdinando Stagno d'Alcontres, 37, 98158 Messina, Messina, Italy
| | - Enza Fazio
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Vincenza Crupi
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Alessia Irrera
- URT "LabSens of Beyond Nano" of the Department of Physical Sciences and Technologies of Matter, National Research Council (CNR- DSFTM-ME), Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy.
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy; Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy; National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy.
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Hakimzadeh A, Asbun AA, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Durling MB, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, Palmer JM, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour 2024; 24:e13847. [PMID: 37548515 PMCID: PMC10847385 DOI: 10.1111/1755-0998.13847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/05/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
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Affiliation(s)
- Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Dominik Buchner
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily Curd
- Vermont Biomedical Research Network, University of Vermont, Burlington, VT, USA
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Mikael B. Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141, Essen, Germany
| | - Zachary Gold
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun S. Gweon
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6EX, UK
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Jonathan M. Palmer
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI USA (current address: Genencor Technology Center, IFF, Palo Alto, CA USA)
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Teresita M. Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, Canada
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen D-72076, Germany
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Haris Zafeiropoulos
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
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Aho VTE, Klee M, Landoulsi Z, Heintz-Buschart A, Pavelka L, Leist AK, Krüger R, May P, Wilmes P. Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease. NPJ Parkinsons Dis 2024; 10:78. [PMID: 38582855 PMCID: PMC10998870 DOI: 10.1038/s41531-024-00687-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Gut microbiome differences between people with Parkinson's disease (PD) and control subjects without Parkinsonism are widely reported, but potential alterations related to PD with mild cognitive impairment (MCI) have yet to be comprehensively explored. We compared gut microbial features of PD with MCI (n = 58) to cognitively unimpaired PD (n = 60) and control subjects (n = 90) with normal cognition. Our results did not support a specific microbiome signature related to MCI in PD.
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Affiliation(s)
- Velma T E Aho
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Matthias Klee
- Institute for Research on Socio-Economic Inequality (IRSEI), Department of Social Sciences, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Swammerdam Institute of Life Sciences at University of Amsterdam, Amsterdam, the Netherlands
| | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Anja K Leist
- Institute for Research on Socio-Economic Inequality (IRSEI), Department of Social Sciences, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Papale M, Giannarelli S, Azzaro di Rosamarina M, Ghezzi L, Lo Giudice A, Rizzo C. Chemical and microbiological insights into two littoral Antarctic demosponge species: Haliclona ( Rhizoniera) dancoi (Topsent 1901) and Haliclona ( Rhizoniera) scotti (Kirkpatrick 1907). Front Microbiol 2024; 15:1341641. [PMID: 38404594 PMCID: PMC10884823 DOI: 10.3389/fmicb.2024.1341641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Antarctic Porifera have gained increasing interest as hosts of diversified associated microbial communities that could provide interesting insights on the holobiome system and its relation with environmental parameters. Methods The Antarctic demosponge species Haliclona dancoi and Haliclona scotti were targeted for the determination of persistent organic pollutant (i. e., polychlorobiphenyls, PCBs, and polycyclic aromatic hydrocarbons, PAHs) and trace metal concentrations, along with the characterization of the associated prokaryotic communities by the 16S rRNA next generation sequencing, to evaluate possible relationships between pollutant accumulation (e.g., as a stress factor) and prokaryotic community composition in Antarctic sponges. To the best of our knowledge, this approach has been never applied before. Results Notably, both chemical and microbiological data on H. scotti (a quite rare species in the Ross Sea) are here reported for the first time, as well as the determination of PAHs in Antarctic Porifera. Both sponge species generally contained higher amounts of pollutants than the surrounding sediment and seawater, thus demonstrating their accumulation capability. The structure of the associated prokaryotic communities, even if differing at order and genus levels between the two sponge species, was dominated by Proteobacteria and Bacteroidota (with Archaea abundances that were negligible) and appeared in sharp contrast to communities inhabiting the bulk environment. Discussions Results suggested that some bacterial groups associated with H. dancoi and H. scotti were significantly (positively or negatively) correlated to the occurrence of certain contaminants.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council, Messina, Italy
| | - Stefania Giannarelli
- Department of Chemical and Industrial Chemistry, University of Pisa, Pisa, Italy
| | | | - Lisa Ghezzi
- Department of Earth Sciences, University of Pisa, Pisa, Italy
| | | | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council, Messina, Italy
- Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
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Kipping L, Jehmlich N, Moll J, Noll M, Gossner MM, Van Den Bossche T, Edelmann P, Borken W, Hofrichter M, Kellner H. Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species. THE ISME JOURNAL 2024; 18:wrae050. [PMID: 38519103 PMCID: PMC11022342 DOI: 10.1093/ismejo/wrae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.
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Affiliation(s)
- Lydia Kipping
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ GmbH, 06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, 8092 Zürich, Switzerland
| | - Tim Van Den Bossche
- VIB—UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Pascal Edelmann
- Department of Ecology and Ecosystem Management, Center of School of Life and Food Sciences Weihenstephan, TU München, 85354 Freising, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
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Klee M, Aho VTE, May P, Heintz-Buschart A, Landoulsi Z, Jónsdóttir SR, Pauly C, Pavelka L, Delacour L, Kaysen A, Krüger R, Wilmes P, Leist AK. Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome. J Prev Alzheimers Dis 2024; 11:759-768. [PMID: 38706292 PMCID: PMC11060993 DOI: 10.14283/jpad.2024.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/03/2023] [Indexed: 05/07/2024]
Abstract
BACKGROUND With differences apparent in the gut microbiome in mild cognitive impairment (MCI) and dementia, and risk factors of dementia linked to alterations of the gut microbiome, the question remains if gut microbiome characteristics may mediate associations of education with MCI. OBJECTIVES We sought to examine potential mediation of the association of education and MCI by gut microbiome diversity or composition. DESIGN Cross-sectional study. SETTING Luxembourg, the Greater Region (surrounding areas in Belgium, France, Germany). PARTICIPANTS Control participants of the Luxembourg Parkinson's Study. MEASUREMENTS Gut microbiome composition, ascertained with 16S rRNA gene amplicon sequencing. Differential abundance, assessed across education groups (0-10, 11-16, 16+ years of education). Alpha diversity (Chao1, Shannon and inverse Simpson indices). Mediation analysis with effect decomposition was conducted with education as exposure, MCI as outcome and gut microbiome metrics as mediators. RESULTS After exclusion of participants below 50, or with missing data, n=258 participants (n=58 MCI) were included (M [SD] Age=64.6 [8.3] years). Higher education (16+ years) was associated with MCI (Odds ratio natural direct effect=0.35 [95% CI 0.15-0.81]. Streptococcus and Lachnospiraceae-UCG-001 genera were more abundant in higher education. CONCLUSIONS Education is associated with gut microbiome composition and MCI risk without clear evidence for mediation. However, our results suggest signatures of the gut microbiome that have been identified previously in AD and MCI to be reflected in lower education and suggest education as important covariate in microbiome studies.
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Affiliation(s)
- M Klee
- Matthias Klee, University of Luxembourg, Institute for Research on Socio-Economic Inequality, Department of Social Sciences, 11, Porte des Sciences, L-4366, Esch-sur-Alzett, Luxembourg, Mail: , Phone: +352 46 66 44 5161
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Hennecke J, Bassi L, Mommer L, Albracht C, Bergmann J, Eisenhauer N, Guerra CA, Heintz-Buschart A, Kuyper TW, Lange M, Solbach MD, Weigelt A. Responses of rhizosphere fungi to the root economics space in grassland monocultures of different age. THE NEW PHYTOLOGIST 2023; 240:2035-2049. [PMID: 37691273 DOI: 10.1111/nph.19261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Recent studies on root traits have shown that there are two axes explaining trait variation belowground: the collaboration axis with mycorrhizal partners and the conservation ('fast - slow') axis. However, it is yet unknown whether these trait axes affect the assembly of soilborne fungi. We expect saprotrophic fungi to link to the conservation axis of root traits, whereas pathogenic and arbuscular mycorrhizal fungi link to the collaboration axis, but in opposite directions, as arbuscular mycorrhizal fungi might provide pathogen protection. To test these hypotheses, we sequenced rhizosphere fungal communities and measured root traits in monocultures of 25 grassland plant species, differing in age. Within the fungal guilds, we evaluated fungal species richness, relative abundance and community composition. Contrary to our hypotheses, fungal diversity and relative abundance were not strongly related to the root trait axes. However, saprotrophic fungal community composition was affected by the conservation gradient and pathogenic community composition by the collaboration gradient. The rhizosphere AMF community composition did not change along the collaboration gradient, even though the root trait axis was in line with the root mycorrhizal colonization rate. Overall, our results indicate that in the long term, the root trait axes are linked with fungal community composition.
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Affiliation(s)
- Justus Hennecke
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Leonardo Bassi
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Liesje Mommer
- Forest Ecology and Forest Management Group, Wageningen University, 6708 PB, Wageningen, the Netherlands
| | - Cynthia Albracht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Joana Bergmann
- Sustainable Grassland Systems, Leibniz Centre for Agricultural Landscape Research (ZALF), 14641, Paulinenaue, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, 06108, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Thomas W Kuyper
- Soil Biology Group, Wageningen University, 6708 PB, Wageningen, the Netherlands
| | - Markus Lange
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, 07745, Jena, Germany
| | - Marcel Dominik Solbach
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, 50674, Cologne, Germany
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
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9
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Roy F, Ibayev O, Arnstadt T, Bässler C, Borken W, Groß C, Hoppe B, Hossen S, Kahl T, Moll J, Noll M, Purahong W, Schreiber J, Weisser WW, Hofrichter M, Kellner H. Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165868. [PMID: 37516186 DOI: 10.1016/j.scitotenv.2023.165868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha-1 yr-1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.
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Affiliation(s)
- Friederike Roy
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Orkhan Ibayev
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Tobias Arnstadt
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Claus Bässler
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; National Park Bavarian Forest, Freyunger Str. 2, D-94481 Grafenau, Germany
| | - Werner Borken
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Christina Groß
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, D-38104 Braunschweig, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Tiemo Kahl
- UNESCO-Biosphärenreservat Thüringer Wald, Schmiedefeld a. Rstg, Brunnenstraße 1, D-98528 Suhl, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Jasper Schreiber
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Technical University of Munich, D-85354 Freising, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany.
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10
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Marchetta A, Papale M, Rappazzo AC, Rizzo C, Camacho A, Rochera C, Azzaro M, Urzì C, Lo Giudice A, De Leo F. A Deep Insight into the Diversity of Microfungal Communities in Arctic and Antarctic Lakes. J Fungi (Basel) 2023; 9:1095. [PMID: 37998900 PMCID: PMC10672340 DOI: 10.3390/jof9111095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
We assessed fungal diversity in water and sediment samples obtained from five Arctic lakes in Ny-Ålesund (Svalbard Islands, High Arctic) and five Antarctic lakes on Livingston and Deception Islands (South Shetland Islands), using DNA metabarcoding. A total of 1,639,074 fungal DNA reads were detected and assigned to 5980 ASVs amplicon sequence variants (ASVs), with only 102 (1.7%) that were shared between the two Polar regions. For Arctic lakes, unknown fungal taxa dominated the sequence assemblages, suggesting the dominance of possibly undescribed fungi. The phylum Chytridiomycota was the most represented in the majority of Arctic and Antarctic samples, followed by Rozellomycota, Ascomycota, Basidiomycota, and the less frequent Monoblepharomycota, Aphelidiomycota, Mortierellomycota, Mucoromycota, and Neocallimastigomycota. At the genus level, the most abundant genera included psychrotolerant and cosmopolitan cold-adapted fungi including Alternaria, Cladosporium, Cadophora, Ulvella (Ascomycota), Leucosporidium, Vishniacozyma (Basidiomycota), and Betamyces (Chytridiomycota). The assemblages displayed high diversity and richness. The assigned diversity was composed mainly of taxa recognized as saprophytic fungi, followed by pathogenic and symbiotic fungi.
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Affiliation(s)
- Alessia Marchetta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Maria Papale
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy (A.L.G.)
| | - Alessandro Ciro Rappazzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy (A.L.G.)
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy (A.L.G.)
- Stazione Zoologica Anton Dohrn, National Institute of Biology, Sicily Marine Centre, Department Ecosustainable Marine Biotechnology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/Catédratico José Beltrán, 2, E46980 Paterna, Spain
| | - Carlos Rochera
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/Catédratico José Beltrán, 2, E46980 Paterna, Spain
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy (A.L.G.)
| | - Clara Urzì
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122 Messina, Italy (A.L.G.)
| | - Filomena De Leo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
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11
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Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Hossen S, Delelegn Y, Buscot F, Lehnert AS, Alves EG, Hilke I, Gleixner G, Schulze ED, Noll M, Purahong W. FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species. MICROBIAL ECOLOGY 2023; 85:411-428. [PMID: 35124727 PMCID: PMC9958157 DOI: 10.1007/s00248-022-01973-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/16/2023]
Abstract
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
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Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, 150040 Harbin, People’s Republic of China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Yoseph Delelegn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
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12
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Wahdan SFM, Ji L, Schädler M, Wu YT, Sansupa C, Tanunchai B, Buscot F, Purahong W. Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks. THE ISME JOURNAL 2023; 17:238-251. [PMID: 36352255 PMCID: PMC9860053 DOI: 10.1038/s41396-022-01336-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Although microbial decomposition of plant litter plays a crucial role in nutrient cycling and soil fertility, we know less about likely links of specific microbial traits and decomposition, especially in relation to climate change. We study here wheat straw decomposition under ambient and manipulated conditions simulating a future climate scenario (next 80 years) in agroecosystems, including decay rates, macronutrient dynamics, enzyme activity, and microbial communities. We show that future climate will accelerate straw decay rates only during the early phase of the decomposition process. Additionally, the projected climate change will increase the relative abundance of saprotrophic fungi in decomposing wheat straw. Moreover, the impact of future climate on microbial community assembly and molecular ecological networks of both bacteria and fungi will strongly depend on the decomposition phase. During the early phase of straw decomposition, stochastic processes dominated microbial assembly under ambient climate conditions, whereas deterministic processes highly dominated bacterial and fungal communities under simulated future climate conditions. In the later decomposition phase, similar assembly processes shaped the microbial communities under both climate scenarios. Furthermore, over the early phases of decomposition, simulated future climate enhanced the complexity of microbial interaction networks. We concluded that the impact of future climate on straw decay rate and associated microbial traits like assembly processes and inter-community interactions is restricted to the early phase of decomposition.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.33003.330000 0000 9889 5690Department of Botany & Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Li Ji
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.440660.00000 0004 1761 0083School of Forestry, Central South University of Forestry and Technology, Changsha, PR China
| | - Martin Schädler
- grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany ,grid.7492.80000 0004 0492 3830Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Yu-Ting Wu
- grid.412083.c0000 0000 9767 1257Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan ,grid.412019.f0000 0000 9476 5696Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Chakriya Sansupa
- grid.7132.70000 0000 9039 7662Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Benjawan Tanunchai
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - François Buscot
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Witoon Purahong
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
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13
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Douanla-Meli C, Moll J. Bark-inhabiting fungal communities of European chestnut undergo substantial alteration by canker formation following chestnut blight infection. Front Microbiol 2023; 14:1052031. [PMID: 36778875 PMCID: PMC9911167 DOI: 10.3389/fmicb.2023.1052031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Background Chestnut forests are severely threatened by chestnut blight caused by the fungal pathogen Cryphonectria parasitica and the infected trees exhibit bark canker in the later stage of the disease. European chestnut (Castanea sativa) is further infected by Gnomoniopsis smithogilvyi, another canker-causing fungal pathogen. We explored whether and how chestnut blight is reflected in bark-inhabiting fungal communities of European chestnut and also assessed the co-occurrence of C. parasitica and G. smithogilvyi. Materials and methods We initially investigated the fungal communities of European chestnut bark tissues and further monitored changes in these fungal communities with regard to disease progression from infection to canker formation by analyzing bark samples from asymptomatic trees, asymptomatic trees with latent C. parasitica infection, and infected trees with canker tissues, using amplicon sequencing of the ITS2 region of rDNA. Results The results showed that fungal community composition and diversity differed between the sample types. The fungal community composition was substantially reshaped by canker formation, whereas latent C. parasitica infection and more specifically pre-canker infection period per se had a weak effect. Fungal communities of canker samples was less diverse and more dissimilar to those of other sample types. C. parasitica dominated the mycobiome of canker samples, whereas G. smithogilvyi was found in only 9% of canker samples at very low abundances. However, G. smithogilvyi was a dominant fungus in the bark of healthy plants. Conclusion This study highlights that canker formation is the principal driver of decreasing diversity and altered composition of the mycobiome in bark tissues of European chestnut infected by C. parasitica infection. It additionally emphasizes the scarce co-occurrence of C. parasitica and G. smithogilvyi on European chestnut.
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Affiliation(s)
- Clovis Douanla-Meli
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Quedlinburg, Germany,*Correspondence: Clovis Douanla-Meli, ✉
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
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14
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Wang D. Amplicon Sequencing Pipelines in Metagenomics. Methods Mol Biol 2023; 2649:69-83. [PMID: 37258858 DOI: 10.1007/978-1-0716-3072-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Taxonomic profiling among a large number of samples is a fundamental task during amplicon sequencing analysis. The heterogeneity and technical noises in the sample handling, library preparation, and sequencing present a major challenge to how the biological conclusions are drawn from the data analysis, and accordingly, many tools have been developed to address specific issues related to each step of the data analysis. Nowadays, several sophisticated computational pipelines with flexible parameters are made available to provide one-stop comprehensive solutions by integrating various tools, which significantly mitigate the burden imposed by the complexity of the metagenomics data analysis. This chapter discusses the best practices related to the data generation and describes bioinformatics approaches to achieving greater accuracy from data processing. It offers two independent stepwise pipelines using mothur and DADA2 in a parallel way, presents the basic principles in the key steps of the analysis, and enables the comparisons between the two pipelines straightforwardly.
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Affiliation(s)
- Dapeng Wang
- National Heart and Lung Institute, Imperial College London, London, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- LeedsOmics, University of Leeds, Leeds, UK.
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15
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Moll J, Hoppe B. Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing. PeerJ 2022; 10:e14567. [PMID: 36573238 PMCID: PMC9789694 DOI: 10.7717/peerj.14567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
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Affiliation(s)
- Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle (Saale), Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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16
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Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Larpkern P, Lehnert AS, Alves EG, Gleixner G, Schulze ED, Noll M, Buscot F, Purahong W. A poisoned apple: First insights into community assembly and networks of the fungal pathobiome of healthy-looking senescing leaves of temperate trees in mixed forest ecosystem. FRONTIERS IN PLANT SCIENCE 2022; 13:968218. [PMID: 36407586 PMCID: PMC9669904 DOI: 10.3389/fpls.2022.968218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Despite the abundance of observations of foliar pathogens, our knowledge is severely lacking regarding how the potential fungal pathobiome is structured and which processes determine community assembly. In this study, we addressed these questions by analysing the potential fungal pathobiome associated with the senescing leaves and needles of 12 temperate tree species. We compared fungal plant pathogen load in the senescing leaves/needles and demonstrated that healthy-looking leaves/needles are inhabited by diverse and distinct fungal plant pathogens. We detected 400 fungal plant pathogenic ASVs belonging to 130 genera. The fungal plant pathogenic generalist, Mycosphaerella, was found to be the potential most significant contributor to foliar disease in seedlings. The analyses of assembly process and co-occurrence network showed that the fungal plant pathogenic communities in different tree types are mainly determined by stochastic processes. However, the homogenising dispersal highly contributes in broadleaf trees, whereas ecological drift plays an important role in coniferious trees. The deterministic assembly processes (dominated by variable selection) contributed more in broadleaf trees as compared to coniferous trees. We found that pH and P level significantly corresponded with fungal plant pathogenic community compositions in both tree types. Our study provides the first insight and mechanistic understanding into the community assembly, networks, and complete taxonomy of the foliar fungal pathobiome in senescing leaves and needles.
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Affiliation(s)
- Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- School of Forestry, Central South of Forestry and Technology, Changsha, China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Panadda Larpkern
- Bodhivijjalaya College, Srinakharinwirot University, Nakhon Nayok, Thailand
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
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17
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Juncheed K, Tanunchai B, Wahdan SFM, Thongsuk K, Schädler M, Noll M, Purahong W. Dark side of a bio-based and biodegradable plastic? Assessment of pathogenic microbes associated with poly(butylene succinate-co-adipate) under ambient and future climates using next-generation sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:966363. [PMID: 36311114 PMCID: PMC9610124 DOI: 10.3389/fpls.2022.966363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Bio-based and biodegradable plastic mulching films have been proposed to replace the non-biodegradable plastic mulch films to solve plastic pollution problems in agricultural soils. However, the impact of bio-based and biodegradable plastics on plant and human health remains largely unexplored. Here, we aimed to assess the risk under field conditions of a bio-based and biodegradable poly(butylene succinate-co-adipate; PBSA), a widely used mulching film as carrier of potential pathogenic microorganisms (bacteria and fungi) at ambient and future climate conditions. Overall, we affiliated 64 fungal and 11 bacterial operational taxonomic units (OTUs) as pathogens by using Next-Generation Sequencing approach. Our results revealed that PBSA hosted at least 53 plant pathogens, of which 51 were classified as fungi, while the other two were bacteria. Most fungal plant pathogens were able to withstand the anticipated future climate changes. We detected 13 fungal and eight bacterial OTUs, which were classified as opportunistic human pathogens. Only one bacterial OTU (Enterococcus faecium) was assigned to a human pathogen. While future climate conditions only significantly impacted on the presence and frequency of detection of few pathogens, incubation time was found to significantly impacted on nine pathogens. This result demonstrates the temporal dynamics of pathogens associated with PBSA. The threats to plant and human health were discussed. We emphasize that the risks to human health are relatively low because we mainly found opportunistic pathogens associated with PBSA and the amount are comparable to the plant debris. However, the risks to plant health may be considered as moderate because many plant pathogens were discovered and/or enriched in PBSA. Furthermore, in soil environments, the pathogenic risk of plastic is highly depending on the surrounding soil pathobiome where plastic is being decomposed.
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Affiliation(s)
- Kantida Juncheed
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | - Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Katikarn Thongsuk
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
| | - Martin Schädler
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Halle (Saale), Germany
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18
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Tanunchai B, Schroeter SA, Ji L, Wahdan SFM, Hossen S, Lehnert AS, Grünberg H, Gleixner G, Buscot F, Schulze ED, Noll M, Purahong W. More than you can see: Unraveling the ecology and biodiversity of lichenized fungi associated with leaves and needles of 12 temperate tree species using high-throughput sequencing. Front Microbiol 2022; 13:907531. [PMID: 36187953 PMCID: PMC9523249 DOI: 10.3389/fmicb.2022.907531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/12/2022] [Indexed: 01/04/2023] Open
Abstract
Currently, lichen surveys are generally based on the examination of fruiting bodies. Lichens in the mycelial stage, in spores, or awaiting conditions for fruiting body formation are usually overlooked, even though they are important for maintaining biodiversity and ecosystem functions. This study aimed to explore the lichenized fungal community composition and richness associated with leaves and needles of 12 temperate tree species using Illumina MiSeq-based amplicon sequencing of the internal transcribed spacer (ITS) 2 region. Picea abies harbored the highest richness and number of lichenized fungal species. We found that the lichenized fungus Physcia adscendens dominated the leaves and needles of the most temperate tree species. Eleven lichenized fungal species detected in this study were recorded for the first time on leaves and needles. In addition, we identified Athallia cerinella, Fellhanera bouteillei, and Melanohalea exasperata that are on the German national red lists. Lichenized fungal richness was higher in conifer compared to broadleaf trees. Overall, tree species (within coniferous trees) and tree types (broadleaved vs. coniferous trees) harbored significantly different lichenized fungal community compositions pointing out the importance of host species. Diversity and community composition patterns of lichenized fungi were correlated mainly with tree species. Our study demonstrates that the diversity of foliicolous lichens associated with leaves and needles of 12 temperate tree species can be appropriately analyzed and functionally assigned using the ITS-based high-throughput sequencing. We highlighted the importance of conifers for maintaining the biodiversity of foliicolous lichens. Based on the discovery of many red list lichens, our methodological approach and results are important contributions to subsequent actions in the bio-conversation approaches.
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Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Simon Andreas Schroeter
- Biogeochemical Processes Department, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- School of Forestry, Central South of Forestry and Technology, Changsha, China
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Ann-Sophie Lehnert
- Biogeochemical Processes Department, Max Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Gerd Gleixner
- Biogeochemical Processes Department, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Ernst-Detlef Schulze
- Biogeochemical Processes Department, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
- Matthias Noll
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- *Correspondence: Witoon Purahong
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19
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Antarctic Salt-Cones: An Oasis of Microbial Life? The Example of Boulder Clay Glacier (Northern Victoria Land). Microorganisms 2022; 10:microorganisms10091753. [PMID: 36144355 PMCID: PMC9504174 DOI: 10.3390/microorganisms10091753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 12/04/2022] Open
Abstract
The evaporation of a localized, highly saline water body of the Boulder Clay debris-covered glacier, in the Northern Victoria Land, probably generated the accumulation of mirabilite (Na2SO4 × 10H2O) and thenardite (Na2SO4) in a glacier salt-cone. Such an extremely cold and salty environment resembles the conditions on Mars, so it can be considered a terrestrial analog. The study was aimed at gaining a first glimpse at the prokaryotic community associated with Antarctic mirabilite and thenardite minerals and also to find clues about the origin of the salts. For this purpose, samples were analyzed by a next generation approach to investigate the prokaryotic (Bacteria and Archaea) diversity. Phylogenetic analysis allowed the identification of Bacteroidota, Actinobacteriota, Firmicutes, and Gammaproteobacteria as the main bacterial lineages, in addition to Archaea in the phylum Halobacterota. The genera Arthrobacter, Rhodoglobus, Gillisia, Marinobacter and Psychrobacter were particularly abundant. Interestingly, several bacterial and archaeal sequences were related to halotolerant and halophilic genera, previously reported in a variety of marine environments and saline habitats, also in Antarctica. The analyzed salt community also included members that are believed to play a major role in the sulfur cycle.
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20
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Thompson LR, Anderson SR, Den Uyl PA, Patin NV, Lim SJ, Sanderson G, Goodwin KD. Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. Gigascience 2022; 11:6651346. [PMID: 35902092 PMCID: PMC9334028 DOI: 10.1093/gigascience/giac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/28/2022] [Accepted: 06/15/2022] [Indexed: 12/21/2022] Open
Abstract
Background Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results. Findings We developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files—a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences—it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm; assigns taxonomy to the resulting representative sequences; performs analyses of taxonomic, alpha, and beta diversity; and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S ribosomal RNA amplicon data set from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks. Conclusion Automated workflows like Tourmaline enable rapid analysis of environmental amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.
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Affiliation(s)
- Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Sean R Anderson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Paul A Den Uyl
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI 48108, USA
| | - Nastassia V Patin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Shen Jean Lim
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Grant Sanderson
- Marine Science Department, University of Hawaii, Hilo, HI 96720, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
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21
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Prada-Salcedo LD, Prada-Salcedo JP, Heintz-Buschart A, Buscot F, Goldmann K. Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests. Front Microbiol 2022; 13:920618. [PMID: 35910637 PMCID: PMC9328770 DOI: 10.3389/fmicb.2022.920618] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/14/2022] [Indexed: 01/04/2023] Open
Abstract
Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.
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Affiliation(s)
- Luis Daniel Prada-Salcedo
- Department Soil Ecology, Helmholtz-Centre for Environmental Research (UFZ), Halle, Germany
- Department of Biology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (IDiv), Leipzig, Germany
- *Correspondence: Luis Daniel Prada-Salcedo
| | | | - Anna Heintz-Buschart
- Department Soil Ecology, Helmholtz-Centre for Environmental Research (UFZ), Halle, Germany
- German Centre for Integrative Biodiversity Research (IDiv), Leipzig, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - François Buscot
- Department Soil Ecology, Helmholtz-Centre for Environmental Research (UFZ), Halle, Germany
- German Centre for Integrative Biodiversity Research (IDiv), Leipzig, Germany
| | - Kezia Goldmann
- Department Soil Ecology, Helmholtz-Centre for Environmental Research (UFZ), Halle, Germany
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22
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Mohsen A, Chen YA, Allendes Osorio RS, Higuchi C, Mizuguchi K. Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2. FRONTIERS IN BIOINFORMATICS 2022; 2:893933. [PMID: 36304319 PMCID: PMC9580898 DOI: 10.3389/fbinf.2022.893933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022] Open
Abstract
Optimizing and automating a protocol for 16S microbiome data analysis with QIIME2 is a challenging task. It involves a multi-step process, and multiple parameters and options that need to be tested and determined. In this article, we describe Snaq, a snakemake pipeline that helps automate and optimize 16S data analysis using QIIME2. Snaq offers an informative file naming system and automatically performs the analysis of a data set by downloading and installing the required databases and classifiers, all through a single command-line instruction. It works natively on Linux and Mac and on Windows through the use of containers, and is potentially extendable by adding new rules. This pipeline will substantially reduce the efforts in sending commands and prevent the confusion caused by the accumulation of analysis results due to testing multiple parameters.
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Affiliation(s)
- Attayeb Mohsen
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- *Correspondence: Attayeb Mohsen,
| | - Yi-An Chen
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Rodolfo S. Allendes Osorio
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Chihiro Higuchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Institute for Protein Research, Osaka University, Osaka, Japan
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23
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Gebauer L, Breitkreuz C, Heintz-Buschart A, Reitz T, Buscot F, Tarkka M, Bouffaud ML. Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming. Front Microbiol 2022; 13:824437. [PMID: 35770171 PMCID: PMC9234553 DOI: 10.3389/fmicb.2022.824437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023] Open
Abstract
Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS+) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions.
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Affiliation(s)
- Lucie Gebauer
- Helmholtz Centre for Environmental Research, Halle, Germany
| | | | - Anna Heintz-Buschart
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Thomas Reitz
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mika Tarkka
- Helmholtz Centre for Environmental Research, Halle, Germany
| | - Marie-Lara Bouffaud
- Helmholtz Centre for Environmental Research, Halle, Germany
- *Correspondence: Marie-Lara Bouffaud
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24
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Okoroafor PU, Mann L, Amin Ngu K, Zaffar N, Monei NL, Boldt C, Reitz T, Heilmeier H, Wiche O. Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030341. [PMID: 35161323 PMCID: PMC8838376 DOI: 10.3390/plants11030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 05/21/2023]
Abstract
Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.
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Affiliation(s)
- Precious Uchenna Okoroafor
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Correspondence:
| | - Lotte Mann
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Kerian Amin Ngu
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nazia Zaffar
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Nthati Lillian Monei
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
- Mining Department, Geology Institute, Tallinn University of Technology, 19086 Tallin, Estonia
| | - Christin Boldt
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research–UFZ, Theodor–Lieser Str. 4, 06120 Halle, Germany;
| | - Hermann Heilmeier
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
| | - Oliver Wiche
- Institute of Biosciences, Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany; (L.M.); (K.A.N.); (N.Z.); (N.L.M.); (C.B.); (H.H.); (O.W.)
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25
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Purahong W, Tanunchai B, Wahdan SFM, Buscot F, Schulze ED. Molecular Screening of Microorganisms Associated with Discolored Wood in Dead European Beech Trees Suffered from Extreme Drought Event Using Next Generation Sequencing. PLANTS (BASEL, SWITZERLAND) 2021; 10:2092. [PMID: 34685901 PMCID: PMC8537330 DOI: 10.3390/plants10102092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 01/04/2023]
Abstract
Drought events weaken trees and make them vulnerable to attacks by diverse plant pathogens. Here, we propose a molecular method for fast screening of microorganisms associated with European beech decline after an extreme drought period (2018) in a forest of Thuringia, Germany. We used Illumina sequencing with a recent bioinformatics approach based on DADA2 to identify archaeal, bacterial, and fungal ASVs (amplicon sequence variants) based on bacterial and archaeal 16S and fungal ITS genes. We show that symptomatic beech trees are associated with both bacterial and fungal plant pathogens. Although the plant pathogen sequences were detected in both discolored and non-discolored wood areas, they were highly enriched in the discolored wood areas. We show that almost each individual tree was associated with a different combination of pathogens. Cytospora spp. and Neonectria coccinea were among the most frequently detected fungal pathogens, whereas Erwinia spp. and Pseudomonas spp. were the dominant bacterial plant pathogens. We demonstrate that bacterial plant pathogens may be of major importance in beech decline.
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Affiliation(s)
- Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; (B.T.); (S.F.M.W.); (F.B.)
| | - Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; (B.T.); (S.F.M.W.); (F.B.)
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; (B.T.); (S.F.M.W.); (F.B.)
- Botany Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; (B.T.); (S.F.M.W.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, D-07745 Jena, Germany;
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26
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Ferlian O, Goldmann K, Eisenhauer N, Tarkka MT, Buscot F, Heintz-Buschart A. Distinct effects of host and neighbour tree identity on arbuscular and ectomycorrhizal fungi along a tree diversity gradient. ISME COMMUNICATIONS 2021; 1:40. [PMID: 37938639 PMCID: PMC9723774 DOI: 10.1038/s43705-021-00042-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 04/26/2023]
Abstract
Plant diversity and plant-related ecosystem functions have been important in biodiversity-ecosystem functioning studies. However, biotic interactions with mycorrhizal fungi have been understudied although they are crucial for plant-resource acquisition. Here, we investigated the effects of tree species richness and tree mycorrhizal type on arbuscular (AMF) and ectomycorrhizal fungal (EMF) communities. We aimed to understand how dissimilarities in taxa composition and beta-diversity are related to target trees and neighbours of the same or different mycorrhizal type. We sampled a tree diversity experiment with saplings (~7 years old), where tree species richness (monocultures, 2-species, and 4-species mixtures) and mycorrhizal type were manipulated. AMF and EMF richness significantly increased with increasing tree species richness. AMF richness of mixture plots resembled that of the sum of the respective monocultures, whereas EMF richness of mixture plots was lower compared to the sum of the respective monocultures. Specialisation scores revealed significantly more specialised AMF than EMF suggesting that, in contrast to previous studies, AMF were more specialised, whereas EMF were not. We further found that AMF communities were little driven by the surrounding trees, whereas EMF communities were. Our study revealed drivers of mycorrhizal fungal communities and further highlights the distinct strategies of AMF and EMF.
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Affiliation(s)
- Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany.
| | - Kezia Goldmann
- Department Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| | - Mika T Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Department Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Department Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Department Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle (Saale), Germany
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27
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Moll J, Roy F, Bässler C, Heilmann-Clausen J, Hofrichter M, Kellner H, Krabel D, Schmidt JH, Buscot F, Hoppe B. First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes. Microorganisms 2021; 9:microorganisms9071454. [PMID: 34361890 PMCID: PMC8304250 DOI: 10.3390/microorganisms9071454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/02/2023] Open
Abstract
Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.
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Affiliation(s)
- Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Correspondence: (J.M.); (B.H.)
| | - Friederike Roy
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Claus Bässler
- Department of Conservation Biology, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Research, National Park Bavarian Forest, 94481 Grafenau, Germany
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Martin Hofrichter
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Harald Kellner
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Doris Krabel
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Jan Henrik Schmidt
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany;
| | - François Buscot
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle—Jena—Leipzig, 04103 Leipzig, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
- Correspondence: (J.M.); (B.H.)
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28
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Breitkreuz C, Herzig L, Buscot F, Reitz T, Tarkka M. Interactions between soil properties, agricultural management and cultivar type drive structural and functional adaptations of the wheat rhizosphere microbiome to drought. Environ Microbiol 2021; 23:5866-5882. [PMID: 34029439 DOI: 10.1111/1462-2920.15607] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
Rhizosphere microbial communities adapt their structural and functional compositions to water scarcity and have the potential to substantially mitigate drought stress of crops. To unlock this potential, it is crucial to understand community responses to drought in the complex interplay between soil properties, agricultural management and crop species. Two winter wheat cultivars, demanding and non-demanding, were exposed to drought stress in loamy Chernozem and sandy Luvisol soils under conventional or organic farming management. Structural and functional adaptations of the rhizosphere bacteria were assessed by 16S amplicon sequencing, the predicted abundance of drought-related functional genes in the bacterial community based on 16S amplicon sequences (Tax4Fun) and the activity potentials of extracellular enzymes involved in the carbon cycle. Bacterial community composition was strongly driven by drought and soil type. Under drought conditions, Gram-positive phyla became relatively more abundant, but either less or more diverse in Luvisol and Chernozem soil respectively. Enzyme activities and functional gene abundances related to carbon degradation were increased under drought in the rhizosphere of the demanding wheat cultivar in organic farming. We demonstrate that soil type, farming system and wheat cultivar each constitute important factors during the structural and/or functional adaptation of rhizobacterial communities in response to drought.
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Affiliation(s)
- Claudia Breitkreuz
- Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany
| | - Laura Herzig
- Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany
| | - François Buscot
- Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Thomas Reitz
- Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Mika Tarkka
- Soil Ecology Department, UFZ - Helmholtz-Centre for Environmental Research, Theodor-Lieser-Straße 4, Halle, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
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29
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Ansorge R, Birolo G, James SA, Telatin A. Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments. Int J Mol Sci 2021; 22:5309. [PMID: 34069990 PMCID: PMC8157834 DOI: 10.3390/ijms22105309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.
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Affiliation(s)
- Rebecca Ansorge
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
| | - Giovanni Birolo
- Medical Sciences Department, University of Turin, 10126 Turin, Italy;
| | - Stephen A. James
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
| | - Andrea Telatin
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (R.A.); (S.A.J.)
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30
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Wahdan SFM, Reitz T, Heintz-Buschart A, Schädler M, Roscher C, Breitkreuz C, Schnabel B, Purahong W, Buscot F. Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns. Environ Microbiol 2021; 23:6163-6176. [PMID: 33780112 DOI: 10.1111/1462-2920.15492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023]
Abstract
Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50-70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterized using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany.,Department of Biology, Leipzig University, Johannisallee 21, Leipzig, 04103, Germany.,Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Thomas Reitz
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Anna Heintz-Buschart
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany.,Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany
| | - Christiane Roscher
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany.,Department of Physiological Diversity, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Claudia Breitkreuz
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
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31
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Gebauer L, Bouffaud ML, Ganther M, Yim B, Vetterlein D, Smalla K, Buscot F, Heintz-Buschart A, Tarkka MT. Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere. Front Microbiol 2021; 12:616828. [PMID: 33613486 PMCID: PMC7891401 DOI: 10.3389/fmicb.2021.616828] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/04/2023] Open
Abstract
Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the acdS gene. We stated the hypothesis that the relative phylogenetic distribution of acdS carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective rth3 mutant in the substrates loam and sand, and harvest was implemented from three depths. Most acdS sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. Variovorax, Acidovorax, and Ralstonia sequences dominated in loam, whereas Streptomyces and Agromyces were more abundant in sand. Soil depth caused strong variations in acdS sequence distribution, with differential levels in the relative abundances of acdS sequences affiliated to Tetrasphaera, Amycolatopsis, and Streptomyces in loam, but Burkholderia, Paraburkholderia, and Variovorax in sand. Maize genotype influenced the distribution of acdS sequences mainly in loam and only in the uppermost depth. Variovorax acdS sequences were more abundant in WT, but Streptomyces, Microbacterium, and Modestobacter in rth3 rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of acdS carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere acdS carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on acdS carrying bacterial populations.
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Affiliation(s)
- Lucie Gebauer
- Helmholtz Centre for Environmental Research, Halle, Germany
| | | | - Minh Ganther
- Helmholtz Centre for Environmental Research, Halle, Germany
| | - Bunlong Yim
- Julius Kühn-Institute, Braunschweig, Germany
| | - Doris Vetterlein
- Helmholtz Centre for Environmental Research, Halle, Germany.,Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | | | - François Buscot
- Helmholtz Centre for Environmental Research, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Anna Heintz-Buschart
- Helmholtz Centre for Environmental Research, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mika T Tarkka
- Helmholtz Centre for Environmental Research, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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