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Rohrbach S, Gkoutselis G, Hink L, Weig AR, Obst M, Diekmann A, Ho A, Rambold G, Horn MA. Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field. Environ Microbiol 2023; 25:2681-2697. [PMID: 36224114 DOI: 10.1111/1462-2920.16234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022]
Abstract
Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.
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Affiliation(s)
- Stephan Rohrbach
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | - Alfons R Weig
- Genomics and Bioinformatics, University of Bayreuth, Bayreuth, Germany
| | - Martin Obst
- Experimental Biogeochemistry, BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Astrid Diekmann
- Deutsches Institut für Kautschuktechnologie e.V., Hannover, Germany
| | - Adrian Ho
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | - Gerhard Rambold
- Department of Mycology, University of Bayreuth, Bayreuth, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
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2
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Xiao Y, Wang X, Wang P, Zhou Z, Wang H, Teng T, Li Y, Yang L. New insights into multi-strategies of sludge granulation in up-flow anaerobic sludge blanket reactors from community succession and interaction. BIORESOURCE TECHNOLOGY 2023; 377:128935. [PMID: 36958683 DOI: 10.1016/j.biortech.2023.128935] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 06/18/2023]
Abstract
This study aimed to elucidate the multiple strategies employed by anaerobes during granulation in a laboratory upflow anaerobic sludge blanket reactor, based on microbial succession and interactions. The anaerobic granulation process featured staged dominance of microbial genera, corresponding well with the environmental traits. Across the stages (selection, seeding, expansion, and maturation), chemotaxis attraction of nitrogen and/or carbon sources and flagellar motion were the primary strategy of microbial assembly. The second messengers - cyclic adenosine and guanosine monophosphates - partially regulated the agglomeration of filamentous Euryachaeota and Chloroflexi as the inner cores, while quorum sensing mediated the expansion of granules prior to maturation. Antagonism or competition governed the interactions within the phylogenetic molecular ecological network during sludge granulation, which were largely driven by the low-abundance (<1%) taxa. These new insights suggest that better engineering solutions to enhance chemotaxis attraction and species selection could achieve more efficient anaerobic granular sludge processes.
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Affiliation(s)
- Yeyuan Xiao
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China.
| | - Xucai Wang
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China
| | - Peiling Wang
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China
| | - Zhongbo Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Tao Teng
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China
| | - Yiwei Li
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China
| | - Lei Yang
- College of Engineering, Shantou University, Shantou, Guangdong 515063, China
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3
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Crosbie DB, Mahmoudi M, Radl V, Brachmann A, Schloter M, Kemen E, Marín M. Microbiome profiling reveals that Pseudomonas antagonises parasitic nodule colonisation of cheater rhizobia in Lotus. THE NEW PHYTOLOGIST 2022; 234:242-255. [PMID: 35067935 DOI: 10.1111/nph.17988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Nodule microbiota are dominated by symbiotic nitrogen-fixing rhizobia, however, other non-rhizobial bacteria also colonise this niche. Although many of these bacteria harbour plant-growth-promoting functions, it is not clear whether these less abundant nodule colonisers impact root-nodule symbiosis. We assessed the relationship between the nodule microbiome and nodulation as influenced by the soil microbiome, by using a metabarcoding approach to characterise the communities inside nodules of healthy and starved Lotus species. A machine learning algorithm and network analyses were used to identify nodule bacteria of interest, which were re-inoculated onto plants in controlled conditions to observe their potential functionality. The nodule microbiome of all tested species differed according to inoculum, but only that of Lotus burttii varied with plant health. Amplicon sequence variants representative of Pseudomonas species were the most indicative non-rhizobial signatures inside healthy L. burttii nodules and negatively correlated with Rhizobium sequences. A representative Pseudomonas isolate co-colonised nodules infected with a beneficial Mesorhizobium, but not with an ineffective Rhizobium isolate and another even reduced the number of ineffective nodules induced on Lotus japonicus. Our results show that nodule endophytes influence the overall outcome of the root-nodule symbiosis, albeit in a plant host-specific manner.
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Affiliation(s)
| | - Maryam Mahmoudi
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Viviane Radl
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
| | | | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Centre for Environmental Health, Oberschleissheim, 85764, Germany
- Chair for Soil Science, Technical University of Munich, Freising, 85354, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Centre for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Macarena Marín
- Genetics, Biocentre, LMU Munich, Martinsried, 82152, Germany
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4
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Sanchez-Cid C, Tignat-Perrier R, Franqueville L, Delaurière L, Schagat T, Vogel TM. Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery. Biomolecules 2022; 12:biom12030364. [PMID: 35327556 PMCID: PMC8945597 DOI: 10.3390/biom12030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.
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Affiliation(s)
- Concepcion Sanchez-Cid
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
- Scientific Applications and Training, Promega France, 69100 Charbonnières-les-Bains, France;
- Correspondence:
| | - Romie Tignat-Perrier
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
- Institut des Géosciences de l’Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, 38400 Saint-Martin-d’Hères, France
| | - Laure Franqueville
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
| | - Laurence Delaurière
- Scientific Applications and Training, Promega France, 69100 Charbonnières-les-Bains, France;
| | - Trista Schagat
- Scientific Applications and Training, Promega Corporation, Madison, WI 53711, USA;
| | - Timothy M. Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 69134 Ecully, France; (R.T.-P.); (L.F.); (T.M.V.)
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5
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Llovet A, Mattana S, Chin-Pampillo J, Gascó G, Sánchez S, Mondini C, Briones MJI, Márquez L, Alcañiz JM, Ribas A, Domene X. Long-term effects of gasification biochar application on soil functions in a Mediterranean agroecosystem: Higher addition rates sequester more carbon but pose a risk to soil faunal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149580. [PMID: 34411789 DOI: 10.1016/j.scitotenv.2021.149580] [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: 05/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Biochar applications can have important implications for many of the soil functions upon which agroecosystems rely, particularly regarding organic carbon storage. This study evaluated the impacts of adding a highly aromatic gasification biochar at different rates (0, 12 and 50 t ha-1) to a barley crop on the provision of crucial soil functions (carbon sequestration, water content, greenhouse gas emissions, nutrient cycling, soil food web functioning, and food production). After natural ageing in the field for six years, a wide range of soil properties representative of the studied soil functions were measured and integrated into a soil quality index. Results showed that C sequestration increased with biochar rate (23 and 68% higher than in the control for the 12 and 50 t biochar ha-1 treatments, respectively). Water content was enhanced at the 50 t ha-1 treatment depending on the sampling date. Despite biochar additions neither abating nor increasing CO2 equivalent emissions (carbon dioxide plus nitrous oxide and methane), the system shifted from being a methane sink (-0.017 ± 0.01 mg CH4-C m-2 h-1 at the 12 t ha-1 treatment), to a net source (0.025 ± 0.02 mg CH4-C m-2 h-1 at the 50 t ha-1 treatment). In addition, biochar ageing provoked a loss of nitrate mitigation potential, and indeed ammonium production was stimulated at the 50 t ha-1 rate. The 50 t ha-1 treatment also adversely affected nematode and collembolan functional diversity. Lastly, biochar did not affect barley yield. The results of the soil quality index indicated that no biochar treatment provided more benefits to our agricultural soil, and, although the 50 t ha-1 treatment increased C sequestration, this was potentially offset by its harmful effects on soil faunal communities. Therefore, application of this biochar at high rates should be avoided to prevent risks to soil biological communities.
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Affiliation(s)
- Alba Llovet
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain.
| | - Stefania Mattana
- Research Group Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Wilrijk B-2610, Belgium
| | - Juan Chin-Pampillo
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain; Centro de Investigación en Contaminación Ambiental (CICA), Universidad de Costa Rica (UCR), San José, Costa Rica
| | - Gabriel Gascó
- Departamento de Producción Agraria, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2, 28040 Madrid, Spain
| | - Sara Sánchez
- Departamento de Medio Ambiente y Agronomía, Instituto Nacional de Investigación y Tecnología, Agraria y Alimentaria, Madrid, Spain
| | - Claudio Mondini
- CREA Research Centre for Viticulture and Enology, Via Trieste 23, 34170 Gorizia, Italy
| | | | - Laura Márquez
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Josep Maria Alcañiz
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Angela Ribas
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Xavier Domene
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
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6
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Hwang Y, Schulze-Makuch D, Arens FL, Saenz JS, Adam PS, Sager C, Bornemann TLV, Zhao W, Zhang Y, Airo A, Schloter M, Probst AJ. Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. MICROBIOME 2021; 9:234. [PMID: 34836555 PMCID: PMC8627038 DOI: 10.1186/s40168-021-01177-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core. RESULTS Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. CONCLUSION We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.
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Affiliation(s)
- Yunha Hwang
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dirk Schulze-Makuch
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany.
- Section Geomicrobiology, German Research Centre for Geosciences (GFZ), 14473, Potsdam, Germany.
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Stechlin, Germany.
- School of the Environment, Washington State University, Pullman, WA, 99164, USA.
| | - Felix L Arens
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Johan S Saenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Christof Sager
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Till L V Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Weishu Zhao
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Alessandro Airo
- Astrobiology Group, Center for Astronomy & Astrophysics, Technische Universität Berlin, 10623, Berlin, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, 85758, Oberschleißheim, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 , Essen, Germany.
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7
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Andrade-Linares DR, Zistl-Schlingmann M, Foesel B, Dannenmann M, Schulz S, Schloter M. Short term effects of climate change and intensification of management on the abundance of microbes driving nitrogen turnover in montane grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146672. [PMID: 34030328 DOI: 10.1016/j.scitotenv.2021.146672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/09/2023]
Abstract
Montane grasslands in Europe are exposed to increasing temperatures twice as fast as the global average. Changes in climatic conditions are possibly accompanied by an increase in land use intensity, caused by a prolongation of the vegetation period and the need to improve productivity. Therefore, the investigation of combined effects of climate change and land use intensity is needed to further implement agricultural management strategies. Here we present results from a study performed in the pre-alpine region of southern Germany, where intact plant-soil mesocosms from grasslands, were translocated along an altitudinal gradient, resulting in an increase in soil temperature (moderate treatment: +0.5 K; strong treatment: +1.9 K warming) during the experimental period. Additionally, we applied an extensive or intensive agricultural management (two vs. five times of mowing and slurry application) on the transplanted mesocosms. After an exposure of one year, we measured plant growth and soil properties and quantified abundances of soil microorganisms catalyzing key steps in the nitrogen (N) cycle. Our data indicate, significant interactions between climate change and management. For example, microbial biomass was significantly reduced (-47.7% and -49.8% for Cmic and Nmic respectively), which was further accompanied by lower abundances of N2-fixing bacteria (up to -89,3%), as well as ammonia oxidizing bacteria (-81.4%) under intensive management, whereas N-mineralizing bacteria increased in abundance (up to +139.8%) under extensive management. Surprisingly, the abundances of denitrifying bacteria as well as mean N2O emissions were not affected by the treatments. Overall, our data suggest pronounced shifts in the abundance of microbes driving the N cycle in soil as a result of combined climate change and land use intensification already after a short simulation period of one year.
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Affiliation(s)
- Diana R Andrade-Linares
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Marcus Zistl-Schlingmann
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Baerbel Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Dannenmann
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Soil Science, Technical University of Munich, Freising, Germany.
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8
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Schulze-Makuch D, Lipus D, Arens FL, Baqué M, Bornemann TLV, de Vera JP, Flury M, Frösler J, Heinz J, Hwang Y, Kounaves SP, Mangelsdorf K, Meckenstock RU, Pannekens M, Probst AJ, Sáenz JS, Schirmack J, Schloter M, Schmitt-Kopplin P, Schneider B, Uhl J, Vestergaard G, Valenzuela B, Zamorano P, Wagner D. Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. Microorganisms 2021; 9:microorganisms9051038. [PMID: 34065975 PMCID: PMC8151210 DOI: 10.3390/microorganisms9051038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
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Affiliation(s)
- Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
| | - Felix L. Arens
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Mickael Baqué
- German Aerospace Center (DLR), Institute of Planetary Research, 12489 Berlin, Germany;
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Microgravity User Support Center (MUSC), 51147 Cologne, Germany;
| | - Markus Flury
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
- Department of Crop and Soil Science, Washington State University, Puyallup, WA 98371, USA
| | - Jan Frösler
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jacob Heinz
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Yunha Hwang
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Samuel P. Kounaves
- Department of Chemistry, Tufts University, Boston, MA 02155, USA;
- Department of Earth Science & Engineering, Imperial College London, London SW7 2AZ, UK
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, 14473 Potsdam, Germany;
| | - Rainer U. Meckenstock
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Johan S. Sáenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Janosch Schirmack
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Beate Schneider
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Jenny Uhl
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
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9
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Duffner C, Holzapfel S, Wunderlich A, Einsiedl F, Schloter M, Schulz S. Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material. FEMS Microbiol Ecol 2021; 97:6081091. [PMID: 33428716 DOI: 10.1093/femsec/fiab004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022] Open
Abstract
Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Sebastian Holzapfel
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Anja Wunderlich
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Florian Einsiedl
- Chair of Hydrogeology, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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10
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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11
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Llovet A, Mattana S, Chin-Pampillo J, Otero N, Carrey R, Mondini C, Gascó G, Martí E, Margalef R, Alcañiz JM, Domene X, Ribas A. Fresh biochar application provokes a reduction of nitrate which is unexplained by conventional mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142430. [PMID: 33011595 DOI: 10.1016/j.scitotenv.2020.142430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/06/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Soil-applied biochar has been reported to possess the potential to mitigate nitrate leaching and thus, exert beneficial effects beyond carbon sequestration. The main objective of the present study is to confirm if a pine gasification biochar that has proven able to decrease soil-soluble nitrate in previous research can indeed exert such an effect and to determine by which mechanism. For this purpose, lysimeters containing soil-biochar mixtures at 0, 12 and 50 t biochar ha-1 were investigated in two different scenarios: a fresh biochar scenario consisting of fresh biochar and a fallow-managed soil, and an aged biochar scenario with a 6-yr naturally aged biochar in a crop-managed soil. Soil columns were assessed under a mimicked Mediterranean ambient within a greenhouse setting during an 8-mo period which included a barley crop cycle. A set of parameters related to nitrogen cycling, and particularly to mechanisms that could directly or indirectly explain nitrate content reduction (i.e., sorption, leaching, microbially-mediated processes, volatilisation, plant uptake, and ecotoxicological effects), were assessed. Specific measurements included soil solution and leachate ionic composition, microbial biomass and activity, greenhouse gas (GHG) emissions, N and O isotopic composition of nitrate, crop yield and quality, and ecotoxicological endpoints, among others. Nitrate content reduction in soil solution was verified for the fresh biochar scenario in both 12 and 50 t ha-1 treatments and was coupled to a significant reduction of chloride, sodium, calcium and magnesium. This effect was noticed only after eight months of biochar application thus suggesting a time-dependent process. All other mechanisms tested being discarded, the formation of an organo-mineral coating emerges as a plausible explanation for the ionic content decrease.
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Affiliation(s)
- Alba Llovet
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain.
| | - Stefania Mattana
- CREAF, Cerdanyola del Vallès 08193, Spain; Research Group Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Wilrijk, B-2610, Belgium
| | - Juan Chin-Pampillo
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain; Centro de Investigación en Contaminación Ambiental (CICA), Universidad de Costa Rica (UCR), San José, Costa Rica
| | - Neus Otero
- Grup de Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Martí i Franquès s/n, 08020 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA) de la Universitat de Barcelona (UB), Spain; Serra Húnter Fellowship, Generalitat de Catalunya, Spain
| | - Raúl Carrey
- Grup de Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Martí i Franquès s/n, 08020 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA) de la Universitat de Barcelona (UB), Spain
| | - Claudio Mondini
- CREA Research Centre for Viticulture and Enology, Via Trieste 23, 34170 Gorizia, Italy
| | - Gabriel Gascó
- Departamento de Producción Agraria, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2, 28040 Madrid, Spain
| | - Esther Martí
- Laboratori d'Edafologia, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
| | - Rosanna Margalef
- Grup de Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Martí i Franquès s/n, 08020 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA) de la Universitat de Barcelona (UB), Spain
| | - Josep Maria Alcañiz
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Xavier Domene
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain; Serra Húnter Fellowship, Generalitat de Catalunya, Spain
| | - Angela Ribas
- CREAF, Cerdanyola del Vallès 08193, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
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12
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Harris E, Diaz-Pines E, Stoll E, Schloter M, Schulz S, Duffner C, Li K, Moore KL, Ingrisch J, Reinthaler D, Zechmeister-Boltenstern S, Glatzel S, Brüggemann N, Bahn M. Denitrifying pathways dominate nitrous oxide emissions from managed grassland during drought and rewetting. SCIENCE ADVANCES 2021; 7:eabb7118. [PMID: 33547069 PMCID: PMC7864578 DOI: 10.1126/sciadv.abb7118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/07/2020] [Indexed: 05/19/2023]
Abstract
Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade.
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Affiliation(s)
- E Harris
- Plant, Soil and Ecosystem Processes Research Group, Department of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria.
| | - E Diaz-Pines
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - E Stoll
- Plant, Soil and Ecosystem Processes Research Group, Department of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
| | - M Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Soil Science, Technical University of Munich, 85354 Freising, Germany
| | - S Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - C Duffner
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Soil Science, Technical University of Munich, 85354 Freising, Germany
| | - K Li
- Department of Materials, Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - K L Moore
- Department of Materials, Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - J Ingrisch
- Plant, Soil and Ecosystem Processes Research Group, Department of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
| | - D Reinthaler
- Plant, Soil and Ecosystem Processes Research Group, Department of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
| | - S Zechmeister-Boltenstern
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - S Glatzel
- Geoecology, Department of Geography and Regional Research, Faculty of Geosciences, Geography, and Astronomy, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - N Brüggemann
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Agrosphere (IBG-3), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M Bahn
- Plant, Soil and Ecosystem Processes Research Group, Department of Ecology, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
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13
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Weithmann N, Mlinar S, Sonnleitner E, Weig AR, Freitag R. Flexible feeding in anaerobic digestion - Impact on process stability, performance and microbial community structures. Anaerobe 2020; 68:102297. [PMID: 33212292 DOI: 10.1016/j.anaerobe.2020.102297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/14/2020] [Accepted: 11/11/2020] [Indexed: 01/26/2023]
Abstract
Biogas has the potential to contribute to some of the most urgent issues of the energy transition, including mobility, energy storage, and grid stability. Flexibilization has been discussed as a means to improve the economics of biogas production, ideally restricting the production of electricity to times of strong need. Here the possibility of demand-driven, flexible biogas production is investigated, which saves substrates and storage capacity, while still enabling control over the production of electricity. Effects of different flexible feeding regimes were tested in a continuously operated 200 L reactor. After a period of 300 days under steady conditions (6.4 kg feed m-3d-1), varying flexible feeding patterns were applied over the next 700 days. Biogas production, volatile organic acid concentrations, and microbial dynamics were documented. Reduction of feeding resulted in reducing the gas production by up to 80% within a day. By increasing the feed, gas production could rapidly be reinitiated at similar levels as before even after fasting periods of up to 22 days. CH4-contents of the produced biogas were nearly constant over the investigation period. As a response to the flexible feeding, a reorganization of the microbial community was observed, which came to an end after 800 days and then was no longer affected by further changes in the feeding patterns or the substrate composition. Dominating archaea were of the order Methanosarcinales. During the experiment, representatives from the class Methanosaetaceae replaced representatives from the class Methanosarcinaceae.
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Affiliation(s)
- Nicolas Weithmann
- Process Biotechnology, Center for Energy Technology (ZET), University of Bayreuth, 95440, Bayreuth, Germany
| | - Stanislava Mlinar
- Process Biotechnology, Center for Energy Technology (ZET), University of Bayreuth, 95440, Bayreuth, Germany
| | | | - Alfons Rupert Weig
- Genomics and Bioinformatics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Ruth Freitag
- Process Biotechnology, Center for Energy Technology (ZET), University of Bayreuth, 95440, Bayreuth, Germany.
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14
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Mlinar S, Weig AR, Freitag R. Influence of mixing and sludge volume on stability, reproducibility, and productivity of laboratory-scale anaerobic digestion. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Waheed H, Xiao Y, Hashmi I, Zhou Y. The selective pressure of quorum quenching on microbial communities in membrane bioreactors. CHEMOSPHERE 2020; 247:125953. [PMID: 32069724 DOI: 10.1016/j.chemosphere.2020.125953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/30/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
In conventional membrane bioreactor (MBR) treatment systems, Gram-negative bacterial population appears to be always outnumbered Gram-positive community. Thereby, acyl homoserine lactones (AHLs), major signaling molecules utilized by Gram-negative bacteria, have been targeted for biofouling control in quorum quenching (QQ) based studies. This study investigated the impact of AHL and autoinducer-2 (AI-2)-degrading QQ consortium on the selective accumulation of microbial communities in a QQ MBR (MBR-QQb). The results show that addition of the QQ consortium (in the form of beads) increased the filtration time of MBR-QQb by 3.5 times. The distribution of mixed liquor extracellular polymeric substances (EPS), especially the tightly bound (TB) proteinous EPS and the floc size were strongly affected by the QQ activity, and the endless 'battle' between QQ and quorum sensing (QS). More importantly, QQ induced the significant suppression of Gram-negative bacterial community. The average abundance of Gram-positive bacteria at the genus level in the biocake of MBR-QQb (51%) was significantly higher than that of the control MBR (11%) and the MBR with vacant beads (28%). These findings suggest that an unintended condition is created to favor the growth of Gram-positive bacteria in QQ MBRs, resulting in a distinct microbial social network in both bulk sludge and biocake.
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Affiliation(s)
- Hira Waheed
- Department of Civil and Environmental Engineering, Shantou University, Guangdong, 515063, China; Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Guangdong, 515063, China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Imran Hashmi
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan.
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
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16
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Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert. DIVERSITY 2019. [DOI: 10.3390/d11110205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.
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17
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Xiao Y, Yaohari H, Zhou Z, Sze CC, Stuckey DC. Autoinducer-2-mediated quorum sensing partially regulates the toxic shock response of anaerobic digestion. WATER RESEARCH 2019; 158:94-105. [PMID: 31022531 DOI: 10.1016/j.watres.2019.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
This study discovered a strong correlation between the autoinducer-2 (AI-2)-mediated quorum sensing (QS) with the performance of a submerged anaerobic membrane bioreactor during its recovery from a pentachlorophenol (PCP) shock: a decrease in AI-2 levels coincided with a reduction in volatile fatty acid concentrations, and corresponded significantly to a decrease in the relative abundance of Firmicutes, and to an increase in the relative abundance of Bacteroidetes and Synergistetes. Further batch experiments with the addition of an AI-2-regulating Escherichia coli mutant culture showed that a reduction in AI-2 levels resulted in the highest biogas production rate during a PCP shock. In contrast, an increase in AI-2 levels via addition of the E. coli wild type strain or an AI-2 precursor showed no obvious effects on biogas production. These results suggest that the AI-2 level in anaerobic sludge was governed primarily by Firmicutes, and the AI-2-mediated QS partially regulates the toxic shock response of anaerobic sludge via tuning the activities of Firmicutes and Synergistetes. A decrease in the AI-2 level might reduce acetogenesis and favor hydrogenotrophic methanogenesis, thus resulting in less VFA accumulation and higher methane production during the PCP shock. This study is the first of this type that exploits the role of quorum sensing in the toxic shock response of anaerobic sludge; it demonstrates a novel approach to shortening the recovery period of anaerobic processes via manipulating the AI-2-mediated QS.
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Affiliation(s)
- Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, 515063, China; Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Hazarki Yaohari
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Zhongbo Zhou
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore
| | - Chun Chau Sze
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - David C Stuckey
- Advanced Environmental Biotechnology Centre (AEBC), Nanyang Environment and Water Research Centre (NEWRI), Nanyang Technological University, 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
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18
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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19
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Grafe M, Goers M, von Tucher S, Baum C, Zimmer D, Leinweber P, Vestergaard G, Kublik S, Schloter M, Schulz S. Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:320-327. [PMID: 29687664 DOI: 10.1111/1758-2229.12651] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 04/05/2018] [Accepted: 04/08/2018] [Indexed: 05/28/2023]
Abstract
Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input.
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Affiliation(s)
- Martin Grafe
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
- Chair of Plant Nutrition, Technische Universität München Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Manuela Goers
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Sabine von Tucher
- Chair of Plant Nutrition, Technische Universität München Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Christel Baum
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Dana Zimmer
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Peter Leinweber
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
- Chair of Soil Science, Technische Universität München, Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
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20
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Baraniya D, Nannipieri P, Kublik S, Vestergaard G, Schloter M, Schöler A. The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley. MICROBIAL ECOLOGY 2018; 75:830-833. [PMID: 29110064 DOI: 10.1007/s00248-017-1101-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
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Affiliation(s)
- Divyashri Baraniya
- Department of Agrifood Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 28, 50144, Florence, Italy
| | - Paolo Nannipieri
- Department of Agrifood Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 28, 50144, Florence, Italy
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | - Anne Schöler
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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21
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Schulz S, Kölbl A, Ebli M, Buegger F, Schloter M, Fiedler S. Field-Scale Pattern of Denitrifying Microorganisms and N 2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil. MICROBIAL ECOLOGY 2017; 74:765-770. [PMID: 28492990 DOI: 10.1007/s00248-017-0991-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.
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Affiliation(s)
- Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Angelika Kölbl
- Department of Ecology and Ecosystem Management, Technical University of Munich, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Martin Ebli
- Institute for Geography, Soil Science, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 21, 55099, Mainz, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Sabine Fiedler
- Institute for Geography, Soil Science, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 21, 55099, Mainz, Germany.
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22
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Schäfer J, Weiß S, Jäckel U. Preliminary Validation of a Method Combining Cultivation and Cloning-Based Approaches to Monitor Airborne Bacteria. Ann Work Expo Health 2017. [DOI: 10.1093/annweh/wxx038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Shen N, Chen Y, Zhou Y. Multi-cycle operation of enhanced biological phosphorus removal (EBPR) with different carbon sources under high temperature. WATER RESEARCH 2017; 114:308-315. [PMID: 28259067 DOI: 10.1016/j.watres.2017.02.051] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/08/2016] [Accepted: 02/21/2017] [Indexed: 05/25/2023]
Abstract
Many studies reported that it is challenging to apply enhanced biological phosphorus removal (EBPR) process at high temperature. Glycogen accumulating organisms (GAOs) could easily gain their dominance over poly-phosphate accumulating organisms (PAOs) when the operating temperature was in the range of 25 °C-30 °C. However, a few successful EBPR processes operated at high temperature have been reported recently. This study aimed to have an in-depth understanding on the impact of feeding strategy and carbon source types on EBPR performance in tropical climate. P-removal performance of two EBPR systems was monitored through tracking effluent quality and cyclic studies. The results confirmed that EBPR was successfully obtained and maintained at high temperature with a multi-cycle strategy. More stable performance was observed with acetate as the sole carbon source compared to propionate. Stoichiometric ratios of phosphorus and carbon transformation during both anaerobic and aerobic phases were higher at high temperature than low temperature (20±1 °C) except anaerobic PHA/C ratios within most of the sub-cycles. Furthermore, the fractions of PHA and glycogen in biomass were lower compared with one-cycle pulse feed operation. The microbial community structure was more stable in acetate-fed sequencing batch reactor (C2-SBR) than that in propionate-fed reactor (C3-SBR). Accumulibacter Clade IIC was found to be highly abundant in both reactors.
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Affiliation(s)
- Nan Shen
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yun Chen
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
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24
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Weithmann N, Weig AR, Freitag R. Process parameters and changes in the microbial community patterns during the first 240 days of an agricultural energy crop digester. AMB Express 2016; 6:53. [PMID: 27485518 PMCID: PMC4970986 DOI: 10.1186/s13568-016-0219-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 07/08/2016] [Indexed: 12/27/2022] Open
Abstract
Commercial biogas production takes place by complex microbial communities enclosed in controlled "technical ecosystems". Once established, the communities tend to be resilient towards disturbances, although the relative abundance of their members may vary. The start-up phase, during which the community establishes itself, is therefore decisive for the later performance of the reactor. In this study, we followed the first 240 days of a standard agricultural energy crop digester consisting of a 400 m(3) plug flow fermenter and a 1000 m(3) agitated post digester, operated at 40-45 °C. The feed consisted of corn and later grass silage augmented by ground wheat. Changes in both the eubacterial and methanogenic archaeal communities were followed by automated ribosomal intergenic spacer analysis (ARISA). In addition the copy number of the methyl-coenzyme reductase A (mcrA)-genes found in all known methanogens were followed by quantitative PCR, while selected samples from two phases-one early, one late-of the community structure development were subjected to high throughput sequencing. Biogas volume and composition (CH4, CO2, H2, H2S, O2), pH, ammonia-N, and volatile fatty acids (VFA), were measured as part of the routine process control. VFA/TIC values were calculated on this basis. Whereas the total gas production of the plant established itself at about 2500 m(3) biogas per day within the first months, the composition of the microbial communities showed distinct spatial and temporal differences over the investigated time period. Absolute values for DNA isolation procedures are difficult to certify, hence comparative results on community structures obtained using standardized ARISA with identical primers are of value. Moreover, ARISA patterns can be statistically analyzed to identify distinct subgroups and transitions between them as well as serial correlations. Thereby the microbial community and its structural development can be correlated with statistical relevance to changes in operational (feed) and process parameters (pH-value, biogas composition). In particular when augmented by deep sequencing data of judiciously chosen samples, this allows a hitherto unknown level of insight into the performance of technical biogas plants.
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Affiliation(s)
- Nicolas Weithmann
- Process Biotechnology, Center for Energy Technology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Alfons Rupert Weig
- Genomics and Bioinformatics, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ruth Freitag
- Process Biotechnology, Center for Energy Technology, University of Bayreuth, 95440 Bayreuth, Germany
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25
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Barbato RA, Garcia-Reyero N, Foley K, Jones R, Courville Z, Douglas T, Perkins E, Reynolds CM. Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside. J Vis Exp 2016. [PMID: 27403572 DOI: 10.3791/54091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect conditions over vast time periods and investigation of biological materials harbored inside could provide insight of ancient environments. To appropriately analyze these ecosystems and extract meaningful biological information from frozen soils and ice, proper collection and processing of the frozen samples is necessary. This is especially critical for microbial and DNA analyses since the communities present may be so uniquely different from modern ones. Here, a protocol is presented to successfully collect and decontaminate frozen cores. Both the absence of the colonies used to dope the outer surface and exogenous DNA suggest that we successfully decontaminated the frozen cores and that the microorganisms detected were from the material, rather than contamination from drilling or processing the cores.
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Affiliation(s)
- Robyn A Barbato
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH;
| | - Natàlia Garcia-Reyero
- Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS
| | - Karen Foley
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Robert Jones
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Zoe Courville
- Terrestrial and Cryospheric Scienes Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Thomas Douglas
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Fairbanks, AK
| | - Edward Perkins
- Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS
| | - Charles M Reynolds
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Fairbanks, AK
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26
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Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil. J Microbiol Methods 2016; 125:91-7. [PMID: 27102665 DOI: 10.1016/j.mimet.2016.04.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/16/2016] [Accepted: 04/16/2016] [Indexed: 11/23/2022]
Abstract
Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.
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27
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Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed. Appl Environ Microbiol 2016; 82:2595-2607. [PMID: 26896137 DOI: 10.1128/aem.00019-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/13/2016] [Indexed: 12/18/2022] Open
Abstract
Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms.
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28
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Weise L, Ulrich A, Moreano M, Gessler A, Kayler ZE, Steger K, Zeller B, Rudolph K, Knezevic-Jaric J, Premke K. Water level changes affect carbon turnover and microbial community composition in lake sediments. FEMS Microbiol Ecol 2016; 92:fiw035. [PMID: 26902802 PMCID: PMC4821186 DOI: 10.1093/femsec/fiw035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 11/14/2022] Open
Abstract
Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. Climate changes can induce higher intensities of drying and rewetting of lake littoral zones, which in turn might result in higher allochthonous organic carbon uptake and decreased carbon storage.
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Affiliation(s)
- Lukas Weise
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany
| | - Matilde Moreano
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany
| | - Arthur Gessler
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany Swiss Federal Research Institute WSL, Zürcherstr. 111, CH-8903 Birmensdorf, Switzerland Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Zachary E Kayler
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany
| | - Kristin Steger
- University of California, Department of Viticulture and Enology, One Shields Avenue, Davis, CA 95616, USA
| | - Bernd Zeller
- INRA, Centre de Nancy Lorraine, UR 1138, Biogéochimie des Ecosystèmes Forestiers (BEF), Labex ARBRE, 54280 Champenoux, France
| | - Kristin Rudolph
- TU Chemnitz, Department of Psychology, Research Methods and Evaluation, 09107 Chemnitz, Germany
| | - Jelena Knezevic-Jaric
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Chemical Analytics and Biogeochemistry Müggelseedamm 310, D-12587 Berlin, Germany
| | - Katrin Premke
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg, Institute for Landscape Biogeochemistry, Eberswalderstr. 84, 15374 Müncheberg, Germany Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Chemical Analytics and Biogeochemistry Müggelseedamm 310, D-12587 Berlin, Germany
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29
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Bergkemper F, Schöler A, Engel M, Lang F, Krüger J, Schloter M, Schulz S. Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems. Environ Microbiol 2016; 18:1988-2000. [PMID: 26690731 DOI: 10.1111/1462-2920.13188] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/13/2015] [Accepted: 12/11/2015] [Indexed: 11/27/2022]
Abstract
Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus but conversely also take up and immobilize P. Therefore, we analysed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic deoxyribonucleic acid. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the data sets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harboured by Rhizobiales, Actinomycetales and Acidobacteriales.
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Affiliation(s)
- Fabian Bergkemper
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anne Schöler
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Friederike Lang
- Professur für Bodenökologie, Albert-Ludwigs-Universität Freiburg, Bertoldstr. 17, 79085, Freiburg i. Br, Germany
| | - Jaane Krüger
- Professur für Bodenökologie, Albert-Ludwigs-Universität Freiburg, Bertoldstr. 17, 79085, Freiburg i. Br, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Stefanie Schulz
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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Leite J, Fischer D, Rouws LFM, Fernandes-Júnior PI, Hofmann A, Kublik S, Schloter M, Xavier GR, Radl V. Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype. FRONTIERS IN PLANT SCIENCE 2016; 7:2064. [PMID: 28163711 PMCID: PMC5247471 DOI: 10.3389/fpls.2016.02064] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/26/2016] [Indexed: 05/04/2023]
Abstract
Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.
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Affiliation(s)
- Jakson Leite
- Soil Science Department, Universidade Federal Rural do Rio de JaneiroSeropédica, Brazil
| | - Doreen Fischer
- Embrapa AgrobiologiaSeropédica, Brazil
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | | | | | - Andreas Hofmann
- Embrapa AgrobiologiaSeropédica, Brazil
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | | | - Viviane Radl
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
- *Correspondence: Viviane Radl,
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Yang Q, Shen N, Lee ZMP, Xu G, Cao Y, Kwok B, Lay W, Liu Y, Zhou Y. Simultaneous nitrification, denitrification and phosphorus removal (SNDPR) in a full-scale water reclamation plant located in warm climate. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:448-456. [PMID: 27438250 DOI: 10.2166/wst.2016.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combination of simultaneous nitrification-denitrification (SND) with enhanced biological phosphorus removal (EBPR) provides a more efficient and economically viable option for nutrient removal from municipal wastewater compared to conventional two-step nitrification-denitrification. This study analyzed the nutrients (N and P) profiles in a full-scale municipal wastewater reclamation plant (WRP) located in the tropical region, in which more than 90% of nitrogen was removed. Interestingly, average SND efficiency in aerobic zones was found to be up to 50%, whereas phosphorus profile displayed a clear cyclic release and uptake pattern with a phosphorus removal efficiency of up to 76%. The capability of sludge to perform SND and EBPR was further confirmed through a series of batch experiments. Microbial analysis revealed the presence of Accumulibacter and Tetrasphaera phosphate accumulating organisms in the plant, while few glycogen accumulating organisms (GAO) was observed. This study showed the significant occurrence of combined SND and EBPR, known as simultaneous nitrification, denitrification and phosphorus removal (SNDPR), in the studied WRP under warm climate. The possible causes behind the observed SNDPR were also discussed.
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Affiliation(s)
- Qin Yang
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Interdisciplinary Graduate School, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Nan Shen
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Zarraz M-P Lee
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail:
| | - Guangjing Xu
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail:
| | - Yeshi Cao
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Beehong Kwok
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Winson Lay
- PUB, 40 Scotts Road # 15-01 Environment Building, Singapore 228231, Singapore
| | - Yu Liu
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore E-mail: ; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Soil bacterial community structure responses to precipitation reduction and forest management in forest ecosystems across Germany. PLoS One 2015; 10:e0122539. [PMID: 25875835 PMCID: PMC4397059 DOI: 10.1371/journal.pone.0122539] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/16/2015] [Indexed: 01/01/2023] Open
Abstract
Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season.
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Tournier E, Amenc L, Pablo AL, Legname E, Blanchart E, Plassard C, Robin A, Bernard L. Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents. MethodsX 2015; 2:182-91. [PMID: 26150987 PMCID: PMC4487712 DOI: 10.1016/j.mex.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/26/2015] [Indexed: 11/26/2022] Open
Abstract
An optimized method, based on the coupling of two commercial kits, is described for the extraction of soil nucleic acids, with simultaneous extraction and purification of DNA and RNA following a cascade scheme and avoiding the use of harmful solvents. The protocol canmonitor the variations in the recovery yield of DNA and RNA from soils of various types.The quantitative version of the protocol was obtained by testing the starting soil quantity, the grinding parameters and the final elution volumes, in order to avoid saturation of both kits. A first soil-crushing step in liquid nitrogen could be added for the assessment of fungal parameters. The protocol was efficienton different tropical soils, including Andosol, while their high contents of clays, including poorly crystalline clays, and Fe and Al oxides usually make the nucleic acid extraction more difficult. The RNA recovery yield from the previous tropical soils appeared to correlate better to soil respiration than DNA, which is positively influenced by soil clay content.
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Affiliation(s)
- E Tournier
- IRD, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - L Amenc
- INRA, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - A L Pablo
- IRD, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - E Legname
- INRA, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - E Blanchart
- IRD, UMR Eco&Sols-Laboratoire des RadioIsotopes (LRI), Ampandrianomby, Antananarivo 101, Madagascar
| | - C Plassard
- INRA, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - A Robin
- CIRAD, UMR Eco&Sols, 2 Place Viala, 34060 Montpellier Cedex 1, France
| | - L Bernard
- IRD, UMR Eco&Sols-Laboratoire des RadioIsotopes (LRI), Ampandrianomby, Antananarivo 101, Madagascar
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Young JM, Rawlence NJ, Weyrich LS, Cooper A. Limitations and recommendations for successful DNA extraction from forensic soil samples: A review. Sci Justice 2014; 54:238-44. [DOI: 10.1016/j.scijus.2014.02.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/12/2014] [Accepted: 02/18/2014] [Indexed: 11/15/2022]
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Fischer D, Pagenkemper S, Nellesen J, Peth S, Horn R, Schloter M. Influence of non-invasive X-ray computed tomography (XRCT) on the microbial community structure and function in soil. J Microbiol Methods 2013; 93:121-3. [DOI: 10.1016/j.mimet.2013.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 02/22/2013] [Accepted: 02/22/2013] [Indexed: 11/29/2022]
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Schäfer J, Klug K, van Kampen V, Jäckel U. Quantification of Saccharopolyspora rectivirgula in composting plants: assessment of the relevance of S. rectivirgula. ACTA ACUST UNITED AC 2013; 57:875-83. [PMID: 23579625 DOI: 10.1093/annhyg/met010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Exposure to bioaerosols in composting plants can lead to negative health effects on compost workers. Health complaints vary between cough, irritation of the eyes and the skin, sinusitis, or dyspnea among others. It is fact that compost materials harbor high concentrations of microorganisms, which were aerosolized during handling compost. Within the present study, total cell numbers between 3.4 × 10(4) and 1.6 × 10(8) cell counts per m(3) air were determined after 4',6-Diamidin-2-phenylindol DAPI staining in 124 samples from German composting plants. Special attention should be paid to some specific microorganisms, which are able to cause health complaints. Saccharopolyspora rectivirgula, known to be one of the major causes of extrinsic allergic alveolitis (EAA, also called hypersensitivity pneumonitis, HP), was often found in environments of agricultural production, where the classical form of EAA ('farmer's lung disease') is common, but also in composting plants. In Germany, cases are known where workers had to terminate their work due to this disease. However, up to now, the relevance of S. rectivirgula at composting plants is unexplained. This study showed that high concentrations of airborne S. rectivirgula were found in composting plants similar to that found in agricultural production. Altogether, in 86.7% of the 124 analyzed samples, S. rectivirgula was detected using quantitative real-time polymerase chain reaction (PCR). Estimated concentrations ranged between 1.24 × 10(2) cell counts of S. rectivirgula per cubic meter air next to the rotted residues and 1.5 × 10(7) cell counts next to a converter. Furthermore, our methodical proceedings were verified. To analyze DNA extraction limits through the amount of cells within one sample, the DNA concentration was compared with total cell counts (TCCs). Altogether, when TCC was <1.4 × 10(5) cells per DNA extraction assay, no DNA was measurable; when TCC reached 3.5 × 10(6) cells, DNA was always detectable by fluorometric method. To overcome limitation of DNA measurement using fluorometric method, samples without measurable DNA were inserted in a PCR assay with universal primers. Results showed that a gain of 37% was possible, when samples were additionally analyzed by universal PCR. Hence, cell counts >2.0 × 10(6) cells were necessary to measure DNA concentrations in 90% of the analyzed samples, whereas cell counts <3.0 × 10(5) are sufficient to detect PCR products. Therefore, sampling of bioaerosols should be done in consideration of the expected cell count per cubic meter air. Note, to get measurable DNA using a fluorometer, >3.5 × 10(6) cells must be sampled for one DNA extraction assay. With this study, the real-time PCR approach for the detection of S. rectivirgula at workplaces in compost plants was revised, and the results revealed that this method is suitable for occupational exposure measurements.
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Affiliation(s)
- Jenny Schäfer
- Federal Institute for Occupational Safety and Health, Berlin, Germany.
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Knauth S, Schmidt H, Tippkötter R. Comparison of commercial kits for the extraction of DNA from paddy soils. Lett Appl Microbiol 2013; 56:222-8. [PMID: 23252687 DOI: 10.1111/lam.12038] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/20/2012] [Accepted: 12/07/2012] [Indexed: 11/28/2022]
Abstract
UNLABELLED The objective of this study was to compare the extraction efficiency of commercial DNA kits by evaluating the quantity and purity of DNA extracts obtained from paddy soils. DNA was extracted from three paddy soils using the FastDNA® SPIN kit for soil (FD), the innuSPEED soil DNA kit (INS) and the NucleoSpin® soil kit (NSP). DNA extracts were analysed by agarose gel electrophoresis and UV spectroscopy. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses were conducted to evaluate the potential bias of the DNA extractions on fingerprinting techniques. Regarding the quantity and the purity of the extracted DNA, the NSP kit was detected superior to the FD kit, while the INS kit failed to extract detectable amounts of DNA. DGGE fingerprints generated from PCR products (FD, NSP) showed high levels of similarity for the amplified 16S rRNA genes of methanogenic archaea (>95%) and bacteria (up to 100%) in each soil. This study suggested that the recently introduced NSP kit allowed for the adjustment of the lysis buffer composition to the soil of interest and is at least equivalent to the well-established FD kit for the extraction of DNA from paddy soils. SIGNIFICANCE AND IMPACT OF THE STUDY The choice of commercial kits (FD, INS, NSP) has been of great importance regarding the quantity and purity of DNA extracted from paddy soils in this study. The composition of the cell lysis buffer represented a key component for successful extractions of DNA from different soils. The possibility of adjusting the lysis buffer to the soil of interest as well as the reproducibility of DGGE banding patterns makes the recently introduced NSP kit a strong competitor to the well-established FD kit for the extraction of DNA from paddy soils.
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Affiliation(s)
- S Knauth
- University of Bremen, UFT, Bremen, Germany.
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Schulz S, Giebler J, Chatzinotas A, Wick LY, Fetzer I, Welzl G, Harms H, Schloter M. Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments. THE ISME JOURNAL 2012; 6:1763-74. [PMID: 22402403 PMCID: PMC3498921 DOI: 10.1038/ismej.2012.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 02/10/2012] [Accepted: 02/10/2012] [Indexed: 11/09/2022]
Abstract
Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.
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Affiliation(s)
- Stephan Schulz
- Chair of Soil Ecology, Technische Universität München, Neuherberg, Germany
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Giebler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Ingo Fetzer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Gerhard Welzl
- Institute of Developmental Genetics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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Sharma S, Mehta R, Gupta R, Schloter M. Improved protocol for the extraction of bacterial mRNA from soils. J Microbiol Methods 2012; 91:62-4. [PMID: 22841738 DOI: 10.1016/j.mimet.2012.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
An improved protocol for extraction of prokaryotic mRNA from soil samples was developed by modifying the extraction procedure to obtain higher yields of mRNA and to reduce co-extraction of humic acids. The modified protocol was found to be more robust and efficient compared to the original protocol by Griffiths et al. (2000) without compromising with the quality and quantity of RNA.
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Affiliation(s)
- Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Marty F, Ghiglione JF, Païssé S, Gueuné H, Quillet L, van Loosdrecht MCM, Muyzer G. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel. BIOFOULING 2012; 28:363-380. [PMID: 22500778 DOI: 10.1080/08927014.2012.672644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high NA yield, quality, purity, representativeness of microbial community and processing time efficiency). The PowerSoil RNA Isolation Kit was the only method which resulted in amplifiable RNA of good quality (ie intact 16S/23S rRNA). Sample homogenization and hot chemical (SDS) cell lysis combined with mechanical (bead-beating) lysis in presence of a DNA competitor (skim milk) contributed to improving substantially (around 23 times) the DNA yield of the PowerSoil DNA Isolation Kit. Apart from presenting NA extraction strategies for optimizing extraction parameters with corrosion samples from carbon steel, this study proposes DNA and RNA extraction procedures suited for comparative molecular analysis of total and active fractions of bacterial communities associated with carbon steel corrosion events, thereby contributing to improved MIC diagnosis and control.
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Affiliation(s)
- Florence Marty
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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