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Espenberg M, Pille K, Yang B, Maddison M, Abdalla M, Smith P, Li X, Chan PL, Mander Ü. Towards an integrated view on microbial CH 4, N 2O and N 2 cycles in brackish coastal marsh soils: A comparative analysis of two sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170641. [PMID: 38325442 PMCID: PMC10884468 DOI: 10.1016/j.scitotenv.2024.170641] [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: 09/17/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.
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Affiliation(s)
- Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia; Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
| | - Kristin Pille
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Bin Yang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mohamed Abdalla
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Xiuzhen Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Ping-Lung Chan
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Malard LA, Bergk-Pinto B, Layton R, Vogel TM, Larose C, Pearce DA. Snow Microorganisms Colonise Arctic Soils Following Snow Melt. MICROBIAL ECOLOGY 2023; 86:1661-1675. [PMID: 36939866 PMCID: PMC10497451 DOI: 10.1007/s00248-023-02204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Benoit Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
- BioIT, TAG (Transversal Activities in Applied Genomics) Sciensano, 1050, Brussels, Belgium
| | - Rose Layton
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
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Lu Y, Cong P, Kuang S, Tang L, Li Y, Dong J, Song W. Long-term excessive application of K 2SO 4 fertilizer alters bacterial community and functional pathway of tobacco-planting soil. FRONTIERS IN PLANT SCIENCE 2022; 13:1005303. [PMID: 36247599 PMCID: PMC9554487 DOI: 10.3389/fpls.2022.1005303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 05/31/2023]
Abstract
To improve tobacco leaf quality, excessive K2SO4 fertilizers were applied to soils in major tobacco-planting areas in China. However, the effects of K2SO4 application on soil microbial community and functions are still unclear. An eight-year field experiment with three kinds of K2SO4 amounts (low amount, K2O 82.57 kg hm-2, LK; moderate amount, K2O 165.07 kg hm-2, MK; high amount, K2O 247.58 kg hm-2, HK) was established to assess the effects of K2SO4 application on the chemical and bacterial characteristics of tobacco-planting soil using 16S rRNA gene and metagenomic sequencing approaches. Results showed that HK led to lower pH and higher nitrogen (N), potassium (K), sulfur(S) and organic matter contents of the soil than LK. The bacterial community composition of HK was significantly different from those of MK and LK, while these of MK and LK were similar. Compared to LK, HK increased the relative abundance of predicted copiotrophic groups (e.g. Burkholderiaceae, Rhodospirillaceae families and Ellin6067 genus) and potentially beneficial bacteria (e.g. Gemmatimonadetes phylum and Bacillus genus) associated with pathogens and heavy metal resistance, N fixation, dissolution of phosphorus and K. While some oligotrophic taxa (e.g. Acidobacteria phylum) related to carbon, N metabolism exhibited adverse responses to HK. Metagenomic analysis suggested that the improvement of pathways related to carbohydrate metabolism and genetic information processing by HK might be the self-protection mechanism of microorganisms against environmental stress. Besides, the redundancy analysis and variation partitioning analysis showed that soil pH, available K and S were the primary soil factors in shifting the bacterial community and KEGG pathways. This study provides a clear understanding of the responses of soil microbial communities and potential functions to excessive application of K2SO4 in tobacco-planting soil.
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Affiliation(s)
- Ya Lu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ping Cong
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Shuai Kuang
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lina Tang
- Tobacco Science Research Institute, Fujian Tobacco Monopoly Administration, Fuzhou, China
| | - Yuyi Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxin Dong
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wenjing Song
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Finn DR, App M, Hertzog L, Tebbe CC. Reconciling concepts of black queen and tragedy of the commons in simulated bulk soil and rhizosphere prokaryote communities. Front Microbiol 2022; 13:969784. [PMID: 36187971 PMCID: PMC9520196 DOI: 10.3389/fmicb.2022.969784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The Black Queen hypothesis describes the evolutionary strategy to lose costly functions in favour of improving growth efficiency. This results in mutants (cheaters) becoming obligately dependent upon a provider (black queen) to produce a necessary resource. Previous analyses demonstrate black queens and cheaters reach a state of equilibrium in pair-wise systems. However, in complex communities, accumulation of cheaters likely poses a serious burden on shared resources. This should result in a Tragedy of the Commons (ToC), whereby over-utilisation of public resources risks making them growth-limiting. With a collection of differential equations, microbial communities composed of twenty prokaryote ‘species’ either from rhizosphere, characterised by abundant carbon and energy sources, or bulk soil, with limited carbon and energy supply, were simulated. Functional trait groups differed based on combinations of cellulase and amino acid production, growth and resource uptake. Randomly generated communities were thus composed of species that acted as cellulolytic prototrophic black queens, groups that were either cellulolytic or prototrophic, or non-cellulolytic auxotrophic cheaters. Groups could evolve to lose functions over time. Biomass production and biodiversity were tracked in 8,000 Monte Carlo simulations over 500 generations. Bulk soil favoured oligotrophic co-operative communities where biodiversity was positively associated with growth. Rhizosphere favoured copiotrophic cheaters. The most successful functional group across both environments was neither black queens nor cheaters, but those that balanced providing an essential growth-limiting function at a relatively low maintenance cost. Accumulation of loss of function mutants in bulk soil risked resulting in loss of cumulative growth by ToC, while cumulative growth increased in the rhizosphere. In the bulk soil, oligotrophic adaptations assisted species in avoiding extinction. This demonstrated that loss of function by mutation is a successful evolutionary strategy in host-associated and/or resource-rich environments, but poses a risk to communities that must co-operate with each other for mutual co-existence. It was concluded that microbial communities must follow different evolutionary and community assembly strategies in bulk soil versus rhizosphere, with bulk soil communities more dependent on traits that promote co-operative interactions between microbial species.
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Finn DR, Samad MS, Tebbe CC. One-step PCR amplicon sequencing libraries perform better than two-step when assessing soil microbial diversity and community profiles. FEMS Microbiol Lett 2022; 369:6674203. [PMID: 35998308 DOI: 10.1093/femsle/fnac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/13/2022] [Accepted: 08/17/2022] [Indexed: 11/14/2022] Open
Abstract
Despite adoption of high-throughput sequencing of PCR-amplified microbial taxonomic markers for ecological analyses, distinct approaches for preparing amplicon libraries exist. One approach utilises long fusion primers and a single PCR (one-step) while another utilises shorter primers in a first reaction, before transferring diluted amplicons to a second reaction for barcode index incorporation (two-step). We investigated whether transferring diluted amplicons risked creating artificially simplified, poorly diverse communities. In soils from three sites with paired cropland and forest, one-step yielded higher alpha-diversity indices, including detection of two-four times more unique taxa. Modelling expected taxa per sequence observation predicted that one-step reaches full coverage by 104 sequences per sample while two-step needs 105-109. Comparisons of rank abundance demonstrated that two-step covered only 38-69% of distributions. Beta-diversity showed better separation of communities in response to land use change under one-step, although both approaches showed a significant effect. Driving differences was underestimation of relatively minor taxa with the two-step procedure. These taxa were low in abundance, yet play important roles in carbon cycling, secondary metabolite production, anaerobic metabolism, and bacterial predation. We conclude that one-step amplicon libraries are advisable for studies focussed on diversity or relatively minor yet functionally important taxa.
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Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany
| | - Md Sainur Samad
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany
| | - Christoph C Tebbe
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany
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Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill. Appl Environ Microbiol 2022; 88:e0243821. [PMID: 35404071 PMCID: PMC9088289 DOI: 10.1128/aem.02438-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities mediate the transformation of organic matter within landfills into methane (CH4). Yet their ecological role in CH4 production is rarely evaluated. To characterize the microbiome associated with this biotransformation, the overall community and methanogenic Archaea were surveyed in an arid landfill using leachate collected from distinctly aged landfill cells (i.e., younger, intermediate, and older). We hypothesized that distinct methanogenic niches exist within an arid landfill, driven by geochemical gradients that developed under extended and age-dependent waste biodegradation stages. Using 16S rRNA and mcrA gene amplicon sequencing, we identified putative methanogenic niches as follows. The order Methanomicrobiales was the most abundant order in leachate from younger cells, where leachate temperature and propionate concentrations were measured at 41.8°C ± 1.7°C and 57.1 ± 10.7 mg L−1. In intermediate-aged cells, the family Methanocellaceae was identified as a putative specialist family under intermediate-temperature and -total dissolved solid (TDS) conditions, wherein samples had a higher alpha diversity index and near CH4 concentrations. In older-aged cells, accumulating metals and TDS supported Methanocorpusculaceae, “Candidatus Bathyarchaeota,” and “Candidatus Verstraetearchaeota” operational taxonomic units (OTUs). Consistent with the mcrA data, we assayed methanogenic activity across the age gradient through stable isotopic measurements of δ13C of CH4 and δ13C of CO2. The majority (80%) of the samples’ carbon fractionation was consistent with hydrogenotrophic methanogenesis. Together, we report age-dependent geochemical gradients detected through leachate in an arid landfill seemingly influencing CH4 production, niche partitioning, and methanogenic activity. IMPORTANCE Microbiome analysis is becoming common in select municipal and service ecosystems, including wastewater treatment and anaerobic digestion, but its potential as a microbial-status-informative tool to promote or mitigate CH4 production has not yet been evaluated in landfills. Methanogenesis mediated by Archaea is highly active in solid-waste microbiomes but is commonly neglected in studies employing next-generation sequencing techniques. Identifying methanogenic niches within a landfill offers detail into operations that positively or negatively impact the commercial production of methane known as biomethanation. We provide evidence that the geochemistry of leachate and its microbiome can be a variable accounting for ecosystem-level (coarse) variation of CH4 production, where we demonstrate through independent assessments of leachate and gas collection that the functional variability of an arid landfill is linked to the composition of methanogenic Archaea.
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Westoby M, Nielsen DA, Gillings MR, Gumerov VM, Madin JS, Paulsen IT, Tetu SG. Strategic traits of bacteria and archaea vary widely within substrate-use groups. FEMS Microbiol Ecol 2021; 97:6402898. [PMID: 34665251 DOI: 10.1093/femsec/fiab142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/14/2021] [Indexed: 11/12/2022] Open
Abstract
Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.
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Affiliation(s)
- Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Daniel A Nielsen
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Michae R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Vadim M Gumerov
- Department of Microbiology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Joshua S Madin
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2019, Australia
| | - Sasha G Tetu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2019, Australia
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Stone W, Lukashe NS, Blake LI, Gwandu T, Hardie AG, Quinton J, Johnson K, Clarke CE. The microbiology of rebuilding soils with water treatment residual co-amendments: Risks and benefits. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:1381-1394. [PMID: 34464455 DOI: 10.1002/jeq2.20286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Water treatment residual (WTR) is composed of sludges from the potable water treatment process, currently largely destined for landfill. This waste can be diverted to rebuild degraded soils, aligning with the UN's Sustainable Development Goals 12 (Consumption and Production) and 15 (Terrestrial Ecosystems). Biosolids are tested against stringent pathogen guidelines, yet few studies have explored the microbial risk of WTR land application, despite anthropogenic impacts on water treatment. We explored the microbial risks and benefits of amending nutrient-poor sandy soil with WTRs. Our results showed that the culturable pathogen load of wet and dry WTRs did not warrant pre-processing before land application, according to South African national quality guidelines, with fecal coliforms not exceeding 104 colony forming units per gram dry weight in wet sludges sampled from four South African and Zimbabwean water treatment plants and decreasing upon drying and processing. There was no culturable pathogenic (fecal coliforms, enterococci, Salmonella, and Shigella) regrowth in soil incubations amended with dry WTR. However, the competition (microbial load and diversity) introduced by a WTR co-amendment did not limit pathogen survival in soils amended with biosolids. Application of WTR to nutrient-poor sandy soils for wheat (Triticum aestivum L.) growth improved the prokaryotic and eukaryotic culturable cell concentrations, similar to compost. However, the compost microbiome more significantly affected the bacterial beta diversity of the receiving soil than WTR when analyzed with automated ribosomal intergenic spacer analysis. Thus, although there was a low pathogen risk for WTR amendment in receiving soils and total soil microbial loads were increased, microbial diversity was more significantly enhanced by compost than WTR.
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Affiliation(s)
- Wendy Stone
- Environmental Microbiology Laboratory, Dep. of Microbiology, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | - Noxolo S Lukashe
- Dep. of Soil Science, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | | | - Tariro Gwandu
- Dep. of Engineering, Durham Univ., Durham, DH1 3LE, UK
- Dep. of Soil Science & Environment, Univ. of Zimbabwe, Harare, Zimbabwe
| | - Ailsa G Hardie
- Dep. of Soil Science, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | - John Quinton
- Lancaster Environment Centre, Lancaster Univ., Lancaster, Lancashire, UK
| | - Karen Johnson
- Dep. of Engineering, Durham Univ., Durham, DH1 3LE, UK
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Finn DR, Lee S, Lanzén A, Bertrand M, Nicol GW, Hazard C. Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial. FEMS Microbiol Ecol 2021; 97:6374554. [PMID: 34555173 DOI: 10.1093/femsec/fiab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022] Open
Abstract
Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species-rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.
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Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, 38116 Braunschweig, Germany.,Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Sungeun Lee
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Anders Lanzén
- NEIKER, Basque Institute of Agricultural Research and Development, c/ Berreaga 1, 48160 Derio, Spain
| | - Michel Bertrand
- UMR Agronomie, INRAE AgroParisTech Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
| | - Christina Hazard
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134 Écully, France
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