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Filippova N, Zvyagina E, Rudykina EA, Ishmanov TF, Filippov IV, Bulyonkova TM, Dobrynina AS. DNA-based occurrence dataset on peatland fungal communities studied by metabarcoding in north-western Siberia. Biodivers Data J 2024; 12:e119851. [PMID: 38586530 PMCID: PMC10998959 DOI: 10.3897/bdj.12.e119851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background The paper represents the first DNA-based occurrence dataset on peatland fungal communities published for north-western Siberia, the first for Russia and complements several existing datasets on metabarcoding of peat soils globally. New information The aim of the present publication is to describe the first DNA-based occurrence dataset on fungal communities in peat soils and other substrates studied by the eDNA approach in the Mukhrino raised bog, located in a large paludified area of north-western Siberia. A comparison of the species diversity of larger fungi identified by the conventional approach and by eDNA showed a high proportion of shared taxa. Other groups (mainly Ascomycota), described by metabarcoding, revealed high diversity compared with conventional observation. Overall, the species richness identified in one peatland locality (the Mukhrino Bog) was comparable in number of species to the global estimation of fungal diversity in peatlands, previously reported in literature.
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Affiliation(s)
- Nina Filippova
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Elena Zvyagina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
- Moscow State University, Moscow, RussiaMoscow State UniversityMoscowRussia
| | - Elena A. Rudykina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Tagir F. Ishmanov
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Ilya V. Filippov
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | | | - Alevtina S. Dobrynina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
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Filippova N, Zvyagina E, Rudykina E, Dobrynina A, Bolshakov S. The diversity of macromycetes in peatlands: nine years of plot-based monitoring and barcoding in the raised bog "Mukhrino", West Siberia. Biodivers Data J 2023; 11:e105111. [PMID: 37901679 PMCID: PMC10612115 DOI: 10.3897/bdj.11.e105111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Background Peatland ecosystems are defined by soils with sufficient under-decomposed organic layer, called peat, formed under anoxic conditions. Peatlands are widespread around the world, with several highly paludified regions, one of which is the Western Siberian Plain. Peatlands store large amounts of carbon and are important in their intact state to counteract climate change, as well as for a variety of other ecosystem functions. From the practical aspect, these ecosystems are used as a source of peat for fuel, peat-based fertilisers and growing media, berries and Sphagnum plantations. Fungi are the key part of the decomposer community of peatlands, playing a critical role in the aerobic decomposition in the upper peat layer. The community of peatland fungi is adapted to decomposition of peat and dead parts of Sphagnum in wet acidic conditions; they form specific mycorrhizal associations with a variety of plants. Thus, the research of fungal diversity of peatlands is important for several reasons: 1) adding knowledge of peatland fungal diversity to local or global biodiversity databases; 2) studying carbon cycling in peatlands; 3) using peat and peatlands for different applications, such as cultivation of Sphagnum with regards to some parasitic species of fungi and 4) peatland restoration and conservation, to mention a few. New information The community of macromycetes of the raised bog "Mukhrino" in Western Siberia was studied using plot-based monitoring throughout a 9-year observation period. The revealed species diversity is represented by approximately 500 specimens in the Fungarium of Yugra State University collection. Selected specimens were used for barcoding of the ITS region to reveal a total of 95 species from 33 genera and three classes. The barcoding effort confirmed morphological identifications for most specimens and identified a number of cryptic species and several potentially new taxa. Based on regular all-season observations, we describe the phenology of the community sporophore production. The quantitative community structure, based on sporophores, revealed a difference in abundance between species by four orders of magnitude, with rare species representing nearly half of the species list. The inter-annual fruiting abundance varied several times by the total number of sporophores per year. To make the comparisons with global studies, we created an open access database of literature-based observations of fungi in peatlands, based on about 120 published papers (comprising about 1300 species) and compared our species list with this database.As a result, the study created an accurate representation of taxonomic and quantitative structure of the community of macromycetes in raised bogs in the region. The raw data of plot-based counts was published as a sampling-event dataset and the sequenced specimens with the sequence information as an DNA-derived extension dataset in GBIF.
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Affiliation(s)
- Nina Filippova
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Elena Zvyagina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
- Lomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State UniversityMoscowRussia
| | - Elena Rudykina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Alevtina Dobrynina
- Yugra State University, Khanty-Mansiysk, RussiaYugra State UniversityKhanty-MansiyskRussia
| | - Sergey Bolshakov
- Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, RussiaKomarov Botanical Institute of the Russian Academy of SciencesSaint PetersburgRussia
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Birnbaum C, Wood J, Lilleskov E, Lamit LJ, Shannon J, Brewer M, Grover S. Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland. MICROBIAL ECOLOGY 2023; 85:875-891. [PMID: 35867139 PMCID: PMC10156627 DOI: 10.1007/s00248-022-02071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/01/2022] [Indexed: 05/04/2023]
Abstract
Peatland ecosystems cover only 3% of the world's land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.
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Affiliation(s)
- Christina Birnbaum
- Applied Chemistry and Environmental Science, School of Science, RMIT University Melbourne, Victoria, 3001, Australia.
- School of Life and Environmental Sciences, Faculty of Science & Built Environment, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia.
- School of Agriculture and Environmental Science, The University of Southern Queensland, Toowoomba, QLD, 4350, Australia.
| | - Jennifer Wood
- Physiology, Anatomy and Microbiology, La Trobe University, Science Drive, Bundoora, VIC, 3086, Australia
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, 410 MacInnes Dr, Houghton, MI, 49931, USA
| | - Louis James Lamit
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - James Shannon
- Research Centre for Applied Alpine Ecology, Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Matthew Brewer
- Physiology, Anatomy and Microbiology, La Trobe University, Science Drive, Bundoora, VIC, 3086, Australia
| | - Samantha Grover
- Applied Chemistry and Environmental Science, School of Science, RMIT University Melbourne, Victoria, 3001, Australia
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Pastukhov A, Kovaleva V, Kaverin D. Microbial Community Structure in Ancient European Arctic Peatlands. PLANTS (BASEL, SWITZERLAND) 2022; 11:2704. [PMID: 36297728 PMCID: PMC9607101 DOI: 10.3390/plants11202704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Northern peatlands, which are crucial reservoirs of carbon and nitrogen (415 ± 150 and 10 ± 7 Pg, respectively), are vulnerable to microbial mineralization after permafrost thaw. This study was carried out in four key sites containing northern permafrost peatland, which are located along the southern cryolithozone. The aim of this study is to characterize amino acids and the microbial community composition in peat strata along a climate gradient. Amino acids and microbiota diversity were studied by liquid chromatography and a quantitative polymerase chain reaction. The share of amino acid fragments was 2.6-7.8, and it is highly significantly correlated (r = 0.87, -0.74 and 0.67, p ˂ 0.05) with the organic nitrogen concentration in the soil, the C/N ratio, and δ15N. The data shows the existence of a large pool of microorganisms concentrated in permafrost peatlands, and a vertical continuum of bacteria, archaea, and microscopic fungi along the peat profile, due to the presence of microorganisms in each layer, throughout all the peat strata. There is no significant correlation between microorganism distribution and the plant macrofossil composition of the peat strata. Determining factors for the development of microorganism abundance are aeration and hydrothermal conditions. The availability of nitrogen will limit the ability of plants and microorganisms to respond to changing environmental conditions; however, with the increased decomposition of organic matter, amino acids will be released as organic sources of nitrogen stored in the protein material of peat-forming plants and microbial communities, which can also affect the organic nitrogen cycle.
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Affiliation(s)
- Alexander Pastukhov
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
- BIO-GEO-CLIM Laboratory, National Research Tomsk State University, Lenina 36, 634050 Tomsk, Russia
| | - Vera Kovaleva
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
| | - Dmitry Kaverin
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
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Panis F, Rompel A. The Novel Role of Tyrosinase Enzymes in the Storage of Globally Significant Amounts of Carbon in Wetland Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11952-11968. [PMID: 35944157 PMCID: PMC9454253 DOI: 10.1021/acs.est.2c03770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
Over the last millennia, wetlands have been sequestering carbon from the atmosphere via photosynthesis at a higher rate than releasing it and, therefore, have globally accumulated 550 × 1015 g of carbon, which is equivalent to 73% of the atmospheric carbon pool. The accumulation of organic carbon in wetlands is effectuated by phenolic compounds, which suppress the degradation of soil organic matter by inhibiting the activity of organic-matter-degrading enzymes. The enzymatic removal of phenolic compounds by bacterial tyrosinases has historically been blocked by anoxic conditions in wetland soils, resulting from waterlogging. Bacterial tyrosinases are a subgroup of oxidoreductases that oxidatively remove phenolic compounds, coupled to the reduction of molecular oxygen to water. The biochemical properties of bacterial tyrosinases have been investigated thoroughly in vitro within recent decades, while investigations focused on carbon fluxes in wetlands on a macroscopic level have remained a thriving yet separated research area so far. In the wake of climate change, however, anoxic conditions in wetland soils are threatened by reduced rainfall and prolonged summer drought. This potentially allows tyrosinase enzymes to reduce the concentration of phenolic compounds, which in turn will increase the release of stored carbon back into the atmosphere. To offer compelling evidence for the novel concept that bacterial tyrosinases are among the key enzymes influencing carbon cycling in wetland ecosystems first, bacterial organisms indigenous to wetland ecosystems that harbor a TYR gene within their respective genome (tyr+) have been identified, which revealed a phylogenetically diverse community of tyr+ bacteria indigenous to wetlands based on genomic sequencing data. Bacterial TYR host organisms covering seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Planctomycetes, and Proteobacteria) have been identified within various wetland ecosystems (peatlands, marshes, mangrove forests, bogs, and alkaline soda lakes) which cover a climatic continuum ranging from high arctic to tropic ecosystems. Second, it is demonstrated that (in vitro) bacterial TYR activity is commonly observed at pH values characteristic for wetland ecosystems (ranging from pH 3.5 in peatlands and freshwater swamps to pH 9.0 in soda lakes and freshwater marshes) and toward phenolic compounds naturally present within wetland environments (p-coumaric acid, gallic acid, protocatechuic acid, p-hydroxybenzoic acid, caffeic acid, catechin, and epicatechin). Third, analyzing the available data confirmed that bacterial host organisms tend to exhibit in vitro growth optima at pH values similar to their respective wetland habitats. Based on these findings, it is concluded that, following increased aeration of previously anoxic wetland soils due to climate change, TYRs are among the enzymes capable of reducing the concentration of phenolic compounds present within wetland ecosystems, which will potentially destabilize vast amounts of carbon stored in these ecosystems. Finally, promising approaches to mitigate the detrimental effects of increased TYR activity in wetland ecosystems and the requirement of future investigations of the abundance and activity of TYRs in an environmental setting are presented.
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Hinzke T, Li G, Tanneberger F, Seeber E, Aggenbach C, Lange J, Kozub Ł, Knorr K, Kreyling J, Kotowski W. Potentially peat‐forming biomass of fen sedges increases with increasing nutrient levels. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tjorven Hinzke
- Department of Experimental Plant Ecology Institute of Botany and Landscape Ecology University of GreifswaldPartner in the Greifswald Mire Centre Greifswald Germany
| | - Guixiang Li
- Department of Ecology and Environmental Conservation Institute of Environmental Biology Faculty of Biology University of Warsaw Warsaw Poland
| | - Franziska Tanneberger
- Department of Experimental Plant Ecology Institute of Botany and Landscape Ecology University of GreifswaldPartner in the Greifswald Mire Centre Greifswald Germany
| | - Elke Seeber
- Department of Experimental Plant Ecology Institute of Botany and Landscape Ecology University of GreifswaldPartner in the Greifswald Mire Centre Greifswald Germany
| | - Camiel Aggenbach
- Ecosystem Management Research Group Department of Biology University of Antwerp Antwerp Belgium
- KWR Water Research Institute Nieuwegein The Netherlands
| | - Jelena Lange
- Department of Experimental Plant Ecology Institute of Botany and Landscape Ecology University of GreifswaldPartner in the Greifswald Mire Centre Greifswald Germany
- Department of Physical Geography and Geoecology, Faculty of Science Charles University Prague Czech Republic
| | - Łukasz Kozub
- Department of Ecology and Environmental Conservation Institute of Environmental Biology Faculty of Biology University of Warsaw Warsaw Poland
| | - Klaus‐Holger Knorr
- Ecohydrology & Biogeochemistry Group Institute of Landscape Ecology University of Münster Münster Germany
| | - Juergen Kreyling
- Department of Experimental Plant Ecology Institute of Botany and Landscape Ecology University of GreifswaldPartner in the Greifswald Mire Centre Greifswald Germany
| | - Wiktor Kotowski
- Department of Ecology and Environmental Conservation Institute of Environmental Biology Faculty of Biology University of Warsaw Warsaw Poland
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Asemaninejad A, Thorn RG, Branfireun BA, Lindo Z. Vertical stratification of peatland microbial communities follows a gradient of functional types across hummock–hollow microtopographies. ECOSCIENCE 2019. [DOI: 10.1080/11956860.2019.1595932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Asma Asemaninejad
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Vale Living with Lakes Centre, Laurentian University, Sudbury, Ontario, Canada
| | - R. Greg Thorn
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Brian A. Branfireun
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Centre for Environment and Sustainability, University of Western Ontario, London, Ontario, Canada
| | - Zoë Lindo
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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Ballaud F, Dufresne A, Francez AJ, Colombet J, Sime-Ngando T, Quaiser A. Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat. Front Microbiol 2016; 6:1494. [PMID: 26779149 PMCID: PMC4701944 DOI: 10.3389/fmicb.2015.01494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/11/2015] [Indexed: 11/23/2022] Open
Abstract
Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 106 to 5.6 x 108 particles mL-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.
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Affiliation(s)
- Flore Ballaud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
| | | | | | - Jonathan Colombet
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Télesphore Sime-Ngando
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Achim Quaiser
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
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Görres CM, Conrad R, Petersen SO. Effect of soil properties and hydrology on archaeal community composition in three temperate grasslands on peat. FEMS Microbiol Ecol 2013; 85:227-40. [PMID: 23521431 DOI: 10.1111/1574-6941.12115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/13/2013] [Accepted: 03/13/2013] [Indexed: 11/28/2022] Open
Abstract
Grasslands established on drained peat soils are regarded as negligible methane (CH4 ) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark. We used terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and clone libraries to characterize the soils' archaeal community composition to gain a better understanding of relationships between peat properties and land use, respectively, and CH4 dynamics. Samples were taken at three different depths and at four different seasons. Archaeal community composition varied considerably between the three peatlands and, to a certain degree, also with peat depth, but seemed to be quite stable at individual sampling depths throughout the year. Archaeal community composition was mainly linked to soil pH. No methanogens were detected at one fen site with soil pH ranging from 3.2 to 4.4. The methanogenic community of the bog (soil pH 3.9-4.6) was dominated by hydrogenotrophs, whereas the second fen site (soil pH 5.0-5.3) comprised both aceticlastic and hydrogenotrophic methanogens. Overall, there seemed to be a significant coupling between peat type and archaeal community composition, with local hydrology modifying the strength of this coupling.
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