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Acetoclastic archaea adaptation under increasing temperature in lake sediments and wetland soils from Alaska. Polar Biol 2023. [DOI: 10.1007/s00300-023-03120-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Rakitin AL, Begmatov S, Beletsky AV, Philippov DA, Kadnikov VV, Mardanov AV, Dedysh SN, Ravin NV. Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire. Microorganisms 2022; 10:microorganisms10010170. [PMID: 35056619 PMCID: PMC8778904 DOI: 10.3390/microorganisms10010170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.
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Affiliation(s)
- Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia;
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
- Correspondence: or
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Wu D, Zhao C, Bai H, Feng F, Sui X, Sun G. Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China. Ecol Evol 2021; 11:10396-10408. [PMID: 34367583 PMCID: PMC8328403 DOI: 10.1002/ece3.7842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/07/2021] [Accepted: 06/10/2021] [Indexed: 01/12/2023] Open
Abstract
Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.
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Affiliation(s)
- Di Wu
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Caihong Zhao
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Hui Bai
- Key Laboratory of Fast‐Growing Tree Cultivating of Heilongjiang ProvinceForestry Science Research Institute of Heilongjiang ProvinceHarbinChina
| | - Fujuan Feng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold RegionSchool of Life SciencesHeilongjiang UniversityHarbinChina
| | - Guangyu Sun
- Key Laboratory of Saline‐Alkali Vegetation Ecology Restoration (Northeast Forestry University)Ministry of EducationHarbinChina
- College of Life ScienceNortheast Forestry UniversityHarbinChina
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L. Bräuer S, Basiliko N, M. P. Siljanen H, H. Zinder S. Methanogenic archaea in peatlands. FEMS Microbiol Lett 2020; 367:5928548. [DOI: 10.1093/femsle/fnaa172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.
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Affiliation(s)
- Suzanna L. Bräuer
- Appalachian State University, Department of Biology, ASU Box 32027, 572 Rivers Street, Boone, NC 28608-2027 USA
| | - Nathan Basiliko
- Laurentian University, Department of Biology and the Vale Living with Lakes Centre, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
| | - Henri M. P. Siljanen
- Eastern Finland University, Department of Environmental and Biological Sciences, Biogeochemistry Research Group, Snellmania Room 4042, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Stephen H. Zinder
- Cornell University, Department of Microbiology, 272 Wing Hall, Ithaca, NY 14850, USA
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Chroňáková A, Bárta J, Kaštovská E, Urbanová Z, Picek T. Spatial heterogeneity of belowground microbial communities linked to peatland microhabitats with different plant dominants. FEMS Microbiol Ecol 2020; 95:5551480. [PMID: 31425589 DOI: 10.1093/femsec/fiz130] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/16/2019] [Indexed: 11/13/2022] Open
Abstract
Peatland vegetation is composed mostly of mosses, graminoids and ericoid shrubs, and these have a distinct impact on peat biogeochemistry. We studied variation in soil microbial communities related to natural peatland microhabitats dominated by Sphagnum, cotton-grass and blueberry. We hypothesized that such microhabitats will be occupied by structurally and functionally different microbial communities, which will vary further during the vegetation season due to changes in temperature and photosynthetic activity of plant dominants. This was addressed using amplicon-based sequencing of prokaryotic and fungal rDNA and qPCR with respect to methane-cycling communities. Fungal communities were highly microhabitat-specific, while prokaryotic communities were additionally directed by soil pH and total N content. Seasonal alternations in microbial community composition were less important; however, they influenced the abundance of methane-cycling communities. Cotton-grass and blueberry bacterial communities contained relatively more α-Proteobacteria but less Chloroflexi, Fibrobacteres, Firmicutes, NC10, OD1 and Spirochaetes than in Sphagnum. Methanogens, syntrophic and anaerobic bacteria (i.e. Clostridiales, Bacteroidales, Opitutae, Chloroflexi and Syntrophorhabdaceae) were suppressed in blueberry indicating greater aeration that enhanced abundance of fungi (mainly Archaeorhizomycetes) and resulted in the highest fungi-to-bacteria ratio. Thus, microhabitats dominated by different vascular plants are inhabited by unique microbial communities, contributing greatly to spatial functional diversity within peatlands.
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Affiliation(s)
- Alica Chroňáková
- Biology Centre, CAS, Institute of Soil Biology and SoWa RI, Na Sádkách 7, České Budějovice 370 05, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Eva Kaštovská
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Zuzana Urbanová
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Tomáš Picek
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
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Ivanova AA, Beletsky AV, Rakitin AL, Kadnikov VV, Philippov DA, Mardanov AV, Ravin NV, Dedysh SN. Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens. Microorganisms 2020; 8:microorganisms8040484. [PMID: 32235351 PMCID: PMC7232223 DOI: 10.3390/microorganisms8040484] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/21/2023] Open
Abstract
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia;
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
- Correspondence:
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
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Juottonen H. Disentangling the effects of methanogen community and environment on peatland greenhouse gas production by a reciprocal transplant experiment. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heli Juottonen
- Department of Biosciences, General Microbiology University of Helsinki Helsinki Finland
- Natural Resources Institute Finland Helsinki Finland
- Department of Biological and Environmental Sciences University of Jyväskylä Jyväskylä Finland
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Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog. Appl Environ Microbiol 2018; 84:AEM.02218-17. [PMID: 29180368 DOI: 10.1128/aem.02218-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA-based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.
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