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Goraj W, Pytlak A, Grządziel J, Gałązka A, Stępniewska Z, Szafranek-Nakonieczna A. Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies. BIOLOGY 2023; 12:1420. [PMID: 37998019 PMCID: PMC10669130 DOI: 10.3390/biology12111420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.
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Affiliation(s)
- Weronika Goraj
- Department of Biology and Biotechnology of Microorganisms, Faculty of Medicine, The John Paul II Catholic University of Lublin, Str. Konstantynów 1I, 20-708 Lublin, Poland;
| | - Anna Pytlak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-280 Lublin, Poland;
| | - Jarosław Grządziel
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation–State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100 Puławy, Poland; (J.G.); (A.G.)
| | - Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation–State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100 Puławy, Poland; (J.G.); (A.G.)
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów 1 I, 20-708 Lublin, Poland;
| | - Anna Szafranek-Nakonieczna
- Department of Biology and Biotechnology of Microorganisms, Faculty of Medicine, The John Paul II Catholic University of Lublin, Str. Konstantynów 1I, 20-708 Lublin, Poland;
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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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Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region. Ecosystems 2021. [DOI: 10.1007/s10021-021-00713-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractPeatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.
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Zhang H, Tuittila ES, Korrensalo A, Laine AM, Uljas S, Welti N, Kerttula J, Maljanen M, Elliott D, Vesala T, Lohila A. Methane production and oxidation potentials along a fen-bog gradient from southern boreal to subarctic peatlands in Finland. GLOBAL CHANGE BIOLOGY 2021; 27:4449-4464. [PMID: 34091981 DOI: 10.1111/gcb.15740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4 ) emissions from northern peatlands are projected to increase due to climate change, primarily because of projected increases in soil temperature. Yet, the rates and temperature responses of the two CH4 emission-related microbial processes (CH4 production by methanogens and oxidation by methanotrophs) are poorly known. Further, peatland sites within a fen-bog gradient are known to differ in the variables that regulate these two mechanisms, yet the interaction between peatland type and temperature lacks quantitative understanding. Here, we investigated potential CH4 production and oxidation rates for 14 peatlands in Finland located between c. 60 and 70°N latitude, representing bogs, poor fens, and rich fens. Potentials were measured at three different temperatures (5, 17.5, and 30℃) using the laboratory incubation method. We linked CH4 production and oxidation patterns to their methanogen and methanotroph abundance, peat properties, and plant functional types. We found that the rich fen-bog gradient-related nutrient availability and methanogen abundance increased the temperature response of CH4 production, with rich fens exhibiting the greatest production potentials. Oxidation potential showed a steeper temperature response than production, which was explained by aerenchymous plant cover, peat water holding capacity, peat nitrogen, and sulfate content. The steeper temperature response of oxidation suggests that, at higher temperatures, CH4 oxidation might balance increased CH4 production. Predicting net CH4 fluxes as an outcome of the two mechanisms is complicated due to their different controls and temperature responses. The lack of correlation between field CH4 fluxes and production/oxidation potentials, and the positive correlation with aerenchymous plants points toward the essential role of CH4 transport for emissions. The scenario of drying peatlands under climate change, which is likely to promote Sphagnum establishment over brown mosses in many places, will potentially reduce the predicted warming-related increase in CH4 emissions by shifting rich fens to Sphagnum-dominated systems.
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Affiliation(s)
- Hui Zhang
- Institute for Atmospheric and Earth System Research (INAR), Department of Physics, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | | | - Aino Korrensalo
- Department of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Anna M Laine
- Department of Forest Sciences, University of Eastern Finland, Joensuu, Finland
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Geological Survey of Finland, Kuopio, Finland
| | - Salli Uljas
- Department of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Nina Welti
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johanna Kerttula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marja Maljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - David Elliott
- Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Timo Vesala
- Institute for Atmospheric and Earth System Research (INAR), Department of Physics, University of Helsinki, Helsinki, Finland
- Institute for Atmospheric and Earth System Research (INAR), Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Yugra State University, Khanty-Mansiysk, Russia
| | - Annalea Lohila
- Institute for Atmospheric and Earth System Research (INAR), Department of Physics, University of Helsinki, Helsinki, Finland
- Climate System Research, Finnish Meteorological Institute, Helsinki, Finland
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Li W, Chen H, Yan Z, Yang G, Rui J, Wu N, He Y. Variation in the Soil Prokaryotic Community Under Simulated Warming and Rainfall Reduction in Different Water Table Peatlands of the Zoige Plateau. Front Microbiol 2020; 11:343. [PMID: 32256463 PMCID: PMC7093333 DOI: 10.3389/fmicb.2020.00343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Climate change and water table drawdown impact the community structure and diversity of peatland soil prokaryotes. Nonetheless, how soil prokaryotes of different water tables respond to climate change remains largely unknown. This study used 16S rRNA gene sequencing to evaluate the variation in soil prokaryotes under scenarios of warming, rainfall reduction, and their combination in different water table peatlands on the Zoige Plateau in China. Stimulated climate change affected some of the diversity indexes and relative abundances of soil prokaryotes in three water table peatlands. Additionally, those from the dry-rewetting event peatland had the most dominant phyla (genera) that showed significant changes in a relative abundance due to the simulated climate change treatments. Regarding functional microbial groups of carbon and nitrogen cycling, simulated climate change did not affect the abundances of the Euryarchaeota, Proteobacteria, Verrucomicrobia, and Methanobacterium in three water table peatlands, except NC10 and Nitrospirae. Redundancy analysis showed that the prokaryotic community variation was primary impacted by site properties of the different water table peatlands rather than the simulated climate change treatments. Moreover, the water table, total carbon, total nitrogen, and soil pH were the primary factors for the overall variation in the soil prokaryotic structure. This study provides a theoretical guidance for management strategies in the Zoige peatland, under climate change scenarios. More attention should be given to the interactive effects of peatland water table drawdown and simulated climate changes for better restorative efforts in water table drawdown, rather than simply adapting to climate change.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
- School of Ecology and Environmental Sciences and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
- Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhiying Yan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Gang Yang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ning Wu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
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6
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Biodiversity of methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00190-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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Zhou X, Zhang Z, Tian L, Li X, Tian C. Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China. Sci Rep 2017; 7:9567. [PMID: 28852134 PMCID: PMC5575048 DOI: 10.1038/s41598-017-10436-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/09/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial communities play crucial roles in the global carbon cycle, particularly in peatland ecosystems under climate change. The peatlands of the Sanjiang Plain could be highly vulnerable to global warming because they are mainly located at the southern limit of northern peatlands. In this study, the alpha diversity and composition of bacterial communities in three different minerotrophic fens along a chronosequence were investigated. We captured a rich microbial community that included many rare operational taxonomic units (OTUs) but was dominated by a few bacterial classes that have frequently been detected in other peatland ecosystems. Notably, a large diversity of methanotrophs affiliated with Alpha- and Gammaproteobacteria was also detected. Bacterial alpha diversity and composition varied as a function of peat depth and its associated physical-chemical properties, such as total carbon, total nitrogen, pH and bulk density. We also found that bacterial community turnover (beta diversity) to be significantly correlated with soil age, whereas bacterial alpha diversity was not.
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Affiliation(s)
- Xue Zhou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
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8
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Zhong Q, Chen H, Liu L, He Y, Zhu D, Jiang L, Zhan W, Hu J. Water table drawdown shapes the depth-dependent variations in prokaryotic diversity and structure in Zoige peatlands. FEMS Microbiol Ecol 2017; 93:3738479. [DOI: 10.1093/femsec/fix049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/15/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Qiuping Zhong
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Science, Beijing 100049, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Liangfeng Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Science, Beijing 100049, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Science, Beijing 100049, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
- Technology Department of Qinghai Normal University, Xining 810008, China
| | - Dan Zhu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Lin Jiang
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Wei Zhan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Science, Beijing 100049, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
| | - Ji Hu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Science, Beijing 100049, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan 624400, China
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9
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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
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10
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Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME JOURNAL 2016; 10:2734-2743. [PMID: 27058508 DOI: 10.1038/ismej.2016.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/05/2016] [Accepted: 02/25/2016] [Indexed: 12/29/2022]
Abstract
Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
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Affiliation(s)
- Olga V Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mette M Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | | | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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11
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Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog. Appl Environ Microbiol 2016; 82:2363-2371. [PMID: 26873322 DOI: 10.1128/aem.03640-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
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Juottonen H, Kotiaho M, Robinson D, Merilä P, Fritze H, Tuittila ES. Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific. FEMS Microbiol Ecol 2015. [PMID: 26220310 DOI: 10.1093/femsec/fiv094] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed more variation of vegetation within a bog with microform than between the bogs. Potential methane production was low and differed among bogs but not consistently with microform. Methane oxidation followed water table position with microform, showing higher rates closer to surface in lawns and hollows than in hummocks. Methanogen community, analysed by mcrA terminal restriction fragment length polymorphism and dominated by Methanoregulaceae or 'Methanoflorentaceae', varied strongly with bog. The extent of microform-related variation of methanogens depended on the bog. Methanotrophs identified as Methylocystis spp. in pmoA denaturing gradient gel electrophoresis similarly showed effect of bog, and microform patterns were stronger within individual bogs. Our results suggest that methane-cycling microbes in boreal Sphagnum bogs with seemingly uniform environmental conditions may show strong site-dependent variation. The bog-intrinsic factor may be related to carbon availability but contrary to expectations appears to be unrelated to current surface vegetation, calling attention to the origin of carbon substrates for microbes in bogs.
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Affiliation(s)
- Heli Juottonen
- Department of Biosciences, General Microbiology, University of Helsinki, FI-00014, Finland
| | - Mirkka Kotiaho
- Peatland Ecology Group, Department of Forest Sciences, University of Helsinki, FI-00014, Finland
| | - Devin Robinson
- Natural Resources Institute Finland, Vantaa Unit, FI-01370 Vantaa, Finland
| | - Päivi Merilä
- Natural Resources Institute Finland, Oulu Unit, University of Oulu, FI-90014, Finland
| | - Hannu Fritze
- Natural Resources Institute Finland, Vantaa Unit, FI-01370 Vantaa, Finland
| | - Eeva-Stiina Tuittila
- Peatland Ecology Group, Department of Forest Sciences, University of Helsinki, FI-00014, Finland
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13
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14
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Danilova OV, Dedysh SN. Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714020040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Putkinen A, Larmola T, Tuomivirta T, Siljanen HMP, Bodrossy L, Tuittila ES, Fritze H. Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs. FEMS Microbiol Ecol 2014; 88:596-611. [PMID: 24701995 DOI: 10.1111/1574-6941.12327] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 01/01/2023] Open
Abstract
Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity.
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Affiliation(s)
- Anuliina Putkinen
- Southern Finland Regional Unit, Finnish Forest Research Institute, Vantaa, Finland
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16
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Deng Y, Cui X, Lüke C, Dumont MG. Aerobic methanotroph diversity in Riganqiao peatlands on the Qinghai-Tibetan Plateau. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:566-574. [PMID: 23864571 DOI: 10.1111/1758-2229.12046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 06/02/2023]
Abstract
The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmospheric methane in the Qinghai-Tibetan Plateau. Methanotrophs play an important role in the global cycling of CH4, but the diversity, identity and activity of methanotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph community was analysed by qPCR and sequencing methane monooxygenase (pmoA and mmoX) genes. The pmoA genes ranged between 10(7) and 10(8) copies g(-1) fresh soil, with a somewhat greater abundance in hummocks than hollows. The pmoA genes were analysed by amplicon pyrosequencing and the mmoX genes by cloning and sequencing. Methylocystis species were found to be the most abundant methanotrophs, but numerous clades were present including three novel pmoA and three novel mmoX clusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib methanotrophs in the hollows. The results indicate that aerobic methanotrophs are abundant in Riganqiao peatland and include previously undetected clades in this geographically isolated and distinctive environment.
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Affiliation(s)
- Yongcui Deng
- University of Chinese Academy of Sciences, 100049, Beijing, China
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17
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Danilova OV, Kulichevskaya IS, Rozova ON, Detkova EN, Bodelier PLE, Trotsenko YA, Dedysh SN. Methylomonas paludis sp. nov., the first acid-tolerant member of the genus
Methylomonas
, from an acidic wetland. Int J Syst Evol Microbiol 2013; 63:2282-2289. [DOI: 10.1099/ijs.0.045658-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30T. Cells of this strain were Gram-negative, pale pink-pigmented, non-motile, thick rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme (pMMO) and utilized only methane and methanol. Carbon was assimilated via the ribulose-monophosphate pathway; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strain MG30T was able to grow at a pH range of 3.8–7.3 (optimum pH 5.8–6.4) and at temperatures between 8 and 30 °C (optimum 20–25 °C). The major cellular fatty acids were C16 : 1ω5t, C16 : 1ω8c, C16 : 1ω7c and C14 : 0; the DNA G+C content was 48.5 mol%. The isolate belongs to the family
Methylococcaceae
of the class
Gammaproteobacteria
and displayed 94.7–96.9 % 16S rRNA gene sequence similarity to members of the genus
Methylomonas
. However, strain MG30T differed from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions and low DNA G+C content. Therefore, we propose to classify this strain as representing a novel, acid-tolerant species of the genus
Methylomonas
, Methylomonas paludis sp. nov. Strain MG30T ( = DSM 24973T = VKM B-2745T) is the type strain.
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Affiliation(s)
- Olga V. Danilova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Irina S. Kulichevskaya
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Olga N. Rozova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Ekaterina N. Detkova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L. E. Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, PO Box 50 6700AB, The Netherlands
| | - Yuri A. Trotsenko
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Svetlana N. Dedysh
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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18
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Artz RRE. Microbial Community Structure and Carbon Substrate use in Northern Peatlands. CARBON CYCLING IN NORTHERN PEATLANDS 2013. [DOI: 10.1029/2008gm000806] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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19
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Liebner S, Svenning MM. Environmental transcription of mmoX by methane-oxidizing Proteobacteria in a subarctic Palsa Peatland. Appl Environ Microbiol 2013; 79:701-6. [PMID: 23104418 PMCID: PMC3553753 DOI: 10.1128/aem.02292-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/24/2012] [Indexed: 11/20/2022] Open
Abstract
Methane-oxidizing bacteria (MOB) that possess the soluble form of methane monooxygenase (sMMO) are present in various environments, but unlike the prevalent particulate methane monooxygenase (pMMO), the in situ activity of sMMO has not been documented. Here we report on the environmental transcription of a gene (mmoX) for this enzyme, which was attributed mainly to MOB lacking a pMMO. Our study indicates that the sMMO is an active enzyme in acidic peat ecosystems, but its importance for the mitigation of methane releases remains unknown.
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Affiliation(s)
- Susanne Liebner
- University of Tromsø, Department of Arctic and Marine Biology, Tromsø, Norway
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20
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Methane-cycling microbial communities and methane emission in natural and restored peatlands. Appl Environ Microbiol 2012; 78:6386-9. [PMID: 22752167 DOI: 10.1128/aem.00261-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We addressed how restoration of forestry-drained peatlands affects CH(4)-cycling microbes. Despite similar community compositions, the abundance of methanogens and methanotrophs was lower in restored than in natural sites and correlated with CH(4) emission. Poor establishment of methanogens may thus explain low CH(4) emissions on restored peatlands even 10 to 12 years after restoration.
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21
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Barbier BA, Dziduch I, Liebner S, Ganzert L, Lantuit H, Pollard W, Wagner D. Methane-cycling communities in a permafrost-affected soil on Herschel Island, Western Canadian Arctic: active layer profiling ofmcrAandpmoAgenes. FEMS Microbiol Ecol 2012; 82:287-302. [DOI: 10.1111/j.1574-6941.2012.01332.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 01/10/2023] Open
Affiliation(s)
- Béatrice A. Barbier
- Alfred Wegener Institute for Polar and Marine Research; Research Unit Potsdam; Potsdam; Germany
| | - Isabel Dziduch
- Alfred Wegener Institute for Polar and Marine Research; Research Unit Potsdam; Potsdam; Germany
| | - Susanne Liebner
- Department of Arctic and Marine Biology; University of Tromsø; Tromsø; Norway
| | - Lars Ganzert
- Department of Arctic and Marine Biology; University of Tromsø; Tromsø; Norway
| | - Hugues Lantuit
- Alfred Wegener Institute for Polar and Marine Research; Research Unit Potsdam; Potsdam; Germany
| | - Wayne Pollard
- Department of Geography; McGill University; Montréal; QC; Canada
| | - Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research; Research Unit Potsdam; Potsdam; Germany
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22
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Gupta V, Smemo KA, Yavitt JB, Basiliko N. Active methanotrophs in two contrasting North American peatland ecosystems revealed using DNA-SIP. MICROBIAL ECOLOGY 2012; 63:438-445. [PMID: 21728037 DOI: 10.1007/s00248-011-9902-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/20/2011] [Indexed: 05/31/2023]
Abstract
The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.
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Affiliation(s)
- Varun Gupta
- Department of Geography, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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23
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Putkinen A, Larmola T, Tuomivirta T, Siljanen HMP, Bodrossy L, Tuittila ES, Fritze H. Water dispersal of methanotrophic bacteria maintains functional methane oxidation in sphagnum mosses. Front Microbiol 2012; 3:15. [PMID: 22291695 PMCID: PMC3263434 DOI: 10.3389/fmicb.2012.00015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 01/09/2012] [Indexed: 11/16/2022] Open
Abstract
It is known that Sphagnum associated methanotrophy (SAM) changes in relation to the peatland water table (WT) level. After drought, rising WT is able to reactivate SAM. We aimed to reveal whether this reactivation is due to activation of indigenous methane (CH4) oxidizing bacteria (MOB) already present in the mosses or to MOB present in water. This was tested through two approaches: in a transplantation experiment, Sphagna lacking SAM activity were transplanted into flark water next to Sphagna oxidizing CH4. Already after 3 days, most of the transplants showed CH4 oxidation activity. Microarray showed that the MOB community compositions of the transplants and the original active mosses had become more similar within 28 days thus indicating MOB movement through water between mosses. Methylocystis-related type II MOB dominated the community. In a following experiment, SAM inactive mosses were bathed overnight in non-sterile and sterile-filtered SAM active site flark water. Only mosses bathed with non-sterile flark water became SAM active, which was also shown by the pmoA copy number increase of over 60 times. Thus, it was evident that MOB present in the water can colonize Sphagnum mosses. This colonization could act as a resilience mechanism for peatland CH4 dynamics by allowing the re-emergence of CH4 oxidation activity in Sphagnum.
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Affiliation(s)
- Anuliina Putkinen
- Finnish Forest Research Institute, Southern Finland Regional Unit Vantaa, Finland
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24
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Belova SE, Baani M, Suzina NE, Bodelier PLE, Liesack W, Dedysh SN. Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:36-46. [PMID: 23761229 DOI: 10.1111/j.1758-2229.2010.00180.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Representatives of the genus Methylocystis are traditionally considered to be obligately methanotrophic bacteria, which are incapable of growth on multicarbon substrates. Here, we describe a novel member of this genus, strain H2s, which represents a numerically abundant and ecologically important methanotroph population in northern Sphagnum-dominated wetlands. This isolate demonstrates a clear preference for growth on methane but is able to grow slowly on acetate in the absence of methane. Strain H2s possesses both forms of methane monooxygenase (particulate and soluble MMO) and a well-developed system of intracytoplasmic membranes (ICM). In cells grown for several transfers on acetate, these ICM are maintained, although in a reduced form, and mRNA transcripts of particulate MMO are detectable. These cells resume their growth on methane faster than those kept for the same period of time without any substrate. Growth on acetate leads to a major shift in the phospholipid fatty acid composition. The re-examination of all type strains of the validly described Methylocystis species showed that Methylocystis heyeri H2(T) and Methylocystis echinoides IMET10491(T) are also capable of slow growth on acetate. This capability might represent an important part of the survival strategy of Methylocystis spp. in environments where methane availability is variable or limited.
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Affiliation(s)
- Svetlana E Belova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia. Max Planck Institute for terrestrial Microbiology, D-35043 Marburg, Germany. G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia. Netherlands Institute of Ecology, NL3631 AC Nieuwersluis, The Netherlands
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25
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Larmola T, Tuittila ES, Tiirola M, Nykänen H, Martikainen PJ, Yrjälä K, Tuomivirta T, Fritze H. The role ofSphagnummosses in the methane cycling of a boreal mire. Ecology 2010; 91:2356-65. [DOI: 10.1890/09-1343.1] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Dedysh SN. Exploring methanotroph diversity in acidic northern wetlands: Molecular and cultivation-based studies. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709060010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Tuomivirta TT, Yrjälä K, Fritze H. Quantitative PCR of pmoA using a novel reverse primer correlates with potential methane oxidation in Finnish fen. Res Microbiol 2009; 160:751-6. [PMID: 19781637 DOI: 10.1016/j.resmic.2009.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/02/2009] [Accepted: 09/03/2009] [Indexed: 11/28/2022]
Abstract
We report a new reverse primer (A621r) for use with A189f in PCR amplification of pmoA alleles in type II methanotrophs. The new primer combination was used to successfully amplify pmoA in peat monolith samples of various depths taken from fen-type peatlands in Finland. In quantitative PCR, pmoA amplicons produced from two sets of three replicate monoliths showed a significant Pearson correlation coefficient (r=0.77 and 0.61) with methane oxidation potential. The maximum methane oxidation potential and number of pmoA amplicons ranged between 8.8-40.5 micromol g (dry weight)(-1) d(-1) and 5.5 x 10(7)-18.7 x 10(7) g (wet weight)(-1), respectively, occurring in depths between 10 and 30 cm beneath the surface in the seven individual monoliths used in this study.
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Affiliation(s)
- Tero T Tuomivirta
- Finnish Forest Research Institute, Vantaa Research Unit, Box 18, FI-01301 Vantaa, Finland.
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28
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Juottonen H, Tuittila ES, Juutinen S, Fritze H, Yrjälä K. Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire. ISME JOURNAL 2008; 2:1157-68. [DOI: 10.1038/ismej.2008.66] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Chen Y, Dumont MG, Neufeld JD, Bodrossy L, Stralis-Pavese N, McNamara NP, Ostle N, Briones MJI, Murrell JC. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ Microbiol 2008; 10:2609-22. [PMID: 18631364 DOI: 10.1111/j.1462-2920.2008.01683.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.
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Affiliation(s)
- Yin Chen
- Department of Biological Sciences, the University of Warwick, Coventry, CV4 7AL, UK
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30
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Urmann K, Schroth MH, Noll M, Gonzalez-Gil G, Zeyer J. Assessment of microbial methane oxidation above a petroleum-contaminated aquifer using a combination of in situ techniques. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2006jg000363] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Karina Urmann
- Institute of Biogeochemistry and Pollutant Dynamics; ETH Zurich; Zurich Switzerland
| | - Martin H. Schroth
- Institute of Biogeochemistry and Pollutant Dynamics; ETH Zurich; Zurich Switzerland
| | - Matthias Noll
- Institute of Biogeochemistry and Pollutant Dynamics; ETH Zurich; Zurich Switzerland
| | | | - Josef Zeyer
- Institute of Biogeochemistry and Pollutant Dynamics; ETH Zurich; Zurich Switzerland
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31
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Chen Y, Dumont MG, McNamara NP, Chamberlain PM, Bodrossy L, Stralis-Pavese N, Murrell JC. Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses. Environ Microbiol 2007; 10:446-59. [PMID: 18093158 DOI: 10.1111/j.1462-2920.2007.01466.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH(4) oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH(4). Soil samples were also labelled with (13)CH(4), and subsequent analysis of the (13)C-labelled phospholipid fatty acids (PLFAs) showed that 16:1 omega 7, 18:1 omega 7 and 18:1 omega 9 were the major labelled PLFAs. The presence of (13)C-labelled 18:1 omega 9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.
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Affiliation(s)
- Yin Chen
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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