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Tang X, Zhang M, Fang Z, Yang Q, Zhang W, Zhou J, Zhao B, Fan T, Wang C, Zhang C, Xia Y, Zheng Y. Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau. FEMS Microbiol Ecol 2023; 99:fiad117. [PMID: 37766397 DOI: 10.1093/femsec/fiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.
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Affiliation(s)
- Xiaotong Tang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhengkun Fang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wan Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxing Zhou
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tongyu Fan
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Congzhen Wang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Zheng
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
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Xing T, Liu P, Ji M, Deng Y, Liu K, Wang W, Liu Y. Sink or Source: Alternative Roles of Glacier Foreland Meadow Soils in Methane Emission Is Regulated by Glacier Melting on the Tibetan Plateau. Front Microbiol 2022; 13:862242. [PMID: 35387086 PMCID: PMC8977769 DOI: 10.3389/fmicb.2022.862242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Glacier foreland soils have long been considered as methane (CH4) sinks. However, they are flooded by glacial meltwater annually during the glacier melting season, altering their redox potential. The impacts of this annual flooding on CH4 emission dynamics and methane-cycling microorganisms are not well understood. Herein, we measured in situ methane flux in glacier foreland soils during the pre-melting and melting seasons on the Tibetan Plateau. In addition, high-throughput sequencing and qPCR were used to investigate the diversity, taxonomic composition, and the abundance of methanogenic archaea and methanotrophic bacteria. Our results showed that the methane flux ranged from -10.11 to 4.81 μg·m-2·h-1 in the pre-melting season, and increased to 7.48-22.57 μg·m-2·h-1 in the melting season. This indicates that glacier foreland soils change from a methane sink to a methane source under the impact of glacial meltwater. The extent of methane flux depends on methane production and oxidation conducted by methanogens and methanotrophs. Among all the environmental factors, pH (but not moisture) is dominant for methanogens, while both pH and moisture are not that strong for methanotrophs. The dominant methanotrophs were Methylobacter and Methylocystis, whereas the methanogens were dominated by methylotrophic Methanomassiliicoccales and hydrogenotrophic Methanomicrobiales. Their distributions were also affected by microtopography and environmental factor differences. This study reveals an alternative role of glacier foreland meadow soils as both methane sink and source, which is regulated by the annual glacial melt. This suggests enhanced glacial retreat may positively feedback global warming by increasing methane emission in glacier foreland soils in the context of climate change.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
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Shen L, Liu Y, Allen MA, Xu B, Wang N, Williams TJ, Wang F, Zhou Y, Liu Q, Cavicchioli R. Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution. MICROBIOME 2021; 9:136. [PMID: 34118971 PMCID: PMC8196931 DOI: 10.1186/s40168-021-01084-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth's expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult. RESULTS Here we examined the bacterial genus Arthrobacter and, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at -1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A Arthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature. CONCLUSION The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting. Video Abstract.
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Affiliation(s)
- Liang Shen
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Baiqing Xu
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ninglian Wang
- College of Urban and Environmental Science, Northwest University, Xian, 710069, China
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Feng Wang
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining. Appl Environ Microbiol 2021; 87:AEM.02355-20. [PMID: 33355115 PMCID: PMC8090869 DOI: 10.1128/aem.02355-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using 13C-CH4 to a co-occurrence network analysis derived from the 13C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.
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Ma L, Jiang X, Liu G, Yao L, Liu W, Pan Y, Zuo Y. Environmental Factors and Microbial Diversity and Abundance Jointly Regulate Soil Nitrogen and Carbon Biogeochemical Processes in Tibetan Wetlands. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3267-3277. [PMID: 32101417 DOI: 10.1021/acs.est.9b06716] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wetlands have numerous critical ecological functions, some of which are regulated by several nitrogen (N) and carbon (C) biogeochemical processes, such as denitrification, organic matter decomposition, and methane emission. Until now, the underlying pathways of the effects of environmental and biological factors on wetland N and C cycling rates are still not fully understood. Here, we investigated soil potential/net nitrification, potential/unamended denitrification, methane production/oxidation rates in 36 riverine, lacustrine, and palustrine wetland sites on the Tibet Plateau. The results showed that all the measured N and C cycling rates did not differ significantly among the wetland types. Stepwise multiple regression analyses revealed that soil physicochemical properties (e.g., moisture, C and N concentration) explained a large amount of the variance in most of the N and C cycling rates. Microbial abundance and diversity were also important in controlling potential and unamended denitrification rates, respectively. Path analysis further revealed that soil moisture and N and C availability could impact wetland C and N processes both directly and indirectly. For instance, the indirect effect of soil moisture on methane production rates was mainly through the regulating the soil C content and methanogenic community structure. Our findings highlight that many N and C cycling processes in high-altitude and remote Tibetan wetlands are jointly regulated by soil environments and functional microorganisms. Soil properties affecting the N and C cycling rates in wetlands through altering their microbial diversity and abundance represent an important but previously underestimated indirect pathway.
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Affiliation(s)
- Lin Ma
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
| | - Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, P. R. China
| | - Lunguang Yao
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, P. R. China
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, P. R. China
| | - Yongtai Pan
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, P. R. China
| | - Yanxia Zuo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China
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6
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Dhakar K, Pandey A. Microbial Ecology from the Himalayan Cryosphere Perspective. Microorganisms 2020; 8:microorganisms8020257. [PMID: 32075196 PMCID: PMC7074745 DOI: 10.3390/microorganisms8020257] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 11/18/2022] Open
Abstract
Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.
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Affiliation(s)
- Kusum Dhakar
- Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishay 30095, Israel;
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement Town, Dehradun 248002, India
- Correspondence:
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Zhang DQ, Zhang WL, Liang YN. Adsorption of perfluoroalkyl and polyfluoroalkyl substances (PFASs) from aqueous solution - A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133606. [PMID: 31401505 DOI: 10.1016/j.scitotenv.2019.133606] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/20/2019] [Accepted: 07/25/2019] [Indexed: 04/14/2023]
Abstract
Perfluoroalkyl and polyfluoroalkyl substances (PFASs) have gained increasingly global attention in recent years. Due to their unique amphiphilic properties and stability, PFASs are recognized as highly persistent, toxic, and environmentally bioaccumulative. Among several physicochemical technologies, adsorption has been extensively used and proved to be an effective method for removing PFASs from aqueous environment. In this review article, the technical feasibility of the use of different adsorbents, such as activated carbon, ion exchange resins, minerals, molecularly imprinted polymer (MIP), carbon nanotubes (CNTs), and a wide range of potentially low-cost biosorbents, for PFASs removal from water or wastewater is critically reviewed. The evaluation and comparison of their PFASs sorption behavior in terms of kinetics and isotherms is presented. The mechanisms involved in PFASs adsorption processes, such as diffusion, electrostatic interaction, hydrophobic interaction, ion exchange and hydrogen bond, are discussed. The effects of the parameters variability on sorption process are highlighted. Based on the literature reviewed, a few recommendations for future research on PFASs adsorption are also elaborated. Capsule: The adsorption behavior and mechanisms of perfluoroalkyl and polyfluoroalkyl substances (PFASs) on various adsorbents are reviewed.
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Affiliation(s)
- D Q Zhang
- College of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - W L Zhang
- Department of Environmental and Sustainable Engineering, College of Engineering and Applied Sciences, University at Albany, State University of New York, 1400 Washington Ave, Albany, NY 12222, United States of America
| | - Y N Liang
- Department of Environmental and Sustainable Engineering, College of Engineering and Applied Sciences, University at Albany, State University of New York, 1400 Washington Ave, Albany, NY 12222, United States of America.
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8
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Horton DJ, Theis KR, Uzarski DG, Learman DR. Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes. FEMS Microbiol Ecol 2019; 95:fiz033. [PMID: 30855669 PMCID: PMC6447756 DOI: 10.1093/femsec/fiz033] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/10/2019] [Indexed: 12/16/2022] Open
Abstract
Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystem services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships among nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa that may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.
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Affiliation(s)
- Dean J Horton
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
| | - Kevin R Theis
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, USA
| | - Donald G Uzarski
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
| | - Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
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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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10
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Blue carbon potential of coastal wetland restoration varies with inundation and rainfall. Sci Rep 2019; 9:4368. [PMID: 30867475 PMCID: PMC6416304 DOI: 10.1038/s41598-019-40763-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 02/19/2019] [Indexed: 01/29/2023] Open
Abstract
There is a growing interest in how the management of 'blue carbon' sequestered by coastal wetlands can influence global greenhouse gas (GHG) budgets. A promising intervention is through restoring tidal exchange to impounded coastal wetlands for reduced methane (CH4) emissions. We monitored an impounded wetland's GHG flux (CO2 and CH4) prior to and following tidal reinstatement. We found that biogeochemical responses varied across an elevation gradient. The low elevation zone experienced a greater increase in water level and an associated greater marine transition in the sediment microbial community (16 S rRNA) than the high elevation zone. The low elevation zone's GHG emissions had a reduced sustained global warming potential of 264 g m-2 yr-1 CO2-e over 100 years, and it increased to 351 g m-2 yr-1 with the removal of extreme rain events. However, emission benefits were achieved through a reduction in CO2 emissions, not CH4 emissions. Overall, the wetland shifted from a prior CH4 sink (-0.07 to -1.74 g C m-2 yr-1) to a variable sink or source depending on the elevation site and rainfall. This highlights the need to consider a wetland's initial GHG emissions, elevation and future rainfall trends when assessing the efficacy of tidal reinstatement for GHG emission control.
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11
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Liao B, Yan X, Zhang J, Chen M, Li Y, Huang J, Lei M, He H, Wang J. Microbial community composition in alpine lake sediments from the Hengduan Mountains. Microbiologyopen 2019; 8:e00832. [PMID: 30848090 PMCID: PMC6741133 DOI: 10.1002/mbo3.832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 11/18/2022] Open
Abstract
Microbial communities in sediments play an important role in alpine lake ecosystems. However, the microbial diversity and community composition of alpine lake sediments from the Hengduan Mountains remain largely unknown. Therefore, based on the Illumina MiSeq platform, high‐throughput sequencing analysis of the 16S rRNA gene was performed on 15 alpine lake sediments collected at different locations in the Hengduan Mountains. The abundance‐based coverage estimate (ACE), Chao1, and Shannon indices indicated that the microbial abundance and diversity of these sediments were high. There are some differences in the composition of microbial communities among sediments. However, in general, Proteobacteria accounted for the largest proportion of all sediments (22.3%–67.6%) and was the dominant phylum. Followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes. In addition, the operational taxonomic unit (OTU) interactions network had modular structures and suggested more cooperation than competition in the microbial community. Besides, we also found that temperature has a significant contribution to the sample–environment relationship. This study revealed the diversity and composition of microbial communities in alpine lake sediments from the Hengduan Mountains, and describe the correlation between microbial community structure and different environmental variables.
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Affiliation(s)
- Binqiang Liao
- School of Life Science Central South University, Changsha, China
| | - Xiaoxin Yan
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, China
| | - Jiang Zhang
- School of Life Science Central South University, Changsha, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, China
| | - Yanling Li
- Key Laboratory of Plateau Lake Ecology and Environment Change, Institute of Plateau Lake Ecology and Pollution Management, School of Resource Environment and Earth Science, Yunnan University, Kunming, China
| | - Jiafeng Huang
- School of Life Science Central South University, Changsha, China
| | - Ming Lei
- School of Life Science Central South University, Changsha, China
| | - Hailun He
- School of Life Science Central South University, Changsha, China
| | - Jun Wang
- School of Life Science Central South University, Changsha, China.,Sanway Gene Technology Inc., Changsha, China
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12
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Mahato NK, Sharma A, Singh Y, Lal R. Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Arch Microbiol 2019; 201:377-388. [PMID: 30683956 DOI: 10.1007/s00203-018-01616-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 12/29/2018] [Indexed: 11/26/2022]
Abstract
Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78-98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.
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Affiliation(s)
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.
- PhiXgen Pvt. Ltd, Gurugram, India.
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13
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Huang W, Chen X, Wang K, Chen J, Zheng B, Jiang X. Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network. Microbiologyopen 2018; 8:e00644. [PMID: 29888529 PMCID: PMC6391271 DOI: 10.1002/mbo3.644] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/04/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022] Open
Abstract
Sediment microbial communities from plain river networks exert different effects on pollutant transformation and migration in lake basins. In this study, we examined millions of Illumina reads (16S rRNA gene amplicons) to compare lake, lake wetland, and estuary bacterial communities through a technically consistent approach. Results showed that bacterial communities in the sampled lake sediments had the highest alpha‐diversity (Group B), than in sampled lake wetland sediments and estuary sediments. Proteobacteria was the most abundant (more than 30%) phyla in all the sediments. The lake sediments had more Nitrospirae (1.63%–11.75%) and Acidobacteria (3.46%–10.21%) than the lake wetland and estuary sediments, and estuary sediments had a greater abundance of the phylum Firmicutes (mean of 22.30%). Statistical analysis (LEfSe) revealed that lake wetland sediments contained greater abundances of the class Anaerolineaceae, orders Xanthomonadales, Pseudomonadales, and genera Flavobacterium, Acinetobacter. The lake sediments had a distinct community of diverse primary producers, such as phylum Acidobacteria, order Ignavibacteriales, and families Nitrospiraceae, Hydrogenophilaceae. Total phosphorus and organic matter were the main factors influencing the bacterial communities in sediments from several parts of the lake wetland and river estuary (p < .05). The novel insights into basin pollution control in plain river networks may be obtained from microbial distribution in sediments from different basin regions.
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Affiliation(s)
- Wei Huang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xing Chen
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Kun Wang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Junyi Chen
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Binghui Zheng
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xia Jiang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, China.,State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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14
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Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A, Johengen TH, Palladino D, Denef VJ. Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One 2018; 13:e0195112. [PMID: 29590198 PMCID: PMC5874073 DOI: 10.1371/journal.pone.0195112] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7–41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.
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Affiliation(s)
- Edna Chiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Marian L. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Michelle A. Berry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, United States of America
| | - Ashley Burtner
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Danna Palladino
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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15
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Gu Y, Bai Y, Xiang Q, Yu X, Zhao K, Zhang X, Li C, Liu S, Chen Q. Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau. Sci Rep 2018; 8:3884. [PMID: 29497087 PMCID: PMC5832768 DOI: 10.1038/s41598-018-21874-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/02/2018] [Indexed: 12/19/2022] Open
Abstract
Soil microbes provide important ecosystem services. Zoige Plateau wetland, the largest alpine peat wetland in the world, has suffered from serious degradation in the past 30 years. We studied the composition of the Zoige Plateau alpine wetland soil microbiota and relations among specific taxa using 16S rRNA amplicon sequencing combined with association network analysis. Compared to the pristine swamp soil, taxons DA101, Aeromicrobium, Bradyrhizobium, and Candidatus Nitrososphaera were enriched and several methanogenic Euryarchaeota were depleted in the moderately degraded meadow soil and highly degraded sandy soil. Soil total potassium contents in soils with different degradation levels were significantly different, being the highest in meadow soil and lowest in swamp soil. The association network analysis showed that total potassium positively correlated with specific bacterial and archaeal taxa. Jiangella, Anaerolinea, Desulfobulbus, Geobacter, Flavobacterium, Methanobacterium and Methanosaeta were identified as the keystone genera in the networks. Soil degradation affected soil properties, and caused changes in the bacterial and archaeal community composition and the association patterns of community members. The changes could serve as early warning signals of soil degradation in alpine wetlands.
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Affiliation(s)
- Yunfu Gu
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Bai
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ke Zhao
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaonan Li
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Songqing Liu
- Department of Microbiology, College of Chemistry and Life Science, Chengdu Normal University, Chengdu, 611130, China
| | - Qiang Chen
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Cui H, Su X, Wei S, Zhu Y, Lu Z, Wang Y, Li Y, Liu H, Zhang S, Pang S. Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China. Curr Microbiol 2017; 75:484-491. [PMID: 29188321 DOI: 10.1007/s00284-017-1407-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Wetlands are an important methane (CH4) emission source. CH4 is mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are overwhelmingly dominant in high moisture samples, while Methylocystis (53.3%) and Methylomonas (42.2%) belonging to types II and I methanotrophs are the predominant groups in low moisture samples. Furthermore, qPCR analysis revealed that the abundance of methanogens and methanotrophs were higher in high moisture samples than that in low moisture samples. Overall, this comparative study between wetlands controlled by two different water regimes on the Qinghai-Tibetan Plateau provides fundamental data for further research on microbial functions within extreme ecosystems.
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Affiliation(s)
- Hongpeng Cui
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China. .,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Youhai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Yanfa Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Yuejiao Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Hui Liu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Shuai Zhang
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Shouji Pang
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
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17
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Cao X, Liu S, Wang J, Wang H, Chen L, Tian X, Zhang L, Chang J, Wang L, Mu Z, Qiao Z. Soil bacterial diversity changes in different broomcorn millet intercropping systems. J Basic Microbiol 2017; 57:989-997. [DOI: 10.1002/jobm.201700133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/11/2017] [Accepted: 08/17/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Xiaoning Cao
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Sichen Liu
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Junjie Wang
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Haigang Wang
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Ling Chen
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Xiang Tian
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Lijun Zhang
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Jianwu Chang
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Lun Wang
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Zhixin Mu
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
| | - Zhijun Qiao
- Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural Sciences; Shanxi Key Laboratory of Genetic Resources; Genetic Improvement of Minor Crops; Key Laboratory of Crop Gene Resources; Germplasm Enhancement on Loess Plateau; Ministry of Agriculture; Taiyuan P.R. China
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18
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Amin A, Ahmed I, Salam N, Kim BY, Singh D, Zhi XY, Xiao M, Li WJ. Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan. MICROBIAL ECOLOGY 2017; 74:116-127. [PMID: 28105510 DOI: 10.1007/s00248-017-0930-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.
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Affiliation(s)
- Arshia Amin
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan
- Department of Microbiology, Quaid-e-Azam University, Islamabad, 45320, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan.
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Byung-Yong Kim
- Chun Lab Inc., Seoul National University, Seoul, 151-742, Republic of South Korea
| | - Dharmesh Singh
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, 440024, India
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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19
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20
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Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island. Appl Microbiol Biotechnol 2017; 101:6241-6252. [DOI: 10.1007/s00253-017-8342-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/30/2023]
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21
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Lynn TM, Liu Q, Hu Y, Yuan H, Wu X, Khai AA, Wu J, Ge T. Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil. Arch Microbiol 2017; 199:711-721. [PMID: 28233042 DOI: 10.1007/s00203-017-1347-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 11/30/2022]
Abstract
Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.
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Affiliation(s)
- Tin Mar Lynn
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China
| | - Qiong Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yajun Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China. .,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China.
| | - Hongzhao Yuan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xiaohong Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Aye Aye Khai
- Biotechnology Research Department, Ministry of Education, Kyaukse, 100301, Myanmar
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.,Changsha Observation and Research Station for Agricultural environment, Chinese Academy of Sciences, Changsha, 410125, China
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22
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Deng Y, Cui X, Dumont MG. Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing. FEMS Microbiol Lett 2016; 363:fnw168. [PMID: 27369086 DOI: 10.1093/femsle/fnw168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.
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Affiliation(s)
- Yongcui Deng
- School of Geography Science Nanjing Normal University, Nanjing 210023, China Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Xiaoyong Cui
- College of Life Sciences University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Marc G Dumont
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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23
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Dai Y, Yan Z, Jia L, Zhang S, Gao L, Wei X, Mei Z, Liu X. The composition, localization and function of low-temperature-adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils. J Appl Microbiol 2016; 121:163-76. [PMID: 27123875 DOI: 10.1111/jam.13164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/26/2015] [Accepted: 01/18/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Y. Dai
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - Z. Yan
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - L. Jia
- The State Key Laboratory of Biotherapy; West China Hospital; Sichuan University; Sichuan China
| | - S. Zhang
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - L. Gao
- Department of Agricultural Engineering; Chongqing Academy of Agricultural Sciences; Chongqing China
| | - X. Wei
- Department of Agricultural Engineering; Chongqing Academy of Agricultural Sciences; Chongqing China
| | - Z. Mei
- Center of Agricultural Engineering; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - X. Liu
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
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24
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Illuminating Anaerobic Microbial Community and Cooccurrence Patterns across a Quality Gradient in Chinese Liquor Fermentation Pit Muds. Appl Environ Microbiol 2016; 82:2506-15. [PMID: 26896127 DOI: 10.1128/aem.03409-15] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/05/2016] [Indexed: 11/20/2022] Open
Abstract
Fermentation pit mud, an important reservoir of diverse anaerobic microorganisms, is essential for Chinese strong-aroma liquor production. Pit mud quality, according to its sensory characteristics, can be divided into three grades: degraded, normal, and high quality. However, the relationship between pit mud microbial community and pit mud quality is poorly understood, as are microbial associations within the pit mud ecosystem. Here, microbial communities at these grades were compared using Illumina MiSeq sequencing of the variable region V4 of the 16S rRNA gene. Our results revealed that the pit mud microbial community was correlated with its quality and environmental factors. Species richness, biodiversity, and relative and/or absolute abundances of Clostridia,Clostridium kluyveri, Bacteroidia, and Methanobacteria significantly increased, with corresponding increases in levels of pH, NH4 (+), and available phosphorus, from degraded to high-quality pit muds, while levels of Lactobacillus, dissolved organic carbon, and lactate significantly decreased, with normal samples in between. Furthermore, 271 pairs of significant and robust correlations (cooccurrence and negative) were identified from 76 genera using network analysis. Thirteen hubs of cooccurrence patterns, mainly under the Clostridia,Bacteroidia,Methanobacteria, and Methanomicrobia, may play important roles in pit mud ecosystem stability, which may be destroyed with rapidly increased levels of lactic acid bacteria (Lactobacillus,Pediococcus, and Streptococcus). This study may help clarify the relationships among microbial community, environmental conditions, and pit mud quality, allow the improvement of pit mud quality by using bioaugmentation and controlling environmental factors, and shed more light on the ecological rules guiding community assembly in pit mud.
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25
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Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol 2016; 92:fiv149. [PMID: 26613748 DOI: 10.1093/femsec/fiv149] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 01/30/2023] Open
Abstract
Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.
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Affiliation(s)
- Andrea Söllinger
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Clarissa Schwab
- Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zurich, Switzerland
| | - Thomas Weinmaier
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
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26
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The genome of Bacillus aryabhattai T61 reveals its adaptation to Tibetan Plateau environment. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0366-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Breidenbach B, Blaser MB, Klose M, Conrad R. Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environ Microbiol 2015; 18:2868-85. [PMID: 26337675 DOI: 10.1111/1462-2920.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/27/2022]
Abstract
Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
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Affiliation(s)
| | - Martin B Blaser
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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28
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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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