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Zhou G, Zhang J, Zhang C, Feng Y, Chen L, Yu Z, Xin X, Zhao B. Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures. Sci Rep 2016; 6:22186. [PMID: 26916902 PMCID: PMC4768159 DOI: 10.1038/srep22186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/03/2016] [Indexed: 12/30/2022] Open
Abstract
Differences in the composition of a bacterial community engaged in decomposing wheat straw in a fluvo-aquic soil at 15 °C, 25 °C, and 35 °C were identified using barcode pyrosequencing. Functional carbon groups in the decomposing wheat straw were evaluated by 13C-NMR (nuclear magnetic resonance). Actinobacteria and Firmicutes were more abundant, whereas Alphaproteobacteria and Bacteroidetes were less abundant, at higher temperatures during the later stages of decomposition. Differences in the chemical properties of straw accounted for 19.3% of the variation in the community composition, whereas soil properties accounted for more (24.0%) and temperature, for less (7.4%). Carbon content of the soil microbial biomass and nitrogen content of straw were significantly correlated with the abundance of Alphaproteobacteria, Actinobacteria, and Bacteroidetes. The chemical properties of straw, especially the NCH/OCH3, alkyl O-C-O, and O-alkyl functional groups, exercised a significant effect on the composition of the bacterial community at different temperatures during decomposition—results that extend our understanding of bacterial communities associated with the decomposition of straw in agro-ecosystems and of the effects of temperature and chemical properties of the decomposing straw and soil on such communities.
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Affiliation(s)
- Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Congzhi Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lin Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental&Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenghong Yu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuli Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bingzi Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Gibbons SM, Gilbert JA. Microbial diversity--exploration of natural ecosystems and microbiomes. Curr Opin Genet Dev 2015; 35:66-72. [PMID: 26598941 DOI: 10.1016/j.gde.2015.10.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 12/24/2022]
Abstract
Microorganisms are the pillars of life on Earth. Over billions of years, they have evolved into every conceivable niche on the planet. Microbes reshaped the oceans and atmosphere and gave rise to conditions conducive to multicellular organisms. Only in the past decade have we started to peer deeply into the microbial cosmos, and what we have found is amazing. Microbial ecosystems behave, in many ways, like large-scale ecosystems, although there are important exceptions. We review recent advances in our understanding of how microbial diversity is distributed across environments, how microbes influence the ecosystems in which they live, and how these nano-machines might be harnessed to advance our understanding of the natural world.
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Affiliation(s)
- Sean M Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jack A Gilbert
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA; Department of Surgery, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Yue H, Wang M, Wang S, Gilbert JA, Sun X, Wu L, Lin Q, Hu Y, Li X, He Z, Zhou J, Yang Y. The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands. ISME JOURNAL 2015; 9:2012-20. [PMID: 25689025 PMCID: PMC4542033 DOI: 10.1038/ismej.2015.19] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 01/06/2015] [Accepted: 01/06/2015] [Indexed: 11/12/2022]
Abstract
Warming has been shown to cause soil carbon (C) loss in northern grasslands owing to accelerated microbial decomposition that offsets increased grass productivity. Yet, a multi-decadal survey indicated that the surface soil C stock in Tibetan alpine grasslands remained relatively stable. To investigate this inconsistency, we analyzed the feedback responses of soil microbial communities to simulated warming by soil transplant in Tibetan grasslands. Whereas microbial functional diversity decreased in response to warming, microbial community structure did not correlate with changes in temperature. The relative abundance of catabolic genes associated with nitrogen (N) and C cycling decreased with warming, most notably in genes encoding enzymes associated with more recalcitrant C substrates. By contrast, genes associated with C fixation increased in relative abundance. The relative abundance of genes associated with urease, glutamate dehydrogenase and ammonia monoxygenase (ureC, gdh and amoA) were significantly correlated with N2O efflux. These results suggest that unlike arid/semiarid grasslands, Tibetan grasslands maintain negative feedback mechanisms that preserve terrestrial C and N pools. To examine whether these trends were applicable to the whole plateau, we included these measurements in a model and verified that topsoil C stocks remained relatively stable. Thus, by establishing linkages between microbial metabolic potential and soil biogeochemical processes, we conclude that long-term C loss in Tibetan grasslands is ameliorated by a reduction in microbial decomposition of recalcitrant C substrates.
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Affiliation(s)
- Haowei Yue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Shiping Wang
- 1] Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China [2] CAS Center for Excellence in Tibetan Plateau Earth Science, Beijing, China
| | - Jack A Gilbert
- 1] Institute of Genomic and Systems Biology, Argonne National Laboratory, Argonne, IL, USA [2] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA [3] College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Linwei Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qiaoyan Lin
- Key Laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yigang Hu
- 1] Key Laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China [2] Shapotou Desert Experiment and Research Station, Cold and Arid Regions and Environmental & Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, China
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- 1] State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China [2] Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA [3] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [4] Collaborative Innovation Center for Regional Environmental Quality, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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