251
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Chen J, Wang P, Wang C, Wang X, Miao L, Liu S, Yuan Q. Bacterial Communities in Riparian Sediments: A Large-Scale Longitudinal Distribution Pattern and Response to Dam Construction. Front Microbiol 2018; 9:999. [PMID: 29867892 PMCID: PMC5964209 DOI: 10.3389/fmicb.2018.00999] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/27/2018] [Indexed: 11/15/2022] Open
Abstract
Sediment microbes play major roles in riparian ecosystems; however, little is known about their longitudinal distribution pattern and their responses to dam construction, the most severe human disturbance in river basins. Here, we investigated the variability of sediment bacterial communities along a large-scale longitudinal gradient and between dam-controlled and dam-affected sites in riparian zone of the Lancang River, China. The abundance, activity and diversity of sediment bacteria gradually increased in a downstream direction, but were significantly lower in the dam-affected sites than in the dam-controlled sites. The bacterial community compositions differed significantly between the upper-middle-reach and downstream sites at all control sites, and also between the dam-affected and dam-controlled sites. In the cascade dam area, the relative importance of spatial distance and environmental heterogeneity for bacterial distribution differed between the dam-controlled and dam-affected sites. Spatial distance was the primary cause of variations in bacterial community in dam-controlled site. By contrast, the environmental heterogeneity had more control over the bacterial communities than did the spatial distance in dam-affected site. Network analysis showed that the bacterial community in the dam-affected sites had lower connectivity and stability when compared with that in dam-controlled sites. These results suggest the distinct variations in sediment bacterial community in dam-affected sites, which could enhance our understanding of potential ecological effects caused by dam construction.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
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252
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Liu J, Li C, Jing J, Zhao P, Luo Z, Cao M, Ma Z, Jia T, Chai B. Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage. WATER RESEARCH 2018; 133:99-109. [PMID: 29367051 DOI: 10.1016/j.watres.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Environmental gradient have strong effects on community assembly processes. In order to reveal the effects of alkaline mine drainage (AlkMD) on bacterial and denitrifying bacterial community compositions and diversity in tailings reservoir, here we conducted an experiment to examine all and core bacterial taxa and denitrifying functional genes's (nirS, nirK, nosZΙ) abundance along a chemical gradient in tailings water in Shibahe copper tailings in Zhongtiaoshan, China. Differences in bacterial and denitrifying bacterial community compositions in different habitats and their relationships with environmental parameters were analyzed. The results showed that the richness and diversity of bacterial community in downstream seeping water (SDSW) were the largest, while that in upstream tailings water (STW1) were the lowest. The diversity and abundance of bacterial communities tended to increase from STW1 to SDSW. The variation of bacterial community diversity was significantly related to electroconductibility (EC), nitrate (NO3-), nitrite (NO2-), total carbon (TC), inorganic carbon (IC) and sulfate (SO42-), but was not correlated with geographic distance in local scale. Core taxa from class to genus were all significantly related to NO3- and NO2-. Core taxa Rhodobacteraceae, Rhodobacter, Acinetobacter and Hydrogenophaga were typical denitrifying bacteria. The variation trends of these groups were consistent with the copy number of nirS, nirK and nosZΙ, demonstrating their importance in the process of nitrogen reduction. The copy number of nirK, nosZΙ and nirS/16S rDNA, nirK/16Sr DNA correlated strongly with NO3-, NO2- and IC, but nirS and nosZI/16SrDNA had no significant correlation with NO3- and NO2-. The copy numbers of denitrifying functional genes (nirS, nirK and nosZΙ) were negatively correlated with heavy metal plumbum (Pb) and zinc (Zn). It showed that heavy metal contamination was an important factor affecting the structure of denitrifying bacterial community in AlkMD. In this study we have identified the distribution pattern of bacterial community along physiochemical gradients in alkaline tailings reservoir and displayed the driving force of shaping the structure of bacterial community. The influence of NO3-, NO2-, IC and heavy metal Pb and Zn on bacterial community might via their influence on the functional groups involving nitrogen, carbon and metal metabolisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, 030006, China
| | - Juhui Jing
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Miaowen Cao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhuanzhuan Ma
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China.
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253
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Drivers of microbial community structure in forest soils. Appl Microbiol Biotechnol 2018; 102:4331-4338. [DOI: 10.1007/s00253-018-8950-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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254
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Wu B, Liu F, Weiser MD, Ning D, Okie JG, Shen L, Li J, Chai B, Deng Y, Feng K, Wu L, Chen S, Zhou J, He Z. Temperature determines the diversity and structure of N
2
O‐reducing microbial assemblages. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center and Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Feifei Liu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- Guangdong Provincial Key Lab of Microbial Culture Collection and Application Guangdong Institute of Microbiology and State Key Laboratory of Applied Microbiology Southern China Guangzhou China
| | | | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Jordan G. Okie
- School of Earth and Space Exploration Arizona State University Tempe AZ USA
- School of Life Sciences Arizona State University Tempe AZ USA
| | - Lina Shen
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Juan Li
- College of Agriculture Hunan Agricultural University Changsha Hunan China
| | - Benli Chai
- Center for Microbial Ecology Michigan State University East Lansing MI USA
| | - Ye Deng
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- CAS Key Laboratory of Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Shouwen Chen
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
- Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources College of Life Sciences Hubei University Wuhan China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- Earth Sciences Division Lawrence Berkeley National Laboratory Berkeley CA USA
- School of Environment Tsinghua University Beijing China
| | - Zhili He
- Environmental Microbiomics Research Center and Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
- College of Agriculture Hunan Agricultural University Changsha Hunan China
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255
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Delgado-Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, Singh BK, Bissett A. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology 2018; 99:583-596. [PMID: 29315530 DOI: 10.1002/ecy.2137] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA.,Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, Móstoles, 28933, Spain
| | - Frank Reith
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia, 5064, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Andrew Young
- National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, 2601, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, New South Wales, 2751, Australia
| | - Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania, 7000, Australia
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256
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Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N. A global atlas of the dominant bacteria found in soil. Science 2018; 359:320-325. [DOI: 10.1126/science.aap9516] [Citation(s) in RCA: 914] [Impact Index Per Article: 152.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022]
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257
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Chen YL, Deng Y, Ding JZ, Hu HW, Xu TL, Li F, Yang GB, Yang YH. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Mol Ecol 2017; 26:6608-6620. [DOI: 10.1111/mec.14396] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 09/29/2017] [Accepted: 10/13/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Yong-Liang Chen
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Jin-Zhi Ding
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Tian-Le Xu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Gui-Biao Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Yuan-He Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
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258
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Changes in the soil bacterial community along a pedogenic gradient. Sci Rep 2017; 7:14593. [PMID: 29109410 PMCID: PMC5674076 DOI: 10.1038/s41598-017-15133-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/20/2017] [Indexed: 11/08/2022] Open
Abstract
Current research on the influence of environmental and physicochemical factors in shaping the soil bacterial structure has seldom been approached from a pedological perspective. We studied the bacterial communities of eight soils selected along a pedogenic gradient at the local scale in a Mediterranean calcareous mountain (Sierra de María, SE Spain). The results showed that the relative abundance of Acidobacteria, Canditate division WPS-1, and Armatimonadetes decreased whereas that of Actinobacteria, Bacteroidetes, and Proteobacteria increased from the less-developed soils (Leptosol) to more-developed soils (Luvisol). This bacterial distribution pattern was also positively correlated with soil-quality parameters such as organic C, water-stable aggregates, porosity, moisture, and acidity. In addition, at a lower taxonomic level, the abundance of Acidobacteria Gp4, Armatimonadetes_gp4, Solirubrobacter, Microvirga, Terrimonas, and Nocardioides paralleled soil development and quality. Therefore, our work indicates that the composition of bacterial populations changes with pedogenesis, which could be considered a factor influencing the communities according to the environmental and physicochemical conditions during the soil formation.
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259
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1293] [Impact Index Per Article: 184.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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260
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Xiao Y, Liu X, Fang J, Liang Y, Zhang X, Meng D, Yin H. Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process. AMB Express 2017; 7:190. [PMID: 29063373 PMCID: PMC5653677 DOI: 10.1186/s13568-017-0491-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/14/2017] [Indexed: 11/15/2022] Open
Abstract
Temperature and energy resources (e.g., iron, sulfur and organic matter) usually undergo dynamic changes, and play important roles during industrial bioleaching process. Thus, it is essential to investigate their synergistic effects and the changes of their independent effects with simultaneous actions of multi-factors. In this study, we explored the synergistic effects of temperature and original mineral compositions (OMCs, energy resources) on the sphalerite bioleaching process. The microbial community structure was monitored by 16S rRNA gene sequencing technology and showed clear segregation along temperature gradients and Shannon diversity decreased at high temperature. On the contrary, the physicochemical parameters (pH and [Fe3+]) in the leachate were significantly affected by the OMCs. Interestingly, the influence of temperature on zinc recovery was greater at relatively simpler OMCs level, whereas the influence of OMCs was stronger at lower temperature. In addition, using [Fe3+], pH, relative abundances of dominant OTUs of microbial community and temperature as variable parameters, several models were constructed to predict zinc leaching efficiency, providing a possibility to predict the metal recovery efficiency under temperature change and variable energy resources.
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261
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Terrat S, Horrigue W, Dequietd S, Saby NPA, Lelièvre M, Nowak V, Tripied J, Régnier T, Jolivet C, Arrouays D, Wincker P, Cruaud C, Karimi B, Bispo A, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L. Mapping and predictive variations of soil bacterial richness across France. PLoS One 2017; 12:e0186766. [PMID: 29059218 PMCID: PMC5653302 DOI: 10.1371/journal.pone.0186766] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/07/2017] [Indexed: 11/18/2022] Open
Abstract
Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.
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Affiliation(s)
- Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequietd
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | | | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | | | | | | | | | | | - Battle Karimi
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Pierre Alain Maron
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
- * E-mail:
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262
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Peay KG, von Sperber C, Cardarelli E, Toju H, Francis CA, Chadwick OA, Vitousek PM. Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient. FEMS Microbiol Ecol 2017; 93:3586621. [PMID: 28402397 DOI: 10.1093/femsec/fix045] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 11/13/2022] Open
Abstract
Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.
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Affiliation(s)
- Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Emily Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | | | - Oliver A Chadwick
- Geography Department, University of California, Santa Barbara CA 93106, USA
| | - Peter M Vitousek
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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263
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Tian J, He N, Hale L, Niu S, Yu G, Liu Y, Blagodatskaya E, Kuzyakov Y, Gao Q, Zhou J. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12952] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Tian
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Lauren Hale
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Yuan Liu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Evgenia Blagodatskaya
- Institute of Physicochemical and Biological Problems in Soil Science Pushchino Russia
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
- Agro‐Technology InstituteRUDN University Moscow Russia
| | - Qun Gao
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
- Earth and Environmental SciencesLawrence Berkeley National Laboratory Berkeley CA USA
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264
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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265
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Zhou Y, Zhu H, Fu S, Yao Q. Metagenomic evidence of stronger effect of stylo (legume) than bahiagrass (grass) on taxonomic and functional profiles of the soil microbial community. Sci Rep 2017; 7:10195. [PMID: 28860520 PMCID: PMC5579253 DOI: 10.1038/s41598-017-10613-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/07/2017] [Indexed: 12/21/2022] Open
Abstract
Plants are key determinants of soil microbial community (SMC). Legumes and grasses are distinct groups in various ecosystems; however, how they differentially shape SMC structure and functioning has yet to be explored. Here, we investigate SMC in soils grown with stylo (legume) or bahiagrass (grass). Soil metagenomic sequencing indicates that Archaea was more abundant in unplanted soils than in planted soils, and that stylo selected higher abundance of fungi than bahiagrass. When the stylo soils enriched Streptomyces, Frankia, Mycobacterium and Amycolatopsis, the bahiagrass soils enriched Sphingomonas and Sphingobium. NMDS reveals that the legume shaped SMC more greatly than the grass (P < 0.004). SMC functional profiles (KEGG and CAZy) were also greatly altered by plants with the legume being more effective (P < 0.000 and P < 0.000). The abundant microbial taxa contributed to the main community functions, with Conexibacter, Sphingomonas, and Burkholderia showing multifunctionality. Moreover, soil chemical property showed much higher direct effect on SMC structure and functional profiles than soil extracts, although the soil total nitrogen and some compounds (e.g. heptadecane, 1-pentadecyne and nonanoic acid) in soil extracts were best correlated with SMC structure and functional profiles. These findings are the first to suggest that legume species shape SMC more greatly than grass species.
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Affiliation(s)
- Yang Zhou
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, 510642, China
| | - Honghui Zhu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, 510070, China.
| | - Shenglei Fu
- College of Environment and Planning, Henan University, Kaifeng, 475004, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou, 510642, China.
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266
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Zhang Z, Qu Y, Li S, Feng K, Wang S, Cai W, Liang Y, Li H, Xu M, Yin H, Deng Y. Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa. Sci Rep 2017; 7:4837. [PMID: 28684789 PMCID: PMC5500469 DOI: 10.1038/s41598-017-05260-w] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/19/2017] [Indexed: 01/19/2023] Open
Abstract
Understanding the abundance change of certain bacterial taxa is quite important for the study of soil microbiology. However, the observed differences of relative abundances by high-throughput techniques may not accurately reflect those of the actual taxon abundances. This study investigated whether soil microbial abundances coupling with microbial quantities can be more informative in describing the microbial population distribution under different locations. We analyzed relative abundances of the major species in soil microbial communities from Beijing and Tibet grasslands by using 16 S rRNA high-throughput sequencing technique, and quantified the absolute bacterial cell numbers directly or indirectly by multiple culture-independent measurements, including adenosine tri-phosphate (ATP), flow cytometry (FCM), quantitative real-time PCR (qPCR), phospholipid fatty acids (PLFA) and microbial biomass Carbon (MBC). By comparison of the relative abundance and the estimated absolute abundances (EAA) of the major components in soil microbial communities, several dominant phyla, including Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonates and Planctomycetes, showed significantly different trends. These results indicated that the change in EAA might be more informative in describing the dynamics of a population in a community. Further studies of soil microbes should combine the quantification and relative abundances of the microbial communities for the comparisons among various locations.
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Affiliation(s)
- Zhaojing Zhang
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.,Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuanyuan Qu
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Shuzhen Li
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.,Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shang Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weiwei Cai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China.,State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin, 150090, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
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267
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Tedersoo L. Correspondence: Analytical flaws in a continental-scale forest soil microbial diversity study. Nat Commun 2017; 8:15572. [PMID: 28585543 PMCID: PMC5467159 DOI: 10.1038/ncomms15572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
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268
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Zhou J, Deng Y, Shen L, Wen C, Yan Q, Ning D, Qin Y, Xue K, Wu L, He Z, Voordeckers JW, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide R, Yang Y, Brown JH. Correspondence: Reply to 'Analytical flaws in a continental-scale forest soil microbial diversity study'. Nat Commun 2017; 8:15583. [PMID: 28585533 PMCID: PMC5467158 DOI: 10.1038/ncomms15583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, USA
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Lina Shen
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Chongqing Wen
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Qingyun Yan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - James W. Voordeckers
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Vanessa Buzzard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Sean T. Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Brian J. Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
- The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, New Mexico 87501, USA
| | - Michael D. Weiser
- EEB Graduate Program, Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Michael Kaspari
- EEB Graduate Program, Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
- Smithsonian Tropical Research Institute, Balboa 0843-03092, Republic of Panama
| | - Robert Waide
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - James H. Brown
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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269
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Bell-Dereske L, Takacs-Vesbach C, Kivlin SN, Emery SM, Rudgers JA. Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes. FEMS Microbiol Ecol 2017; 93:3071445. [PMID: 28334408 PMCID: PMC5827620 DOI: 10.1093/femsec/fix036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/10/2017] [Indexed: 11/13/2022] Open
Abstract
Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multiyear field experiment (2010-2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community. Epichloë addition increased host root biomass at the plot scale, but reduced the length of extraradical arbuscular mycorrhizal (AM) fungal hyphae in the soil. Under ambient precipitation alone, the addition of Epichloë increased root biomass per aboveground tiller and reduced the diversity of AM fungi in A. breviligulata roots. Furthermore, with Epichloë added, the diversity of root-associated bacteria declined with higher soil moisture, whereas in its absence, bacterial diversity increased with higher soil moisture. Thus, the aboveground fungal mutualist not only altered the abundance and composition of belowground microbial communities but also affected how belowground communities responded to climate, suggesting that aboveground microbes have potential for cascading influences on community dynamics and ecosystem processes that occur belowground.
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Affiliation(s)
- Lukas Bell-Dereske
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Stephanie N. Kivlin
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Sarah M. Emery
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Jennifer A. Rudgers
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
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270
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Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level. Nat Commun 2016; 7:13736. [PMID: 28004657 PMCID: PMC5192166 DOI: 10.1038/ncomms13736] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/28/2016] [Indexed: 12/20/2022] Open
Abstract
The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities. Explaining species richness patterns is a key question in ecology. Peters et al. sample diverse plant and animal groups across elevation on Mt. Kilimanjaro to show that, while disparate factors drive distributions of individual taxa, diversity overall decreases with elevation, mostly driven by effects of temperature.
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271
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Wang J, Pan F, Soininen J, Heino J, Shen J. Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments. Nat Commun 2016; 7:13960. [PMID: 28000677 PMCID: PMC5187590 DOI: 10.1038/ncomms13960] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Climate effects and human impacts, that is, nutrient enrichment, simultaneously drive spatial biodiversity patterns. However, there is little consensus about their independent effects on biodiversity. Here we manipulate nutrient enrichment in aquatic microcosms in subtropical and subarctic regions (China and Norway, respectively) to show clear segregation of bacterial species along temperature gradients, and decreasing alpha and gamma diversity toward higher nutrients. The temperature dependence of species richness is greatest at extreme nutrient levels, whereas the nutrient dependence of species richness is strongest at intermediate temperatures. For species turnover rates, temperature effects are strongest at intermediate and two extreme ends of nutrient gradients in subtropical and subarctic regions, respectively. Species turnover rates caused by nutrients do not increase toward higher temperatures. These findings illustrate direct effects of temperature and nutrients on biodiversity, and indirect effects via primary productivity, thus providing insights into how nutrient enrichment could alter biodiversity under future climate scenarios.
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Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
- Department of Geosciences and Geography, University of Helsinki, Helsinki FIN-00014, Finland
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing 210023, China
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki FIN-00014, Finland
| | - Jani Heino
- Finnish Environment Institute, Natural Environment Centre, Biodiversity, Oulu FI-90014, Finland
| | - Ji Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing 210008, China
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272
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Shen C, Shi Y, Ni Y, Deng Y, Van Nostrand JD, He Z, Zhou J, Chu H. Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain. Front Microbiol 2016; 7:1184. [PMID: 27524983 PMCID: PMC4965465 DOI: 10.3389/fmicb.2016.01184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022] Open
Abstract
The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.
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Affiliation(s)
- Congcong Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; University of the Chinese Academy of SciencesBeijing, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; State Key Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
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