Global diversity and biogeography of bacterial communities in wastewater treatment plants

doi:10.1038/s41564-019-0426-5

. 2019 Jul;4(7):1183-1195.

doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13.

Global diversity and biogeography of bacterial communities in wastewater treatment plants

Linwei Wu^#^{1

2}, Daliang Ning^#^{1

2

3}, Bing Zhang^#^{1

2}, Yong Li⁴, Ping Zhang^{2

5}, Xiaoyu Shan¹, Qiuting Zhang¹, Mathew Robert Brown⁶, Zhenxin Li⁷, Joy D Van Nostrand², Fangqiong Ling⁸, Naijia Xiao^{2

3}, Ya Zhang², Julia Vierheilig^{9

10}, George F Wells¹¹, Yunfeng Yang¹, Ye Deng^{12

13}, Qichao Tu¹², Aijie Wang¹³; Global Water Microbiome Consortium; Tong Zhang¹⁴, Zhili He^{15

16}, Jurg Keller¹⁷, Per H Nielsen¹⁸, Pedro J J Alvarez¹⁹, Craig S Criddle²⁰, Michael Wagner⁹, James M Tiedje²¹, Qiang He^{22

23}, Thomas P Curtis²⁴, David A Stahl²⁵, Lisa Alvarez-Cohen^{26

27}, Bruce E Rittmann²⁸, Xianghua Wen²⁹, Jizhong Zhou^{30

31

32}

Collaborators, Affiliations

Collaborators

Global Water Microbiome Consortium:
Dany Acevedo, Miriam Agullo-Barcelo, Pedro J J Alvarez, Lisa Alvarez-Cohen, Gary L Andersen, Juliana Calabria de Araujo, Kevin F Boehnke, Philip Bond, Charles B Bott, Patricia Bovio, Rebecca K Brewster, Faizal Bux, Angela Cabezas, Léa Cabrol, Si Chen, Craig S Criddle, Ye Deng, Claudia Etchebehere, Amanda Ford, Dominic Frigon, Janeth Sanabria, James S Griffin, April Z Gu, Moshe Habagil, Lauren Hale, Steven D Hardeman, Marc Harmon, Harald Horn, Zhiqiang Hu, Shameem Jauffur, David R Johnson, Jurg Keller, Alexander Keucken, Sheena Kumari, Cintia Dutra Leal, Laura A Lebrun, Jangho Lee, Minjoo Lee, Zarraz M P Lee, Yong Li, Zhenxin Li, Mengyan Li, Xu Li, Fangqiong Ling, Yu Liu, Richard G Luthy, Leda C Mendonça-Hagler, Francisca Gleire Rodriguez de Menezes, Arthur J Meyers, Amin Mohebbi, Per H Nielsen, Daliang Ning, Adrian Oehmen, Andrew Palmer, Prathap Parameswaran, Joonhong Park, Deborah Patsch, Valeria Reginatto, Francis L de Los Reyes 3rd, Bruce E Rittmann, Adalberto Noyola, Simona Rossetti, Xiaoyu Shan, Jatinder Sidhu, William T Sloan, Kylie Smith, Oscarina Viana de Sousa, David A Stahl, Kyle Stephens, Renmao Tian, James M Tiedje, Nicholas B Tooker, Qichao Tu, Joy D Van Nostrand, Daniel De Los Cobos Vasconcelos, Julia Vierheilig, Michael Wagner, Steve Wakelin, Aijie Wang, Bei Wang, Joseph E Weaver, George F Wells, Stephanie West, Paul Wilmes, Sung-Geun Woo, Linwei Wu, Jer-Horng Wu, Liyou Wu, Chuanwu Xi, Naijia Xiao, Meiying Xu, Tao Yan, Yunfeng Yang, Min Yang, Michelle Young, Haowei Yue, Bing Zhang, Ping Zhang, Qiuting Zhang, Ya Zhang, Tong Zhang, Qian Zhang, Wen Zhang, Yu Zhang, Hongde Zhou, Jizhong Zhou, Xianghua Wen, Thomas P Curtis, Qiang He, Zhili He, Mathew Robert Brown

Affiliations

¹ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
² Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
³ Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.
⁴ College of Resource and Environment Southwest University, Chongqing, China.
⁵ Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
⁶ School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
⁷ School of Environment, Northeastern Normal University, Changchun, China.
⁸ Department of Energy, Environmental and Chemical Engineering, Washington University in St Louis, St Louis, MO, USA.
⁹ Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria.
¹⁰ Karl Landsteiner University of Health Sciences, Division of Water Quality and Health, Krems, Austria and Interuniversity Cooperation Centre for Water and Health, Krems, Austria.
¹¹ Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
¹² Institute for Marine Science and Technology, Shandong University, Qingdao, China.
¹³ Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
¹⁴ Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.
¹⁵ Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China.
¹⁶ Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.
¹⁷ Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia.
¹⁸ Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
¹⁹ Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA.
²⁰ Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
²¹ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
²² Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA. qianghe@utk.edu.
²³ Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, TN, USA. qianghe@utk.edu.
²⁴ School of Engineering, Newcastle University, Newcastle upon Tyne, UK. tom.curtis@newcastle.ac.uk.
²⁵ Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
²⁶ Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA.
²⁷ Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
²⁸ Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA.
²⁹ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. xhwen@tsinghua.edu.cn.
³⁰ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. jzhou@ou.edu.
³¹ Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
³² Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jzhou@ou.edu.

^# Contributed equally.

PMID: 31086312
DOI: 10.1038/s41564-019-0426-5

Free article

Global diversity and biogeography of bacterial communities in wastewater treatment plants

Linwei Wu et al. Nat Microbiol. 2019 Jul.

Free article

. 2019 Jul;4(7):1183-1195.

doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13.

Authors

Collaborators

Global Water Microbiome Consortium:
Dany Acevedo, Miriam Agullo-Barcelo, Pedro J J Alvarez, Lisa Alvarez-Cohen, Gary L Andersen, Juliana Calabria de Araujo, Kevin F Boehnke, Philip Bond, Charles B Bott, Patricia Bovio, Rebecca K Brewster, Faizal Bux, Angela Cabezas, Léa Cabrol, Si Chen, Craig S Criddle, Ye Deng, Claudia Etchebehere, Amanda Ford, Dominic Frigon, Janeth Sanabria, James S Griffin, April Z Gu, Moshe Habagil, Lauren Hale, Steven D Hardeman, Marc Harmon, Harald Horn, Zhiqiang Hu, Shameem Jauffur, David R Johnson, Jurg Keller, Alexander Keucken, Sheena Kumari, Cintia Dutra Leal, Laura A Lebrun, Jangho Lee, Minjoo Lee, Zarraz M P Lee, Yong Li, Zhenxin Li, Mengyan Li, Xu Li, Fangqiong Ling, Yu Liu, Richard G Luthy, Leda C Mendonça-Hagler, Francisca Gleire Rodriguez de Menezes, Arthur J Meyers, Amin Mohebbi, Per H Nielsen, Daliang Ning, Adrian Oehmen, Andrew Palmer, Prathap Parameswaran, Joonhong Park, Deborah Patsch, Valeria Reginatto, Francis L de Los Reyes 3rd, Bruce E Rittmann, Adalberto Noyola, Simona Rossetti, Xiaoyu Shan, Jatinder Sidhu, William T Sloan, Kylie Smith, Oscarina Viana de Sousa, David A Stahl, Kyle Stephens, Renmao Tian, James M Tiedje, Nicholas B Tooker, Qichao Tu, Joy D Van Nostrand, Daniel De Los Cobos Vasconcelos, Julia Vierheilig, Michael Wagner, Steve Wakelin, Aijie Wang, Bei Wang, Joseph E Weaver, George F Wells, Stephanie West, Paul Wilmes, Sung-Geun Woo, Linwei Wu, Jer-Horng Wu, Liyou Wu, Chuanwu Xi, Naijia Xiao, Meiying Xu, Tao Yan, Yunfeng Yang, Min Yang, Michelle Young, Haowei Yue, Bing Zhang, Ping Zhang, Qiuting Zhang, Ya Zhang, Tong Zhang, Qian Zhang, Wen Zhang, Yu Zhang, Hongde Zhou, Jizhong Zhou, Xianghua Wen, Thomas P Curtis, Qiang He, Zhili He, Mathew Robert Brown

Affiliations

¹ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
² Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
³ Consolidated Core Laboratory, University of Oklahoma, Norman, OK, USA.
⁴ College of Resource and Environment Southwest University, Chongqing, China.
⁵ Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
⁶ School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
⁷ School of Environment, Northeastern Normal University, Changchun, China.
⁸ Department of Energy, Environmental and Chemical Engineering, Washington University in St Louis, St Louis, MO, USA.
⁹ Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria.
¹⁰ Karl Landsteiner University of Health Sciences, Division of Water Quality and Health, Krems, Austria and Interuniversity Cooperation Centre for Water and Health, Krems, Austria.
¹¹ Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
¹² Institute for Marine Science and Technology, Shandong University, Qingdao, China.
¹³ Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
¹⁴ Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.
¹⁵ Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China.
¹⁶ Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.
¹⁷ Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland, Australia.
¹⁸ Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
¹⁹ Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA.
²⁰ Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
²¹ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
²² Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA. qianghe@utk.edu.
²³ Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, TN, USA. qianghe@utk.edu.
²⁴ School of Engineering, Newcastle University, Newcastle upon Tyne, UK. tom.curtis@newcastle.ac.uk.
²⁵ Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
²⁶ Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA.
²⁷ Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
²⁸ Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA.
²⁹ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. xhwen@tsinghua.edu.cn.
³⁰ State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. jzhou@ou.edu.
³¹ Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
³² Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jzhou@ou.edu.

^# Contributed equally.

PMID: 31086312
DOI: 10.1038/s41564-019-0426-5

Erratum in

Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.
Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium; Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J. Wu L, et al. Nat Microbiol. 2019 Dec;4(12):2579. doi: 10.1038/s41564-019-0617-0. Nat Microbiol. 2019. PMID: 31728072

Abstract

Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

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References

1. Torsvik, V., Øvreås, L. & Thingstad, T. F. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296, 1064–1066 (2002). - PubMed - DOI
1. Chase, J. M. & Myers, J. A. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2351–2363 (2011). - PubMed - PMC - DOI
1. Ofiţeru, I. D. et al. Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl Acad. Sci. USA 107, 15345–15350 (2010). - PubMed - DOI - PMC
1. Zhou, J. et al. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 6, e02288-14 (2015). - PubMed - PMC - DOI
1. Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017). - PubMed - PMC - DOI

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[1] Torsvik, V., Øvreås, L. & Thingstad, T. F. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296, 1064–1066 (2002). - PubMed - DOI

[2] Torsvik, V., Øvreås, L. & Thingstad, T. F. Prokaryotic diversity—magnitude, dynamics, and controlling factors. Science 296, 1064–1066 (2002). - PubMed - DOI

[3] Chase, J. M. & Myers, J. A. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2351–2363 (2011). - PubMed - PMC - DOI

[4] Chase, J. M. & Myers, J. A. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2351–2363 (2011). - PubMed - PMC - DOI

[5] Ofiţeru, I. D. et al. Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl Acad. Sci. USA 107, 15345–15350 (2010). - PubMed - DOI - PMC

[6] Ofiţeru, I. D. et al. Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl Acad. Sci. USA 107, 15345–15350 (2010). - PubMed - DOI - PMC

[7] Zhou, J. et al. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 6, e02288-14 (2015). - PubMed - PMC - DOI

[8] Zhou, J. et al. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 6, e02288-14 (2015). - PubMed - PMC - DOI

[9] Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017). - PubMed - PMC - DOI

[10] Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017). - PubMed - PMC - DOI

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Global diversity and biogeography of bacterial communities in wastewater treatment plants

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