Environmental stress mediates groundwater microbial community assembly

Daliang Ning; Yajiao Wang; Yupeng Fan; Jianjun Wang; Joy D Van Nostrand; Liyou Wu; Ping Zhang; Daniel J Curtis; Renmao Tian; Lauren Lui; Terry C Hazen; Eric J Alm; Matthew W Fields; Farris Poole; Michael W W Adams; Romy Chakraborty; David A Stahl; Paul D Adams; Adam P Arkin; Zhili He; Jizhong Zhou

doi:10.1038/s41564-023-01573-x

Environmental stress mediates groundwater microbial community assembly

Nat Microbiol. 2024 Feb;9(2):490-501. doi: 10.1038/s41564-023-01573-x. Epub 2024 Jan 11.

Authors

Daliang Ning^{1

2}, Yajiao Wang^{1

2}, Yupeng Fan^{1

2}, Jianjun Wang^{1

3}, Joy D Van Nostrand¹, Liyou Wu^{1

2}, Ping Zhang^{1

4}, Daniel J Curtis¹, Renmao Tian^{1

5}, Lauren Lui⁶, Terry C Hazen^{7

8

9}, Eric J Alm¹⁰, Matthew W Fields¹¹, Farris Poole¹², Michael W W Adams¹², Romy Chakraborty¹³, David A Stahl¹⁴, Paul D Adams^{6

9}, Adam P Arkin^{6

9}, Zhili He^{1

15}, Jizhong Zhou^{16

17

18

19

20}

Affiliations

¹ Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
² School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
³ State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
⁴ Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
⁵ Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA.
⁶ Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁷ Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA.
⁸ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁹ Department of Bioengineering, University of California, Berkeley, CA, USA.
¹⁰ Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹¹ Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
¹² Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
¹³ Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁴ Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
¹⁵ Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.
¹⁶ Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
¹⁷ School of Biological Sciences, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
¹⁸ Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jzhou@ou.edu.
¹⁹ School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
²⁰ School of Computer Science, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.

PMID: 38212658
DOI: 10.1038/s41564-023-01573-x

Abstract

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

MeSH terms

Groundwater*
Microbiota*
Phylogeny
Stochastic Processes

Abstract

MeSH terms

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