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Title: Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

Abstract

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

Authors:
 [1];  [2];  [1]; ORCiD logo [3];  [1];  [1];  [4];  [1];  [1];  [1];  [1];  [1];  [4];  [4]; ORCiD logo [5];  [6];  [6]; ORCiD logo [1]; ORCiD logo [7];  [8] more »;  [9];  [5];  [6];  [4];  [8]; ORCiD logo [4] « less
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Johns Hopkins Univ., Baltimore, MD (United States)
  3. Colorado State Univ., Fort Collins, CO (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  5. Univ. of Oklahoma, Norman, OK (United States)
  6. Univ. of Georgia, Athens, GA (United States)
  7. Montana State Univ., Bozeman, MT (United States)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1348330
Alternate Identifier(s):
OSTI ID: 1476466
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Science and Technology
Additional Journal Information:
Journal Volume: 51; Journal Issue: 5; Journal ID: ISSN 0013-936X
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Bioreactor; Microbial Community; Groundwater

Citation Formats

King, Andrew J., Preheim, Sarah P., Bailey, Kathryn L., Robeson, Michael S., Roy Chowdhury, Taniya, Crable, Bryan R., Hurt, Richard A., Mehlhorn, Tonia, Lowe, Kenneth A., Phelps, Tommy J., Palumbo, Anthony V., Brandt, Craig C., Brown, Steven D., Podar, Mircea, Zhang, Ping, Lancaster, W. Andrew, Poole, Farris, Watson, David B., W. Fields, Matthew, Chandonia, John-Marc, Alm, Eric J., Zhou, Jizhong, Adams, Michael W. W., Hazen, Terry C., Arkin, Adam P., and Elias, Dwayne A. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. United States: N. p., 2017. Web. doi:10.1021/acs.est.6b04751.
King, Andrew J., Preheim, Sarah P., Bailey, Kathryn L., Robeson, Michael S., Roy Chowdhury, Taniya, Crable, Bryan R., Hurt, Richard A., Mehlhorn, Tonia, Lowe, Kenneth A., Phelps, Tommy J., Palumbo, Anthony V., Brandt, Craig C., Brown, Steven D., Podar, Mircea, Zhang, Ping, Lancaster, W. Andrew, Poole, Farris, Watson, David B., W. Fields, Matthew, Chandonia, John-Marc, Alm, Eric J., Zhou, Jizhong, Adams, Michael W. W., Hazen, Terry C., Arkin, Adam P., & Elias, Dwayne A. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. United States. doi:10.1021/acs.est.6b04751.
King, Andrew J., Preheim, Sarah P., Bailey, Kathryn L., Robeson, Michael S., Roy Chowdhury, Taniya, Crable, Bryan R., Hurt, Richard A., Mehlhorn, Tonia, Lowe, Kenneth A., Phelps, Tommy J., Palumbo, Anthony V., Brandt, Craig C., Brown, Steven D., Podar, Mircea, Zhang, Ping, Lancaster, W. Andrew, Poole, Farris, Watson, David B., W. Fields, Matthew, Chandonia, John-Marc, Alm, Eric J., Zhou, Jizhong, Adams, Michael W. W., Hazen, Terry C., Arkin, Adam P., and Elias, Dwayne A. Mon . "Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation". United States. doi:10.1021/acs.est.6b04751. https://www.osti.gov/servlets/purl/1348330.
@article{osti_1348330,
title = {Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation},
author = {King, Andrew J. and Preheim, Sarah P. and Bailey, Kathryn L. and Robeson, Michael S. and Roy Chowdhury, Taniya and Crable, Bryan R. and Hurt, Richard A. and Mehlhorn, Tonia and Lowe, Kenneth A. and Phelps, Tommy J. and Palumbo, Anthony V. and Brandt, Craig C. and Brown, Steven D. and Podar, Mircea and Zhang, Ping and Lancaster, W. Andrew and Poole, Farris and Watson, David B. and W. Fields, Matthew and Chandonia, John-Marc and Alm, Eric J. and Zhou, Jizhong and Adams, Michael W. W. and Hazen, Terry C. and Arkin, Adam P. and Elias, Dwayne A.},
abstractNote = {Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in-situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads) and biogeochemical parameters monitored by quantifying 53 metals, 12 organic acids, 14 anions and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community, and responded to DO. This also directly influenced the pH and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.},
doi = {10.1021/acs.est.6b04751},
journal = {Environmental Science and Technology},
number = 5,
volume = 51,
place = {United States},
year = {2017},
month = {1}
}

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Works referencing / citing this record:

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China
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