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Title: Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

Abstract

ABSTRACT Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series. Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites thatmore » we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “ Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.« less

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [4];  [5];  [6];
  1. Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
  2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
  3. Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
  4. Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA, Computation Institute, University of Chicago, Chicago, Illinois, USA, Department of Ecology and Evolution, Department of Surgery, University of Chicago, Chicago, Illinois, USA
  5. Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California, USA, Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California, USA, Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
  6. Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA, Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1618367
Alternate Identifier(s):
OSTI ID: 1418265
Grant/Contract Number:  
AC02-06CH11357; DGE-1256259
Resource Type:
Published Article
Journal Name:
mSphere
Additional Journal Information:
Journal Name: mSphere Journal Volume: 2 Journal Issue: 3; Journal ID: ISSN 2379-5042
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; freshwater; 16S rRNA; microbial communities; microbial ecology; time series

Citation Formats

Linz, Alexandra M., Crary, Benjamin C., Shade, Ashley, Owens, Sarah, Gilbert, Jack A., Knight, Rob, McMahon, Katherine D., and LaPara, ed., Timothy M. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. United States: N. p., 2017. Web. doi:10.1128/mSphere.00169-17.
Linz, Alexandra M., Crary, Benjamin C., Shade, Ashley, Owens, Sarah, Gilbert, Jack A., Knight, Rob, McMahon, Katherine D., & LaPara, ed., Timothy M. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes. United States. doi:10.1128/mSphere.00169-17.
Linz, Alexandra M., Crary, Benjamin C., Shade, Ashley, Owens, Sarah, Gilbert, Jack A., Knight, Rob, McMahon, Katherine D., and LaPara, ed., Timothy M. Wed . "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes". United States. doi:10.1128/mSphere.00169-17.
@article{osti_1618367,
title = {Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes},
author = {Linz, Alexandra M. and Crary, Benjamin C. and Shade, Ashley and Owens, Sarah and Gilbert, Jack A. and Knight, Rob and McMahon, Katherine D. and LaPara, ed., Timothy M.},
abstractNote = {ABSTRACT Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series. Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “ Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.},
doi = {10.1128/mSphere.00169-17},
journal = {mSphere},
number = 3,
volume = 2,
place = {United States},
year = {2017},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1128/mSphere.00169-17

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Cited by: 12 works
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