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

ABSTRACT 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 freshwa...

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Autores principales:	Alexandra M. Linz, Benjamin C. Crary, Ashley Shade, Sarah Owens, Jack A. Gilbert, Rob Knight, Katherine D. McMahon
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	16S rRNA freshwater microbial communities microbial ecology time series Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6780147582094a2f8920a014f8f5b7ce
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spelling	oai:doaj.org-article:6780147582094a2f8920a014f8f5b7ce2021-11-15T15:21:46ZBacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes10.1128/mSphere.00169-172379-5042https://doaj.org/article/6780147582094a2f8920a014f8f5b7ce2017-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00169-17https://doaj.org/toc/2379-5042ABSTRACT 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.Alexandra M. LinzBenjamin C. CraryAshley ShadeSarah OwensJack A. GilbertRob KnightKatherine D. McMahonAmerican Society for Microbiologyarticle16S rRNAfreshwatermicrobial communitiesmicrobial ecologytime seriesMicrobiologyQR1-502ENmSphere, Vol 2, Iss 3 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA freshwater microbial communities microbial ecology time series Microbiology QR1-502
spellingShingle	16S rRNA freshwater microbial communities microbial ecology time series Microbiology QR1-502 Alexandra M. Linz Benjamin C. Crary Ashley Shade Sarah Owens Jack A. Gilbert Rob Knight Katherine D. McMahon Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
description	ABSTRACT 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.
format	article
author	Alexandra M. Linz Benjamin C. Crary Ashley Shade Sarah Owens Jack A. Gilbert Rob Knight Katherine D. McMahon
author_facet	Alexandra M. Linz Benjamin C. Crary Ashley Shade Sarah Owens Jack A. Gilbert Rob Knight Katherine D. McMahon
author_sort	Alexandra M. Linz
title	Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
title_short	Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
title_full	Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
title_fullStr	Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
title_full_unstemmed	Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
title_sort	bacterial community composition and dynamics spanning five years in freshwater bog lakes
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/6780147582094a2f8920a014f8f5b7ce
work_keys_str_mv	AT alexandramlinz bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT benjaminccrary bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT ashleyshade bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT sarahowens bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT jackagilbert bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT robknight bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes AT katherinedmcmahon bacterialcommunitycompositionanddynamicsspanningfiveyearsinfreshwaterboglakes
_version_	1718428132401217536

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

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