Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery
Abstract Background Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes tha...
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doaj-70cd980bae004a3c92c1320e8f75aaaa2021-04-04T11:41:28ZengBMCEnvironmental Microbiome2524-63722021-03-0116111210.1186/s40793-021-00376-zCoupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatcheryEmma Timmins-Schiffman0Samuel J. White1Rhonda Elliott Thompson2Brent Vadopalas3Benoit Eudeline4Brook L. Nunn5Steven B. Roberts6Department of Genome Sciences, University of WashingtonSchool of Aquatic and Fishery Sciences, University of WashingtonTaylor Shellfish HatcheryWashington Sea Grant, University of WashingtonTaylor Shellfish HatcheryDepartment of Genome Sciences, University of WashingtonSchool of Aquatic and Fishery Sciences, University of WashingtonAbstract Background Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events. Results We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides. Conclusion The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships.https://doi.org/10.1186/s40793-021-00376-zMicrobiomeShellfishGeoduckLarvaeMetagenomicsMetaproteomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Emma Timmins-Schiffman Samuel J. White Rhonda Elliott Thompson Brent Vadopalas Benoit Eudeline Brook L. Nunn Steven B. Roberts |
spellingShingle |
Emma Timmins-Schiffman Samuel J. White Rhonda Elliott Thompson Brent Vadopalas Benoit Eudeline Brook L. Nunn Steven B. Roberts Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery Environmental Microbiome Microbiome Shellfish Geoduck Larvae Metagenomics Metaproteomics |
author_facet |
Emma Timmins-Schiffman Samuel J. White Rhonda Elliott Thompson Brent Vadopalas Benoit Eudeline Brook L. Nunn Steven B. Roberts |
author_sort |
Emma Timmins-Schiffman |
title |
Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
title_short |
Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
title_full |
Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
title_fullStr |
Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
title_full_unstemmed |
Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
title_sort |
coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery |
publisher |
BMC |
series |
Environmental Microbiome |
issn |
2524-6372 |
publishDate |
2021-03-01 |
description |
Abstract Background Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events. Results We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides. Conclusion The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships. |
topic |
Microbiome Shellfish Geoduck Larvae Metagenomics Metaproteomics |
url |
https://doi.org/10.1186/s40793-021-00376-z |
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