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How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence da...

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Autores principales: Reid, Thomas, Bergsveinson, Jordyn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138469/
https://www.ncbi.nlm.nih.gov/pubmed/34026835
http://dx.doi.org/10.3389/fmolb.2021.662888
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author Reid, Thomas
Bergsveinson, Jordyn
author_facet Reid, Thomas
Bergsveinson, Jordyn
author_sort Reid, Thomas
collection PubMed
description Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.
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spelling pubmed-81384692021-05-22 How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes Reid, Thomas Bergsveinson, Jordyn Front Mol Biosci Molecular Biosciences Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments. Frontiers Media S.A. 2021-05-07 /pmc/articles/PMC8138469/ /pubmed/34026835 http://dx.doi.org/10.3389/fmolb.2021.662888 Text en Copyright © 2021 Reid and Bergsveinson. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Reid, Thomas
Bergsveinson, Jordyn
How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title_full How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title_fullStr How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title_full_unstemmed How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title_short How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes
title_sort how do the players play? a post-genomic analysis paradigm to understand aquatic ecosystem processes
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138469/
https://www.ncbi.nlm.nih.gov/pubmed/34026835
http://dx.doi.org/10.3389/fmolb.2021.662888
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