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A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System

A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumin...

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Autores principales: Beale, David J., Karpe, Avinash V., Ahmed, Warish, Cook, Stephen, Morrison, Paul D., Staley, Christopher, Sadowsky, Michael J., Palombo, Enzo A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369139/
https://www.ncbi.nlm.nih.gov/pubmed/28335448
http://dx.doi.org/10.3390/ijerph14030303
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author Beale, David J.
Karpe, Avinash V.
Ahmed, Warish
Cook, Stephen
Morrison, Paul D.
Staley, Christopher
Sadowsky, Michael J.
Palombo, Enzo A.
author_facet Beale, David J.
Karpe, Avinash V.
Ahmed, Warish
Cook, Stephen
Morrison, Paul D.
Staley, Christopher
Sadowsky, Michael J.
Palombo, Enzo A.
author_sort Beale, David J.
collection PubMed
description A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5–V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem. Sites sampled represented the transition from less affected (upstream) to polluted (downstream) environments along the BR. Chemometric analysis of the combined datasets indicated a clear separation between the sampled environments. Burkholderiales and Cyanobacteria were common key factors for differentiation of pristine waters. Increased sugar alcohol and short-chain fatty acid production was observed by Actinomycetales and Rhodospirillaceae that are known to form biofilms in urban polluted and brackish waters. Results from this study indicate that a multi-omics approach enables a deep understanding of the health of an aquatic ecosystem, providing insight into the bacterial diversity present and the metabolic output of the population when exposed to environmental contaminants.
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spelling pubmed-53691392017-04-05 A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System Beale, David J. Karpe, Avinash V. Ahmed, Warish Cook, Stephen Morrison, Paul D. Staley, Christopher Sadowsky, Michael J. Palombo, Enzo A. Int J Environ Res Public Health Article A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5–V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem. Sites sampled represented the transition from less affected (upstream) to polluted (downstream) environments along the BR. Chemometric analysis of the combined datasets indicated a clear separation between the sampled environments. Burkholderiales and Cyanobacteria were common key factors for differentiation of pristine waters. Increased sugar alcohol and short-chain fatty acid production was observed by Actinomycetales and Rhodospirillaceae that are known to form biofilms in urban polluted and brackish waters. Results from this study indicate that a multi-omics approach enables a deep understanding of the health of an aquatic ecosystem, providing insight into the bacterial diversity present and the metabolic output of the population when exposed to environmental contaminants. MDPI 2017-03-14 2017-03 /pmc/articles/PMC5369139/ /pubmed/28335448 http://dx.doi.org/10.3390/ijerph14030303 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Beale, David J.
Karpe, Avinash V.
Ahmed, Warish
Cook, Stephen
Morrison, Paul D.
Staley, Christopher
Sadowsky, Michael J.
Palombo, Enzo A.
A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title_full A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title_fullStr A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title_full_unstemmed A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title_short A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System
title_sort community multi-omics approach towards the assessment of surface water quality in an urban river system
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369139/
https://www.ncbi.nlm.nih.gov/pubmed/28335448
http://dx.doi.org/10.3390/ijerph14030303
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