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Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

BACKGROUND: Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine b...

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Autores principales: Bengtsson-Palme, Johan, Alm Rosenblad, Magnus, Molin, Mikael, Blomberg, Anders
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161860/
https://www.ncbi.nlm.nih.gov/pubmed/25179155
http://dx.doi.org/10.1186/1471-2164-15-749
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author Bengtsson-Palme, Johan
Alm Rosenblad, Magnus
Molin, Mikael
Blomberg, Anders
author_facet Bengtsson-Palme, Johan
Alm Rosenblad, Magnus
Molin, Mikael
Blomberg, Anders
author_sort Bengtsson-Palme, Johan
collection PubMed
description BACKGROUND: Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals. RESULTS: Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu. CONCLUSIONS: We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-749) contains supplementary material, which is available to authorized users.
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spelling pubmed-41618602014-09-19 Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities Bengtsson-Palme, Johan Alm Rosenblad, Magnus Molin, Mikael Blomberg, Anders BMC Genomics Research Article BACKGROUND: Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals. RESULTS: Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu. CONCLUSIONS: We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-749) contains supplementary material, which is available to authorized users. BioMed Central 2014-09-01 /pmc/articles/PMC4161860/ /pubmed/25179155 http://dx.doi.org/10.1186/1471-2164-15-749 Text en © Bengtsson-Palme et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Bengtsson-Palme, Johan
Alm Rosenblad, Magnus
Molin, Mikael
Blomberg, Anders
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title_full Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title_fullStr Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title_full_unstemmed Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title_short Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
title_sort metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161860/
https://www.ncbi.nlm.nih.gov/pubmed/25179155
http://dx.doi.org/10.1186/1471-2164-15-749
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