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Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Journal article
Authors Johan Bengtsson-Palme
Magnus Alm Rosenblad
Mikael Molin
Anders Blomberg
Published in BMC Genomics
Volume 15
Issue 749
ISSN 1471-2164
Publication year 2014
Published at Department of Chemistry and Molecular Biology
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links www.biomedcentral.com/1471-2164/15/...
Keywords Detoxification, Ecotoxicology, Global ocean sampling, Marine, Metagenomics, Oxidative stress, Toxic metals
Subject categories Microbiology, Bioinformatics and Systems Biology, Marine ecology

Abstract

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.

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