Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments

Abstract

Aim: The goal of this study was to identify functional targets to detect polycyclic aromatic hydrocarbon (PAH)‐degrading bacterial populations in cold marine ecosystems. Methods and Results: We designed a degenerate primer set targeting genes encoding the α subunit of PAH‐dioxygenases from Gram‐positive bacteria. This primer set was used to amplify gene fragments from metagenomic DNA isolated from Subantarctic marine sediments (Ushuaia Bay, Argentina). These gene fragments were cloned and sequenced. We identified 14 distinct groups of genes, most of them showing significant relatedness with dioxygenases from Gram‐positive bacteria of the genera Rhodococcus, Mycobacterium, Nocardioides, Terrabacter and Bacillus. The level of identity with these genes, however, was low to moderate (33–62% at the amino acid level). Conclusion: These results indicate the presence of a high diversity of hitherto unidentified dioxygenase genes in this cold polluted environment. Significance and Impact of the Study: Subantarctic marine ecosystems are particularly vulnerable to hydrocarbon pollution, and the development of environmental restoration strategies for these environments is pressing. The information obtained in this work will be the starting point for the design of quantitative molecular tools to analyse the abundance and dynamics of these aromatic hydrocarbon‐degrading bacterial populations in the marine environment.

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

“…There are important knowledge gaps on the structure and diversity of ARHD enzymes, making it difficult to classify them (Marcos et al, 2009). In addition, many reports regarding dioxygenase diversity are related to chronically polluted environments, which is not the case of ADE soils in general.…”

Abundance, Dynamics, and Biogeographic Distribution of Seven Polycyclic Aromatic Hydrocarbon Dioxygenase Gene Variants in Coastal Sediments of Patagonia

“…2A; see Table S1 in the supplemental material). One possible explanation for the observed decline in PAH dioxygenase gene abundance could be that populations carrying these genes were outcompeted by other PAH-degrading populations not targeted in this study but present at this site, such as Gram-positive bacteria (10). Further studies should explore this possibility.…”

Heterologous Expression of Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenase Genes from a Novel Pyrene-Degrading Betaproteobacterium

“…Surveys of contaminated sites using degenerate primers for genes associated with PAH degradation have revealed gene clusters with low similarity to homologous genes from described organisms (34,36) that were presumably derived from organisms that have yet to be cultivated or closely examined in the laboratory.…”