Integron diversity in bacterial communities of freshwater sediments at different contamination levels.

Integrons, genetic elements known to be involved in the adaptation of pathogenic bacteria, were first discovered in the clinical setting. However, they are ancient structures found in various environments. When clinical integrons have a low diversity, with three integrases and gene cassettes essentially encoding antibiotic resistance, in natural environments, integrons show a greater diversity, of both gene cassettes and integrases. Although a large number of gene cassettes from environmental samples have been identified, integrase diversity remains poorly documented, and has not yet been investigated in freshwater environments. The work presented here explores environmental integrons in sediments from a freshwater environment, with emphasis on integrases. Integron diversity in bacterial communities was analyzed at sampling stations with different contamination levels and contaminant types. A total of 684 integrase sequences were obtained and grouped into 322 previously undescribed integron classes, revealing a diversity wider than that previously expected in non-clinical environments. The bacterial community structures did not fully explain the integron diversity suggesting that integrase diversity could be influenced by contamination level, and that contaminant type could influence gene cassette diversity. These results provide further arguments for the involvement of integrons in the adaptation of bacterial communities in response to contaminants in natural environments.

Integron diversity in marine environments.

Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments.

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.