Metagenomic investigation of the antibiotic resistance in coastal marine ecosystems
Bays adjacent to developed land are sinks for runoff and municipal wastewater. These inflows carry residual antibiotic compounds and antibiotic-resistant bacteria (ARB) that pose a threat to human and environmental health. This study aims to investigate the abundance and richness of antibiotic resistance genes (ARGs) in Copano Bay, Galveston Bay, Nueces Bay, and 1852 Pass, Texas. Each water body receives a different type of major wastewater inflow dependent on the surrounding land use, and each inflow likely carries a unique suspension of chemical inducers of ARG development. This study proposes that oysters, which can bioaccumulate contaminants from the surrounding water, are an indicator species for the investigation of antibiotic resistance in the coastal environment. Bacterial metagenomes of oyster stomach contents and overlying water were collected and sequenced using Illumina HiSeq technology. The raw sequence reads were filtered for quality and length. The 16S rRNA reads were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and the Metagenome Analyzer (MEGAN) to determine the taxonomic composition of the microbial communities. The filtered reads were also compared against the Microbial Ecology Group Antibiotic Resistance (MEGARes) database to determine the abundance and richness of ARGs. The dominant bacterial classes in each sample reflected the major wastewater inflow and the surrounding land use. Further, the oyster bacterial communities differed between (but not within) sites while the free-living bacterial communities were very similar across all sampling sites. These findings suggest that local conditions select for distinct oyster microbiota, but those same conditions do not select for distinct free-living microbiota. The abundance of ARGs ranged from 28 to 826 genes while the richness of ARGs ranged from 10 to 32 distinct types. The most abundant ARGs were the mutated tuf, rpoB, and gyrB genes. Overall, fewer ARGs were detected in the oyster samples compared to the water samples, indicating that oysters were buffered from the bioaccumulation of ARGs. Data describing the prevalence of ARGs – a promising proxy for coastal sewage pollution – can aid officials in managing healthy coastal ecosystems and safeguarding human health.