Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire

Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Both types of sediment contained many unclassified bacterial sequences, including the mollusk pathogen Perkinsus marinus, and detectable xenobiotic degradation and nitrogen transformation genes.

Assessment of the petroleum hydrocarbon biodegradation potential of the sediment microbial community from an urban fringing tidal marsh of Northern New England

We assessed the impact of dodecane,n-hexane and gasoline on the microbial diversity of chronically polluted fringing tidal marsh sediment from the Great Bay Estuary of New Hampshire. Dilution cultures containing saturated alkane concentrations were sampled at zero, one and 10 days, andalkBandcyp153A1alkane hydroxylase gene libraries and 16S rRNA sequences were analyzed. The initial sediment had the most diverse alkane hydroxylase sequences and phylogenetic composition whereas treated sediments became less functionally and phylogenetically diverse with alkane substrates apparently enriching a few dominant taxa. All 1-and 10-day samples were dominated byPseudomonas-type alkane hydroxylase sequences except in dodecane treatments where primarilyRhodococcus--type alkane hydroxylases were detected. 16S rRNA profiling revealed that the Gammaproteobacteria, particularlyPseudomonas, dominated all one day samples, especially then-hexane and gasoline treatments (63.2 and 47.2% respectively) and the 10-dayn-hexane treatment (which contained 60.8%Pseudomonasand 18.6%Marinobacter).In contrast, the 10 days of dodecane treatment enriched for Actinobacteria (26.2%Rhodococcusand 32.4%Mycobacterium)and gasoline treatment enriched for Firmicutes (29.7%; mainlyBacillus, LysinibacillusandRumelibacillus).Our data indicate that fringing tidal marshes contain microbial communities with alkane-degrading abilities similar to larger meadow marshes, and support the hypothesis that alkane exposure reduces the functional and phylogenetic diversity of microbial communities in an alkane-specific manner. Further research to evaluate the ability of such fringing marsh communities to rebound to pre-pollutant diversity levels should be conducted to better assess the threat of petroleum to these habitats.

Bacterial community profiles andVibrio parahaemolyticusabundance in individual oysters and their association with estuarine ecology

ABSTRACTOysters naturally harbor the human gastric pathogenVibrio parahaemolyticus, but the nature of this association is unknown. Because microbial interactions could influence the accumulation ofV. parahaemolyticusin oysters, we investigated the composition of the microbiome in water and oysters at two ecologically unique sites in the Great Bay Estuary, New Hampshire using 16s rRNA profiling. We then evaluated correlations between bacteria inhabiting the oyster withV. parahaemolyticusabundance quantified using a most probable number (MPN) analysis. Even though oysters filter-feed, their microbiomes were not a direct snapshot of the bacterial community in overlaying water, suggesting they selectively accumulate some bacterial phyla. The microbiome of individual oysters harvested more centrally in the bay were relatively more similar to each other and had fewer unique phylotypes, but overall more taxonomic and metabolic diversity, than the microbiomes from tributary-harvested oysters that were individually more variable with lower taxonomic and metabolic diversity. Oysters harvested from the same location varied inV. parahaemolyticusabundance, with the highest abundance oysters collected from one location. This study, which to our knowledge is the first of its kind to evaluate associations ofV. parahaemolyticusabundance with members of individual oyster microbiomes, implies that sufficient sampling and depth of sequencing may reveal microbiome members that could impactV. parahaemolyticusabundance.