The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modeling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free-living or particle-associated). Assemblages from the upper waters represent sets of co-occurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters., and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically-active bacterial community that is compositionally distinct compared to surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine Myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.

The full methods is available in the published article. The article has been accepted for publicaiton.

The dataset consists of two files. The first file (LSLE_16S.fasta) is the nucleotide algnment of all 16S rRNA amplicons and the second file (LSLE_16S.groups) maps each amplicon to its sample of origin. FD is free-living DNA fraction, FR is free-living RNA fraction, PD is particle-associated DNA fraction, PR is particle-associated RNA fraction.