Diversity patterns of benthic bacterial communities along the salinity continuum of the Humber estuary (UK)

Abstract

Intertidal mudflats are fluctuating environments that support highly diverse microbial communities. The highly variable physico-chemical conditions complicate the understanding of the environmental controls on diversity patterns in estuarine systems. We investigated the bacterial diversity in the surface and subsurface sediments along the salinity gradient of the Humber estuary (UK) using amplicon sequencing of the 16S rRNA gene and correlated its variations with environmental variables. The sediment depths sampled were selected based on the local resuspension patterns. In general, bacterial communities showed similar composition at the different sites and depths, with Proteobacteria being the most abundant phylum. The richness of operational taxonomic units (OTUs) was uniform along the salinity gradient. However, Hill numbers, as bacterial diversity measures, showed that the common and dominant OTUs exhibited a decreasing trend from the inner towards the outer estuary sites. Additionally, surface and subsurface bacterial communities were separated by non-metric multi-dimensional scaling (NMDS) analysis only in the mid- and outer estuary samples, where redox transitions with depth were more abrupt. Salinity, porewater ammonium concentration and acid-extractable Fe(II) in solids were the subset of environmental factors that best correlated with community dissimilarities. Analysis of regional diversity indicated that the dataset may include 2 potentially distinct communities: (1) a near-surface community that is the product of regular mixing and transport and is subjected to a wide range of salinity conditions, and (2) a bacterial community indigenous to the more reducing subsurface sediments of the mudflats of the mid- and outer estuary.