An amplicon sequencing based study investigating the spatiotemporal dynamics of microbial communities in the Tamar estuary, UK.
Estuarine and coastal ecosystems host some of the most diverse and productive microbial communities on Earth. Dynamic physiochemical gradients and various anthropogenic and natural factors are known to dictate the microbial ecology of these environments, yet elucidating the drivers shaping prokaryotic and microeukaryotic communities can be highly complex. In light of the increasing anthropogenic pressures estuaries face, a thorough understanding of the factors influencing the microbial community dynamics of these systems is critical. Here, over a 3-year period, we assess the physiochemical characteristics and variations in microbial community structure along the salinity gradient of the Tamar estuary, Southwest UK, and the coastal waters of Western Channel Observatory station L4.  Through 16S and 18S rRNA gene sequencing, we reveal a high degree of spatiotemporal heterogeneity of microbial communities across this ecosystem, with salinity, temperature and nutrient loading appearing to structure both prokaryotic and microeukaryotic communities. Via novel co-occurrence analyses, we highlight distinct niche partitioning patterns within and across domains. We observe marked temporal shifts, particularly between March 2020 and other dates, and report pronounced transitions in community composition from river to sea. Upstream, fungi were prevalent alongside common freshwater prokaryotes such as Actinobacteria, with an influx of bovine associated taxa such as Peptostreptococcaceae (class Clostridia) and Acinetobacter (class Gammaproteobacteria) in March 2020 indicative of anthropogenic influence. We demonstrate that brackish waters are dominated by phytoplankton such as diatoms and chlorophytes, particularly in warmer months, which share these waters with common Alphaproteobacterial marine taxa such as SAR11 Clade Ia and Planktomarina. Dinoflagellates such as Dinophyceae were also prevalent across the transect, although poor characterisation highlights an important need for further research into many of these prominent microeukaryotes. At high salinity sites and at L4 we demonstrate that clades such as Marine Group II archaea, Aurantivirga (class Bacteroidia) and the SAR92 clade (class Gammaproteobacteria) are prevalent, with the latter exhibiting interesting co-occurrence patterns with its known common phytoplankton symbiont Phaeocystis. This research sets a foundation for future studies encompassing this ecologically critical coastal region, whilst shedding new light on the dynamics of microbial communities within these complex ecosystems.