Within New Zealand fjords depth and location influence prokaryotic and eukaryotic microbial community composition, but two sources of organic matter shape microbial activity

Fjords are semi-enclosed marine systems with unique environmental conditions that influence microbial community structures. Pronounced physicochemical gradients (e.g. depth, and salinity) within fjords are expected to drive changes in both microbial phylogenetic and metabolic response, providing a natural experiment allowing for a deeper understanding of the ecology of marine ecotones. In this study, we explored six New Zealand fjords and identified depth-linked changes in community diversity and structure. Increased depth resulted in significant increases in the abundance of Proteobacteria and SAR, while decreasing Opisthokonta, and Bacteroidetes. This was consistent along a head to mouth transect within fjords. The metabolic diversity and activity were also influenced by similar parameters as prokaryotic and eukaryotic microbial communities. Based on metabolic potential we predict that photosynthesis at surface sites supply organic matter to deeper aphotic layers, sustaining microbial activity. However, metabolic diversity and potential shifts were identified at near bottom (aphotic) sites, without corresponding community composition changes. These aphotic increases in metabolic diversity are consistent with sediment influences. Thus, while composition and function of the microbial community in the upper water column was likely shaped by marine snow and sinking particulate organic matter generated by new surface production, deeper sites were strongly influenced by benthic organic matter resuspension. This resuspension of organic matter uncouples the community composition from the functional dynamics. This analysis sheds light into the microbial dynamics across marine ecotones, as well as providing the first in-depth view into the ecological drivers of microbial community variation within New Zealand fjords.