Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords Metagenome

Marine microbes are key players in marine ecosystems, driving the cycling of energy and matter. It is therefore critical to understand the factors that influence the microbial community structure. Systems with strong horizontal and vertical gradients, such as fjords, can be extremely useful in studying the response of microbial communities to environmental factors. The New Zealand Fiordland region, which harbours 15 deep-water fjords, is subject to 1200-8000 mm of annual rainfall. High rainfall and linked runoff from native forested catchments result in a surface low salinity layer (LSL) with high tannin concentrations within each fjord. These gradients are expected to drive microbial (both prokaryotic and eukaryotic) community differences but this is so far unexplored. Here we examine changes in microbial communities associated with the LSL and underlying seawater in multiple fjords. Our results represent the first study to utilise both 16S and 18S amplicon sequencing to assess microbial community patterns within a fjord and their relationships with environmental parameters. Also, it is the first time that microbial diversity and community structure is determined using next generation sequencing in NZ fjords. Marine water samples were collected from the surface and deep water at multiple stations along the length of six fjords. In one fjord a depth profile was also sampled. We found that depth, amongst the environmental variables examined, showed the strongest correlation with patterns in microbial diversity and community structure. We also observed differences in community structure changes along the axis of individual fjords within different depth strata, indicating horizontal community changes. Changes in the prokaryotic community coincided with changes in eukaryotic communities. Overall, depth, through direct or indirect effects, seem to be the main factor controlling Fiordland's prokaryotic and eukaryotic richness, community diversity and taxonomic composition patterns.