Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred
to as meiofauna) are ubiquitous in marine sediments and likely play
pivotal roles in maintaining ecosystem function. Although the deep-sea
benthos represents one of the world’s largest habitats, we lack a firm
understanding of the biodiversity and community interactions amongst
meiobenthic organisms in this ecosystem. Within this vast environment key
questions concerning the historical genetic structure of species remain a
mystery, yet have profound implications for our understanding of global
biodiversity and how we perceive and mitigate the impact of environmental
change and anthropogenic disturbance. Using a metagenetic approach, we
present an intensive assessment of microbial eukaryote communities across
depth gradients (shallow water to abyssal) and ocean basins (deep-sea
Pacific and Atlantic). Our results show that while some taxa can maintain
eurybathic ranges and cosmopolitan deep-sea distributions, the majority of
species appear to be regionally restricted in marine habitats. For OCTUs
reporting wide distributions, there appears to be a taxonomic bias towards
a small subset of taxa in most phyla; such bias may be driven by specific
life history traits amongst these organisms. In addition, low genetic
divergence between geographically disparate deep-sea sites suggests either
a shorter coalescence time between deep-sea regions or slower rates of
evolution across this vast oceanic ecosystem. While high-throughput
studies allow for broad assessment of genetic patterns across microbial
eukaryote communities, intragenomic variation in rRNA gene copies and the
patchy coverage of reference databases currently present substantial
challenges for robust taxonomic interpretations of eukaryotic datasets.