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

Abstract

Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and probably 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 assessment of microbial eukaryote communities across depth (shallow water to abyssal) and ocean basins (deep-sea Pacific and Atlantic). Within the 12 sites examined, our results suggest that some taxa can maintain eurybathic ranges and cosmopolitan deep-sea distributions, but the majority of species appear to be regionally restricted. For Operationally Clustered Taxonomic Units (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 data sets.

Figure 1. Rarefaction Curves compiled using Chao1 estimation (top) and observed species counts (bottom)

All high-quality sequence reads (>200bps) clustered with UCLUST (99% similarity cutoff) prior to calculation of alpha diversity.

Figure 2. Eukaryotic community assemblages present across marine sites

Taxonomic assemblages inferred from non-chimeric OCTUs recovered from UCLUST analysis at a 99% pairwise similarity cutoff; similar proportions were reported for all sites under relaxed 95% clustering.

Figure 3. Results of phylogenetic community analyses using the Fast Unifrac toolkit (Hamady et al. 2010)

Data represents forward sequencing reads from Region 1 of the 18S gene. Principle Coordinate analysis of OCTUs clustered using a 95% (A) and 99% (C) pairwise identity cutoff in the OCTUPUS pipeline. Jackknifed Cluster Analysis of OCTUs clustered at 95% (B) and 99% (D); colors represent geographic origin, and support values >50% are reported.

Figure 4. Proportions of eukaryotic taxa recovered under relaxed (95%) and stringent (99%) clustering in the OCTUPUS pipeline

Proportions calculated from non-chimeric OCTUs representing forward sequencing reads from both 18S gene regions. Only significant proportional increases (+) and decreases (−) are outlined across datasets; Black symbols represent changes observed between differential clustering of non-chimeric sequence reads at 95% (A) versus 99% (D) cutoffs. White symbols represent proportional changes between all non-chimeric OCTUs and subsets of OCTUs with observed eurybathic (B, E) and cosmopolitan (C, F) distributions.