Unexpected biodiversity of ciliates in marine samples from below the photic zone

Abstract

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high-throughput sequencing (HTS) to analyse the spatial distribution of planktonic ciliate diversity from shallow waters (<30 m depth) to beyond the continental shelf (>800 m depth) along a 163 km transect off the coast of New England, USA. We focus on ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), as these taxa are major components of marine food webs. We did not observe the decrease of diversity below the photic zone expected based on productivity and previous analyses. Instead, we saw an increase of diversity with depth. We also observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors. Across our samples, abundant OTUs tend to match previously characterized morphospecies while rare OTUs are more often undescribed, consistent with the idea that species in the rare biosphere remain to be characterized by microscopy. Finally, samples taken below the photic zone also reveal the prevalence of two uncharacterized (i.e. lacking sequenced morphospecies) clades - clusters X1 and X2 - that are enriched within the nano-sized fraction (2-10 μm) and are defined by deletions within the region of the SSU-rDNA analysed here. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deep-waters that may be a reservoir for rare species and uncharacterized taxa.

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf

“…We hypothesized that ciliate communities will be the similar in samples taken close together and that beyond some minimum distance, the community membership changes. We also expected to find strong assemblage changes related to the distance from shore as previously observed [16, 17, 19] such that communities are more diverse offshore. To evaluate these hypotheses, we contrasted the biogeographies of individual taxa (operational taxonomic units, or OTUs) with those of whole assemblages and evaluated patterns associated with physical and biological features of the environment.…”

“…5, 18] show that, within the Spirotrichea, the subclasses Oligotrichia and Choreotrichia dominate the marine planktonic ciliates. Analyses of oligotrich and choreotrich ciliates, the main focus of the current study, have found complex patterns of diversity on a large spatial scale (transect of 130 km with samples every 6 km) [16, 17]. These studies reveal that the patterns of variation in ciliate communities are related to distance from shore and to the degree of water column stratification, as evidenced both by analyses of DGGE and HTS [16, 17, 19].…”

“…The raw reads are available under the BioProject PRJNA339757 and Sequence Read Archive SRP082687. We analyzed the data following recommendations from previous studies [16, 19, 33, 34]. In summary, OTU libraries were built in QIIME version 1.9.1 [35], clustering with Uclust 1.2.22q at 99% similarity [36].…”

“…HTS, DGGE) focusing on Spirotrichea [e.g. 16, 17] or all microbial eukaryotes [e.g. 5, 18] show that, within the Spirotrichea, the subclasses Oligotrichia and Choreotrichia dominate the marine planktonic ciliates.…”

Ciliate micrograzer dynamics of the New England Shelf

“…Choreotrichia comprise a majority of the herbivorous ciliate community at MVCO, they typically dominate planktonic ciliates (Grattepanche et al, 2015;Massana et al, 2015;Grattepanche et al, 2016). While it is difficult to directly compare data between morphotypes and genotypes because sampling efforts were different, we used two methods to do so; one indirect (comparisons of beta diversity) and one direct (comparisons between N OTU and C IFCB ).…”