Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

Abstract

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

“…As shown above, the high number of Basidiomycota in deepsea samples (Pernice et al, 2016) is supported by our findings of a large number of fungi. Direct counts and 16S/18S diversity approaches also agree in the relative abundance of diplonemids for deep-sea environments (Lara et al, 2009;Morgan-Smith et al, 2013;Lukeš et al, 2015;Pernice et al, 2016).…”

“…Given our result of an extreme enrichment of fungi on marine snow, it is very likely that fungi in these samples came primarily from marine snow. The variability in taxonomic composition of eukaryotic microbes was high in that study with much of the variance explained by water mass (Pernice et al, 2016). As the amount of deep-sea marine snow changes dramatically by water mass and location (Bochdansky et al, , 2016, some of the high variability in microbial eukaryotes is very likely due to the relative abundance and type of marine snow in these layers.…”

“…colonies (Sheridan et al, 2002) and in the surface waters of upwelling regions where fungi episodically exceed prokaryote biomass (Gutiérrez et al, 2011). Recently, a survey of bathypelagic eukaryotic microbes concluded that Basidiomycota (a major group of fungi) are among the four most dominant groups (Pernice et al, 2016). That study did not distinguish between marine snow and ambient water but screened their samples through a 20 μm mesh.…”

“…In a study employing stable isotope probing, specific particle-associated clades were identified that specialize in the degradation of highmolecular weight compounds (Orsi et al, 2016). Recently, Pernice et al (2016) described a highly variable eukaryotic microbial community composition that was affected by depth, water masses, as well as the number of prokaryotes. It is thus possible that the relative amount and type of marine snow significantly contributes to this observed variability.…”

Methodological Studies on Estimates of Abundance and Diversity of Heterotrophic Flagellates from the Deep-Sea Floor

“…Concerning investigations of the bathypelagic deep sea, analysis revealed the occurrence of heterotrophic protists (11˘1 cells mL´1) at depths down to 4000 m [7]. A global survey of bathypelagic microbial eukaryote communities identified a few groups as the dominant part of deep-sea communities, whereas the proportional composition of the dominant groups varied on a global scale [8]. Until the end of the last century, besides morphology based studies of foraminiferans [9], only anecdotal reports for other protists existed [10,11] mainly due to methodological issues.…”