High throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations

Abstract

We performed high throughput 18S rDNA V9 region sequencing analyses of micro-eukaryote communities at seven sites with depths ranging from 0–1450 m in the southern part of Lake Baikal. We show that micro-eukaryotic diversity differed according to water column depth and sediment depth. Chrysophytes and perkinsids were diverse in subsurface samples, novel radiations of petalomonads and Ichthyobodo relatives were found in benthic samples, and a broad range of divergent OTUs were detected in deep sub-benthic samples. Members of clades usually associated with marine habitats were also detected, including syndinians for the first time in freshwater systems. Fungal- and cercozoan-specific c. 1,200 bp amplicon clone libraries also revealed many novel lineages in both planktonic and sediment samples at all depths, a novel radiation of aphelids in shallower benthic samples, and partitioning of sarcomonad lineages in shallow vs deep benthic samples. Putative parasitic lineages accounted for 12.4% of reads overall, including a novel radiation of Ichthyobodo (fish parasite) relatives. Micrometazoans were also analysed, including crustaceans, rotifers, and nematodes. The deepest (> 1,000 m) sub-surface sediment samples harboured some highly divergent sequence types, including heterotrophic flagellates, parasites, putative metazoans, and sequences likely representing organisms originating from higher up in the water column.

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