Prokaryotic assemblages of halophilic protists in laboratory cultures

Protists inhabit waters with different salinities up to saturation, and play significant roles in the food webs. In hypersaline environments, the simplified communities are composed of mainly pro- and eukaryotic halophilic microorganisms. The aim of this study was to characterize the prokaryotic assemblages associated with uniprotist cultures of heterotrophic and phototrophic halophilic protists isolated from inland saline water bodies and maintained under laboratory conditions for a long time. The cultures were represented by chlorophycean algae Dunaliella and Asteromonas, as well as by heterotrophic protozoa of the phylum Heterolobosea. DNA metabarcoding revealed that the prokaryotic assemblages differed drastically between the phototrophic and heterotrophic protists in richness, diversity and taxonomic composition. Generally, the prokaryotic assemblages of Heterolobosea protozoa were richer than those of chlorophycean algae. In the algal microbiomes, only few prokaryotic genera were revealed. They were represented by the bacterial phylum Pseudomonadota and the archaeal phylum Halobacteriota. Rather diverse prokaryotic assemblages were associated with the cultures of halophilic Heterolobosea protozoa. They were composed of the phyla Pseudomonadota, Bacteroidota, Balneolota, Thermodesulfobacteriota, Halobacteriota, and Nanohaloarchaeota. Predicted functional profiles of the prokaryotic assemblages revealed the pathways responsible for close metabolic interactions between the halophilic protists and their prokaryotic associates, including synthesis of organic osmotic solutes and their conversion, degradation of sugar and organic aromatic compounds, biosynthesis of cofactors and vitamins. The dramatic differences between prokaryotic assemblages of heterotrophic and phototrophic protists suggest the existence of different selection mechanisms shaping microbiomes of the halophilic protists that still have to be elucidated.