Diversity Of Ciliate-associated Microbiomes In Benthic Habitats In Shandong Province

Microbes in marine sediments constitute up to five-sixths of the planet’s total biomass,but their diversity is little explored,especially for those forming associations with unicellular protists.Heterotrophic ciliates are among the most dominant and diversified marine benthic protists,and comprise hotspot niches of bacterial colonization.To date,studies using culture-independent single cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent,even for the most ubiquitous species.Most of the ciliate groups in the marine benthic habitat are not culturable,and the information of the marine benthic bacteria carried or symbiotic by them is almost blank,which limits the cognition of the diversity of Marine benthic bacteria.Currently,researchers are beginning to use culture-independent single-cell methods to study the natural habitat protist-associated microbiome,which has not been studied in Marine benthic ciliates.Here,we characterize the prokaryotic community associated with representative marine benthic ciliate,Geleia sp.YT,Paraspathidium and Trachelocercidae,collected directly from the coastal zone of Yantai,China.PacBio sequencing of the nearly fulllength-16 Sr RNA genes was performed on single cells.Fluorescence in situ hybridization(FISH)analysis with genus-specific probes was further applied to locate the dominant bacterial groups.The main results and conclusions of this work are as follows:In Geleia sp.YT,we identified a Variovorax paradoxus-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host.We provide evidence of an exclusively intranuclear undescribed bacterium related to the human pathogen Mycoplasma,which persisted for 4 months in the ciliate population.The most abundant bacterial taxa associated with Geleia sp.YT likely represent its core microbiome and are degraders of recalcitrant biogenic and anthropogenic compounds,hinting at important roles of the ciliate-bacteria consortium in biochemical cycles in the marine benthos.In Paraspathidium sp.,Pseudoalteromonas lipolytica,Moraxella osloensis,Peredibacter sp.and Oceanobacter sp.were found as the dominant bacteria.The most abundant bacteria,Pseudoalteromonas lipolytica,was identified by fluorescence in situ hybridization as being on the body surface of host ciliates,which may be potential symbiotic bacteria because of its adhesion properties and the ability to produce extracellular polysaccharide.In addition,the presence of potential pathogenic bacteria was also found in its microbiome.The proportion of microbial communities in the Trachelocercidae is dynamic and may exhibit species-specific and spatiotemporal specificity.Interestingly,Parcubacteria,Candidatus Magasanikbacteria,Candidatus Campbellbacteria,and Candidatus Uhrbacteria were found in Tracheloraphis colubis.These bacterial members do not respire and lack genes for the tricarboxylic acid cycle and electron transport,and are associated with hydrogen and sulfur cycling in anoxic sediments.Parcubacteria genomes are typically lacking in genes for biosynthesis of amino acids,nucleotides,vitamins,and lipids,suggesting they have potential symbiotic roles.Overall,this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic and its symbioses.