The core microbiome of sessile ciliate Stentor coeruleus is not shaped by the environment

Olivia Lanzoni,Giulio Petroni,Alexey Potekhin,Andrey Plotnikov,Yuri Khlopko,Giulio Munz

doi:10.1038/s41598-019-47701-8

Abstract

Microbiomes of multicellular organisms are one of the hottest topics in microbiology and physiology, while only few studies addressed bacterial communities associated with protists. Protists are widespread in all environments and can be colonized by plethora of different bacteria, including also human pathogens. The aim of this study was to characterize the prokaryotic community associated with the sessile ciliate Stentor coeruleus. 16S rRNA gene metabarcoding was performed on single cells of S. coeruleus and on their environment, water from the sewage stream. Our results showed that the prokaryotic community composition differed significantly between Stentor cells and their environment. The core microbiome common for all ciliate specimens analyzed could be defined, and it was composed mainly by representatives of bacterial genera which include also potential human pathogens and commensals, such as Neisseria, Streptococcus, Capnocytophaga, Porphyromonas. Numerous 16S rRNA gene contigs belonged to endosymbiont “Candidatus Megaira polyxenophila”. Our data suggest that each ciliate cell can be considered as an ecological microniche harboring diverse prokaryotic organisms. Possible benefits for persistence and transmission in nature for bacteria associated with protists are discussed. Our results support the hypothesis that ciliates attract potentially pathogenic bacteria and play the role of natural reservoirs for them.

Highlights

All possible forms of coexistence of prokaryotes with metazoan organisms became one of the most rapidly developing research fields in microbiology, and in physiology[1,2]
A total number of 554260 reads were assembled, and after denoising and chimera filtering the obtained contigs clustered at 97% similarity threshold in 473 Operational Taxonomic Units (OTUs)
Both rarefaction curves reached plateau indicating that OTUs forming respective communities were almost completely determined

Summary

Introduction

All possible forms of coexistence of prokaryotes with metazoan organisms became one of the most rapidly developing research fields in microbiology, and in physiology[1,2]. This gap in knowledge extends to other groups of protists, as there were only few attempts to assess the microbiomes of free-living amoebae[43,44] applying NGS, and in several works bacterial diversity in association with protists was estimated by cloning and sequencing[45,46,47,48,49]. Few reports analyzed microbial consortia associated to cyanobacteria[50,51,52] proving that even bacteria may organize and maintain stable communities of cohabiting prokaryotes All these few studies assume that unicellular organisms do have their own microbiomes. We provide further support to the hypothesis that ciliates may host some opportunistic bacteria and should be considered as potential reservoirs of human pathogens

Objectives

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Results

Conclusion