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Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study

  • Host Microbe Interactions
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Abstract

Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.

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Acknowledgements

This work was supported by the University of Pisa (565-60%2016, 565-60%2017, PRA_2018_63) and by the Italian Ministry of University and Research (565-FFABR 2017). The authors wish to thank Simone Gabrielli for the help with graphic artworks and Irene Barbagli for the help in sampling. The authors are grateful to the Migliarino San Rossore Massaciuccoli Regional Park for giving permission for sampling.

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Authors and Affiliations

  1. Department of Biology, University of Pisa, Pisa, Italy

    Alessia Rossi, Alessio Bellone, Sergei I. Fokin, Vittorio Boscaro & Claudia Vannini

  2. Department of Invertebrate Zoology, St.-Petersburg State University, St. Petersburg, Russia

    Sergei I. Fokin

  3. St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia

    Sergei I. Fokin

  4. Department of Botany, University of British Columbia, Vancouver, Canada

    Vittorio Boscaro

Authors
  1. Alessia Rossi
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  2. Alessio Bellone
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  3. Sergei I. Fokin
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  4. Vittorio Boscaro
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  5. Claudia Vannini
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Corresponding author

Correspondence to Claudia Vannini.

Additional information

The nucleotide sequence data reported are available in the ENA database under the accession numbers LT985649-LT985676 and study number PRJEB25414.

Electronic Supplementary Material

Online Resource 1

Table of biodiversity indexes. Average values of evenness and richness indexes (DOC 29.5 kb)

Online Resource 2

Tables with results of Permanova tests between different groups performed with different metrics. (DOC 32 kb)

Online Resource 3

Relative abundances of the ten most frequent bacterial phyla in the obtained libraries are shown in the bar plot. Proteobacteria is always the dominant phylum. The total number of phyla is higher in control communities then in ciliate microbiomes. CM: ciliate microbiomes. CC: control communities (EPS 525 kb)

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Rossi, A., Bellone, A., Fokin, S.I. et al. Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study. Microb Ecol 78, 232–242 (2019). https://doi.org/10.1007/s00248-018-1279-9

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  • DOI: https://doi.org/10.1007/s00248-018-1279-9

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