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Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species

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Abstract

The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.

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Data Availability

All the raw read files are available from the DDBJ database (DRA accession number: DRA014777).

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Acknowledgements

We thank H. Ohtsuki, W. Makino, and N. Maruoka for their help with the laboratory work.

Funding

This study was financially supported by the Japan Science and Technology Agency for the SPRING program (JPMJSP2114) and the Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (KAKENHI:20H03315 and 23H05482).

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  1. Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-Ku, Sendai, 980-8578, Japan

    Ryotaro Ichige & Jotaro Urabe

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  1. Ryotaro Ichige
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I. R. and J. U. designed the study; I. R. performed the experiments; and I. R. and J. U. analyzed the data and wrote the manuscript.

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Correspondence to Ryotaro Ichige.

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Ichige, R., Urabe, J. Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species. Microb Ecol 86, 2097–2108 (2023). https://doi.org/10.1007/s00248-023-02219-5

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