Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

YOSHIDA, Y.; Nishimura, Y.; Itoh, H.; Hasegawa-Takano, M.; Takano, T.; Wada, N.; Tominaga, K.; Ogawa, A.; Iwasaki, W.; Gotoh, Y.; Itoh, T.; Hayashi, T.; Yoshizawa, S.

doi:10.64898/2026.08.10.742674

bioRxiv · 10.64898/2026.08.10.742674

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

YOSHIDA, Y.·Nishimura, Y.·Itoh, H.·Hasegawa-Takano, M.·Takano, T.·Wada, N.·Tominaga, K.·Ogawa, A.·Iwasaki, W.·Gotoh, Y.·Itoh, T.·Hayashi, T.·Yoshizawa, S.

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Abstract

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, "Candidatus Abyssoplasma scotoplanesicola", within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. "Candidatus Abyssoplasma scotoplanesicola" occupied 76.4-98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

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YOSHIDA, Y., Nishimura, Y., Itoh, H., Hasegawa-Takano, M., Takano, T., Wada, N., Tominaga, K., Ogawa, A., Iwasaki, W., Gotoh, Y., Itoh, T., Hayashi, T., Yoshizawa, S.. 2026-08-10. Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians. https://doi.org/10.64898/2026.08.10.742674

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