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.
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.
Blood-feeding insects typically depend on obligate intracellular bacterial symbionts that provide essential B vitamins absent from vertebrate blood. In contrast, kissing bugs (Triatominae) have long been considered atypical because they rely primarily on extracellular gut-associated bacteria. Recent reports of the genus Symbiopectobacterium in Rhodnius species raise questions about the diversity and evolution of symbiosis in these insects. Here, we investigate the distribution, genome evolution, and tissue localization of Symbiopectobacterium in the genus Rhodnius. Using comparative metagenomics, phylogenomics, fluorescence in situ hybridization, transmission electron microscopy, and hemolymph screening, we characterize a Symbiopectobacterium genome from Rhodnius prolixus and assess its occurrence across publicly available datasets representing multiple Rhodnius species. The R. prolixus strain possesses a large, highly dynamic genome enriched in mobile genetic elements, pseudogenes, and remnants of secretion systems, while retaining biosynthetic pathways for several B vitamins. Comparative analysis revealed variation in genome reduction among Rhodnius-associated strains, suggesting ongoing and potentially independent transitions toward host-restricted symbiosis. Localization analyses detected Symbiopectobacterium intracellularly within posterior midgut epithelial cells and occasionally in the hemolymph, consistent with a facultative intracellular lifestyle. However, no bacteriomes or stable intracellular structures were observed. Together, these findings indicate that Symbiopectobacterium represents an intermediate stage in the transition from environmentally associated bacteria to obligate intracellular mutualists in Triatominae.
Tanisha Moons, S. Mendiola, Hassan Tarabai et al.· bioRxiv· 0 citations
An integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1, isolated from halophytic rice, and opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.
Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin et al.· Microbial Genomics· 0 citations
A high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19 are presented, establishing a valuable foundation for future functional studies and providing keys for developing a new chassis for potential industrial applications.
Bartosz Wąsik, Patryk Kupaj, Paweł Moroz et al.· BMC Genomics· 0 citations
The plastids of peridinin-containing dinoflagellates ultimately derive from a red alga acquired by secondary endosymbiosis, an event that required extensive endosymbiotic gene transfer (EGT) from the endosymbiont to the host nucleus. Although many individual studies have recovered a red-algal phylogenetic signal in nucleus-encoded, plastid-targeted dinoflagellate proteins, this evidence remains scattered across genome papers, transcriptome surveys, plastid-proteome predictions and single-gene phylogenies, and has never been compiled systematically. Conducted and reported in accordance with the PRISMA 2020 guideline adapted for evolutionary genomics, this systematic review aimed to map and grade that evidence at the level of individual genes, lineages and functional categories. Bibliographic databases and sequence repositories, including Web of Science, Scopus, PubMed, MMETSP and EukProt, were searched up to 31 January 2026, and a four-tier evidence-grading scheme (strong, moderate, weak, ambiguous) together with a phylogenomic risk-of-bias appraisal was applied. Twenty-four studies met the eligibility criteria. The strongest and most consistent red-algal signals were recovered among nucleus-encoded proteins of the photosynthetic electron-transport chain, the Calvin–Benson cycle, tetrapyrrole and carotenoid biosynthesis, and plastid gene expression, consistent with a chromalveolate origin of the peridinin plastid. Peridinean lineages carried the clearest red-derived signal, whereas haptophyte-derived (Kareniaceae) and diatom-derived (dinotom) lineages showed a younger layer of donor-specific ancestry that frequently obscured the original red signal. The number of recovered EGT candidates was also an order of magnitude greater in secondary than in tertiary plastid contexts.
Anssam Hassan Ali, Amjad Abd Ali· International Journal of Sci...· 0 citations
Introduction Fish nocardiosis is a chronic and economically significant bacterial disease in aquaculture, yet its genomic basis remains poorly resolved beyond single-species studies. It remains unclear whether fish-associated Nocardia share conserved persistence-associated features or exhibit lineage-specific genomic diversification. Materials and methods We conducted a comparative genomic analysis of 22 Nocardia genomes, including 20 N. seriolae isolates and single representatives of N. salmonicida and N. crassostreae. Genome-wide analyses included phylogenomics, gene-content comparison, pangenome analysis, functional annotation, virulence-associated homolog screening, genomic island detection, and secondary biosynthetic gene cluster prediction. Results The conserved genome core was enriched in central metabolism, lipid-associated cell envelope biogenesis, iron acquisition, and stress-response pathways. Virulence-associated homologs were dominated by persistence-associated and metabolic functions, whereas classical toxin systems were limited, although several transport- and secretion-associated homologs were detected, consistent with their potential contribution to host interaction and intracellular persistence. Phylogenomic and gene-content analyses revealed clear species-level divergence but limited host-associated structuring within N. seriolae. Pangenome analysis supported a robust open pangenome structure (γ = 0.386), with extensive accessory gene diversity enriched in regulatory functions, mobile genetic elements, and secondary metabolic pathways. Genomic islands were dominated by insertion-sequence-associated genes, recombinases, regulators, and hypothetical proteins, whereas prophage- and toxin-related signatures were rare. Secondary metabolite analysis revealed extensive biosynthetic diversity, with most biosynthetic gene clusters showing low similarity to characterized reference pathways. However, ectoine- and nocobactin-associated pathways were broadly conserved. Conclusion These genome findings are consistent with a persistence-associated pathogenicity model in which fish-associated Nocardia, particularly N. seriolae, may depend more on metabolic resilience, stress adaptation, iron acquisition, and accessory genome plasticity than on classical toxin-mediated virulence. Collectively, the results highlight the importance of accessory genome diversification, iron acquisition, and stress adaptation in shaping host-associated lifestyles and provide a comparative genomic foundation for future functional investigations and aquaculture disease-management strategies.
Kiran Kumar Eripogu, P. Maharathi, Wen-Hsiung Li· Frontiers in Microbiology· 0 citations
