Marine nematodes exhibit widespread symbiosis, novel chemoautotrophy, and evolutionary conservation of holobiont taxa

Discovering 25 novel phyla that fill gaps in the eukaryotic tree of life

Protists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity1,2. While most commonly found protist species are well known to science, our global-scale environmental DNA survey across soil, water, and sediments reveals dozens of novel, phylum-level phylogenetic lineages that remain to be characterized for basic morphology and function. A vast majority of these undescribed taxa occur in marine water and sediments, but some are common in soil. Most of these novel taxa have distinct substrate and habitat preferences and biogeographic patterns. To accord these lineages scientific agency and enable unambiguous scientific communication, we propose formal names for 150 species to phylum-level taxa from 25 deep lineages based on eDNA and rRNA gene long-read sequence information.

Hyperdiversity and functional potential of the coral mycobiome: characterising host-specific and environmentally driven niches across the South China Sea reefs using long-read 28S rRNA metabarcoding.

Coral-associated fungi are an integral yet understudied component of the coral holobiont. To elucidate their diversity, drivers, and potential functions, we conducted a comprehensive survey of 104 coral samples representing eight genera across three environmentally distinct reef regions in the South China Sea. Utilizing long-read 28S rRNA gene sequencing and a curated multi-source reference database, we significantly enhanced the taxonomic resolution of coral-associated fungi. A total of 15,244 OTUs belonging to fungi were clustered, representing 16 phyla, 61 classes, 84 orders, 117 families, 156 genera, and 187 species. Ascomycota dominated the fungal communities, followed by Basidiomycota and Chytridiomycota. Phylogenetic analyses revealed a deeply divergent fungal lineage distinct from known phyla. Pending further molecular and morphological validation, this lineage is provisionally designated Candidate.Coralgong. For community assembly, host identity explained 11.7% of the variation in fungal community composition (R2 = 0.117, p = 0.001), whereas geographic location significantly affected observed OTU richness and Pielou's evenness (p < 0.001) but not overall community composition. Mantel tests likewise revealed no significant associations between fungal community structure and the measured environmental variables. Functional predictions showed that fungal communities comprised major guilds, including animal parasites, fungal parasites, plant pathogens, endophytes, and saprotrophs. Functional community composition was primarily shaped by host identity (R2 = 0.183, p = 0.001), whereas geographic effects were comparatively weak. Overall, our results demonstrate strong host-associated structuring, substantial unexplored diversity and conserved functional organization of coral fungal communities, providing a baseline coral mycobiome for future multi-omics and phylogenomic studies.

Genomic analysis of picocyanobacteria of the genus Synechococcus from Lake Baikal

The genusSynechococcuscomprises photosynthetic picocyanobacteria that, as autotrophic microorganisms, make a significant contribution to the production of organic matter and oxygen in marine and freshwater ecosystems. The wide distribution of representatives of the genusSynechococcusis due to their genetic diversity and ecological plasticity. Of particular interest is the study of these microorganisms in unique natural ecosystems, such as Lake Baikal – a freshwater oligotrophic deep-water lake with a high percentage of endemism among its inhabiting species. This work presents an analysis of two genomes ofSynechococcusrepresentatives recovered from metagenomic data of microbial communities from the water of Lake Baikal (MAGs):Synechococcussp. bin7 andSynechococcussp. bin8. A structural and functional characterization of the genomes is provided, and genes for antibiotic resistance and secondary metabolite synthesis are identified. Phylogenetic analysis, including 90 closely related freshwater and marine representatives of the genusSynechococcusalongside the studied MAGs, showed that the genomes belong to different, rather distant, phylogenetic clades.

Ancestral phototrophic Rhizobiaceae evolved in association with algae, then plants

Rhizobiaceae serve as classical models for elucidating mutualistic plant-microbe interactions yet they represent a narrow phylogenetic subgroup of Alphaproteobacteria. Studying additional lineages of Rhizobiaceae, we observed broad associations with oxygenic phototrophs beyond land plants, including early branching clades of submerged plants, multicellular and unicellular algae, as well as cyanobacteria. In particular, bacteria of the genus Hoeflea were often affiliated with cyanobacteria or microbial algae, whereas Peteryoungia spp. colonized roots of submerged plants. While both genera were originally described as nonpigmented heterotrophs, our detailed genomic, biochemical and physiological analyses revealed that most strains actually contained genes for anoxygenic photosynthesis. Under oligotrophic, oxic growth conditions, each characterized representative expressed bacteriochlorophyll a-containing functional photosynthetic complexes. Photosynthesis genes shared the highest homology among phylogenetically closest relatives, displaying topologies congruent to cognate house-keeping gene phylogenies, and maintained highly conserved gene synteny across the chromosomes of different species. Together, this indicated a vertical inheritance and long ancestral history of aerobic anoxygenic photosynthesis in Rhizobiaceae rather than multiple recent horizontal transfers. Subsequent time-scale phylogenetic analysis suggested that the last common ancestor of Rhizobiaceae was an aquatic phototroph, with different lineages of Rhizobiaceae consecutively evolving in association with algae, land plants, then later legumes. While aquatic lineages maintained photosynthetic machinery till today, Rhizobia which developed symbioses with land plants either as mutualistic endosymbiosis within root nodules or as plant pathogens, concomitantly lost photosynthetic capability. Based on our results, multiple biotic interactions with diverse oxygenic phototrophs drove the early evolution of Rhizobiaceae.

Caught in transition: facultative intracellularity and genome evolution of Symbiopectobacterium in Rhodnius species

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.

Ca. Steroidedax gorgoniicola, a heterotrophic coral associate with horizontally acquired genes from Endozoicomonadaceae