In deep-sea hydrothermal vent ecosystems, most animals harbor symbiotic communities that support their nutrition. This is the case for the shrimp Rimicaris exoculata and Rimicaris chacei, two endemic species of the Mid-Atlantic Ridge (MAR), housing three distinct bacterial symbiotic communities playing a major role in their nutrition and scaling up their immune systems. One is located in the cephalothoracic cavity, another in the foregut and the third in the midgut that is mostly represented by Candidatus Microvillispirillaceae. However, recent metabarcoding and metagenomics studies reported for the first time the presence of another abundant potential digestive symbiont representing a novel family of Lachnospirales. To date, their role and organization in the holobiont remain unknown. We combined Fluorescent in situ Hybridization, metabarcoding and genome-resolved metagenomics data to investigate their contribution to the holobiont functioning and their metabolic potential. For this purpose, we used the raw reads of a recent metabarcoding analysis and Metagenome-Assembled Genomes (MAGs) obtained in a previous study. We studied two MAGs reconstructed from TAG and Snake Pit sites (MAR) revealing a novel midgut-associated Lachnospirales family. This novel symbiont shows the capacity to degrade host chitin, utilize oxygen and encode flagellar genes involved in host-symbiont recognition. In addition, this Lachnospirales family harbors CRISPR/cas genes that may contribute to the holobiont’s defense. This symbiotic lineage seems to colonize the ectoperitrophic space, undergo elongation without dividing and may be acquired after juvenile settlement at active vent sites. Consequently, they share many commonalities with Candidatus Microvillispirillaceae, with which they co-occur. Our data suggest that the Lachnospirales may engage in a syntrophic relationship with Candidatus Microvillispirillaceae. They may be able to degrade chitin, allowing Ca. Microvillispirillaceae to use degradation products for their metabolism. Like Ca. Microvillispirillaceae, Lachnospirales are acquired post-installation of juveniles between stage B and subadult metamorphosis. Consequently, both symbionts may strongly contribute to the holobiont fitness.
Mycorrhizal fungi are an important component of the root microbiota in most land plants as they play fundamental roles in plant nutrition and health. Orchids, one of the largest plant families, are particularly dependent on mycorrhizal fungi for seed germination and plant development. Orchid mycorrhizal (OrM) fungi identified in the roots of most green orchids belong to the ‘rhizoctonia’ complex, a polyphyletic group of Tulasnellaceae, Ceratobasidiaceae, Serendipitaceae and Sebacinaceae (Agaricomycotina), and are generally assumed to colonize their host from soil, where they live as saprotrophs. However, some rhizoctonia OrM fungi were rarely detected by metabarcoding in soil around orchid roots, and we have tested the hypothesis that these fungi may use adult orchid plants as a habitat by colonizing not only their roots, but also other organs. The occurrence of OrM rhizoctonias inside roots, stems and leaves of three terrestrial orchid species (Spiranthes spiralis, Serapias vomeracea and Neottia ovata) was investigated by metabarcoding. In all orchid species, a broad majority of putative OrM fungi found in roots was also detected in either stems or leaves of the same plant. Putative OrM fungi were also detected in the capsules of all three species and in seeds of S. spiralis. Systemic occurrence of mycorrhizal fungi in plants is a novel finding. In particular, identification of OrM symbionts in all orchid tissues raises important questions on the plant-fungus relationship in the aerial organs.
Aquatic macrophytes shape microbial habitats in shallow coastal systems, yet the relative influence of plant-driven effects versus local hydrology and seasonal environmental variation remains poorly resolved. We investigated how Phragmites australis influences sediment, water, and phyllosphere bacterial communities in two shallow Baltic Sea bays, Haapsalu and Pärnu, that are approximately 83 km from each other. Bacterial communities clustered strongly by substrate (sediment, water, and phyllosphere). Sediments exhibited higher 𝛼-diversity and stronger site specificity than water or phyllosphere habitats, with bulk sediments harboring greater richness than Phragmites-associated sediments. Seasonal 𝛼-diversity peaked in summer–autumn and reached minima in spring across sediments, whereas water communities showed weaker seasonality. β-diversity analyses revealed that sediments maintained lower seasonal turnover (i.e., more temporally stable) and site-specific communities compared to water and phyllosphere habitats, which showed rapid compositional shifts and higher seasonal dissimilarity. Pärnu Bay, which experiences stronger riverine influence, exhibits larger temporal shifts in both 𝛼- and β-diversity than Haapsalu Bay. Taxonomic differences between bays included the dominance of Cyanobium in Haapsalu Bay and Synechococcus in Pärnu Bay, most likely driven by site-specific hydrology and nutrient regimes. After accounting for environmental gradients, P. australis had only modest, context-dependent effects on the bacterial community composition. Local hydrology and seasonal variation, particularly riverine inputs and salinity dynamics, exert stronger control over coastal bacterial community composition in top-layer sediment and water than the presence of P. australis. While sediments act as relatively stable, site-specific reservoirs, water, and phyllosphere communities were more labile and seasonally dynamic. These findings underscore the importance of site-specific assessments in shallow coastal studies and caution against generalizing results across bays.
Giant sulfur-oxidizing bacteria of the family Beggiatoaceae and their symbiotic relatives (Candidatus Epulonipiscium and related taxa) represent some of the largest and most morphologically conspicuous prokaryotes, yet their accessory genomic repertoires beyond chemolithoautotrophy remain poorly characterized. These lineages have independently evolved gigantism and contrasting lifestyles —free-living chemolithoautotrophy versus host-associated fermentative symbiosis—providing a comparative framework to test how lifestyle shapes accessory genome evolution. I conducted a genomic survey of 82 assemblies representing eight taxa, including free-living Beggiatoa, Thioploca, Candidatus Thiomargarita, and Thiomargarita; and symbiotic Candidatus Epulonipiscium, Candidatus Epulonipiscioides, Candidatus Parepulonipiscium, and Epulopiscium. Putative antimicrobial resistance genes (ARGs) were identified using DeepARG and ABRicate; biosynthetic gene clusters (BGCs) with antiSMASH; defense systems with DefenseFinder and CRISPRCas++; plasmids and prophages with geNomad, PHASTEST, VirSorter2, and PhaMer followed by CheckV quality filtering; and phage protein co-evolution with HyPhy/GARD/BGM. Lifestyle-associated differences were tested with negative-binomial models using genome size as an offset. After curation, 214 high-confidence putative ARGs and 350 BGCs were retained. Symbiotic lineages were strongly enriched in ARGs (IRR = 4.60) but depleted in total BGC density (IRR = 0.55), driven by loss of NRPS, terpene, PKS, and arylpolyene clusters and partially offset by enrichment of RiPP clusters. Defense systems were heterogeneously distributed, and genus-level differences largely disappeared after genome-size adjustment. Defense ORFs were not enriched inside BGC cores but were modestly over-represented within a 50–100 kb neighbourhood. Ten plasmids and eleven curated prophage-like sequences were recovered, most showing limited similarity to public databases. Co-evolutionary signal was stronger in structural phage proteins than in lytic and tail-associated proteins. These findings indicate that giant sulfur bacteria reallocate accessory genomic investment between biosynthetic capacity and antimicrobial resistance according to lifestyle, and that their mobile genetic elements remain poorly represented in current databases. Not applicable.
Globally, eutrophication, coastal pollution and thermal stress threaten seagrass ecosystems ecosystems. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. Our cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, including 17 potentially novel species, as well as genera not detected in our amplicon sequencing survey. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51
