Torsten Thomas

Sponges host phylogenetically highly diverse yet stable microbial symbiont communities that underpin the ecological success of the holobiont through functions such as nutrient cycling and secondary metabolite production. Here we describe 17 MAGs recovered from deep-sea sponges that belong to an uncultivated and previously uncharacterised, globally distributed microbial clade historically assigned a variety of placeholder names (AncK6, SAUL, PAUC34f and JAAXHH01). Using comprehensive phylogenetic analyses, we propose the phylum name Spongivicinota for this clade. While members of this group were detected across a range of marine and aquatic environments, their preferred lifestyle appear to be as symbionts of sponges and corals, where they consistently co-occur with members of their sister phylum Latescibacterota. Genome-based metabolic reconstruction supported by transcriptomic evidence reveals a specialisation of the Spongivicinota on the degradation of complex peptides and an enhanced capacity for vitamin B12 and iron uptake, with likely cross-phylum acquisition of vitamins B1, B2, B5 and B7. Several evolutionary divergences between Spongivicinota and Latescibacterota highlight the breadth of possible niches and adaptations these symbionts may exploit in the host environment.

Marine sponges harbor diverse communities of microorganisms that are essential for the host survival and function. Omics analyses have in recent years described the functional diversity and potential of sponge symbionts, however it is unclear if and how they interacted with each other and the host to provide essential metabolites for growth. To address this knowledge gap, we generated and curated genome-scale metabolic model (GSMM) for 19 bacterial symbionts that account for 95 % of the community abundance in the sponge Phyllospongia foliascens. We next employed spatio-temporal resolved flux-balance analysis to the community of models using sponge-derived substrates identified by metabolomics as nutrient constraint. We identified nutrient conditions that resulted in stable community structures that reflected observed those seen in nature. Under those conditions, cross-feeding of multiple metabolites were found to be important for sustaining the community structure. The exchange of B-vitamins and amino acids also resulted in excess metabolite production potentially available for the sponge. Our analysis reveals the metabolic dependencies and interactions that are important for the symbiont community and how this can provide benefit to the host.

Deep-sea corals (DSC) are ecologically important, yet their microbiomes’ composition, structure, and host specificity remain largely unresolved in the South Atlantic, especially for octocorals. Here, we provide a comprehensive characterization of DSC microbiomes, spanning Hexacorallia (Desmophyllum pertusum, Solenosmilia variabilis) and Octocorallia (Candidella imbricata, three Malacalcyonacea species), collected at ∼710 m depth in the Campos Basin, an active oil- and gas-producing region. Abiotic characterization revealed total hydrocarbon concentrations. Seawater and sediment samples provided further environmental context. Amplicon sequencing (16S rRNA gene), combined with alpha and beta diversity analyses, differential abundance analysis, and indicator species analysis, revealed that each coral species harboured a microbial community structure distinct from the surrounding environment, with host specificity varying along a continuum. Candidella imbricata was the individually resolved coral species with the most specialized microbiome, dominated by Endozoicomonadaceae, the lowest Shannon diversity, the highest intragroup homogeneity, and the largest number of indicator amplicon sequencing variants (ASVs). Desmophyllum pertusum showed no exclusive indicators, overlapping broadly with environmental communities, but selectively enriched the potentially hydrocarbon-degrading family Halieaceae. To our knowledge, these findings establish the first microbial baseline for DSC holobionts in this region, documenting contrasting host-specificity across scleractinian and octocoral taxa.

Microbial symbionts play key roles in macroalgal development, yet the processes structuring early‐life microbiomes remain poorly understood. Using laboratory outgrowth experiments and 16S rRNA gene amplicon sequencing we compared microbiome acquisition and assembly during the early development of three distinct macroalgae: Ulva australis (Chlorophyta), Hormosira banksii (Phaeophyceae) and Delisea pulchra (Rhodophyta). All species established distinct bacterial communities within the first week of outgrowth, with significant shifts in community composition and structure associated with major developmental stages. Stage‐enriched taxa included Phaeobacter , Roseobacter and Maribacter , which include members reported to influence algal growth or morphogenesis. Vertical inheritance contributed unevenly to the microbiome assembly across hosts. U. australis recruited low‐abundance environmental bacteria, possibly via strong host filtering. H. banksii selectively retained a small, consistent subset of adult‐derived bacteria, whereas D. pulchra retained fewer of its inherited bacteria. These results suggest that macroalgae can employ diverse transmission and recruitment strategies to assemble early microbiomes, combining selective inheritance with stage‐specific retention and/or environmental acquisition.

Host-associated microbiomes often display host specificity and heritability, yet the evolutionary processes under which such structured communities first emerge are still unclear. In particular, the conditions by which intergenerational (i.e., vertical) transmission of microbes can evolve and generate host-specific microbiomes are still unresolved. Here, we present an eco-evolutionary theory of microbiome assembly under minimal assumptions of microbial dynamics (i.e., neutrally driven by environmental fluctuations) and host control. We consider the adaptive evolution of microbial and host traits, including microbiome size and vertical transmission. We show that environmental fluctuations can generate enough among-host microbial variation to enable host-level selection favoring beneficial microbiome configurations. Vertical transmission can then evolve and, even when weak, allow microbiome specificity to be inherited and amplified across generations despite continuous influx from the external environment. Selection is most effective at intermediate levels of environmental fluctuation and host lifespan, revealing fundamental trade-offs between stochastic assembly, inheritance, and dispersal of microbes. The resulting microbiomes are dense, host-specific, and heritable, yet retain high intraspecific variability and lack strict phylosymbiosis. Simulated patterns of microbial dominance, diversity, and host–microbiome dissimilarity closely match those observed in nature, as evidenced using marine sponge microbiomes. Our results provide a mechanistic theory for the early evolution of host-associated microbiomes, showing that beneficial and species-specific communities can arise through selection and inheritance prior to the evolution of dedicated host-control mechanisms.

Environmental shifts can cause epigenetic modifications in corals associated with changes in gene expression and physiology, although it remains unclear if associated bacteria can also induce such changes. Here, we inoculate nubbins of the coral Pocillopora verrucosa with an opportunistic pathogen, Vibrio coralliilyticus, and/or a coral probiotic, Cobetia sp., and subject the nubbins to heat stress. We show that pathogen exposure leads to distinct DNA methylation changes compared to the control, probiotic, and co-inoculation groups. We also confirm that DNA methylation broadly correlates with coral gene expression; however, individual correlations are restricted to a subset of genes. We then highlight genes altered by pathogen inoculation that show similar responses in their expression and methylation. Notably, coral probiotic exposure mitigates specific epigenetic changes caused by pathogen inoculation, which correlates with increased stress resilience and higher coral survival rates. Although many aspects remain to be resolved, evidence that bacteria alter coral epigenomes may help clarify the role of microbiome interactions in coral resilience.

Marine sponges host complex and specific microbiomes, yet the role of these microbial symbionts in sponge responses to acute environmental stress is not fully understood. We investigated how altering the microbiome influences physiological responses to temperature in the temperate calcareous sponge Rowella lancifera under simulated marine heatwave (MHW) conditions. Sponges were treated with broad‐spectrum antibiotics to disrupt their microbiome and then exposed to sub‐lethal MHW temperatures. Microbial community composition was analysed using 16S rRNA gene sequencing, including assessing diversity and differential abundance, while sponge physiological response to temperature was quantified via respiration rates. Antibiotic treatment significantly altered microbial community structure but did not independently induce a physiological response. Heat exposure increased respiration rates, with a stronger response observed in microbiome‐altered sponges. Multivariate analyses revealed a relationship between microbial community structure and respiration rate, suggesting an association between microbiome composition and host physiological responses. Overall, these findings indicate that sponge‐microbe symbioses may play a role in modulating physiological responses to increased temperatures. As MHWs become more frequent and severe under climate change, understanding sponge‐microbe partnerships will be important for predicting responses of sponges and the stability of benthic ecosystems.

Background: Dysbiosis of the gut microbiota is common in children with autism spectrum disorder (ASD). Probiotics have the potential to improve outcomes in ASD by modulating the gut microbiota–brain axis. Methods: In a pilot randomised trial, children (2 to 5 years) with confirmed ASD (DSM-5 criteria) received either a multi-strain probiotic (450 billion CFU twice daily for one month, followed by once daily for three months) or placebo supplementation. Faecal microbiota profiles were assessed using pre- and post-supplementation samples. The primary outcome involved changes in gut microbiota diversity. Secondary outcomes included faecal short-chain fatty acid levels and behavioural changes. Results: Difficulties in recruitment and loss to follow-up for reasons including COVID-19 resulted in the enrolment of only 23 (probiotic: 9; placebo: 14) instead of the planned 40 children. There was no evidence of changes in the gut microbiota in probiotic-supplemented children. The common phyla were Bacillota_A (~50%), Bacteroidota (~18%) and Actinobacteriota (~10%). Alpha- and Beta-diversity showed no significant difference between pre- vs. post-supplementation samples. Bifodobacteriaceae increased significantly in the probiotic-supplemented group (p = 0.046). Conclusions: The increase in faecal Bifodobacteriaceae supports an evaluation of probiotics in ASD. Addressing the reasons for loss to follow-up is important when designing trials in this field.

The cyanobacterium Dolichospermum circinale is a known producer of the neurotoxin saxitoxin and its analogues, collectively known as the paralytic shellfish toxins (PSTs). PSTs vary in potency, and the reported toxin profiles of D. circinale blooms vary in the quantities of individual PSTs, with the regulation of these profiles being poorly understood. In this study, we present the genomes of four D. circinale strains (ACBU01, ACMB03, ACMB13 and FSS-124) with unique PST profiles and perform genome-wide comparisons and specific analysis of the PST-producing biosynthetic gene cluster (sxt) to understand the variability in PST quotas. A reassessment of the previously published D. circinale AWQC131C genome was also performed to collate genomic variation between all strains. Analysis at the nucleotide and amino acid sequence level revealed that toxic strains maintain high genome-wide similarities, corroborated by the analysis of the pan- and variable genomes of each strain. Specifically, the sxt gene sequences were 99-100% identical across all strains. Novel tailoring (sxtSUL, sxtDIOX) and transport (sxtM4) genes were identified within the sxt cluster that were not reported previously in D. circinale. Taken together, these results indicate that the genetic machinery involved in PST production is conserved in this species, suggesting that the regulation of PST biosynthesis in D. circinale does not occur at the genomic level.