Sen-Lin Tang

Probiotics hold promise for enhancing coral resilience under climate-driven thermal stress, yet their mechanisms remain poorly understood. Although the bacterial genus Endozoicomonas has been proposed to benefit corals, in vivo evidence of beneficial effects on the host remains limited. Here, we establish Endozoicomonas acroporae Acr-14T as a coral probiotic and characterize its effects on the reef-building coral Stylophora pistillata. We show that E. acroporae Acr-14T enhances host thermal tolerance, colonizes coral tissues, and forms coral-associated microbial aggregates (CAMAs). Microbial profiling indicates that probiotic treatment is associated with reduced relative abundances of opportunistic microbes and enrichment of putatively beneficial taxa. To support transcriptomic analyses, we assembled a chromosome-level genome of S. pistillata clade 1 (Pacific lineage) and found that E. acroporae Acr-14T treatment mitigates heat-induced protein-folding stress and apoptotic signaling. Single-cell transcriptomics further revealed altered expression of genes involved in S-adenosylmethionine (SAMe) metabolism and pro-survival signaling in gastrodermal cells of probiotic-treated corals. Together, our results provide a cell-type-resolved view of host responses linked to Endozoicomonas-mediated coral thermal resilience and offer insight into molecular mechanisms implicated in host–microbe interactions under environmental stress.

-short: Land-locked meromictic lakes are characterized by long-term stratification and steep redox gradients that sustain vertically structured microbial communities and tightly coupled biogeochemical processes. Because complete overturns of the lake are rare, the dynamics of microbial reassembly after redox gradients collapse and subsequently recover remain poorly resolved. We investigated a mixing–restratification transition in Lake Shira (Siberia) with depth-stratified sampling of oxic, chemocline, anoxic, and water–sediment interface layers across four stages: intermittent holomictic (IH), complete holomictic (CH), developing meromictic (DM), and stable meromictic (M). 16S rRNA gene amplicons showed that CH homogenized the water column, dominated by Gamma - and Alphaproteobacteria , Campylobacteria , and Cyanobacteriia . As stratification re-formed (DM–M), communities became strongly depth-partitioned, with Desulfobacterota and other anaerobes re-established in sulfidic deep waters and assemblages concentrating near the redox transition. Nanopore metagenomics reconstructed 401 MAGs, revealing stage- and depth-specific functional repertoires consistent with redox zonation. Core MAGs, including Yoonia spp., persisted across phases, suggesting functional continuity underpinning rapid ecosystem recovery. These data provide a system-wide view of biogeochemical reassembly during collapse and restoration of stratification meromictic lake.

Black band disease (BBD), which overgrows and kills scleractinian coral, is known to have various phases. The initial phase is the cyanobacterial patches (CPs) phase, followed by the intermediate phase (IP), and finally the mature BBD phase. Here, we hypothesize, pending further evidence, that when coral fragments infected with mature BBD are placed under shaded conditions, the BBD band shifts into a CP-like condition, with the shading causing a complex shift in the microbial consortium. While these microbial changes are beyond the scope of this paper, the photographs within provide interesting potential insights into this transition.

Endozoicomonas is an omnipresent marine bacterial genus, associated with various marine organisms, that contributes to host health, nutrient cycling and disease resistance. Nonetheless, its genomic features remain poorly characterised due to a paucity of high‐quality genomes. In this study, we sequenced 5 novel Endozoicomonas strains and re‐sequenced 1 known strain to improve genomic resolution. By integrating these 6 high‐quality genomes with 31 qualified published genomes, our pan‐genomic analysis revealed variation in genetic traits among clades. Notably, Endozoicomonas lacks quorum‐sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the capacity to synthesise and transport vitamin B12, indicating that it does not supply this nutrient to holobionts. Remarkably, Endozoicomonas genomes encode 92 identified giant proteins (15–65 kbp). These proteins cluster into three major groups associated with antimicrobial peptide synthesis, exotoxin production and cell adhesion. Additionally, we found that Endozoicomonas has acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR‐Cas sequences suggest evolutionary trajectories independent of both prophage acquisition and phylogenetic lineage, implying potential geographic influences or environmental pressures. This study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptations to diverse hosts.

The coral-killing sponge, Terpios hoshinota, poses a significant ecological threat to coral reefs, exhibiting rapid expansion and competitive overgrowth. Despite its invasiveness, the genomic basis underlying its adaptability and resilience remains largely unexplored. Here, we present a high-quality genome assembly of T. hoshinota, comprising 169.4 Mb with 40,945 predicted genes. Phylogenomic analysis estimated its divergence from other demosponges during the Ordovician (~ 471 million years ago), even though its simple morphology suggests a more ancient evolutionary origin. Comparative genomic analyses revealed enrichment of genes related to substrate adhesion, innate immunity, and developmental pathways, including expansions of Wnt signaling, homeobox genes, and cell migration gene ontologies which may contribute to its aggressive growth and resilience. Transcriptomic responses under simulated climate stress conditions (heat stress at 31 °C and acidification at 700 ppm pCO₂) indicated dynamic gene regulation, with upregulation of neurotransmitter metabolism, cellular maintenance, and ion homeostasis responses. Despite these stressors, it remained stable. This suggests that T. hoshinota exhibits strong adaptability and resilience through rapid gene regulation. In conclusion, these findings provide molecular insights into T. hoshinota’s ecological success, its potential expansion under climate change, and its broader impact on coral reef ecosystems.

Meretrix is a commercially valuable bivalve genus in Asia, but only one reference genome has hindered comprehensive genetic studies and germplasm resource evaluation. In this study, we present three reference genomes of Meretrix species: Meretrix sp. MF1, Meretrix sp. MT1, and Meretrix lamarckii JML1. Meretrix sp. MF1 was assembled at the chromosome level using Nanopore sequencing and Hi-C technologies, whereas Meretrix sp. MT1 and Meretrix lamarckii were assembled as scaffold-level assemblies. The chromosome-level genome of Meretrix sp. MF1 consists of 36 contigs, including 19 chromosomes and 17 scaffolds, with a total length of 883.3 Mb and a scaffold N50 of 46.87 Mb. Notably, the genome of Meretrix sp. MF1, a putative novel species, exhibits an Average Nucleotide Identity (ANI) of 94.33% with its closest relative, Meretrix lamarckii. These genomic resources not only provide a crucial foundation for genetic research on Meretrix but also contribute to the development of effective conservation strategies for its sustainable management.

Background: Endozoicomonas is a widely distributed genus of marine bacteria, associated with various marine organisms, and recognized for its ecological importance in host health, nutrient cycling, and disease dynamics. Despite its significance, genomic features of Endozoicomonas remain poorly characterized due to limited availability of high-quality genome assemblies. Results: In this study, we sequenced 5 novel Endozoicomonas strains and re-sequenced 1 known strain to improve genomic resolution. By integrating these 6 high-quality genomes with 31 others that were publicly available, we identified a distinct, coral-associated clade not recognized by the previous two-clade classification. Pan-genomic analysis revealed significant variation in genetic trait distribution among clades. Notably, Endozoicomonas lacks quorum sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the ability to synthesize and transport vitamin B12, indicating that it is not a primary source of this nutrient for holobionts. A remarkable feature of Endozoicomonas is its abundance of giant proteins, ranging from 15 to 65 kbp. We identified 92 such proteins, which clustered into three major groups based on amino acid similarity, each associated with specialized functions, such as antimicrobial synthesis, exotoxin production, and cell adhesion. Additionally, we explored prophages and CRISPR-Cas systems. We found that Endozoicomonas acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR-Cas sequences suggest independent evolutionary trajectories from both prophage acquisition and phylogenetic lineage, implying a potential influence of geographic or environmental pressures. Conclusions: This study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptation to diverse hosts. Identification of novel genomic features, including deficiencies in B12 synthesis and quorum sensing, the presence of giant proteins, prophages, and CRISPR-Cas systems, underscores its ecological roles in various holobionts. These findings open new avenues for research on Endozoicomonas and its ecological interactions.

Microfluidic systems commenced a new era of coral research, reducing demands for experimental material and minimizing scientific impacts on natural environments. Reduced size also allows continuous microscopy during experiments at unprecedented spatial–temporal resolutions and ensures greater homogeneity of environmental factors among samples. Since the report of the coral‐on‐a‐chip platform in 2016 by Shapiro and colleagues, modifications of coral microfluidic chips have been reported for various experimental purposes. However, existing coral cultivation chips were mostly designed for isolated polyps and for specific experimental setups, limiting their flexibility. Moreover, maintenance of coral health in miniaturized environments has proven challenging, preventing applications of coral chips to experiments with long timescales, which are more relevant to natural environmental events. Here, we present two new coral chips that enable long‐term (over a month), stable coral cultivation in the laboratory without laborious maintenance. Through experiments involving several research topics that are of paramount importance, for example flow speed, heating, osmolarity fluctuation and pathogen inoculation, we tested the applicability of our miniaturized system to coral research. Our results demonstrate the usefulness of our miniaturized system with different experimental objectives. Furthermore, by employing coral microcolonies, that is small coral fragments, our system is suitable for a wider spectrum of corals and is compatible with various analyses, compared to polyp‐based microfluidic systems in previous studies. The miniaturized system presented here considerably extends the applicability of existing coral cultivation chips and provides a convenient, cost‐effective and environmentally friendly platform for future coral studies.

Fungi engage in diverse symbiotic relationships with phototrophs. Lichens, symbiotic complexes involving fungi and either cyanobacteria, green algae, or both, have fungi forming the external layer and much of the interior. We found an erect thallus resembling a lichen yet with an unexpected thallus structure composed of interwoven cyanobacterial filaments with numerous fungal hyphae inserted within individual cyanobacterial sheaths, contrasting with typical lichen structure. Phylogenetics identified the fungus as a previously undescribed species, Serendipita cyanobacteriicola , closely related to endophytes, and the cyanobacterium belongs to the family Coleofasciculaceae, representing a genus and species not yet classified, Symbiothallus taiwanensis . These thalli exhibit nitrogen-fixing activity similar to mosses but lower than cyanolichens. Both symbiotic partners are distinct from known lichen-forming symbionts, uncovering a phylogenetically and morphologically unprecedented thallus-forming fungus-cyanobacterium symbiosis. We propose the name “phyllosymbia” for these thalli to underscore their unique symbiotic nature and leaf-like appearance. This finding marks a previously unknown instance of fungi solely residing within structures generated by cyanobacteria.

Coral skeletons constitute sources of nutrients and energy for holobiont. Although bacteria predominate in endolithic microbiomes of corals, their ecological functions have long been masked by those of symbiotic microalgae. In the skeleton of Isopora palifera, previous studies showed the absence of microalgae and a green layer dominated by green sulfur bacteria. This system, which excludes a contribution from microalgae, provides a perfect model for studying the role of endolithic bacteria in corals. Using this model, we examined the metabolite profile and translocation of organic matter between coral tissue and skeleton. Chromatography-time-of-flight-mass spectrometry and ultra-high-performance liquid chromatography tandem mass spectrometry revealed distinct metabolic profiles in tissue and different skeletal layers. A stable isotope incubation experiment further demonstrated ¹³C translocation between tissue and the green layer, but no translocation of ¹⁵N. These findings suggest communication between the two compartments that is generally carbon-based, possibly in the form of carbohydrates and bioactive compounds, such as corticosterone and domoic acid. Nevertheless, some nitrogenous compounds appear to have an endolithic source, indicating a possible contribution of the skeleton to coral animal. Notably, antibiotic treatment greatly increased ¹⁵N translocation in the tissue but not in the green layer. This highlights an important role of bacteria in nitrogen cycling in the holobiont and in establishing the nitrogen-limiting green layer. Altogether, this study provides the first data about coral skeletal metabolomes. Based on these findings, we propose a model of interactions between coral animal and skeletal bacterial communities, offering a new perspective on the ecological role of endolithic bacteria in corals.