Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis

The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms

Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE

In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.

Integrative morphological, mitogenomic and phylogenetic analyses reveal new vent-dwelling scallop species

Delectopecten is a small genus of the family Pectinidae (Bivalvia: Pectinida) that remains poorly studied in terms of both morphology and phylogeny. Here, we describe the first member of this genus from deep-sea hydrothermal vent ecosystems, D. thermus sp. nov., based on morphological investigations and molecular analyses of a specimen collected from the Higashi-Ensei vent field (962-m depth) in the northern Okinawa Trough. Morphologically, this new species resembles D. vancouverensis and D. gelatinosus in shell size, shape, auricle size and sculpture. However, D. thermus sp. nov. can be distinguished from its congeneric species (including 9 extant and 12 fossil species) by its unequal auricles (the anterior one being larger than the posterior), inwardly recurved anterior auricle of the left valve and a large byssal notch angle of ~90°. Comparisons of genetic sequences from three mitochondrial and three nuclear gene fragments supported the placement of the new species in the genus Delectopecten . Further phylogenetic analyses using these gene markers support that Delectopecten is monophyletic and positioned as an early diverging clade of the family Pectinidae. Additionally, the mitogenome of D. thermus sp. nov. was assembled and annotated, a first for its genus - revealing significant divergences in gene order compared to other pectinids. The 16S rRNA amplicon analysis of the gill tissue indicated that this vent-dwelling scallop does not exhibit symbiosis with chemosynthetic bacteria. A key to all known species of Delectopecten is provided to aid the identification of species in this understudied genus. ZooBank: urn:lsid:zoobank.org:pub:D3D5D4AD-EE39-49F0-9782-12A5D6752A67.

lafK contributes the regulation of swarming motility of Pseudomonas plecoglossicida and bacterial-host interaction

Flagella-mediated swarming motility plays a crucial role in facilitating the rapid colonization and dissemination of bacterial within the host. The swarming motility of Pseudomonas plecoglossicida is intricately associated with its lateral flagella, and notably, the lateral flagella system of P. plecoglossicida encompasses a transcriptional regulator known as LafK. However, the regulatory role of LafK and its impact on bacteria-host interactions remain to be elucidated. In this study, we systematically investigated the regulatory role of LafK by constructing lafK deletion strain on the biological characteristics, virulence, and pathogenic process of P. plecoglossicida, as well as its impact on the host immune response. Our findings demonstrated that the deletion of lafK led to a significant down-regulation in the expression of type III secretion system-associated genes within the lateral flagella of P. plecoglossicida, consequently impairing bacterial swarming motility, biofilm formation, adhesion, and chemotaxis ability. Furthermore, in vitro infection experiments demonstrated that the deletion of lafK resulted in a diminished pathogenicity of P. plecoglossicida through down-regulation of flagella-related genes, thereby triggering an expedited immune response for bacterial clearance, and subsequently leading to reduced bacterial load within the host and attenuated tissue damage during infection. In summary, this study presents a novel theoretical framework for elucidating the regulatory mechanism of virulence in P. plecoglossicida.

sRNA113 regulates Pseudomonas plecoglossicida motility to affect immune response against infection in pearl gentian grouper

Small RNAs (sRNAs) are a class of molecules capable of perceiving environmental changes and exerting post-transcriptional regulation over target gene expression, thereby influencing bacterial virulence and host immune responses. Pseudomonas plecoglossicida is a pathogenic bacterium that poses a significant threat to aquatic animal health. However, the regulatory mechanisms of sRNAs in P. plecoglossicida remain unclear. This study focused on sRNA113, previously identified as a potential regulator of the fliP gene, a key component of the lateral flagellar type III secretion system. To investigate the effects of sRNA113 on P. plecoglossicida virulence, as well as its role in regulating pathogenic processes and host immune responses, mutant strains lacking this sRNA were generated and analyzed. Deletion of sRNA113 resulted in the up-regulation of lateral flagellar type III secretion system-related genes in P. plecoglossicida, which enhanced bacterial swarming motility, biofilm formation, and chemotaxis ability in vitro. In vivo infection experiments with pearl gentian grouper revealed that sRNA113 deletion enhanced the pathogenicity of P. plecoglossicida. This heightened virulence was attributed to the up-regulation of genes associated with the lateral flagellar type III secretion system, resulting in higher bacterial loads within host tissues. This amplification of pathogenic activity intensified tissue damage, disrupted immune responses, and impaired the ability of the host to clear infection, ultimately leading to mortality. These findings underscore the critical role of sRNA113 in regulating the virulence of P. plecoglossicida and its interaction with host immune defenses. This study provides a foundation for further exploration of sRNA-mediated mechanisms in bacterial pathogenesis and host-pathogen interactions, contributing to a deeper understanding of virulence regulation and immune evasion in aquatic pathogens.

Specificity of benthic invertebrate gill-associated microbiome contributes to host fitness to localized heterogeneous environment in the cold seep

The deep hydrocarbon fluids discharged into the water column at cold seeps create diverse and heterogeneous habitats on the seafloor. Symbiosis is essential for the survival of marine life in extreme deep-sea environments. Although the symbiotic relationship between chemoautotrophic bacteria and invertebrates has been reported, our understanding of these host-microbe interactions under heterogeneous environment remains limited. In this study, we evaluated the bacterial community structures, histological and subcellular localization, and potential functions of the gill microbiomes of six invertebrates in the Haima cold seep, South China Sea. The results showed distinct gill-associated microbiomes in these six invertebrates. Gigantidas haimaensis and Archivesica marissinica exhibit a highly dependent symbiotic relationship with their intracellular gill symbionts, characterized by a simple composition. In contrast, Alvinocaris longirostris, Shinkaia crosnieri, Phymorhynchus buccinoides, and Paraescarpia echinospica display a loosely dependent association with their extracellular gill-associated microbes, which are notably complex in composition. Moreover, gill microbiome specificity was seen among six invertebrates and host selection could be an underlying mechanism. The potential functional components of these six invertebrate gill microbiomes contribute to host fitness in heterogeneous local environments. The results obtained from our study provide insights into the ecology and evolution of host-microbe interactions and the underlying mechanisms in extreme marine environments. This information is critical for predicting the responses of benthic fauna to environmental changes in cold seeps.

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliate Zoothamnium niveum and its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup, Z. niveum holds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.

The hidden acceleration pump uncovers the role of shellfish in oceanic carbon sequestration

Whether shellfish mariculture should be included in the blue carbon profile as a strategy to combat climate change has been controversial. It is highly demanding not only to provide calibration quantitation, but also to provide an ecosystem-based mechanism. In this study, we chose mussel farms as a case study to evaluate their contributions to carbon sinks and their responses to sedimentary carbon fixation and sequestration. First, we quantified the air-sea CO2 flux in the mussel aquacultural zone and observed a weak carbon sink (-0.15 ± 0.07 mmol·m-2·d-1) during spring. Next, by analyzing the carbon composition in the sediment, we recorded a noticeable and unexpected increase in the sedimentary recalcitrant carbon (RC) content in the mussel farming case. To address this surprising sedimentary phenomenon, a long-term indoor experimental test was conducted to distinguish the consequences of mussel engagement with sedimentary RC. Our observational data support the idea that mussel engagement promotes accumulation of RC in sediments by 2.5-fold. Furthermore, the relative intensity of carboxylic-rich alicyclic molecule (CRAM)-like compounds (recalcitrant dissolved organic matter (RDOM)) increased by 451.4 % in the mussel-engaged sedimentary dissolved organic matter (DOM) in comparison to the initial state. Mussel engagement had a significantly positive effect on the abundance of sedimentary carbon-fixing genes. Therefore, we definitively conclude that mussel farming is blue carbon positive and propose a new alternative theory that mussel farming areas may have high carbon sequestration potential via an ecologically integrated "3 M" (microalgae-mussel-microbiota) consortium. The "mussel pump" accelerates carbon sequestration and enhances climate-related ecosystem services.

Achieving partial nitrification by sludge treatment using sulfide: Optimal conditions determination, long-term stability evaluation and microbial mechanism exploration

This study proposes an innovative strategy for achieving PN in synthetic domestic wastewater by side-stream sludge treatment using sulfide as the sole control factor. By conducting controllable batch experiments and response surface analysis, optimal sulfide treatment conditions were firstly determined as 90 mg/L of sulfide, 7.5 of pH, 100 rpm of rotation and 12 h of treatment time. After treatment, half of ammonia oxidizing bacteria (AOB) activity remained, but nitrite oxidizing bacteria (NOB) activity was barely detected. Nitrite accumulation rate of long-term running PN steadily reached 83.9 % with 99.1 % of ammonia removal efficiency. Sulfide treatment increased community diversity and facilitated stability of microbiota functioning with PN phenotype, which might be sustained by the positive correlation between ammonia oxidation gene (amoA) and sulfur oxidation gene (soxB). Correspondingly, the network analysis identified the keystone microbial taxa of persistent PN microbiota as Nitrosomonas, Thauera, Truepera, Defluviimonas and Sulitalea in the later stage of long-term reactor.

Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress

Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.

Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses

Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.

Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration

Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.

Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum

One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.