Chemosynthetic Ecosystems Research Articles

Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma.

Vestimentiferan tubeworms are representative members of deep-sea chemosynthetic ecosystems. In this study, we developed a draft genome and gene models and performed genomic and transcriptomic analyses of Lamellibrachia satsuma, the only vestimentiferan reported from the euphotic zone. The quality of the genome assembly and gene models is comparable to or higher than those of previously reported vestimentiferan tubeworms. Tissue-specific transcriptome sequencing revealed that Toll-like receptor genes and lineage-specific expanded bacteriolytic enzyme genes are highly expressed in the obturacular and vestimental regions, respectively, suggesting the importance of these tissues in defense against pathogens. On the other hand, globin subunit genes are expressed almost exclusively in the trunk region, supporting the hypothesis that the trophosome is the site of haemoglobin biosynthesis. Vestimentiferan-specific expanded gene families included chitinases, ion channels, and C-type lectins, suggesting the importance of these functions for vestimentiferans. C-type lectins in the trunk region, in particular, may be involved in recognition of pathogens, or in interactions between tubeworms and symbiotic bacteria. Our genomic and transcriptomic analyses enhance understanding of molecular mechanisms underlying the unique lifestyle of vestimentiferan tubeworms, particularly their obligate mutualism with chemosynthetic bacteria.

Life-history traits of alvinocaridid shrimps inhabiting chemosynthetic ecosystems around Japan

Life-history traits of alvinocaridid shrimps inhabiting chemosynthetic ecosystems around Japan

High Microeukaryotic Diversity in the Cold-Seep Sediment.

Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.

MAPR: PMEL’s Miniature Autonomous Plume Recorder

The NOAA Vents program was established in 1983 at the Pacific Marine Environmental Laboratory (PMEL; Hammond et al., 2015), just six years after the discovery of hydrothermal vents and their unique chemosynthetic ecosystems (Corliss et al., 1979). Because seafloor hydrothermal venting contributes significantly to the transfer of heat and mass from the solid Earth to the ocean, the program’s mission was to systematically explore, discover, and characterize the environmental impacts of submarine volcanism and hydrothermal venting on ocean physical, chemical, and biological processes. The program initially focused on the mid-ocean spreading centers in PMEL’s “backyard” (i.e., the Gorda, Juan de Fuca, and Endeavour Ridges in the Northeast Pacific) where segment-scale surveys detected plumes in the water column above the ridge crest that led to the discovery of numerous individual vent fields (see Hammond et al., 2015, and references therein). New technologies and techniques were created and/or adapted to address the challenges of finding and studying these vents. Repeat visits to the Northeast Pacific sites documented spatial and temporal changes, stimulating the development of new hypotheses about their associated biogeochemical processes. However, testing how broadly applicable these hypotheses would be on a global scale required discovering new vent sites from a far wider range of geological settings, and global-scale exploration requires significant resources.

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

Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.

A New Paralepetopsis Limpet from a South China Sea Seep Hints at a Paraphyletic Neolepetopsidae.

Neolepetopsidae is a little-studied true limpet family only known from deep-sea chemosynthetic ecosystems, containing just over a dozen species in three genera: Neolepetopsis, Paralepetopsis, and Eulepetopsis. Although considered monophyletic by a recent phylogenetic analysis, a lack of Paralepetopsis sequence linked to morphology casts some uncertainty. Here, we discovered a new species of Paralepetopsis from the Haima methane seep in the South China Sea, described as Paralepetopsis polita sp. nov. The new species is distinct from all other described Paralepetopsis by its smooth and semi-transparent shell, combined with a radula exhibiting pluricuspid teeth with two cusps. We tested its relationship with other neolepetopsids using a molecular phylogeny reconstructed from the mitochondrial COI gene, revealing a surprising position nested within Lepetidae, a family with a very different radula morphology. The clade containing lepetids and our new species was recovered sister to other neolepetopsids with sequence data available. This hints at a paraphyletic Neolepetopsidae, and suggests the neolepetopsid-type radula might not be exclusive to one monophyletic group of limpets.

A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

Abstract The alvinocaridid shrimp Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, is an evolutionarily important deep-sea species in hydrothermal vents of north-western Pacific. A genome survey of S. leurokolos was carried out in order to provide a foundation for its whole-genome sequencing. A total of 599 Gb high-quality sequence data were obtained in the study, representing approximately 118× coverage of the S. leurokolos genome. According to the 17-mer distribution frequency, the estimated genome size was 5.08 Gb, and its heterozygosity ratio and percentage of repeated sequences were 2.85 and 87.03%, respectively, showing a complex genome. The final scaffold assembly accounted for a total size of 9.53 Gb (32,796,062 scaffolds, N50 = 597 bp). Repetitive elements nearly constituted 45% of the nuclear genome, among which the most ubiquitous were long interspersed nuclear elements, DNA transposons and long-terminal repeat elements. A total of 12,121,553 genomic simple sequence repeats were identified, with the most frequent repeat motif being di-nucleotide (70.27%), followed by tri-nucleotide and tetra-nucleotide. From the genome survey sequences, the mitochondrial genome of S. leurokolos was also constructed and 71 single nucleotide polymorphisms were identified by comparison with previous published reference. This is the first report of de novo whole-genome sequencing and assembly of S. leurokolos. These newly developed genomic data contribute to a better understanding of genomic characteristics of shrimps from deep-sea chemosynthetic ecosystems, and provides valuable resources for further molecular marker development.

Same (sea) bed different dreams: Biological community structure of the Haima seep reveals distinct biogeographic affinities

<p>Deep-sea chemosynthetic communities, including hydrothermal vents and cold seeps, harbour hundreds of endemic species currently threatened by deep-sea mining and hydrocarbon extraction. The South China Sea (SCS), a semi-enclosed marginal sea with two well-investigated active seeps (Haima in the west and Site F in the east), provides an opportunity to understand the biogeography of chemosynthetic ecosystems. Here, we conducted extensive field surveys using Remotely Operated Vehicles (ROVs) and collected specimens for morphological observations, molecular barcoding, phylogenetic analysis, and stable isotope analysis. Cluster analyses were applied to reveal the community structure of vents and seeps in the Western Pacific and Northern Indian Ocean. A total of 65 species covering seven phyla and 14 classes have been identified from Haima, doubling the number of species reported previously. Among them, 35 species are currently known only from Haima. Stable isotope analysis shows a typical chemosynthesis-based biological community. Community structure analysis at the genus level clustered Haima with Site F, though the species compositions and dominance of two seeps are fairly distinct. Between the two active seeps in the SCS, the higher species richness and endemism at Haima are potentially due to multiple factors, including the unique environmental factors there and the geographic isolation in the northwestern corner of the SCS. Moreover, a similarity in community compositions at the genus level between seeps in the SCS and North Indian Ocean was revealed, potentially mediated by the Early Pliocene opening of the Indonesian islands and the strong westward Indonesia Throughflow. Given the ongoing gas hydrate exploration activities in the SCS, our results will contribute to establishing a global network of marine protected areas for chemosynthetic-based ecosystems. The rich and endemic biodiversity at Haima calls for policymakers to formulate regulations to conserve the unique biodiversity there.</p>

The development and applications of a controllable lander for in-situ, long-term observation of deep sea chemosynthetic communities

Understanding the evolution of chemosynthetic communities and environmental changes near fluid seepages in the deep sea requires in-situ long-term observation data. However, in-situ detection or sampling for the investigation of cold seeps, hydrothermal vents, and nearby chemosynthetic ecosystems, by manned submersibles and remotely operated vehicles (ROVs), has great restrictions in terms of time. The observation parameters of a free-fall mode Lander cannot be adjusted in real time because there is no communication channel once the Lander is separated from the vessel. A long-term ocean observation platform (LOOP), that uses a new controllable mode for launching and recovery with the aid of a research vessel and submarine vehicles, has been developed and used in the cold seep area of the South China Sea. The LOOP can be operated in an online real-time control mode allowing landing site selection and adjustment of observation parameters during the launching process, with subsequent switched to an offline stand-alone operation mode for long-term, continuous observation. The effective observation times were 375 days and 414 days, respectively, during the 2016 and 2018 deployments in the cold seep area in the South China Sea. Results of these deployments show that salinity and dissolved oxygen parameters have strong spatial heterogeneity in both the horizontal and vertical directions within the cold seep vent. The spatial heterogeneity of environmental parameters may be one of the main driving factors for the uneven spatial distribution of chemosynthetic communities in cold seep areas. Overall, the LOOP provides an innovative and controllable launching and recovery mode and is expected to become a universal underwater observation platform for in-situ, long-term, and continuous data acquisition.

Munidopsis geyeri and M. exuta (Crustacea: Munidopsidae): A study of two deep-sea, amphi-Atlantic species that co-occur in the southern Gulf of Mexico

The history of colonization and dispersal of fauna among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood. The distribution of squat lobsters of the genus Munidopsis Whiteaves, 1874 can be influenced by the rich organic matter and associated organism communities of chemosynthetic ecosystems. The present work analyzed the molecular relationships and morphology of individuals from different populations of Munidopsis exuta Macpherson & Segonzac, 2005 and M. geyeri Pequegnat & Pequegnat, 1970 in such ecosystems along the Atlantic Equatorial Belt, including the Chapopote Knoll, in the southern Gulf of Mexico. Munidopsis geyeri is re-described based on the present findings and reference to the literature. This analysis documented the genetic distances, as well as range of variation in the diagnostic characters that support the separation of M. exuta and M. geyeri. Our results confirm that the two species coexist in seep ecosystems and have an amphi-Atlantic distribution.

RV Kronprins Håkon (cruise no. 2019708)

The HACON cruise is a major component of the FRINATEK HACON project, which aims at investigating the role of the Gakkel Ridge and Arctic Ocean in biological connectivity amongst ocean basins and global biogeography of chemosynthetic ecosystems. The HACON cruise was designed to conduct a multidisciplinary survey of the Aurora seamount centred around the identified black smokers in 2014. The scientific goal was to obtain visual and physical samples of the different habitats on the seamount to better understand hydrothermal vent communities on the Gakkel ridge and abyssal communities of an Arctic seamount, to assess the sphere of influence of the Aurora vent field across the seamount and adjacent seafloor regions The cruise may be known as: Hacon19

Element variation in a clam shell and its implications for cold seep irregular eruptions: Calyptogena sp. in the Haima cold seep

Cold seep is characterized by methane-rich fluids released from subsurface reservoirs, and it sustains the chemosynthetic ecosystems on the seafloor. Previous studies suggest that the activity of cold seep could affect the seawater chemistry and ambient temperature. However, the short-term seep activity was hardly reconstructed due to the focus of studies on carbonate or sediment. Vent macrofauna provide such an opportunity by recording in shells the immediate environment in which they grow. The carbonate skeleton of organisms could theoretically preserve environmental variation. Therefore, high-resolution archives are urgently required to understand the influence of cold seep activity on biogeochemistry. In this study, SEM, EDS mapping, EBSD mapping, and LA-ICP-MS analyses were conducted on a clam (Calyptogena sp.) shell collected alive in 2018 from the Haima cold seep in South China Sea. The CaCO3, Na, Mg, Sr, and Ba contents and the Sr/Ca, Ba/Ca, and Na/Ca ratios in the hinge plate were measured on LA-ICP-MS by spot analysis and line scanning. The element contents in the hinge are as follows: Mg (38.5–109 μg/g), Na (3117–5246 μg/g), Sr (970–5371 μg/g), and Ba (2.9–11.5 μg/g). The results show that Sr, Re, and Ba content vary synchronously along the direction of growth, but Na has an opposite trend. The element analyses indicate that the eruption of the Haima cold seep was irregular, causing temperature, redox state, and pH changes in the cold seep ecosystem. These findings show that the irregular cold seep activities exert vital influences on the biogeochemistry of the cold seep ecosystem, which shed a light on cold seep biomonitoring.

Hot Vents in an Ice-Covered Ocean - HACON21 expedition

The HACON cruise is a major component of the FRINATEK HACON project, which aims at investigating the role of the Gakkel Ridge and Arctic Ocean in biological connectivity amongst ocean basins and global biogeography of chemosynthetic ecosystems. The HACON cruise was designed to conduct a multidisciplinary survey of the Aurora seamount centred around the identified black smokers in 2014. The scientific goal was to obtain visual and physical samples of the different habitats on the seamount to better understand hydrothermal vent communities on the Gakkel ridge and abyssal communities of an Arctic seamount, to assess the sphere of influence of the Aurora vent field across the seamount and adjacent seafloor regions. The cruise may be known as: Hacon21

Interactions of Microplastics and Methane Seepage in the Deep-Sea Environment

Microplastics (MPs) are important exempla of the Anthropocene and are exerting an increasing impact on Earth’s carbon cycle. The huge imbalance between the MPs floating on the marine surface and those that are estimated to have been introduced into the ocean necessitates a detailed assessment of marine MP sinks. Here, we demonstrate that cold seep sediments, which are characterized by methane fluid seepage and a chemosynthetic ecosystem, effectively capture and accommodate small-scale (< 100 μm) MPs, with 16 types of MPs being detected. The abundance of MPs in the surface of the sediment is higher in methane-seepage locations than in non-seepage areas. Methane seepage is beneficial to the accumulation, fragmentation, increased diversity, and aging of MPs. In turn, the rough surfaces of MPs contribute to the sequestration of the electron acceptor ferric oxide, which is associated with the anaerobic oxidation of methane (AOM). The efficiency of the AOM determines whether the seeping methane (which has a greenhouse effect 83 times greater than that of CO2 over a 20-year period) can enter the atmosphere, which is important to the global methane cycle, since the deep-sea environment is regarded as the largest methane reservoir associated with natural gas hydrates.

Phylogeny and adaptative evolution to chemosynthetic habitat in barnacle (Cirripedia: Thoracica) revealed by mitogenomes

Thoracican barnacles represent a unique group that has evolved in parallel identical somatotype s (sessile, stalked and asymmetric) in both normal and chemosynthetic environments. Hydrothermal vents and methane seeps are typical extreme deep-sea chemosynthetic habitats for marine macrobenthos. Characterizing the evolutionary history and adaptive strategy of barnacles is fundamentally important for understanding their origin, speciation, and diversification. Herein, we performed a series of phylogenetic analyses focusing on the mitochondrial genomes of the main extant barnacle lineages. Phylogenetic inferences and topology tests contradict the view of the sister relationship between verrucomorphs and balanomorphs, instead revealing that pollicipedids, calanticids and balanomorphs share common ancestor. Selective pressure analyses indicate that the two barnacle lineages of chemosynthetic ecosystems exhibit similar patterns in their evolution of adaptive characters, but have diverse and specific positive substitution sites of mitogenomes. Divergence times suggest that chemosynthetic barnacles originated in the Cenozoic, coinciding with the origins of other metazoan animals in chemosynthetic habitats as well as the Paleogene mass extinction and oceanic anoxic events. It is reasonable to suppose that ecological niche vacancy, sitotaxis, gene specificity in adaptive stress responses, and the subdivision of the ecological niche contributed to the origin and diversification of barnacles in chemosynthetic ecosystems.

Effects of scale worm parasitism on interactions between the symbiotic gill microbiome and gene regulation in deep sea mussel hosts.

Diverse adaptations to the challenging deep sea environment are expected to be found across all deep sea organisms. Scale worms Branchipolynoe pettiboneae are believed to adapt to the deep sea environment by parasitizing deep sea mussels; this biotic interaction is one of most known in the deep sea chemosynthetic ecosystem. However, the mechanisms underlying the effects of scale worm parasitism on hosts are unclear. Previous studies have revealed that the microbiota plays an important role in host adaptability. Here, we compared gill-microbiota, gene expression and host-microorganism interactions in a group of deep sea mussels (Gigantidas haimaensis) parasitized by scale worm (PA group) and a no parasitic control group (NPA group). The symbiotic microorganism diversity of the PA group significantly decreased than NPA group, while the relative abundance of chemoautotrophic symbiotic bacteria that provide the host with organic carbon compounds significantly increased in PA. Interestingly, RNA-seq revealed that G. haimaensis hosts responded to B. pettiboneaei parasitism through significant upregulation of protein and lipid anabolism related genes, and that this parasitism may enhance host mussel nutrient anabolism but inhibit the host’s ability to absorb nutrients, thus potentially helping the parasite obtain nutrients from the host. In an integrated analysis of the interactions between changes in the microbiota and host gene dysregulation, we found an agreement between the microbiota and transcriptomic responses to B. pettiboneaei parasitism. Together, our findings provide new insights into the effects of parasite scale worms on changes in symbiotic bacteria and gene expression in deep sea mussel hosts. We explored the potential role of host-microorganism interactions between scale worms and deep sea mussels, and revealed the mechanisms through which scale worm parasitism affects hosts in deep sea chemosynthetic ecosystem.

Characterization and Comparison of Eye Development and Phototransduction Genes in Deep- and Shallow-Water Shrimp Alvinocaris longirostris and Palaemon carinicauda

The investigations of the molecular components of eye development and phototransduction in deep-sea species are important to elucidate the mechanism of their adaptation to dim light. In this study, eye transcriptomes of the shrimp Alvinocaris longirostris from the deep-sea chemosynthetic ecosystem and the shallow-water shrimp Palaemon carinicauda were compared. Two Pax6 homologs with low expression levels were identified in both species, which are essential transcription factors in eye development. This finding implies that the development of the two shrimp eyes at early embryo–larvae stages might be similar. The multiple components of the phototransduction pathway were identified in both species. However, the number of phototransduction components was significantly reduced in A. longirostris, as well as expression level. Particularly, short-wavelength/UV-sensitive (SWS/UVS) opsins were absent in A. longirostris and only one putative middle-wavelength-sensitive (MWS) opsin was identified in this species. The conserved sites and structures of the putative LWS opsins were found between deep-sea and shallow-water decapods, indicating that the opsins in deep-sea crustaceans may also conserve their spectral absorption and signal transduction function. Phylogenetic analyses supported the monophyly of LWS opsins and SWS/UVS opsins in arthropods, while the MWS clade fell outside of the main arthropod LWS clade. The results are expected to provide baseline for study of visual adaptation in deep-sea shrimps.

Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps.

ABSTRACTRemarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation.IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts.

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

Reproduction in deep-sea vent shrimps is influenced by diet, with rhythms apparently unlinked to surface production.

Variations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non‐photosynthetic primary production, these relationships remain largely under‐studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis—R. exoculata and R. kairei—and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long‐standing paradigm in deep‐sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year‐round observations in order to understand the life history of vent animals.