scholarly journals Host–Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

2020 ◽  
Author(s):  
Jack Chi-Ho Ip ◽  
Ting Xu ◽  
Jin Sun ◽  
Runsheng Li ◽  
Chong Chen ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Carbon Fixation ◽  
Sulfur Oxidation ◽  
Gene Families ◽  
Cold Seeps ◽  
Cellular Processes ◽  
Metabolic Integration ◽  
Metabolite Exchange ◽  
Chemosynthetic Bacteria

Abstract Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host–symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.

scholarly journals Genomic Insights Into Chemosynthetic Symbiosis in a Deep-Sea Hydrothermal Vent Mussel

2022 ◽  
Author(s):  
Kai Zhang ◽  
Yao Xiao ◽  
Jin Sun ◽  
Ting Xu ◽  
Kun Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
Functional Differentiation ◽  
Cold Seeps ◽  
Proteomic Approach ◽  
Immune Related Genes ◽  
Self Protection

Abstract Background Symbiosis with chemosynthetic bacteria has allowed many invertebrates to flourish in ‘extreme’ deep-sea chemosynthesis-based ecosystems, such as hydrothermal vents and cold seeps. Bathymodioline mussels are considered as models of deep-sea animal-bacteria symbiosis, but the diversity of molecular mechanisms governing host-symbiont interactions remains understudied owing to the lack of hologenomes. In this study, we adopted a total hologenome approach in sequencing the hydrothermal vent mussel Bathymodiolus marisindicus and the endosymbiont genomes combined with a transcriptomic and proteomic approach that explore the mechanisms of symbiosis. Results Here, we provide the first coupled mussel-endosymbiont genome assembly. Comparative genome analysis revealed that both Bathymodiolus marisindicus and its endosymbiont reshape their genomes through the expansion of gene families, likely due to chemosymbiotic adaptation. Functional differentiation of host immune-related genes and attributes of symbiont self-protection that likely facilitate the establishment of endosymbiosis. Hologenomic analyses offer new evidence that metabolic complementarity between the host and endosymbionts enables the host to compensate for its inability to synthesize some essential nutrients, and two pathways (digestion of symbionts and molecular leakage of symbionts) that can supply the host with symbiontderived nutrients. Results also showed that bacteriocin and abundant toxins of symbiont may contribute to the defense of the B. marisindicus holobiont. Moreover, an exceptionally large number of anti-virus systems were identified in the B. marisindicus symbiont, which likely work synergistically to efficiently protect their hosts from phage infection, indicating virus-bacteria interactions in intracellular environments of a deepsea vent mussel. Conclusions Our study provides novel insights into the mechanisms of symbiosis enabling deep-sea mussels to successfully colonize the special hydrothermal vent habitats.

Distribution of Pogonophora in Canyons of the Bay of Biscay: Factors Controlling Abundance and Depth Range

1988 ◽  
Vol 68 (4) ◽  
pp. 627-638 ◽  
Author(s):  
A. J. Southward ◽  
P. R. Dando
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Mouth Opening ◽  
Quantitative Information ◽  
Sediment Chemistry ◽  
Cold Seeps ◽  
Depth Range ◽  
Bay Of Biscay ◽  
Tube Worms ◽  
Chemosynthetic Bacteria

The Pogonophora are tube-worms of predominantly deep sea distribution. They lack a functioning alimentary canal in the adult stage and are then dependent for nutrition on internal symbiotic chemosynthetic bacteria that occupy tissue derived from the larval endoderm (Southward, 1982, 1987, 1988; Southward & Southward, 1987; Southwardet al.1981). Of the two main subgroups, the small perviate Pogonophora are widely distributed in reducing sediments in the oceans, while the large vestimentiferan or obturate Pogonophora are restricted to hydrothermal vents or cold seeps. The small Pogonophora are often most abundant on steep slopes and in the Bay of BiscaySiboglinum atlanticum(Southward & Southward, 1958) can be a dominant element of the infauna of the sediments on the sides of canyons. This animal, like other small Pogonophora, lies buried in the sediment, in contrast to the vestimentifera which are attached to hard substrates. Until now there has been no fully quantitative information on the distribution ofS. atlanticumand associated pogonophores of the Bay of Biscay. Dredges or trawls have been used for most previous sampling of pogonophores along the continental slope (Southward, 1979, 1985). Even the Plymouth-pattern deep-sea anchor dredge (Southward & Southward, 1963), which is designed to dig into the sediment immediately it is towed on the bottom, may drag for some distance through soft sediments before digging in, and then samples the upper few centimetres over a wider area than its mouth opening. During the last season of operation of R.R.S. ‘Frederick Russell’, before this vessel was disposed of by N.E.R.C., opportunity was taken to make a combined quantitative biological and chemical survey, using box-corers. The samples from the corers were large enough to allow the sample to be used for assessment of the population density of the pogonophores and analysis of sediment chemistry. Some inferences can now be drawn about the factors controlling pogonophore abundance.

scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

scholarly journals Deep-sea ophiuroids (Echinodermata) from reducing and non-reducing environments in the North Atlantic Ocean

2005 ◽  
Vol 85 (2) ◽  
pp. 383-402 ◽  
Author(s):  
Sabine Stöhr ◽  
Michel Segonzac
Keyword(s):  
South Carolina ◽  
Gulf Of Mexico ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Cold Seep ◽  
Chemical Compositions ◽  
Cold Seeps ◽  
Additional Species ◽  
Blake Ridge ◽  
Reducing Environment

The animal communities associated with the deep-sea reducing environment have been studied for almost 30 years, but until now only a single species of ophiuroid, Ophioctenella acies, has been found at both hydrothermal vents and methane cold seeps. Since the faunal overlap between vent and seep communities is small and many endemic species have been found among other taxa (e.g. Mollusca, Crustacea), additional species of ophiuroids were expected at previously unstudied sites. Chemical compositions at reducing sites differ greatly from the nearby bathyal environment. Generally, species adapted to chemosynthetic environments are not found in non-chemosynthetic habitats, but occasional visitors of other bathyal species to vent and seep sites have been recorded among many taxa except ophiuroids. This paper presents an analysis of the ophiuroid fauna found at hydrothermal vents and non-reducing nearby sites on the Mid-Atlantic Ridge and on methane cold seeps in the Gulf of Mexico, at Blake Ridge off South Carolina and south of Barbados. In addition to O. acies, four species were found at vents, Ophiactis tyleri sp. nov., Ophiocten centobi, Ophiomitra spinea and Ophiotreta valenciennesi rufescens. While Ophioctenella acies appears to be restricted to chemosynthetic areas, the other four species were also found in other bathyal habitats. They also occur in low numbers (mostly single individuals), whereas species adapted to hydrothermal areas typically occur in large numbers. Ophioscolex tripapillatus sp. nov. and Ophiophyllum atlanticum sp. nov. are described from nearby non-chemosynthetic sites. In a cold seep south of Barbados, three species of ophiuroids were found, including Ophioctenella acies, Amphiura sp., Ophiacantha longispina sp. nov. and Ophioplinthaca chelys. From the cold seeps at Blake Ridge and the Gulf of Mexico, Ophienigma spinilimbatum gen. et sp. nov. is described, likely restricted to the reducing environment. Ophiotreta valenciennesi rufescens occurred abundantly among Lophelia corals in the Gulf of Mexico seeps, which is the first record of this species from the West Atlantic. Habitat descriptions complement the taxonomic considerations, and the distribution of the animals in reducing environments is discussed.

scholarly journals Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Marie-Anne Cambon-Bonavita ◽  
Johanne Aubé ◽  
Valérie Cueff-Gauchard ◽  
Julie Reveillaud
Keyword(s):  
Hydrothermal Vents ◽  
Carbon Fixation ◽  
Iron Sulfide ◽  
Hydrogen Oxidation ◽  
Niche Partitioning ◽  
Sulfur Oxidation ◽  
Single Copy ◽  
Trophic Levels ◽  
Rimicaris Exoculata ◽  
Close Relatives

Abstract Background Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris–microbe associations. Results Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences. Conclusion These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents.

Deep-sea hydrothermal vents and cold seeps

2020 ◽  
pp. 238-292 ◽  
Author(s):  
Richard J. Léveillé ◽  
S. Kim Juniper
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Cold Seeps

scholarly journals Chiridota heheva—the cosmopolitan holothurian

2020 ◽  
Vol 50 (6) ◽  
Author(s):  
Elin A. Thomas ◽  
Ruoyu Liu ◽  
Diva Amon ◽  
Jon T. Copley ◽  
Adrian G. Glover ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Deep Sea ◽  
Species Complex ◽  
Hydrothermal Vents ◽  
Novel Species ◽  
Cold Seeps ◽  
Ecological Studies ◽  
Chemosynthetic Ecosystems ◽  
Relationship Of ◽  
The Relationship

AbstractChemosynthetic ecosystems have long been acknowledged as key areas of enrichment for deep-sea life, supporting hundreds of endemic species. Echinoderms are among the most common taxa inhabiting the periphery of chemosynthetic environments, and of these, chiridotid holothurians are often the most frequently observed. Yet, published records of chiridotids in these habitats are often noted only as supplemental information to larger ecological studies and several remain taxonomically unverified. This study therefore aimed to collate and review all known records attributed to Chiridota Eschscholtz, 1829, and to conduct the first phylogenetic analysis into the relationship of these chiridotid holothurians across global chemosynthetic habitats. We show that Chiridota heheva Pawson & Vance, 2004 is a globally widespread, cosmopolitan holothurian that occupies all three types of deep-sea chemosynthetic ecosystem—hydrothermal vents, cold seeps and organic falls—as an organic-enrichment opportunist. Furthermore, we hypothesise that C. heheva may be synonymous with another vent-endemic chiridotid, Chiridota hydrothermica Smirnov et al., 2000, owing to the strong morphological, ecological and biogeographical parallels between the two species, and predict that any chiridotid holothurians subsequently discovered at global reducing environments will belong to this novel species complex. This study highlights the importance of understudied, peripheral taxa, such as holothurians, to provide insights to biogeography, connectivity and speciation at insular deep-sea habitats.

scholarly journals A new species and phylogenetic insights in Hesiospina (Annelida, Hesionidae) 

Zootaxa ◽  
2018 ◽  
Vol 4441 (1) ◽  
pp. 59 ◽  
Author(s):  
PAULO BONIFÁCIO ◽  
YANN LELIÈVRE ◽  
EMMANUELLE OMNES
Keyword(s):  
New Species ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Juan De Fuca Ridge ◽  
Cold Seeps ◽  
Molecular Analyses ◽  
The Third ◽  
Juan De Fuca ◽  
Ne Pacific ◽  
A New Species

Hesionids are a very speciose group of polychaetes. In the deep sea, they occur in different environments such as hydrothermal vents, cold seeps, abyssal depths or whale falls. In the present study, a new species of Hesionidae, Hesiospina legendrei sp. nov. has been identified based on morphological and molecular (16S and COI genes) data from hydrothermal vents located in Juan de Fuca Ridge (NE Pacific Ocean). This new species is characterized by trapezoid prostomium; proboscis with high number of distal papillae (20–27), a pair of sac-like structures inserted ventro-laterally in proboscis; notopodia lobe reduced with multiple, slender aciculae on segments 1–5; and neuropodia developed with single, simple chaeta, and numerous, heterogomph falcigers, with 1–2 inferiormost having elongated hood. Hesiospina legendrei sp. nov. is the third described species in the genus. Sequences from the two previously described Hesiospina species are included in the molecular analyses, and although the genes used in this study are not sufficient to resolve the relationships on genus level, the result raises questions about the cosmopolitan aspect of H. vestimentifera. 

scholarly journals A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11282
Author(s):  
Mengna Li ◽  
Hao Chen ◽  
Minxiao Wang ◽  
Zhaoshan Zhong ◽  
Hao Wang ◽  
...  
Keyword(s):  
Hydrothermal Vents ◽  
Lipid A ◽  
Cold Seeps ◽  
Immune Recognition ◽  
Recognition Mechanism ◽  
Surface Plasmon Resonance Analysis ◽  
Resonance Analysis ◽  
Methane Oxidizing Bacteria ◽  
Chemosynthetic Bacteria ◽  
Lipid A Structure

Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels.

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