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Ecophysiological differences between vesicomyid species and metabolic capabilities of their symbionts influence distribution patterns of the deep‐sea clams
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This study provides an analysis of vesicomyid bivalve–symbiont community distribution across cold seep and hydrothermal vent areas in the Guaymas Basin (Gulf of California, Mexico). Using a combination of morphological and molecular approaches including fluorescent in situ hybridization (FISH), and electronic microscopy observations, vesicomyid clam species and their associated symbionts were characterized and results were analyzed in light of geochemical conditions and other on‐site observations. A greater diversity of vesicomyids was found at cold seep areas, where three different species were present (Phreagena soyoae [syn. kilmeri], Archivesica gigas, and Calyptogena pacifica). In contrast, A. gigas was the only species sampled across the hydrothermal vent area. The same haplotype of A. gigas was found in both hydrothermal vent and cold seep areas, highlighting possible contemporary exchanges among neighboring vents and seeps. In either ecosystem, molecular characterization of the symbionts confirmed the specificity between symbionts and hosts and supported the hypothesis of a predominantly vertical transmission. In addition, patterns of clams could reflect potential niche preferences for each species. The occurrence of numerous traces of vesicomyid movements on sediments in the sites colonized by A. gigas seemed to indicate that this species might have a better ability to move. Furthermore, variation in gill sulfur content could reveal a higher plasticity and sulfur storage capacity in A. gigas. Thus, the distribution of vesicomyid species across the chemosynthetic areas of the Guaymas Basin could be explained by differences in biological traits of the vesicomyid species that would allow A. gigas to more easily exploit transient and punctual sources of available sulfide than P. soyoae.
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... NBC37-1 within the afferent vessel, epithelial principal cells and pilaster cells in the gills suggests an endosymbiont relationship between the SOB and the vent crab. The widespread occurrence of the SOB in X. testudinatus gills is reminiscent of findings made in the gills of vesicomyid clams (Cruaud et al., 2019), mytilid mussels (Halary et al., 2008;Szafranski et al., 2015;Duperron et al., 2016), and bresiliid shrimps (Tokuda et al., 2008) from hydrothermal vent habitats. Since the gills serve as a boundary between an aquatic animal's internal organs and the external environment, these tissues appear to be an enclave for SOBs to carry out sulfide detoxification and organic production for the hosts (Felbeck and Somero, 1982). ...
The shallow-water hydrothermal vent (HV) system off Kueishan Island lies at the end of the Okinawa Trough to the northeast of Taiwan. Near its submarine vent openings, aperiodic vent discharges generate a dynamic acidic (pH 5.5-8.1) and sulfidic (9-3000 μM) ecosystem. The dominant metazoan in this unique environment is the brachyuran vent crab, Xenograpsus testudinatus, which has developed robust metabolic strategies and highly adaptive acid-base regulatory mechanisms to maintain its physiological homeostasis. X. testudinatus is considered a holobiont, but the symbiotic mechanisms underlying acid and sulfur tolerance in the host-microbe system remain largely unclear. In this study, we used LoopSeq long-read sequencing of the full-length 16S rRNA gene to identify the bacterial communities present in the gills and carapace surface of X. testudinatus. The alpha diversity analysis, Venn diagram, and principal coordinate analysis (PCoA) indicated that the gills and carapace surface exhibit different bacterial constituents. Further measurements of relative abundance, coupled with functional predictions and fluorescence in situ hybridization (FISH), revealed a predominance of Sulfurovum sp. NBC37-1, a key bacterium that can perform sulfur and hydrogen oxidation to support denitrification processes. Consequently, our findings suggest that the symbiotic bacteria may play a critical role in conferring the extraordinary acid and sulfur tolerances of X. testudinatus, allowing the crustacean holobiont to thrive in its ecological niche within one of the most extreme marine habitats on Earth.
... Ruthia magnifica and Ca. Vesicomyosocius okutanii possess intermediate genome sizes (1.16 Mbp versus 1.02 Mbp) and levels of AT enrichment (66% versus 68%) compared to other host-restricted symbionts, while contrasting levels of gene decay and GC content for 10 housekeeping genes were observed across their respective clades [25].Variations in host affiliation and genome reduction between symbiont clades do not appear to be driven by adaptation to different broad-scale habitat types, as host species of both clades have been found at hydrothermal vents and hydrocarbon seeps and often cooccur at the same locality [11,14,26,27]. However, limited genetic data suggest that the two symbiont clades differ in physiological characteristics related to nitrate reduction and sulfur metabolism, which may affect microhabitat exploitation [14,26], and could, thus, influence patterns of gene conservation. ...
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017–1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
... Ruthia magnifica and Ca. Vesicomyosocius okutanii possess intermediate genome sizes (1.16 Mbp versus 1.02 Mbp) and levels of AT enrichment (66% versus 68%) compared to other host-restricted symbionts, while contrasting levels of gene decay and GC content for 10 housekeeping genes were observed across their respective clades [25].Variations in host affiliation and genome reduction between symbiont clades do not appear to be driven by adaptation to different broad-scale habitat types, as host species of both clades have been found at hydrothermal vents and hydrocarbon seeps and often cooccur at the same locality [11,14,26,27]. However, limited genetic data suggest that the two symbiont clades differ in physiological characteristics related to nitrate reduction and sulfur metabolism, which may affect microhabitat exploitation [14,26], and could, thus, influence patterns of gene conservation. ...
Given their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts' mitochondria. Our investigation confirmed that nearly-neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that can provide insights into adaptation to divergent ecological niches. While patterns of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is relatively rare. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Differences in nitrogen and sulfur physiology between the two dominant symbiont groups, Ca. Ruthia and Ca. Vesicomyosocius, have been hypothesized to influence niche exploitation, which likely affects gene content evolution in these symbionts. However, genomic data are currently limited to confirm this assumption. In the present study we sequenced and compared 11 vesicomyid symbiont genomes with existing assemblies for Ca. Vesicomyosocius okutanii and Ca. Ruthia magnifica. Our analyses indicate that the two vesicomyid symbiont groups have a common core genome related to chemosynthetic metabolism, but differ in their potential for nitrate respiration and flexibility to environmental sulfide concentrations. Moreover, Ca. Vesicomyosocius and Ca. Ruthia have different enzymatic requirements for cobalamin and nickel and show contrasting capacities to acquire foreign genetic material. Tests for site-specific positive selection in metabolic candidate genes imply that the observed physiological differences are adaptive and thus likely correspond to ecological niches available to each symbiont group. These findings highlight the role of niche differentiation in creating divergent paths of reductive genome evolution in vertically transmitted symbionts.
Pliocardiines (Bivalvia: Vesicomyidae: Pliocardiinae) are symbiotrophic vesicomyid molluscs harbouring symbiotic sulphide-oxidizing chemoautotrophic bacteria in their gills. The pliocardiines, Phreagena soyoae and Archivesica gigas, are a common component of numerous deep-sea chemosynthesis-based communities in the Eastern and Western North Pacific. We examined the stable isotope composition of carbon, nitrogen and sulphur as well as the fatty acid composition of P. soyoae and A. gigas from two methane seep sites, Clam Hill (1427 – 1443 m) and Barite Ridge (1455 – 1548 m) in the Deryugin Basin in the Sea of Okhotsk. For identification of bacterial endosymbiont lineages, we determined the nucleotide sequences of COI genes of symbionts of P. soyoae and A. gigas and confirmed that both species have the same bacterial lineages as their Eastern Pacific counterpart populations. Stable isotope analysis showed that site-specific differences between pliocardiines from the two seeps of the Deryugin Basin far exceeded interspecies variations. There were obvious differences in the sulphur isotopic compositions among pliocardiines from Clam Hill and from Barite Ridge suggesting that the intensity of anaerobic methane oxidation and methane flow varied in different cold seeps from the Deryugin Basin. The δ¹³C values recorded for P. soyoae and A. gigas samples were in the narrow range typical for studied pliocardiines. Both species showed an unusually broad range of δ¹⁵N values (∼18‰) that overlapped the known range of this signature for pliocardiines. The main polyunsaturated fatty acids in P. soyoae and A. gigas were nonmethylene-interrupted 20:2(5,13), 20:3(5,13,16) and 20:4(5,13,16,19), which were synthesized by the molluscs themselves and not by their symbionts.
Insights into the factors controlling fluid circulation through the crust and the nature of fluid venting at the seafloor are first steps in understanding their effect on ocean properties and climate change. New data on the seafloor morphology, sub-surface sedimentary stratification, and water column of the sedimented Southern Trough hydrothermal field (Guaymas basin) were acquired during the BIG cruise in 2010. These data provide accurate and high-resolution information on the geological context of the vents, on the distribution of acoustic anomalies in the water column, and on the possible nature of the fluid generating these echoes. More than 40 hydrothermal edifices were observed. The southern zone of the study area hosts hydrothermal sites that differ from the northern area. The southern vents are located inside or at the edge of small sub-circular depressions and the relationship between active edifices and collapsed areas involves different steps in the continous hydrothermal setting. Sub-bottom data show surface and sub-surface events, with some reflection layers possibly indicating subsurface hydrothermal precipitates or lithification with an estimated age of approximately 10 000 to 20 000 years. Based on the position and maximum altitude of the acoustic anomalies above the seafloor, two types of fluid emission echoes are distinguished: 1) anomalies reaching a maximal altitude of ∼350 m above the seafloor and seen both at the northern and southern fields and 2) strong, narrow and straight anomalies reaching 1334 or 1702 m above the seafloor that are only present in the southern hydrothermal fields of the studied area. We suggest that there are two types of echoes reflecting different fluid escapes based on the physical conditions of fluid venting and degassing and their relationship to geologic features: hydrothermal fluids or hydrothermal fluid mixed with hydrocarbon gas, oil or condensates rising through the water column. The collapsed depressions observed in the southern part facilitate the release of light hydrocarbon (gas, oil, and condensates) soluble at a high temperature and transported by hydrothermal fluids towards the shallow sedimentary levels where they accumulate. These light hydrocarbons rapidly migrate at high levels in the water column. This contrasts with the northern fields where hydrothermal circulation linked to deeper faults, re-mobilize heavier non-soluble hydrocarbons which do not migrate at high levels in the water column.
In the Guaymas Basin, the presence at a few tens of kilometers of cold seeps and hydrothermal vents coupled with comparable sedimentary settings and depths offer a unique opportunity to assess and compare the microbial community composition of these deep-sea ecosystems. The microbial diversity in sediments from three cold seep and two hydrothermal vent assemblages were investigated using high-throughput 16S rRNA-sequencing. Numerous bacterial and archaeal lineages were detected in both cold seep and hydrothermal vent sediments. Various potential organic matter degraders (e.g., Chloroflexi, Atribacteria, MBG-D) and methane and sulfur cycling related microorganisms (e.g., ANME and methanogenic lineages, sulfate-reducing lineages) were detected in both ecosystems. This suggests that analogous metabolic processes such as organic matter degradation and anaerobic methane oxidation coupled to sulfate reduction, were probably occurring in these two contrasted ecosystems. These highlighted “core microbiome” of the Guaymas Basin chemosynthetic ecosystems might therefore result from the combined presence of up-rising fluid emissions and high sedimentary rates of organic matter in the Basin. These results, coupled with the detailed ribotype analysis of major archaeal lineages (ANME-1, ANME-2, and MBG-D), also suggest a potential connectivity among deep-sea ecosystems of the Guaymas Basin likely due to the sedimentary context and the absence of physical border. However, thermophilic and hyperthermophilic lineages (e.g., Thermodesulfobacteria, Desulfurococcales, etc.) were exclusively identified in hydrothermally impacted sediments highlighting the strong influence of temperature gradients and other hydrothermally-related factors such as thermogenic sulfate reduction and sulfide formation on microbial community composition.
Understanding the ecological processes and connectivity of chemosynthetic
deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf
of California, Mexico), the presence of seeps and vents in the absence of a
biogeographic barrier, and comparable sedimentary settings and depths offers a
unique opportunity to assess the role of ecosystem-specific environmental
conditions on macrofaunal communities. Six seep and four vent assemblages
were studied, three of which were characterised by common major foundation
taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats.
Macrofaunal community structure at the family level showed that density,
diversity and composition patterns were primarily shaped by seep- and vent-common abiotic factors including methane and hydrogen sulfide concentrations, whereas vent environmental specificities (higher
temperature, higher metal concentrations and lower pH) were not significant.
The type of substratum and the heterogeneity provided by foundation species
were identified as additional structuring factors and their roles were found
to vary according to fluid regimes. At the family level, seep and vent
similarity reached at least 58 %. All vent families were found at seeps
and each seep-specific family displayed low relative abundances (< 5 %). Moreover, 85 % of the identified species among dominant families
were shared between seep and vent ecosystems. This study provides further
support to the hypothesis of continuity among deep-sea seep and vent
ecosystems.
Two species of the bivalve family Vesicomyidae living at a depth of 940 m in the central Gulf of Mexico were photographed, counted and measured. These species, which are related to bivalves in chemmouatotrophic communities in the Gulf of Mexico and at hydrothermal vents in the Pacific Ocean, occurred here in two apparently distinct aggregations clearly visible on the sea floor surface. Living vesicomyids were generally found amid a scatter of dead shells and occurred in densities of 0.5-9.6 individuals per m2. Distribution of living individuals within the aggregations was patchy. Living clams appear to plow actively through a substrate of silty clay, leaving behind distinctive, curving furrows up to 205 cm in length. Estimates of density, size distribution and spatial distribution provide a basis for detection of change in the aggregations over time and for comparison with similar aggregations.
Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano (AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. (14)C-radiotracer measurements showed that methylamines/methanol, H(2)/CO(2) and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16S PCR-DGGE and mcrA gene libraries, and enrichments of methanogens showed the presence of Methanococcoides in the shallow sediment layers. Overall acetoclastic methanogenesis was higher than hydrogenotrophic methanogenesis, which is unusual for cold seep sediments. Interestingly, acetate porewater concentrations were extremely high in the AMV sediments. This might be the result of organic matter cracking in deeper hotter sediment layers. Methane was also produced from hexadecanes. For the most part, the methanogenic community diversity was in accordance with the depth distribution of the H(2)/CO(2) and acetate methanogenesis. These results demonstrate the importance of methanogenic communities in the centres of marine mud volcanoes.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Methane-rich fluids arising from organic matter diagenesis in deep sediment layers sustain chemosynthesis-based ecosystems along continental margins. This type of cold seep develops on pockmarks along the Congo margin, where fluids migrate from deep-buried paleo-channels of the Congo River, acting as reservoirs. Similar ecosystems based on shallow methane production occur in the terminal lobes of the present-day Congo deep-sea fan, which is supplied by huge quantities of primarily terrestrial material carried by turbiditic currents along the 800 km channel, and deposited at depths of up to nearly 5000 m. In this paper, we explore the effect of this carbon enrichment of deep-sea sediments on benthic macrofauna, along the prograding lobes fed by the current active channel, and on older lobes receiving less turbiditic inputs. Macrofaunal communities were sampled using either USNEL cores on the channel levees, or ROV blade cores in the chemosynthesis-based habitats patchily distributed in the active lobe complex.
Vesicomyids live in endosymbiosis with sulfur-oxidizing bacteria and therefore need hydrogen sulfide to survive. They can nevertheless live in a wide range of sulfide and oxygen levels and depths, which may explain the exceptional diversity of this clam family in deep-sea habitats. In the Gulf of Guinea, nine species of vesicomyid clams are known to live in cold-seep areas with pockmarks from 600 to 3200 m deep, as well as in the organic-rich sediments of the Congo deep-sea fan at 5000 m deep. Our previous study showed that two species living in a giant pockmark have different oxygen carriers, suggesting different adaptations to hypoxia. Here, we studied the hemoglobin structure and oxygen affinity in three other species, Calyptogena valdiviae, Elenaconcha guiness and Abyssogena southwardae to determine whether the characteristics of their oxygen carriers contribute to their distribution in sulfide-rich sediments at a regional scale. Documenting pairwise species associations in various proportions, we give a semi-quantitative account of their local distribution and oxygen and sulfide measurements at seven sites. Mass spectrometry showed that each vesicomyid species has four intracellular monomeric hemoglobin molecules of 15–16 kDa, all differing in their molecular mass. As expected, the monomers showed no cooperativity in oxygen binding. Their oxygen affinities were very high (below 1 Torr), but differed significantly. C. valdiviae had the highest affinity and was dominant in the Harp pockmark, the site with the lowest oxygen content (half the value of fully oxygenated water). A. southwardae dominated in the Congo Lobe area, the site with the deepest sulfides. We discuss how hemoglobin may favor an active, vertical distribution of vesicomyids in sulfide-rich sediments.
Vesicomyid clams are a dominant and common component of the megafauna inhabiting most cold seep and hydrothermal vent communities. The bivalve family Vesicomyidae includes more than 50 species found nearly exclusively in sulphide-rich habitats such as cold seeps, hydrothermal vents, and accumulations of organic debris (e.g. whale carcasses), from 450 m to greater than 3000 m depth. All species investigated have been shown to rely nutritionally on sulphide-oxidizing endosymbiotic chemoautotrophic bacteria held in ctenidia (Fiala-Medioni et al., 1994). Thus, these bivalves require access to sulphide-rich pore fluids, but must also contend with the potentially extreme toxicity of sulphide. In this paper, we investigate aspects of the physiology of Calyptogena pacifica and C. kilmeri that influence their habitat distribution, including results of growth rate studies that suggest potential metabolic constraints imposed by differences in sulphide physiology.