Deep-sea Tubeworm Research Articles

Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm

Endosymbiosis with chemosynthetic Gammaproteobacteria is widely recognized as an adaptive mechanism of siboglinid tubeworms, yet evolution of these endosymbionts and their driving forces remain elusive. Here, we report a finished endosymbiont genome (HMS1) of the cold-seep tubeworm Sclerolinum annulatum. The HMS1 genome is small in size, with abundant prophages and transposable elements but lacking gene sets coding for denitrification, hydrogen oxidization, oxidative phosphorylation, vitamin biosynthesis, cell pH and/or sodium homeostasis, environmental sensing, and motility, indicative of early genome erosion and adaptive evolution toward obligate endosymbiosis. Unexpectedly, a prophage embedded in the HMS1 genome undergoes lytic cycle. Highly expressed ROS scavenger and LexA repressor genes indicate that the tubeworm host likely activates the lysogenic phage into lytic cycle through the SOS response to regulate endosymbiont population and harvest nutrients. Our findings indicate progressive evolution of Sclerolinum endosymbionts toward obligate endosymbiosis and expand the knowledge about phage-symbiont-host interaction in deep-sea tubeworms.

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

BackgroundVestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated.ResultWe assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae.ConclusionRidgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.

Discovery of a readily heterologously expressed Rubisco from the deep sea with potential for CO2 capture

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the key CO2-fixing enzyme in photosynthesis, is notorious for its low carboxylation. We report a highly active and assembly-competent Form II Rubisco from the endosymbiont of a deep-sea tubeworm Riftia pachyptila (RPE Rubisco), which shows a 50.5% higher carboxylation efficiency than that of a high functioning Rubisco from Synechococcus sp. PCC7002 (7002 Rubisco). It is a simpler hexamer with three pairs of large subunit homodimers around a central threefold symmetry axis. Compared with 7002 Rubisco, it showed a 3.6-fold higher carbon capture efficiency in vivo using a designed CO2 capture model. The simple structure, high carboxylation efficiency, easy heterologous soluble expression/assembly make RPE Rubisco a ready-to-deploy enzyme for CO2 capture that does not require complex co-expression of chaperones. The chemosynthetic CO2 fixation machinery of chemolithoautotrophs, CO2-fixing endosymbionts, may be more efficient than previously realized with great potential for next-generation microbial CO2 sequestration platforms.

Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica.

Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.

Centrifugation-Based Enrichment of Bacterial Cell Populations for Metaproteomic Studies on Bacteria-Invertebrate Symbioses.

Owing to high sample complexity, metaproteomic investigations on bacteria-animal symbioses with two or more uncultured partners can be challenging. A selective isolation or enrichment of distinct (sub-)populations within those consortia can solve this problem. Subsequent discrete proteomic analyses benefit from increased sample purity and higher proteome coverage for each of the individual organisms. Here, we describe centrifugation-based methods that allow for a separation of the host and its bacterial symbiont population(s), or even for an enrichment of distinct symbiotic cell cycle stages in the deep-sea mussels Bathymodiolus azoricus and B. thermophilus, the gutless oligochaete Olavius algarvensis and the deep-sea tube worm Riftia pachyptila, respectively.

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro­benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

A chemosynthetic weed: the tubeworm Sclerolinum contortum is a bipolar, cosmopolitan species.

BackgroundSclerolinum (Annelida: Siboglinidae) is a genus of small, wiry deep-sea tubeworms that depend on an endosymbiosis with chemosynthetic bacteria for their nutrition, notable for their ability to colonise a multitude of reducing environments. Since the early 2000s, a Sclerolinum population has been known to inhabit sediment-hosted hydrothermal vents within the Bransfield Strait, Southern Ocean, and whilst remaining undescribed, it has been suggested to play an important ecological role in this ecosystem. Here, we show that the Southern Ocean Sclerolinum population is not a new species, but more remarkably in fact belongs to the species S. contortum, first described from an Arctic mud volcano located nearly 16,000 km away.ResultsOur new data coupled with existing genetic studies extend the range of this species across both polar oceans and the Gulf of Mexico. Our analyses show that the populations of this species are structured on a regional scale, with greater genetic differentiation occurring between rather than within populations. Further details of the external morphology and tube structure of S. contortum are revealed through confocal and SEM imaging, and the ecology of this worm is discussed.ConclusionsThese results shed further insight into the plasticity and adaptability of this siboglinid group to a range of reducing conditions, and into the levels of gene flow that occur between populations of the same species over a global extent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0559-y) contains supplementary material, which is available to authorized users.

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida)

Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts.

Identification and amplification of microsatellite loci in deep-sea tubeworms of the genus Escarpia (Polychaeta, Siboglinidae)

Deep-sea cold seeps support diverse communities that include vestimentiferan tubeworms of the genus Escarpia. To investigate population structure to understand how deep-sea communities are established, several polymorphic microsatellites were developed using 454 pyrosequencing. Eleven and sixteen loci were identified in Escarpia laminata (n = 129) and Escarpia southwardae (n = 80). Additionally, the amplification of microsatellites is expected to be successful in closely related species and can help resolve their phylogenetic relationships. Nine of the E. laminata loci were amplified across three Escarpia species (n = 229). Four of the twenty-eight loci deviated from Hardy–Weinburg Equilibrium and no linkage disequilibrium was found in the loci tested here.

Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics

The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments.

Status quo in physiological proteomics of the unculturedRiftia pachyptilaendosymbiont

Riftia pachyptila, the giant deep-sea tube worm, inhabits hydrothermal vents in the Eastern Pacific ocean. The worms are nourished by a dense population of chemoautotrophic bacterial endosymbionts. Using the energy derived from sulfide oxidation, the symbionts fix CO(2) and produce organic carbon, which provides the nutrition of the host. Although the endosymbionts have never been cultured, cultivation-independent techniques based on density gradient centrifugation and the sequencing of their (meta-) genome enabled a detailed physiological examination on the proteomic level. In this study, the Riftia symbionts' soluble proteome map was extended to a total of 493 identified proteins, which allowed for an explicit description of vital metabolic processes such as the energy-generating sulfide oxidation pathway or the Calvin cycle, which seems to involve a reversible pyrophosphate-dependent phosphofructokinase. Furthermore, the proteomic view supports the hypothesis that the symbiont uses nitrate as an alternative electron acceptor. Finally, the membrane-associated proteome of the Riftia symbiont was selectively enriched and analyzed. As a result, 275 additional proteins were identified, most of which have putative functions in electron transfer, transport processes, secretion, signal transduction and other cell surface-related functions. Integrating this information into complex pathway models a comprehensive survey of the symbiotic physiology was established.

The animal turn: Into the sea with the fish-knights of Perceforest

In his contribution to this volume, Cary Wolfe points out the ‘terrestrialist bias that still obtains in [an] animal studies’ that concentrates on ‘dogs, cats, horses, and farm animals,’ and perhaps less frequently, on birds and hideous fabulists. The world, on land and on sea, comprises many far less familiar ‘critters’ than these: anemones symbiotically reliant on ‘little marshes of algae, ocean plantlets of a species that has come to live only in them’ (Lingis, 2003, 165), deep-sea tube worms, cetaceans, or, legendarily, the whale-like aspidochelone, whose rocky and verdant back, resembling an island, lured unwary sailors to their deaths (Guillaume le Clerc, 1852, ll. 2095–2120; Coulter, 1926; Szabo, 2008, 47–50). Few medieval critters so confused distinctions between land and sea, animal and land, and life and nonlife, but we do find other examples of beings that inhabit both land and sea in medieval texts. We turn, then, to the curious figure of the fish-knight in an epilogue that aims to extend the inquiries and conclusions of the preceding essays and to further unsettle the terrestrial and vitalist biases underlying many critical perspectives on nonhumans. In what is surely one of the stranger episodes in medieval literature, found in the fourteenth-century Roman de Perceforest, the knight Bethides has been

Population structure of two deep sea tubeworms, Lamellibrachia luymesi and Seepiophila jonesi, from the hydrocarbon seeps of the Gulf of Mexico

Vestimentiferan tubeworms are a group of large sessile marine polychaete annelids (family Siboglinidae) found in the regions of hydrothermal venting or seepage of the reduced chemical hydrogen sulfide. Hydrocarbon seeps on the Louisiana Slope of the Gulf of Mexico support large communities of the co-occurring vestimentiferan species Lamellibrachia luymesi and Seepiophila jonesi. These sessile species have the opportunity to disperse between the patchy sites of active seepage on the seafloor during a planktonic larval stage. However, it is unclear whether dispersal occurs at a local or global scale. Four ( L. luymesi) and seven ( S. jonesi) microsatellite loci were used to test for population substructure among ten hydrocarbon seep sites on the Louisiana Slope. Both species showed high levels of allelic diversity, averaging 18.5 ( L. luymesi) and 22 ( S. jonesi) alleles/locus, respectively, and high observed heterozygosity at all microsatellite loci (0.71–0.9 in L. luymesi, 0.27–0.84 in S. jonesi). The two species showed a significant deficiency in heterozygotes compared to that predicted under the Hardy–Weinberg equilibrium. L. luymesi showed a small but significant amount of population structure, with a positive correlation between genetic and geographic distance among the sample sites spanning 540 km. S. jonesi, in contrast, showed no evidence for isolation by distance, but did show a significant genetic difference between aggregations of different ages. These results suggest that these two species differ in how larvae are able to colonize new seep sites through space ( L. luymesi) and though time ( S. jonesi).

Free-Living Tube Worm Endosymbionts Found at Deep-Sea Vents

Recent evidence suggests that deep-sea vestimentiferan tube worms acquire their endosymbiotic bacteria from the environment each generation; thus, free-living symbionts should exist. Here, free-living tube worm symbiont phylotypes were detected in vent seawater and in biofilms at multiple deep-sea vent habitats by PCR amplification, DNA sequence analysis, and fluorescence in situ hybridization. These findings support environmental transmission as a means of symbiont acquisition for deep-sea tube worms.

Biodiversity maintenance in food webs with regulatory environmental feedbacks

Although the food web is one of the most fundamental and oldest concepts in ecology, elucidating the strategies and structures by which natural communities of species persist remains a challenge to empirical and theoretical ecologists. We show that simple regulatory feedbacks between autotrophs and their environment when embedded within complex and realistic food-web models enhance biodiversity. The food webs are generated through the niche-model algorithm and coupled with predator–prey dynamics, with and without environmental feedbacks at the autotroph level. With high probability and especially at lower, more realistic connectance levels, regulatory environmental feedbacks result in fewer species extinctions, that is, in increased species persistence. These same feedback couplings, however, also sensitize food webs to environmental stresses leading to abrupt collapses in biodiversity with increased forcing. Feedback interactions between species and their material environments anchor food-web persistence, adding another dimension to biodiversity conservation. We suggest that the regulatory features of two natural systems, deep-sea tubeworms with their microbial consortia and a soil ecosystem manifesting adaptive homeostatic changes, can be embedded within niche-model food-web dynamics.

Arginine Metabolism in the Deep Sea Tube Worm Riftia pachyptila and Its Bacterial Endosymbiont

The present study describes the distribution and properties of enzymes involved in arginine metabolism in Riftia pachyptila, a tubeworm living around deep sea hydrothermal vents and known to be engaged in a highly specific symbiotic association with a bacterium. The results obtained show that the arginine biosynthetic enzymes, carbamyl phosphate synthetase, ornithine transcarbamylase, and argininosuccinate synthetase are present in all of the tissues of the worm and in the bacteria. Thus, Riftia and its bacterial endosymbiont can assimilate nitrogen and carbon via this arginine biosynthetic pathway. The kinetic properties of ornithine transcarbamylase strongly suggest that neither Riftia nor the bacteria possess the catabolic form of this enzyme belonging to the arginine deiminase pathway, the absence of this pathway being confirmed by the lack of arginine deiminase activity. Arginine decarboxylase and ornithine decarboxylase are involved in the biosynthesis of polyamines such as putrescine and agmatine. These activities are present in the trophosome, the symbiont-harboring tissue, and are higher in the isolated bacteria than in the trophosome, indicating that these enzymes are of bacterial origin. This finding indicates that Riftia is dependent on its bacterial endosymbiont for the biosynthesis of polyamines that are important for its metabolism and physiology. These results emphasize a particular organization of the arginine metabolism and the exchanges of metabolites between the two partners of this symbiosis.

Contribution of the Bacterial Endosymbiont to the Biosynthesis of Pyrimidine Nucleotides in the Deep-sea Tube Worm Riftia pachyptila

The deep-sea tube worm Riftia pachyptila (Vestimentifera) from hydrothermal vents lives in an intimate symbiosis with a sulfur-oxidizing bacterium. That involves specific interactions and obligatory metabolic exchanges between the two organisms. In this work, we analyzed the contribution of the two partners to the biosynthesis of pyrimidine nucleotides through both the "de novo" and "salvage" pathways. The first three enzymes of the de novo pathway, carbamyl-phosphate synthetase, aspartate transcarbamylase, and dihydroorotase, were present only in the trophosome, the symbiont-containing tissue. The study of these enzymes in terms of their catalytic and regulatory properties in both the trophosome and the isolated symbiotic bacteria provided a clear indication of the microbial origin of these enzymes. In contrast, the succeeding enzymes of this de novo pathway, dihydroorotate dehydrogenase and orotate phosphoribosyltransferase, were present in all body parts of the worm. This finding indicates that the animal is fully dependent on the symbiont for the de novo biosynthesis of pyrimidines. In addition, it suggests that the synthesis of pyrimidines in other tissues is possible from the intermediary metabolites provided by the trophosomal tissue and from nucleic acid degradation products since the enzymes of the salvage pathway appear to be present in all tissues of the worm. Analysis of these salvage pathway enzymes in the trophosome strongly suggested that these enzymes belong to the worm. In accordance with this conclusion, none of these enzyme activities was found in the isolated bacteria. The enzymes involved in the production of the precursors of carbamyl phosphate and nitrogen assimilation, glutamine synthetase and nitrate reductase, were also investigated, and it appears that these two enzymes are present in the bacteria.

The enzymes involved in synthesis and utilization of carbamylphosphate in the deep-sea tube worm Riftia pachyptila

The obligate symbiosis of the deep-sea tube worm Riftia pachyptila with a sulphur-oxidizing bacterium raises important questions concerning its metabolism and metabolic exchanges. In this study, the presence and properties of the enzymes synthesizing and utilizing carbamylphosphate in the arginine and pyrimidine nucleotide pathways were investigated in this worm. The results show that the ammonium-dependent carbamylphosphate synthetase and ornithine transcarbamylase, enzymes involved in the arginine pathway, are present in all body parts of the worm. In contrast, the glutamine-dependent carbamylphosphate synthetase and aspartate transcarbamylase, enzymes involved in the de novo pathway for pyrimidine nucleotides biosynthesis, are present only in the trophosome, the symbiont-harbouring tissue. Although the bacterial nature of these enzymes is not unambigously established, these results strongly suggest that the de novo biosynthesis of pyrimidine nucleotides is limited to the trophosome, the organ where the production of metabolic energy takes place, while the other parts of the worm's body rely on the salvage pathway for the production of the pyrimidine triphosphate nucleotides.

Preliminary data on carbon production of deep-sea vent tubeworms

The deep-sea tubeworm Riftia pachyptila and its endosymbiotic bacteria are thought to be major primary producers of the East Pacific Rise hydrothermal vent ecosystem. Tube production rates were measured for worms maintained alive in pressure aquaria. These rates (y) correlate to the fresh weight (x) of individuals, following an almost square-root relationship (y = 0.192x 0.492 ). Extrapolation of experimental data to in situ animal densities (in dense clumps) leads to rates that may exceed 1 g C m -2 d -1 for worms from the Parigo site (13°N). Thus, vestimentiferan tube growth alone would indicate that this vent site is a remarkable benthic hotspot for carbon production. Finally, it seems that these rates differ depending on the in situ origin of the animals, thus suggesting that in the future this type of experiment may provide quantitative information concerning the vitality of different vent sites.

Partially glucose-capped oligosaccharides are found on the hemoglobins of the deep-sea tube worm Riftia pachyptila.

We report here the structural determination of N-linked oligosaccharides found on extracellular hemoglobins of the hydrothermal vent tube worm Riftia pachyptila. Structures were elucidated by a combination of electrospray ionization tandem mass spectrometry, matrix-assisted laser desorption/ionization mass spectrometry, normal-phase high performance liquid chromatography, and exoglycosidase digestion. The sugar chains were found to consist mainly of high-mannose-type glycans with some structures partially capped by one or two terminal glucose residues. The present study represents the first report of the occurrence of glucose capping of N-linked carbohydrates in a secreted glycoprotein of a metazoan. Previously, glucose capping has only been described for a membrane-bound surface glycoprotein from the unicellular parasite Leishmania mexicana amazonensis.