Phenotypic variation and fitness in a metapopulation of tubeworms (Ridgeia piscesae Jones) at hydrothermal vents

Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes

The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

Shining light on a deep-sea bacterial symbiont population structure with CRISPR

Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.

Emergent "core communities" of microbes, meiofauna and macrofauna at hydrothermal vents

Assessment of ecosystem health entails consideration of species interactions within and between size classes to determine their contributions to ecosystem function. Elucidating microbial involvement in these interactions requires tools to distil diverse microbial information down to relevant, manageable elements. We used covariance ratios (proportionality) between pairs of species and patterns of enrichment to identify "core communities" of likely interacting microbial (<64 µm), meiofaunal (64 µm to 1 mm) and macrofaunal (>1 mm) taxa within assemblages hosted by a foundation species, the hydrothermal vent tubeworm Ridgeia piscesae. Compared with samples from co-located hydrothermal fluids, microbial communities within R. piscesae assemblages are hotspots of taxonomic richness and are high in novelty (unclassified OTUs) and in relative abundance of Bacteroidetes. We also observed a robust temperature-driven distinction in assemblage composition above and below ~25 °C that spanned micro to macro size classes. The core high-temperature community included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota, particularly the genera Carboxylicivirga, Nitratifractor and Arcobacter. The core low-temperature community included more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria. Inferred associations among high-temperature core community taxa suggest increased reliance on species interactions under more severe hydrothermal conditions. We propose refinement of species diversity to "core communities" as a tool to simplify investigations of relationships between taxonomic and functional diversity across domains and scales by narrowing the taxonomic scope.

Geochemistry drives the allometric growth of the hydrothermal vent tubeworm Riftia pachyptila (Annelida: Siboglinidae)

The tubeworm Riftia pachyptila is a key primarily producer in hydrothermal vent communities due to the symbiosis with sulphur-oxidizing bacteria, which provide nourishment to the worm from sulphides, oxygen and carbon dioxide. These substances diffuse from the vent water into the bloodstream of the worm through their tentacular crowns, and then to the bacteria, hosted in a specialized organ of the worm, called a trophosome. The uptake rates of these substances depend on the surface/volume relationship of the tentacles. We here describe two morphotypes, ‘fat’ and ‘slim’, respectively, from the basalt sulphide-rich vents at 9 °N and 21 °N at the East Pacific Rise, and the highly sedimented, sulphide-poor vents at 27 °N in the Guaymas Basin. The ‘fat’ morphotype has a thicker body and tube, longer trunk and smaller tentacular crowns, whereas the ‘slim’ morphotype has shorter trunk, thinner body and tube, and presents longer tentacular crowns and has a higher number of tentacular lamellae. Given the dependence on sulphides for the growth of R. pachyptila, as well as high genetic connectivity of the worm’s populations along the studied localities, we suggest that such morphological differences are adaptive and selected to keep the sulphide uptake near to the optimum values for the symbionts. ‘Fat’ and ‘slim’ morphotypes are also found in the vestimentiferan Ridgeia piscesae in similar sulphide-rich and poor environments in the northern Pacific.

Southernmost records of Escarpia spicata and Lamellibrachia barhami (Annelida: Siboglinidae) confirmed with DNA obtained from dried tubes collected from undiscovered reducing environments in northern Chile

Deep-sea fishing bycatch enables collection of samples of rare species that are not easily accessible, for research purposes. However, these specimens are often degraded, losing diagnostic morphological characteristics. Several tubes of vestimentiferans, conspicuous annelids endemic to chemosynthetic environments, were obtained from a single batch of deep-sea fishing bycatch at depths of around 1,500 m off Huasco, northern Chile, as part of an ongoing study examining bycatch species. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and an intron region within the hemoglobin subunit B2 (hbB2i) were successfully determined using vestimentiferans’ dried-up tubes and their degraded inner tissue. Molecular phylogenetic analyses based on DNA sequence identified the samples as Escarpia spicata Jones, 1985, and Lamellibrachia barhami Webb, 1969. These are the southernmost records, vastly extending the geographical ranges of both species from Santa Catalina Island, California to northern Chile for E. spicata (over 8,000 km), and from Vancouver Island Margin to northern Chile for L. barhami (over 10,000 km). We also determined a 16S rRNA sequence of symbiotic bacteria of L. barhami. The sequence of the bacteria is the same as that of E. laminata, Lamellibrachia sp. 1, and Lamellibrachia sp.2 known from the Gulf of Mexico. The present study provides sound evidence forthe presence of reducing environments along the continental margin of northern Chile.

Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity

Hydrothermal vent communities are distributed along mid-ocean spreading ridges as isolated patches. While distance is a key factor influencing connectivity among sites, habitat characteristics are also critical. The Pescadero Basin (PB) and Alarcón Rise (AR) vent fields, recently discovered in the southern Gulf of California, are bounded by previously known vent localities (e.g. Guaymas Basin and 21° N East Pacific Rise); yet, the newly discovered vents differ markedly in substrata and vent fluid attributes. Out of 116 macrofaunal species observed or collected, only three species are shared among all four vent fields, while 73 occur at only one locality. Foundation species at basalt-hosted sulfide chimneys on the AR differ from the functional equivalents inhabiting sediment-hosted carbonate chimneys in the PB, only 75 km away. The dominant species of symbiont-hosting tubeworms and clams, and peripheral suspension-feeding taxa, differ between the sites. Notably, the PB vents host a limited and specialized fauna in which 17 of 26 species are unknown at other regional vents and many are new species. Rare sightings and captured larvae of the 'missing' species revealed that dispersal limitation is not responsible for differences in community composition at the neighbouring vent localities. Instead, larval recruitment-limiting habitat suitability probably favours species differentially. As scenarios develop to design conservation strategies around mining of seafloor sulfide deposits, these results illustrate that models encompassing habitat characteristics are needed to predict metacommunity structure.

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

BACKGROUND

Sclerolinum (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.

RESULTS

Our 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.

CONCLUSIONS

These 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.