Phylogeny and shell form evolution of the hydrothermal vent asymmetrical barnacles (Cirripedia, Thoracicalcarea, Neoverrucidae).

Imbricaverruca and Neoverruca are two genera of hydrothermal vent asymmetrical barnacles in Neoverrucidae, but found in vents of the Southwest Pacific and Northwest Pacific Oceans, respectively. Imbricaverruca has a flattened operculum and the shell base with multiple whorls of imbricating plates, while Neoverruca has an inclined operculum and the shell base with fewer developed imbricating plates. It has been hypothesized that Imbricaverruca has apomorphic shell characters in Neoverrucidae. Although the monophyletic relationship of the vent barnacle members in the superfamily Neolepadoidea were confirmed based on molecular phylogeny, the relationships between Neobrachylepadidae and Neoverrucidae, and between Neoverruca and Imbricaverruca have not been determined because there are no molecular data on Imbricaverruca. In this study, we sequenced three nuclear (18S rDNA, 28S rDNA, histone 3) and one mitochondrial (CO1) genes of I. yamaguchii from the Southwest Pacific. Our phylogenetic results showed that Neobrahchylepadidae is the sister taxon to Neoverrucidae (Imbricaverruca + Neoverruca), and Imbricaverruca and Neoverruca are monophyletic sister taxa each other, which not supporting the previous hypothesis that Neoverruca is sister to the clade containing Neobrahchylepadidae and Neolepadidae. These implied that the differences in shell forms between Neoverruca and Imbricaverruca are a result of independent divergent evolution in different deep-sea basins.

Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents.

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.

The complete mitochondrial genome of deep-sea ophiuroid Ophioleila elegans (Echinodermata: Ophiuroidea) from the Shkolnik Guyot, a northwest Pacific seamount.

Ophiuroids are a diversified benthic taxon in the deep sea. Given their various dispersal strategies, they are considered an adequate group to assess genetic connectivity, especially in the seamounts that function as islands. Ophioleila elegans A.H. Clark, 1949, in the family Ophiothamnidae, was previously reported from the Caiwei Guyot, a seamount in the northwest Pacific Ocean. Here, we described the mitochondrial genome of O. elegans collected from another seamount in the northwest Pacific. The whole mitogenome is 16,376 bp in length and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on the mitogenome sequences showed that O. elegans was clustered with Histampica sp., the only species for which mitogenome sequence has been reported within the family Ophiothamnidae. The complete mitogenome of O. elegans first reported in the present study provides useful information for population genetics and evolutionary relationship of this taxon, especially in the northwest Pacific seamounts.

Carbonate compensation depth drives abyssal biogeography in the northeast Pacific.

Abyssal seafloor communities cover more than 60% of Earth's surface. Despite their great size, abyssal plains extend across modest environmental gradients compared to other marine ecosystems. However, little is known about the patterns and processes regulating biodiversity or potentially delimiting biogeographical boundaries at regional scales in the abyss. Improved macroecological understanding of remote abyssal environments is urgent as threats of widespread anthropogenic disturbance grow in the deep ocean. Here, we use a new, basin-scale dataset to show the existence of clear regional zonation in abyssal communities across the 5,000 km span of the Clarion-Clipperton Zone (northeast Pacific), an area targeted for deep-sea mining. We found two pronounced biogeographic provinces, deep and shallow-abyssal, separated by a transition zone between 4,300 and 4,800 m depth. Surprisingly, species richness was maintained across this boundary by phylum-level taxonomic replacements. These regional transitions are probably related to calcium carbonate saturation boundaries as taxa dependent on calcium carbonate structures, such as shelled molluscs, appear restricted to the shallower province. Our results suggest geochemical and climatic forcing on distributions of abyssal populations over large spatial scales and provide a potential paradigm for deep-sea macroecology, opening a new basis for regional-scale biodiversity research and conservation strategies in Earth's largest biome.

The mitochondrial genome of hydrothermal vent barnacle Eochionelasmus coreana (Cirripedia: Thoracica) from the Indian Ocean.

Balanomorph Eochionelasmus species are hydrothermal vent endemic barnacles. In the genus Eochionelasmus, three species are known to date and they distribute at three different vent fields in Pacific and Indian Oceans, E. ohtai in the Southwest Pacific Ocean, E. paquensis in the East Pacific Ocean, and E. coreana in the Indian Ocean. Therefore, Eochionelasmus species are considered to be a meaningful model taxon to elucidate the evolutionary history of vent organism in relation to geotectonic events. Here, we characterized the partial mitogenome of a newly described vent barnacle Eochionelasmus coreana Chan et al., 2020 from the Solitaire vent field in the Indian Ocean. The length of mitogenome was 16,804 bp with 64.0% AT content. Its gene content and organization was identical to those of E. ohtai. There was one significant part in the mitogenome of E. coreana, which was a long intergenic region over 2 kb found between tRNAPro and tRNAThr. The phylogenetic tree suggested the monophyly of E. ohtai and E. coreana with high supporting values. In the future, additional mitogenome analysis of the last Eochionelasmus species, E. paquensis, could expand our understanding about the speciation and global distribution of Eochionelasmus species.

Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc.

Host-symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co-occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill-associated symbiotic bacteria (gill symbionts) of five co-occurring hosts, three mollusks ("Bathymodiolus" manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ-proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co-occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.

A new species of hydrothermal vent stalked barnacle Vulcanolepas (Scalpelliforms: Eolepadidae) from the North Fiji Basin, Southwestern Pacific Ocean.

A new species of eolepadid stalked barnacle, Vulcanolepas fijiensis sp. nov., was collected from a hydrothermal vent in the North Fiji Basin, Southwestern Pacific Ocean, at a depth of 1988 m. Based on morphological characteristics, this new species was distinguished from its relatives, V. osheai Buckeridge, 2000, V. parensis Southward, 2005, V. scotiaensis Buckeridge, Linse Jackson, 2013, and V. buckeridgei Chan Chang, 2018. Based on morphological characteristics, Vulcanolepas species are divided mainly into two groups by the size of the first mandibular tooth; the first group has a large mandibular first tooth (V. parensis, V. scotiaensis, and V. fijiensis sp. nov., the second a small mandibular first tooth (V. osheai and V. buckeridgei). The new species can be easily distinguished from V. parensis and V. scotiaensis by the length ratio of antenniform segments to robust segments of the rami of cirrus I. Vulcanolepas fijiensis sp. nov. also differs from V. parensis by the length ratio of the penis and cirrus VI (1/10 vs 1/4), and the extension the carinal apex to the tergum (extended vs not extended). Additionally, the sequence divergence of the cytochrome c oxidase 1 gene between V. fijiensis sp. nov. and the other neolepadid species (except V. parensis from its original locations) ranged from 4.2% to 14.0%. In a neighbor-joining tree, V. fijiensis sp. nov. formed an independent branch. These results infer that V. fijiensis sp. nov. is a new species, distinct from the other known neolepadids.

Complete mitochondrial genome of the hydrothermal vent shrimp Rimicaris variabilis (Decapoda: Caridea: Alvinocarididae) from the North Fiji basin.

The family Alvinocarididae is the monophyletic taxon which lives restrictively at chemosynthesis-based environments in the deep-sea. Here, for the first time, we report the complete mitogenome of the alvinocaridid vent shrimp Rimicaris variabilis from the North Fiji Basin. The mitogenome was 15,909 bp in length, with 65.6% AT content. Its protein-coding gene organization was typical of other alvinocaridid shrimps. Based on the phylogenetic tree, R. variabilis was most closely related to Shinkaicaris leurokolos, rather than with other Rimicaris species. To resolve this incongruence between traditional morphological classification and molecular analyses, further mitogenomic analysis of undetermined alvinocaridid taxa is necessary.

Complete mitochondrial genome of the hydrothermal vent stalked barnacle Vulcanolepas fijiensis (Cirripedia, Scalpelliforms, Eolepadidae).

The family Eolepadidae is the only stalked barnacle in hydrothermal vent regions. Here, we determined the mitogenome of the eolepadid Vulcanolepas fijiensis. The mitogenome was 17,374 bp long, with 76.6% AT content. Its protein-coding gene organization was identical to that of the deep-sea scalpellid Arcoscalpellum epeeum. On the mitogenomic tree, two scalpellomorphan families (Eolepadidae and Scalpellidae) were monophyletic while the other scalpellomorphan family Pollicipedidae did not form the monophyletic group with them. Further mitogenomic analysis of undetermined taxa in hydrothermal vents is required to deepen our understanding of their phylogenetic relationships.

Population genetic differentiation of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae) in the Southwest Pacific Ocean.

To understand the origin, migration, and distribution of organisms across disjunct deep-sea vent habitats, previous studies have documented the population genetic structures of widely distributed fauna, such as gastropods, bivalves, barnacles, and squat lobsters. However, a limited number of investigations has been conducted in the Southwest Pacific Ocean, and many questions remain. In this study, we determined the population structure of the bythograeid crab Austinograea alayseae from three adjacent vent systems (Manus Basin, North Fiji Basin, and Tonga Arc) in the Southwest Pacific Ocean using the sequences of two mitochondrial genes (COI and 16S rDNA) and one nuclear gene (28S rDNA). Populations were divided into a Manus clade and a North Fiji-Tonga clade, with sequence divergence values in the middle of the barcoding gap for bythograeids. We inferred that hydrographic and/or physical barriers act on the gene flow of A. alayseae between the Manus and North Fiji basins. Austinograea alayseae individuals interact freely between the North Fiji Basin and the Lau Basin (Tonga Arc). Although further studies of genetic differentiation over a geological time scale, life-history attributes, and genome-based population genetics are needed to improve our understanding of the evolutionary history of A. alayseae, our results contribute to elucidating the phylogeny, evolution, and biogeography of bythograeids.

Complete mitochondrial genome of the hydrothermal vent barnacle Eochionelasmus ohtai (Cirripedia, Thoracica).

Thoracican barnacles are common in hydrothermal vent fields. Here, we characterized the first mitogenome of a hydrothermal vent barnacle. The mitogenome of Eochionelasmus ohtai was 15,585 bp in length and had the typical pancrustacean gene arrangement. Its protein-coding genes (PCGs) were very similar in terms of length, AT content, and start and stop codons to those of other thoracican species. The phylogenetic tree constructed with 13 PCGs divided balanomorph barnacles, including E. ohtai, into two clades. This will further our understanding of the evolution of hydrothermal vent barnacles using mitogenomes, although further mitogenomic analysis of undetermined taxa is required.

Complete mitochondrial genome of the deep-sea asymmetrical barnacle Altiverruca navicula (Cirripedia, Thoracica, Verrucumorpha).

The hitherto suborder Verrucomorpha contains asymmetrical barnacles of two groups: the true Verrucomorpha (Eoverruca + Verrucidae) and the Neoverrucidae. Here, we determined the mitochondrial genome (mitogenome) of Altiverruca navicula, a true Verrucomorpha species. The mitogenome was 15,976 base pairs in length and had the typical pancrustacean gene arrangement. Its protein-coding genes were very similar to those of other thoracican species in terms of length, AT content, and start and stop codons. In phylogenetic trees constructed with 13 protein-coding genes, A. navicula was positioned at an ancestral node of sessile barnacles, consistent with the findings of previous studies.

Complete mitochondrial genome of the blind vent crab Gandalfus puia (Crustacea: Bythograeidae) from the Tonga Arc.

The brachyuran crab Gandalfus puia is a species endemic to the hydrothermal vent fields in the Tonga-Kermadec Arc. In order to understand G. puia at the genomic level, we sequenced its mitochondrial genome (mitogenome) and then compared to other bythograeids. The mitogenome is 15,548 bp in length and exhibits brachyuran-typical gene arrangement. Its protein-coding genes were very similar to other bythograeid species with respect to length, AT content and start and stop codons. Additionally, we compared the mitogenomes of Gandalfus and the closely related Austinograea. The inter-specific nucleotide divergence was 13.4% in Gandalfus and 13.7-14.0% in Austinograea. The inter-generic nucleotide divergence between Gandalfus and Austinograea was 16.3-19.7%. Based on the phylogenetic tree constructed with maximum likelihood and Bayesian inference, bythograeid crabs were recognized as the monophyletic taxon with the high supporting values (100% bootstrap proportions and 1.00 posterior probabilities). These results are useful for understanding the phylogenetic relationships and evolution of bythograeid crabs.

Complete mitochondrial genome of the hydrothermal vent ghost shrimp Paraglypturus tonganus (Crustacea, Axiidea, Callianassidae).

Ghost shrimps are burrowing decapods that serve as bioturbators and habitat providers in seafloor environments. The hydrothermal vent ghost shrimp, Paraglypturus tonganus, was collected from a hydrothermal vent in the Tonga Arc. This species has a mitochondrial genome (mitogenome) of 15,924 bp in length with an AT content of 66.1%. The mitogenome was identical to the typical gene arrangement and transcriptional polarity of the infraorder Axiidea. Paraglypturus tonganus showed 65.3-70.1% nucleotide similarity with the known mitogenomes of other axiid shrimps. These results are useful for understanding the phylogenetic relationships among the members of Axiidea within the decapods.

Mitochondrial genome of the hydrothermal vent shrimp Nautilocaris saintlaurentae (Crustacea: Caridea: Alvinocarididae).

We determined the mitochondrial genome (mitogenome) of Nautilocaris saintlaurentae, sampled at vent fields of the Tofua Arc in the southwestern Pacific. The genome was 15,928 bp in length and had the typical mitogenome structure of the infraorder Caridea. Its protein-coding genes were very similar to other alvinocaridid species in respect to length, AT content, and start and stop codons. However, N. saintlaurentae showed a 17.4--19.2% divergence in the nucleotide sequence from other alvinocaridid species. This information will be helpful in understanding the genetic relationship among members of the alvinocaridid shrimps.

Mercury accumulation in hydrothermal vent mollusks from the southern Tonga Arc, southwestern Pacific Ocean.

We provide the mercury (Hg) and monomethylmercury (MMHg) levels of the plume water, sulfide ore, sediment, and mollusks located at the hydrothermal vent fields of the southern Tonga Arc, where active volcanism and intense seismic activity occur frequently. Our objectives were: (1) to address the potential release of Hg from hydrothermal fluids and (2) to examine the distribution of Hg and MMHg levels in hydrothermal mollusks (mussels and snails) harboring chemotrophic bacteria. While high concentrations of Hg in the sediment and Hg, As, and Sb in the sulfide ore indicates that their source is likely hydrothermal fluids, the MMHg concentration in the sediment was orders of magnitude lower than the Hg (<0.001%). It suggests that Hg methylation may have not been favorable in the vent field sediment. In addition, Hg concentrations in the mollusks were much higher (10-100 times) than in other hydrothermal vent environments, indicating that organisms located at the Tonga Arc are exposed to exceedingly high Hg levels. While Hg concentration was higher in the gills and digestive glands than in the mantles and residues of snails and mussels, the MMHg concentrations in the gills and digestive glands were orders of magnitude lower (0.004-0.04%) than Hg concentrations. In summary, our results suggest that the release of Hg from the hydrothermal vent fields of the Tonga Arc and subsequent bioaccumulation are substantial, but not for MMHg.

Morphological, molecular, and biochemical characterization of astaxanthin-producing green microalga Haematococcus sp. KORDI03 (Haematococcaceae, Chlorophyta) isolated from Korea.

A unicellular red microalga was isolated from environmental freshwater in Korea, and its morphological, molecular, and biochemical properties were characterized. Morphological analysis revealed that the isolate was a unicellular biflagellated green microalga that formed a non-motile, thick-walled palmelloid or red aplanospore. To determine the taxonomical position of the isolate, its 18S rRNA and rbcL genes were sequenced and phylogenetic analysis was performed. We found that the isolate was clustered together with other related Haematococcus strains showing differences in the rbcL gene. Therefore, the isolated microalga was classified into the genus Haematococcus, and finally designated Haematococcus sp. KORDI03. The microalga could be cultivated in various culture media under a broad range of pH and temperature conditions. Compositions of the microalgal cellular components were analyzed, and its protein, carbohydrate, and lipid compositions were estimated to be 21.1 ± 0.2%, 48.8 ± 1.8%, and 22.2 ± 0.9%, respectively. In addition, D-glucose and D-mannose were the dominant monosaccharides in the isolate, and its amino acids were composed mainly of aspartic acid, glutamic acid, alanine, and leucine. Moreover, several polyunsaturated fatty acids accounted for about 80% of the total fatty acids in Haematococcus sp. KORDI03, and the astaxanthin content in the red aplanospores was estimated to be 1.8% of the dry cell weight. To the best of our knowledge, this is the first report of an Haematococcus sp. isolated from Korea, which may be used for bioresource production in the microalgal industry.

Morphological, Molecular, and Biochemical Characterization of Monounsaturated Fatty Acids-Rich Chlamydomonas sp. KIOST-1 Isolated from Korea.

Microalgae hold promise as producers of sustainable biomass for the production of biofuels and other biomaterials. However, the selection of strains with efficient and robust production of desirable resources remains challenging. In this study, we isolated a green microalga from Korea and analyzed its morphological, molecular, and biochemical characteristics. Microscopic and phylogenetic analyses demonstrated that the isolate could be classified into the genus Chlamydomonas, and we designated the isolate Chlamydomonas s p. K IOST -1. Compositions of protein, lipid, and carbohydrate in the microalgal cells were estimated to be 58.8 ± 0.2%, 22.7 ± 1.2%, and 18.5 ± 1.0%, respectively. Similar to other microalgae belonging to Chlorophyceae, the dominant amino acid and monosaccharide in Chlamydomonas sp. KIOST-1 were glutamic acid and glucose. On the other hand, the proportions of saturated fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids clearly differed from other species in the genus Chlamydomonas, and monounsaturated fatty acids accounted for a large portion (41.3%) of the total fatty acids in the isolate. Based on these results, Chlamydomonas sp. KIOST-1 has advantageous characteristics for biomass production.

Mitochondrial genome of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae): genetic differences between individuals from Tofua Arc and Manus Basin.

The brachyuran crab Austinograea alayseae is one of the most common species found in hydrothermal vent fields of the southwestern Pacific Ocean. In this study, we found that the mitochondrial genome (mitogenome) of A. alayseae from Tofua Arc is 15,611 bp in length and has the typical gene arrangement of a brachyuran. We also compared the mitogenomes of A. alayseae from two different regions, Tofua Arc and Manus Basin. Their genomes were identical, except for the control region, which showed 82.29% nucleotide similarity. These results will be helpful in developing stable markers for the identification of A. alayseae at the sub-species level.

Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding.

Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.