Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans.

BACKGROUND: Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the intertidal zone and shallow waters, but a few species inhabit the deep-sea floor. It is of interest to investigate how such sessile crustaceans became adapted to extreme deep-sea environments. We sequenced the transcriptomes of a deep-sea barnacle, Glyptelasma gigas collected at a depth of 731 m from the northern area of the Zhongjiannan Basin, and a shallow-water coordinal relative, Octolasmis warwicki. The purpose of this study was to provide genetic resources for investigating adaptation mechanisms of deep-sea barnacles. RESULTS: Totals of 62,470 and 51,585 unigenes were assembled for G. gigas and O. warwicki, respectively, and functional annotation of these unigenes was made using public databases. Comparison of the protein-coding genes between the deep- and shallow-water barnacles, and with those of four other shallow-water crustaceans, revealed 26 gene families that had experienced significant expansion in G. gigas. Functional annotation showed that these expanded genes were predominately related to DNA repair, signal transduction and carbohydrate metabolism. Base substitution analysis on the 11,611 single-copy orthologs between G. gigas and O. warwicki indicated that 25 of them were distinctly positive selected in the deep-sea barnacle, including genes related to transcription, DNA repair, ligand binding, ion channels and energy metabolism, potentially indicating their importance for survival of G. gigas in the deep-sea environment. CONCLUSIONS: The barnacle G. gigas has adopted strategies of expansion of specific gene families and of positive selection of key genes to counteract the negative effects of high hydrostatic pressure, hypoxia, low temperature and food limitation on the deep-sea floor. These expanded gene families and genes under positive selection would tend to enhance the capacities of G. gigas for signal transduction, genetic information processing and energy metabolism, and facilitate networks for perceiving and responding physiologically to the environmental conditions in deep-sea habitats. In short, our results provide genomic evidence relating to deep-sea adaptation of G. gigas, which provide a basis for further biological studies of sessile crustaceans in the deep sea.

First record of the hippolytid shrimp Hippolyteaustraliensis (Stimpson, 1860) (Crustacea, Decapoda) from China.

Background: Two specimens of the genus Hippolyte were examined from the caridean collections of the Marine Biological Museum, Chinese Academy of Sciences. These specimens were captured in the South China Sea in 1987. Detailed inspection revealed that their morphological features closely match the (re)descriptions of Hippolyteaustraliensis, especially in the presence of a long, distinct lateral carina on the rostrum, a dorsally unarmed rostral border, and four prominent terminal spines on the dactylus of the last three pereiopods. New information: The discovery of Hippolyteaustraliensis in Chinese waters represents a significant expansion of its geographic distribution from the South Pacific to the North Pacific. Furthermore, an additional taxonomical report of H.australiensis is provided since its retrieval in 2001.

Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes.

The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.

Deep-sea caridean shrimps collected from the South China Sea with emphasizing their phylogenetic relationships.

Despite the high biological and ecological diversity of the South China Sea, limited research has been conducted on the deep-sea species diversity of caridean shrimps. Based on the collections from three scientific expeditions conducted in the South China Sea, 31 caridean species, belonging to nine families, were reported, including the identification of two species not previously documented in this region, namely Janicella spinicauda (A. Milne-Edwards, 1883) and Systellaspis curvispina Crosnier, 1988. In addition to morphological features, the COI and 16S gene sequences of these species were analyzed to assess their evolutionary relationships within each family. Phylogenetic analyses, with highest species coverage to date, indicated that similarity in morphological characteristics does not always lead to closer phylogenetic relationships and some defining characteristics for specific taxa are not always synapomorphies but may be the result of convergent evolution. Our results establish reliable evolutionary relationships within specific taxa and highlight the necessity for further taxonomic revisions within these taxa.

A new chemosymbiotic bivalve species of the genus Acharax Dall, 1908 (Bivalvia, Solemyida, Solemyidae) from the Haima cold seep of the South China Sea.

Solemyidae is an ancient group of protobranch bivalves that typically inhabit unusual environments, such as deep-sea chemosynthetic environments, and are symbiotic with chemoautotrophic and gill-hosted bacteria. In May 2018, a living solemyid bivalve was collected using a remotely operated vehicle at a depth of 1,390 m from the Haima cold seep in the northwestern slope of the South China Sea. Through a comprehensive taxonomic approach combining morphological observations and molecular phylogeny reconstruction of concatenated mitochondrial COI,16S rRNA and 18S rRNA gene sequences, a new species, Acharaxhaimaensissp. nov. is identified and described. The discovery of this new species contributes to the diversity of known solemyids in deep-sea chemosynthetic environments.

Phylogenetic relationships among genera of the Periclimenes complex (Crustacea: Decapoda: Pontoniinae) based on mitochondrial and nuclear DNA.

The genus Periclimenes Costa, 1844 is the most species-rich genus in the subfamily Pontoniinae. Recent studies have suggested that it might be a polyphyletic taxon and could be further subdivided. In this study, three protein-coding nuclear genes and one mitochondrial ribosomal gene were used to analyze the phylogenetic relationships among the genera of the Periclimenes complex, includes the genus Periclimenes and 15 related genera, viz. Ancylomenes, Brucecaris, Crinotonia, Cuapetes, Harpiliopsis, Harpilius, Laomenes, Leptomenaeus, Manipontonia, Palaemonella, Periclimenella, Philarius, Phycomenes, Unguicaris and Vir. Based on both independent and combined data analyses, the results support that the genus Periclimenes is a polyphyletic group. Furthermore, the studied Periclimenes species could be divided into several independent groups, and the taxonomic status of P. commensalis, P. brevicarpalis and P. digitalis may need to be reconsidered. Besides, the majority of the related genera of Periclimenes are suggested to be monophyletic. Our analyses also reveal that these genera approximately form two main clades, despite some deep relationships are still obscure.

First records of three Nematocarcinus species (Crustacea, Decapoda, Nematocarcinidae) in the deep-waters of the north-western Pacific.

Background: During two scientific expeditions in the South China Sea and the Kyushu-Palau Ridge area, several specimens of thread-leg shrimp were collected from deep waters. Amongst them, three species, Nematocarcinusevansi Burukovsky, 2000, N.exilis (Spence Bate, 1888) and N.machaerophorus Burukovsky, 2003 were newly recorded from the north-western Pacific. The morphological features of these specimens are in concordance with the original description. New information: Nematocarcinusevansi and N.machaerophorus were recorded for the second time since their original descriptions and newly found from the South China Sea. Nematocarcinusexilis, collected from the Kyushu-Palau Ridge area, represents a great distribution expansion from the eastern Atlantic and the Mediterranean to the Pacific, making it the fourth Atlantic-Pacific distributed Nematocarcinus species. Their detailed morphological characteristics, colour patterns and partial sequences of the COI and 16S rRNA genes are provided, respectively.

Solvent bonding of poly(methyl methacrylate) microfluidic chip using phase-changing agar hydrogel as a sacrificial layer.

In this report, a solvent bonding method based on phase-changing agar hydrogel has been developed for the fabrication of poly(methyl methacrylate) (PMMA) microfluidic chips. Prior to bonding, the channels and the reservoir ports on PMMA channel plates were filled with molten agar hydrogel that could gelate to form solid sacrificial layers at room temperature. Subsequently, PMMA cover sheets were covered on the channeled plates and 1,2-dichlororethane was applied to the interspaces between them. The agar hydrogel in the channels could prevent the bonding solvent and the softened surface of the PMMA cover sheets from filling in the channels. After solvent bonding, the agar hydrogel in the channels and the reservoir ports was melted and removed under pressure. The sealed channels in the complete microchips had been examined by an optical microscope and a scanning electron microscope. The results indicated that high-quality bonding was achieved at room temperature. The prepared microfluidic microchips have been successfully employed in the electrophoresis separation and detection of three cations in combination with contactless conductivity detection.

Facile preparation of carbon nanotube/poly(ethyl 2-cyanoacrylate) composite electrode by water-vapor-initiated polymerization for enhanced amperometric detection.

A carbon nanotube/poly(ethyl 2-cyanoacrylate) (CNT/PECA) composite electrode was developed for enhanced amperometric detection. The composite electrode was fabricated on the basis of water-vapor-initiated polymerization of a mixture of CNTs and ethyl 2-cyanoacrylate in the bore of a piece of fused silica capillary. The morphology and structure of the composite were investigated by scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and thermogravimetric analysis. The results indicate that the CNTs were well dispersed and embedded throughout the PECA matrix to form an interconnected CNT network. The analytical performance of this unique CNT-based detector has been demonstrated by separating and detecting six flavones in combination with capillary electrophoresis. The advantages of the CNT/PECA composite detector include lower operating potential, higher sensitivity, low expense of fabrication, satisfactory resistance to surface fouling, and enhanced stability; these properties indicate great promise for a wide range of applications.

Report of epibenthic macrofauna found from Haima cold seeps and adjacent deep-sea habitats, South China Sea.

This work reports on a preliminary taxonomic study of epibenthic macroinvertebrates collected or observed by underwater video at the Haima cold seeps and in adjacent deep-sea habitats, including a mud volcano field and Ganquan Plateau, during an expedition in the South China Sea by the Chinese-manned submersible Shenhai Yongshi in May 2018. A total of 41 species belonging to 6 phyla were identified, among which 34 species were collected from the Haima cold seeps. Mollusks and crustaceans that are specialized in reducing habitats were predominant in biotopes of the Haima cold seeps, whereas sponges and cold-water corals and their commensals were prominent in communities of the mud volcano field and the slopes of Ganquan Plateau. The distribution and faunal composition of each taxonomic group are discussed.

Report on four deep-water barnacles (Cirripedia, Thoracica) from the north west Pacific, with remarks on Trianguloscalpellum regium (Wyville-Thomson, 1873).

Four deep-water species of stalked barnacles were collected by the manned submersibles Jiaolong and Shenhaiyongshi during recent expeditions. Trianguloscalpellum regium (Wyville-Thomson, 1873), collected from the Mariana Trench at a depth of 5,462 m, represents a new distribution record. Glyptelasma gigas (Annandale, 1916), Poecilasma litum Pilsbry, 1907 and Poecilasma obliqua Hoek, 1907, collected from the South China Sea, are recorded for the first time from a mud volcano environment. Detailed photographs of these four species are presented and their partial sequences of 16S rRNA and mt COI genes are provided.

Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy.

Hippolyte shrimps exhibit abundant biological diversity and display great ecological significance in seaweed bed ecosystems. Dozens of Hippolyte specimens were collected from Hainan Island and the Xisha Islands in the South China Sea. Detailed examination indicates that some of these specimens represent new Hippolyte species. Based on morphological, genetic, and ecological data, Hippolyte chacei sp. nov. and H. nanhaiensis sp. nov. are described. H. chacei sp. nov. was collected from the Sargassum sp. biotope in Hainan Island and is distinguished from congeners by its unique mandible and the dactylus of the third to fifth pereiopods; this species has a basal position in the Indo-West Pacific species clade in the phylogenetic tree which is reconstructed based on 16S rRNA gene. H. nanhaiensis sp. nov. was collected from the biotopes of Galaxaura sp. or Halimeda sp. in the Xisha Islands, and it differs from congeners in a series of characters associated with rostrum, scaphocerite, antennular peduncle, and spines on the dactylus of the third to fifth pereiopods. Additionally, it is sister to H. australiensis in the phylogenetic tree. A key to identifying mature female Hippolyte species of the Indo-West Pacific and neighboring seas is provided.

Spatiotemporal patterns of the macrofaunal community structure in the East China Sea, off the coast of Zhejiang, China, and the impact of the Kuroshio Branch Current.

The Kuroshio Current intrudes in the bottom layer of the East China Sea continental shelf from the northeast of Taiwan via two bottom branches named the Nearshore Kuroshio Branch Current (NKBC, along the 60 m isobath) and the Offshore Kuroshio Branch Current (OKBC, along the 100 m isobath). However, knowledge on the macrofaunal responses to these bottom branches is limited. This study examined the variations in the benthic macrofaunal community in a section of the East China Sea under the influence of the NKBC. Seven sites corresponding to three regions (the west, middle and east region) were sampled using an Agassiz trawl net at a monthly rate from February to November 2015 (except in August). A total of 270 macrofaunal species were collected in this study. Cluster analysis and nMDS ordination revealed three communities: the inshore, Kuroshio and offshore communities, roughly corresponding to the west, middle and east of NKBC route. Significant differences in the species composition (one-way PERMANOVA) and diversity indices (one-way ANOVA) among the regions and communities were observed, while no statistically significant difference among the months was detected. The indicator species also varied among the communities, with Sternaspis scutata and Odontamblyopus rubicundus dominating the inshore community, Camatopsis rubida, Schizaster lacunosus and Craspidaster hesperus dominating the Kuroshio community, and Portunus argentatus, Champsodon snyderi and Coelorinchus multispinulosus dominating the offshore community. Some rare species (e.g., Neobythites sivicola) may indicate the passage of the NKBC better than the indicator species. A redundancy analysis was used to describe the relationship between the macrofaunal species and environmental variables in this study. Water depth and turbidity played important roles in the distribution of the macrofauna. S. scutata and O. rubicundus were associated with high turbidity and shallow depth, while Plesionika izumiae and P. argentatus were associated with low turbidity and deep depth. This study outlines the impact of the NKBC on the distribution patterns of the macrofaunal community of the East China Sea. More studies are needed to understand the detailed interactions between macrofauna and the NKBC in the future.

Lysmata leptodactylus, a new species of lysmatid shrimp (Crustacea: Decapoda: Caridea) from China.

A new species of lysmatid shrimp, Lysmata leptodactylus n. sp., is described and illustrated based on specimens collected from the subtidal zone in Guangdong province, South China Sea. The new species bears distinctly unequal second pereiopods and uniquely elongated gracile dactyli of the ambulatory pereiopods. These characters, combined with the rostral formula, and stylocerite proportion, immediately distinguish Lysmata leptodactylus n. sp. from all known species of lysmatid shrimp.

[Ecological characteristics and seasonal variation of macrobenthos near the Ningjin coastal water of Shandong, East China].

The coastal water off Ningjin is located at the eastern end of the Shandong Peninsula, the boundary of the Northern and Southern Yellow Sea. In this paper, the ecological characteristics and seasonal variation of macrobenthic community in this region were studied, based on the investigation data collected from the four cruises in January (winter), April (spring), July (summer), and October (autumn), 2007. A total of 243 macrobenthic species were identified, of which, 96 species were of Polychaeta, 77 were of Crustacea, 43 were of Mollusca, 13 were of Echinodermata, and the rest 14 species were of other benthic groups. The dominant species varied with seasons, but Paralacydonia paradoxa (Polychaeta) and Amphioplus japonicus (Echinodermata) were dominant throughout the four seasons. The average biomass of the macrobenthos estimated from the four cruises was 9.5 g x m(-2), with the highest biomass during the spring cruise and the lowest one during the winter cruise. The average abundance estimated from the four cruises was 219.6 ind x m(-2), with the highest abundance during the winter cruise and the lowest one during the autumn cruise. The Shannon index (H) of the macrobenthos community varied from 2.82 to 3.23, the species richness index (D) varied from 2.28 to 2.75, and the species evenness index (J) varied from 0.82 to 0.86. The Bray-Curtis similarity cluster analysis and MDS ordination analyses indicated that there was a distinct distribution of macrobenthic communities from seashore to offshore, which was closely correlated with the spatial structure of bathymetry and the sediment type in the study region.