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Upogebia major (De Haan 1841) is a decapod widely distributed in tidal flats in East Asia and Russia and is a dominant species in some regions. Nevertheless, because the inhabiting deep burrows exceeding a depth of 2 m, conducting quantitative surveys is extremely challenging. These challenges are not unique to this species but are also common to infaunal marine benthos. Therefore, this study focuses on environmental DNA (eDNA). eDNA consists of DNA fragments present in water and sediments and serves as an indicator of the presence and abundance of organisms. In particular, sedimentary DNA (sedDNA) is highly concentrated compared with that found in water. When sedDNA is used as an indicator of abundance, it is essential to first comprehensively understand the relationship between abundance and sedDNA concentration. Hence, the number of burrow openings in U. major was considered as abundance, and the relationship between the seasonal variation in abundance and sedDNA concentration was investigated in three tidal flats with different burrow distributions and topographies. During the growth period of this species in stable bottom environments such as bag-shaped lagoons, 10 5 copies/g sediment of sedDNA was detected in burrow-rich areas, which was significantly higher than in other areas. This indicated a correlation between abundance and concentration. However, it was found that events such as spawning, strong wave action, and changes in activity due to increase in water temperature induced fluctuations in concentration. Therefore, while the sedDNA concentration has the potential to reflect abundance, it is susceptible to biological and physical influences; hence, caution is required regarding the location and timing of surveys. This study sheds light on a fraction of the relationship between U. major abundance and sedDNA concentration, offering initial insights into the applicability of sedDNA analysis for estimating the abundance of various marine benthos.

Amino acids play essential roles in various biological processes. In humans, most amino acids are present in the l -form; however, small amounts of d -amino acids also exist and have significant physiological roles, highlighting the importance of dietary intake from foods or drinks. In this study, we investigated the amino acid composition of the geoduck clam Panopea japonica , emphasizing its remarkably high d -alanine ( d -Ala) content in the siphon tissue. The d -Ala content (6.99–14.2 mmol/100 g-wet) amounted to 91–94% of the total Ala, far exceeding that of other bivalves such as Tresus keenae (74%). Enzyme assays revealed alanine racemase and d -amino acid oxidase activities, suggesting active d -Ala biosynthesis and metabolism. The high concentrations of d -Ala enhance its value as a delicacy owing to its unique sweetness. This study provides new insights into the biosynthesis and metabolic characteristics of d -Ala in bivalves, highlighting its physiological and food ingredient significance.

Surface sediments and at least one edible bivalve species (Ruditapes philippinarum, Mytilus galloprovincialis, and Crassostrea gigas) were collected from each of seven intertidal sites in Japan in 2013. The sites had experienced varying levels of tsunami and fire disturbance following the major earthquake of 2011. Eight polycyclic aromatic hydrocarbons (PAHs) were identified and analyzed by gas chromatography-mass spectrometry. Total sediment PAH concentration (CT), the sum of the average concentrations of the eight PAHs, was 21-1447 μg kg-1-dry. Relative to the average level of one type of PAH in sediments collected around Japan in 2002 (benzo[a]pyrene = 21 μg kg-1-dry), five of the seven sites showed concentrations significantly lower than this average in 2013. The CTs for the three bivalves (134-450 μg kg-1-dry) were within the range of the previous reports (2.2-5335 μg kg-1-dry). The data suggest that the natural disaster did not increase PAH concentrations or affect the distribution within sediment or bivalves in Tohoku district. Although PAH concentrations at the sites pose no risk to human health, the findings highlight that the observed PAH levels derive from pre- rather than post-quake processes.

In this study, we investigated the composition of free amino acids and lactate (Lac) in polychaetes in river estuaries and inner bays using chromatographic techniques. Both l -amino acids and d -amino acids ( d -asparagine, d -alanine ( d -Ala), d -serine, d -aspartic acid, and d -proline ( d -Pro)) were detected, indicating that polychaetes contain some d -amino acids. Some polychaete species exhibited notable amino acid levels, such as glycine in Capitellidae sp. and Thelepus sp., d -Pro in Glycera sp., and β-Ala in Scoletoma nipponica and Scoletoma sp.. High d -Lac levels were detected in Tylorrhynchus osawai and Hediste diadroma , (691 and 797 μmol/100 g-wet, respectively), with the d -form exceeding 98%. T. osawai was dominant in the upper tidal-sensitive zone, wherein other organisms were less abundant because of low salinity (3–8 PSU). Seasonal differences in the concentrations of components in T. osawai were observed, particularly a significant increase in d -Lac in the reproductive period. Notably, the d -Lac concentrations of T. osawai were higher upstream than downstream. Thus, d -Lac might be involved in strategies underlying adaptations to low salinity and reproductive activity. These results suggest that both the d -form of Lac and amino acids may play certain physiological roles in the life of polychaetes.

Taurine (Tau) has some important ameliorating effects on human health and is present in bivalve. For the selective analysis of Tau with other amino acids, we designed a derivatization reagent, 2,5-dioxopyrrolidin-1-yl(4-(((2-nitrophenyl)sulfonyl)oxy)-6-(3-oxomorpholino)quinoline-2-carbonyl)pyrrolidine-3-carboxylate (Ns-MOK-β-Pro-OSu). After derivatization with Ns-MOK-β-Pro-OSu, amino acids with Tau in Japanese littleneck clams were determined through ultra-high-performance-liquid chromatography with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) using an octadecyl silica column. We could detect 18 amino acids within 10 min. Tau, valine, glutamine, glutamic acid, and arginine in the clams were determined in the negative ion mode using the characteristic fragment ion, C6H4N1O5S, which corresponded to the 2-nitrobenzenesulfonylate moiety. The fragment ion, C6H4N1O5S, was recognized as a common feature regardless of the amino acid to be derivatized, and it was convenient for detecting amino acid derivatives with high selectivity and sensitivity. Therefore, highly selective quantification using UHPLC-HRMS/MS was possible using Ns-MOK-β-Pro-OSu.

An investigation of the distribution and habitat utilization of spionid polychaetes in Tokyo Bay revealed eight shell-boring and 18 non-boring (interstitial, epifaunal, and infaunal) species, of these 11 species were recorded in the area for the first time. Most of the boring and interstitial species, which are associated with mollusc shells, were mainly distributed in exposed environments favoured by their host species outside Tokyo Bay. Only two boring species, Polydora websteri and Polydora haswelli preferred the enclosed waters of Tokyo Bay. Epifaunal and infaunal species were mainly distributed in the sandy and/or muddy sediment within Tokyo Bay. A widespread or localized distribution pattern within species was observed corresponding to the larval developmental mode. We concluded that habitat availability determines distribution patterns of spionid polychaetes around Tokyo Bay. Novel habitats for Boccardiella hamata , Boccardia proboscidea , Carazziella spongilla , and Polydora cornuta were recorded. Boccardia pseudonatrix , which was recorded for the first time from Japan with clear locality information, is considered to be a potential alien species.

There are unique ecosystems in the ocean that are driven by chemosynthesis. Whale-fall communities are one of these reducing habitats, and many unknowns are left to be resolved to understand their uniqueness. A new species of the genus Protodrilus was discovered on the exposed bones of sperm whale carcasses found in the waters off Cape Nomamisaki in the northwest Pacific. Protodrilus puniceus sp. nov. was the most abundant annelid to be found on the 2.5-y-old carcasses; the exposed bone surfaces appeared bright red due to the coloration of the innumerable worms covering them. Closer inspection revealed that this species was found in the small pores of both the internal and external surfaces of the bones. P. puniceus shows simple morphology; it has paired palps and pygidial lobes, but no eyespots, nuchal organs, statocysts, or ciliary rings dorso-anteriorly—an exceptional finding in this group. A ventral ciliary band was conspicuous, extending over each segment of the animal. The male of the species possessed paired, separated lateral organs on segments 6–11; salivary glands were inconspicuous. From morphological, biological, and ecological characteristics, P. puniceus showed differences from the already known Protodrilus group of shallow interstitial inhabitants. P. puniceus is thought to be a unique deposit feeder, acquiring nutrients by adhering to organic substances from whale carcasses. This is the first description of this group to be found in the organically enriched whale-fall environments of the deep sea below 200 m and from Japanese waters. Information on a nuclear, 18S ribosomal RNA gene sequence is included.

Abstract Polydorid species (Annelida, Spionidae), which inhabit the shells of the commercially important oyster Crassostrea gigas, were investigated along the coast of Normandy, France. Eight species, including five new records for Normandy (Polydora onagawaensis, Polydora websteri, Boccardia pseudonatrix, Boccardia proboscidea, and Boccardiella hamata) and two first records in European waters (P. onagawaensis and B. pseudonatrix), were identified based on morphological, molecular biological, and ecological characteristics. Polydora onagawaensis, which belongs to the Polydora ciliata/websteri complex, was discovered in the shells of wild and suspended cultured oysters, as well as in limestone substrates. In the phylogenetic analysis of mitochondrial COI gene sequences, specimens of P. onagawaensis collected from Normandy were grouped together with specimens from the USA into a single clade and were distinguished from the other three lineages that comprised Japanese and USA specimens. Polydora websteri inhabited shells of suspended cultured oysters. Polydora hoplura, Dipolydora giardi, and Dipolydora sp. were observed in shells from the sandy oyster culture grounds. Boccardiella hamata has been found in wild oyster shells from muddy oyster culture grounds. Boccardia pseudonatrix was observed in the shells of both the wild and cultured oysters. Adult and juvenile Boccardia proboscidea were observed in coralline algae, as well as in suspended cultured oysters. Mud tubes were observed to protrude from the outer surface of the shells, and abnormal black and calcareous deposits were secreted on the inner surface of the shells against polydorid penetration.

The Great East Japan Earthquake and accompanying tsunamis occurred on 11 March 2011, causing huge damage to marine organisms. The invasive naticid gastropod Laguncula pulchella (Euspira fortunei), which was introduced with the imported clam Ruditapes philippinarum from China and Korea, survived the earthquake. The “growth break line” observed on the shell surface in over 90% of the individuals collected in Matsushima Bay and Matsukawa-ura Lagoon after the tsunamis was examined by scanning electron microscopy. Each shell presented three layers before and three after the growth break. However, the fracture surface consisted of five layers—two prismatic and three crossed lamellar—around the growth break line. This suggests that shell formation temporarily ceased following the tsunamis and that the five-layered shell may have developed in response to the stress caused by the tsunamis. The newly formed middle layer became thinner after the “tsunami break,” which may be the result of a rapid change in the mineralization process, including rapid shell growth and/or repair. These results suggest that the damage to and forcible removal of habitats by the tsunamis was stressful for L. pulchella. A decrease in or the cessation of shell formation after a tsunami may be a common phenomenon in mollusks that inhabit tidal flats.

The purpose of this study was to investigate shell growth performance in two thin-shelled pelagic gastropods from cold seawater habitats. The shells of Arctic Limacina helicina and Antarctic Limacina helicina antarctica forma antarctica are very thin, approximately 2–9 μm for shells of 0.5–6 mm in diameter. Many axial ribbed growth lines were observed on the surface of the shell of both Limacina species. Distinct axial ribs were observed on the outermost whorl, while weak or no rib-like structures were observed on the inner whorls in the larger shell of L. helicina antarctica forma antarctica . For L. helicina , no ribs were observed on small individuals with three whorls, while larger individuals had distinct ribs on the outer whorls. Shell microstructure was examined in both species. There is an inner crossed-lamellar and extremely thin outer prismatic layer in small individuals of both species, and a distinct thick inner prismatic layer was observed beneath the crossed-lamellar layer in large Antarctic individuals. Various orientations of the crossed-lamellar structure were observed in one individual. Shell structure appeared to be different between the Antarctic and Arctic species and among shells of different size.