Search

An unexpected new Metapenaeus shrimp species has arrived to the coastal water of Alexandria City, Egypt. Morphological and molecular studies were conducted for its identification. The results revealed that it is the Indo-West Pacific species, Metapenaeus affinis (H. Milne Edwards, 1837), which is considered as a new addition to the already present local penaeidae species; Metapenaeus monoceros (Fabricius, 1798) and Metapenaeus stebbingi (Nobili, 1904). Large numbers of Metapenaeus affinis were observed and collected by the Egyptian fishermen from the coastal waters of Alexandria City, Egypt, during the study period (2020–2021), which indicates its establishment in the area. A recommendation was presented for further studies regarding the suggested ways of introduction and the prediction for future new species appearance. Such phenomenon requires international efforts to deal with the non-indigenous species’ entries that are recently intensified on the global and regional level.

Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals in the Western Pacific Ocean. To determine the source of outbreaking COTS larvae and their dispersal routes across the Western Pacific, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS comprise two major clades, an East-Central Pacific clade (ECP-C) and a Pan-Pacific clade (PP-C). The ECP-C consists of COTS from French Polynesia (FP), Fiji, Vanuatu and the Great Barrier Reef (GBR), and does not appear prone to outbreaks. In contrast, the PP-C, which repeatedly spawns outbreaks, is a large clade comprising COTS from FP, Fiji, Vanuatu, GBR, Papua New Guinea, Vietnam, the Philippines, Japan, Micronesia, and the Marshall Islands. Given the nature of Pacific Ocean currents, the vast area encompassing FP, Fiji, Vanuatu, and the GBR likely supplies larvae for repeated outbreaks, exacerbated by anthropogenic environmental changes, such as eutrophication.

Recently, sea cucumbers (Echinodermata: Holothuroidea) have been over-exploited in many areas of the world, including in the Ryukyu Islands, southern Japan, due to increases in their economic importance. Nevertheless, management and protection of sea cucumbers are insufficient worldwide. The black sea cucumber Holothuria (Halodeima) atra Jaeger, 1833, inhabits a large range across the Indo-West Pacific Ocean and is a widely harvested species. Here we conducted population genetic analyses on H. atra using partial mitochondrial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) to examine 11 different populations around three island groups in the middle Ryukyus; Okinawajima Island, the Kerama Islands, and the Sakishima Islands, all within Okinawa Prefecture. We found 27 haplotypes for COI and 16 haplotypes for 16S. Locations within national and quasi-national parks (Zamami Island, Keramas, and Manza, Okinawajima; managed by the national Ministry of Environment and Okinawa Prefecture, respectively) had the highest number of haplotypes, whereas locations with less management and more anthropogenic pressure had lower numbers The mean of all samples' genetic diversity indices was moderate with regards to both haplotype and nucleotide diversity. According to our results, Zamami Ama was the most genetically diverse location based on both markers used, likely because it is located within Kerama-Shoto National Park with comparatively stricter regulations than most other locations. Based on our COI sequences, three-quarters of the locations with the highest haplotype diversity were found to be distant from Okinawajima Island, indicating that the genetic diversity of H. atra was reduced around Okinawajima Island. Our results possibly reflect negative impacts from anthropogenic pressures such as over-harvesting and coastal development, although future comprehensive research including sequences of nuclear loci is needed to confirm this hypothesis.

We examined genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatus and M. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.

Our knowledge of the ecology and habitat of juveniles of many sea cucumber species is limited, due to their cryptic habitats and differing color and shape from adults. In the present study, a juvenile specimen of the sea cucumber Thelenota anax H. L. Clark, 1921, collected from 30 m at Rukan Reef, Okinawa, Japan, is described. We confirmed specific identity using cytochrome oxidase subunit I (COI) sequences. We show that the pseudotable ossicles in Thelenota are table ossicles, and document synallactid-like ossicles not previously recorded in the Stichopodidae.

Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ ST = 0.49, P

Japan is known for its marine biodiversity and diverse ecosystem due to its unique geological composition and water currents creating suitable habitats for a wider range of marine species. A rich deep-sea shark community with high endemism occurs on the continental shelf. Yet, the deep-sea shark taxonomy is still under development and poorly documented. Here, a DNA barcoding technique was adopted using the mitochondrial cytochrome oxidase I (COI) and NADH2 genes of samples collected from Japan with additional samples from genetic databases to draft out a phylogenetic tree of the deep-sea shark genus Squalus (dogfishes). The morphological divergence of congeners was further examined. Bayesian and maximum-likelihood-based species-level phylogenetic analyses of mitochondrial COI, ND2 and combined sequences provided strong support for distinct clades corresponding to the parental species with substantial sequence divergence between parental species. The combined dataset of the COI and ND2 gene was most suitable for barcoding of Squalus dogfishes. A multivariate analysis of morphological traits was largely consistent with the genetic data showing small but discrete differences in phenotypic characteristics allowing to separate Squalus species. Genetic samples of the taxonomically problematic Shortspine spurdog ‘Squalus mitsukurii’ from the Atlantic Ocean and Taiwan did not match with the type material of S. mitsukurii Jordan & Snyder, 1903 from mainland Japan. Squalus mitsukurii once considered a globally distributed species is a single, unique spurdog restricted to temperate Japan and Korea and may present an endemic in the Northwestern Pacific. This study further resolved two genetically and phenotypically distinct species of Squalus dogfishes in Japan, one in sympatry with S. mitsukurii in mainland Japan and one in sympatry with subtropical waters associated congeners in the Ryukyu Archipelago. The occurrence of populations of the ‘high-fin’ Taiwan spurdog, Squalus formosus, in subtropical Japan is herein confirmed.

In this study we investigated the phylogenetics of two sea urchin species, Arbacia lixula and Paracentrotus lividus from the Mediterranean Sea. Specimens were collected from the east coast of Alexandria City, Egypt. Pigmentation examination showed four sympatric color morphotypes (black, purple, reddish brown, and olive green). Mitochondrial DNA was extracted from specimens and mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S) were sequenced. The results showed that all black specimens constituted the species A . lixula . All other colors belonged to P . lividus , with no apparent differentiation between color morphotypes. Moreover, P . lividus showed high haplotype diversity (COI; H = 0.9500 and 16S; H = 0.8580) and low values of nucleotide diversity (COI; π = 0.0075 and 16S; π = 0.0049), indicating a high degree of polymorphism within this species. This study represents the first attempt at DNA barcoding of echinoid species in the southeast Mediterranean off the Egyptian coast, and will provide a base for future phylogenetic analyses.

Scoliorhapis dianthus, new species, was collected from depths of 0.20–1 m in the Sea of Japan. It is distinctive in having ten tentacles with six pairs of digits of equal size. Ossicles in the body wall have a sigmoid shape and average 75 ± 5 μm in length. An identification key to all species of the genus is provided.

Studies of phylogenetic diversity of fish gut flora often focus on bacteria, leaving a gap in characterization of flora from other domains. This study focused on first exploring of phylogenetic composition of the gut flora, belonging to all domains, eukaryotes, bacteria and archaea, of the tilapia fish, Oreochromis niloticus, inhabiting Lake Nasser, Egypt, based on rRNA gene high-throughput sequencing. Specimens were collected from four distant lake natural fish feeding niches, Khor Kalabsha, Khor Wadi Abyad, Khor Korosko and Khor Toshka. Metagenomic DNA was extracted from fish gut contents, followed by PCR and next generation sequencing of both of eukaryotic 18S- and prokaryotic 16S rRNA genes. A total of 2491, 19005 and 9032 rRNA gene OTUs, were recorded, for eukaryotes, bacteria and archaea, respectively, in the guts from the four niches. Fish guts from Khor Toshka, harbored the highest diversity of bacterial and archaeal 16S rRNA gene sequences. Some 18S rRNA gene OTUs, belonging to members of class Ostracoda, molluscs, and phylum Bacillariophyta, diatoms, beside of 16S rRNA gene OTUs assigned to genus Synechococcus, phylum Cyanobacteria, were recorded in guts from all studied niches, suggesting favorite foods for the fish throughout the lake. Other rRNA gene OTUs, affiliated with the diatom genus Fragilaria, cyanobacterial family Pseudanabaenaceae and genus Oscillatoria, characterized guts from Khor Toshka and Khor Kalabsha, respectively. OTUs, belonging to genus Cetobacterium, phylum Fusobacteria; genera, Methanobacterium and Methanosaeta, phylum Euryarchaeota, constituted the core gut microbiome. Neoechinorhynchus-like OTUs were recorded in guts from all niches, implicating common tilapia gut parasites at Lake Nasser. Guts from all niches harbored several unique archaeal 16S rRNA gene OTUs, but did not match known archaeal phyla. Hence, a large number of phylogenetic shared taxa persist across guts from distant niches, with respect to some OTUs, characterizing gut contents of specific niches.

The Japanese sea cucumber Apostichopus japonicus has a pelagic-lecithotrophic larva. Here, we clarify larval dispersal among Japanese sea cucumber populations by describing the levels of distinctiveness and gene flow among red and green variant populations of A. japonicus across Toyama Bay using 11 polymorphic microsatellite markers. Samples of Japanese sea cucumber populations were collected from three localities (Noto, Shinminato, and Uozu) around Toyama Bay. Geographically separated populations of red and green variants were determined to be genetically distinct, supported by phylogenetic analysis and the distinctiveness range values of pairwise multilocus estimates of F ST. Contemporary migration analyses indicated that the majority of estimated migration events occurred within A. japonicus populations comprised of only either red or green variants. In a historical gene flow analysis, two best-fit models (n-island and stepping stone models) showed circulation for the gene migration in Toyama Bay among red variant populations. Our results provide useful information on the genetic structure of Japanese sea cucumber populations and will be helpful for genetic conservation and fisheries management of sea cucumber populations in Toyama Bay.

We report the spontaneous spawning, larval development, survival rate and larval growth rate patterns observed in the green and red variants of the Japanese sea cucumber Apostichopus japonicus. The green variant adapted well to the captive conditions in the Sasebo City Fisheries Center and spontaneously spawned without any induction or stimulation. One hundred individual green variants spawned nine times and produced approximately 155 million eggs. In contrast, 50 individual red variants showed poor adaptation to captivity and spawned spontaneously only three times, producing about 12 million eggs. Larval development and growth rate pattern was almost identical between the two variants of A. japonicus. In contrast, the larval survival rate for the green variant was over 90% up to the auricularia stage (10 days), but much low (less than 30%) for the red variant. We demonstrated that the green variant of A. japonicus was easier to rear in captivity. This provides a useful method for maintaining sustainable harvests and eventually contributing to restocking and sea ranching of the existing population. Further studies about optimal ecological conditions and behaviour are needed to improve egg production and survival rate of the red variant of A. japonicus.

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil®DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin®Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA;P

The greenfish sea cucumberStichopus chloronotusis an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction.Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies ofS. chloronotusin southern Japan.