Influence of submarine topography and sediment environment on microbial assemblages in a coastal lagoon in northeastern Japan.

The relationships among eutrophication, anoxia, and microbial distribution were investigated for Nagatsura-Ura Lagoon on the northeastern Pacific coast of Japan. In September 2017, the bottom environment in a small area of the inner part of the lagoon (which has a basin-shaped bottom topology) was eutrophic and anoxic, with high carbon, nitrogen, phosphate, acid-volatile sulfide, and low dissolved oxygen and oxidation-reduction potential. Dissolved oxygen levels improved during the winter. Bacillariophyta (diatoms) were the main organic component according to pigment analysis and next-generation sequencing of nucleic acids in seawater samples. Phylum Proteobacteria was dominant among the bacterial flora in the sediment but the proportions of Class Epsilon-proteobacteria and Chlorobium (a green sulfur-utilizing bacterium) were high in the inner part of the lagoon compared to other stations, and these groups were also present in winter. Apparently groups able to thrive in both anoxic and aerobic conditions were predominant in the inner part of the lagoon.

Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation.

The genetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, Haliotis discus and H. madaka, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than that in other genes, suggesting that nucleotide divergence also accumulates in the genes with GCNVs. GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and de novo mutations. Our findings suggest that GCNVs have been accumulated in the early phase of free-spawning abalone speciation.

Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates.

How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.

Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters.

BACKGROUND: Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. METHODS: We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. RESULTS: In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to a raft, which was applied to half of the oyster culture rafts to improve oyster growth. The area of seagrass meadows has been expanding since 2013. Although the lagoon had experienced frequent oyster mass mortality events in summer before the tsunami, these events have not occurred since 2011. The 2011 earthquake and tsunami deepened the sill depth and widened the entrance to enhance water exchange and improve water quality in the lagoon. These changes brought the expansion of seagrass meadows and reduction of mass mortality events to allow sustainable oyster culture in the lagoon. Mapping and monitoring of seagrass meadows and aquaculture facilities via satellite remote sensing can provide clear visualization of their temporal changes. This can in turn facilitate effective aquaculture management and conservation of coastal ecosystems, which are crucial for the sustainable development of coastal waters.

Analysis of environmental and microbiological changes in Onagawa Bay immediately after the tsunami of the Great East Japan Earthquake based on sediment cores.

We investigated two sediment cores to understand whether a tsunami in Onagawa Bay, Japan caused environmental changes. The value of δ13C ranged from -21.9‰ to -24.3‰ and of δ15N ranged from 5.1 to 5.9‰. We conclude that the source of the sediment in the present study area was mainly oceanic and not terrestrial. The chlorophyll concentration ranged from 1.8 to 4.0 µg/g ww, and did not vary greatly between surface and bottom layers. We inferred that all layers were deposited after the tsunami. The major phytoplankton taxa in sediments were diatoms from DNA sequencing. The presence of harmful dinoflagellates was minor. The concentrations of several heavy metals decreased slightly after the tsunami. We inferred that heavy metals in sediments were diluted by the tsunami disturbance. The land in Onagawa suffered serious damage, but disturbance of the seabed was much less evident.

Genetic differences between hatchery stocks and natural populations in Pacific abalone (Haliotis discus) estimated using microsatellite dNA markers.

Genetic variations within and between nine hatchery stocks and seven natural populations of abalone including Ezo-abalone (Haliotis discus hannai) and Kuro-abalone (H. d. discus) were assayed with nine microsatellite markers. Marked reductions of genetic variability in the hatchery stocks were recognized in the allelic diversity and mean heterozygosity compared with the natural populations. Thirteen of 16 significant HWE deviations in hatchery stocks revealed heterozygotes excess, while all natural populations did not show such a tendency. Highly significant F (ST) values were observed for all cases between the hatchery stocks, and between the hatchery stocks and natural populations. Genetic distance (D (A)) between each hatchery stock and the geographically proximal population (mean +/- SD, 0.108 +/- 0.035) were similar to those estimated for between the natural Ezo-abalone and Kuro-abalone (0.101 +/- 0.021). The self-assignment test, which allocated individuals to their own stock with a high success rate, provided evidence of solid genetic differences among the nine hatchery stocks. These results suggests that the allelic composition and diversity in the natural populations was not necessarily reflected in the hatchery stocks owing to population bottleneck and genetic drift through seedling process, and thus the seedling and stocking practice of these hatchery stocks should take much notice of the results to conserve the genetic diversity of natural populations.

Linkage maps for the Pacific abalone (genus Haliotis) based on microsatellite DNA markers.

This study presents linkage maps for the Pacific abalone (Haliotis discus hannai) based on 180 microsatellite DNA markers. Linkage mapping was performed using three F1 outbred families, and a composite linkage map for each sex was generated by incorporating map information from the multiple families. A total of 160 markers are placed on the consolidated female map and 167 markers on the male map. The numbers of linkage groups in the composite female and male maps are 19 and 18, respectively; however, by aligning the two maps, 18 linkage groups are formed, which are consistent with the haploid chromosome number of H. discus hannai. The female map spans 888.1 cM (Kosambi) with an average spacing of 6.3 cM; the male map spans 702.4 cM with an average spacing of 4.7 cM. However, we encountered several linkage groups that show a high level of heterogeneity in recombination rate between families even within the same sex, which reduces the precision of the consolidated maps. Nevertheless, we suggest that the composite maps are of significant potential use as a scaffold to further extend the coverage of the H. discus hannai genome with additional markers.

Segregation and linkage analysis of 75 novel microsatellite DNA markers in pair crosses of Japanese abalone (Haliotis discus hannai) using the 5'-tailed primer method.

We present novel microsatellite markers of the Japanese abalone (Haliotis discus hannai) for general mapping studies in this species. A total of 75 microsatellite markers were developed, and the allele-transmission patterns of these markers were studied in three families generated by pair crosses. For allele scoring, we employed the 5'-tailed primer polymerase chain reaction (PCR) technique, which substantially reduces the cost for fluorescent labeling of primers. Of the 225 possible marker-family combinations (75 markers x 3 families), 18 cases of informative null-allele segregation were inferred. When such null-allele segregations were allowed, more than 70% of the 75 markers in the families turned out to be markers with an expected segregation ratio of 1:1:1:1, allowing maximal exploitation of the codominant nature of microsatellite markers. There were 16 instances of segregation distortion at the 5% significance level. The test for independence of segregation assigned the 75 markers into 17 linkage groups, which is in close agreement with the haploid chromosome number of H. discus hannai (n = 18). Six markers could not be placed into any linkage group. We suggest that these markers could help construct a H. discus hannai linkage map.

Androgenic gland cell structure and spermatogenesis during the molt cycle and correlation to morphotypic differentiation in the giant freshwater prawn, Macrobrachium rosenbergii.

The freshwater prawn Macrobrachium rosenbergii shows three male morphotypes: blue-claw males (final stage having high mating activity), orange-claw males (transitional stage showing rapid somatic growth), and small males (primary stage showing sneak copulation). This morphotypic differentiation is considered to be controlled by androgenic gland hormone, which is probably a peptide hormone. However, its physiological roles are not fully understood. In the present study, we examined the correlation of androgenic gland cell structure to spermatogenic activity and morphotypic differentiation histologically in M. rosenbergii. spermatogenic activity showed close correlation to the molt cycle in orange-claw males and small males. spermatogonia increased in number in the late premolt stage, becoming spermatocytes in the postmolt stage, and spermatocytes differentiated into spermatozoa in the intermolt and early premolt stages. Ultrastructure of the androgenic gland was additionally compared among the molt stages, but, distinct histological changes were not observed in relation to spermatogenesis during the molt cycle. On the other hand, among the three morphotypes, the androgenic gland was largest in the blue-claw males, containing developed rough endoplasmic reticulum in the cytoplasm. These results suggest that, during spermatogenesis which is related to the molt cycle, the androgenic gland hormone is at rather constant levels and plays a role in maintaining spermatogenesis rather than directly regulating the onset of a specific spermatogenesis stage and that, during the morphotypic differentiation, the androgenic gland is most active in the blue-claw males and plays a role in regulating the observed high mating activity in M. rosenbergii.