Trophic interactions of reef-associated predatory fishes (Hexagrammos otakii and Sebastes schlegelii) in natural and artificial reefs along the coast of North Yellow Sea, China

Whole-Genome Sequencing of Hexagrammos otakii Provides Insights into Its Genomic Characteristics and Population Dynamics

Hexagrammos otakii, also commonly called "Fat Greenling", is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70-15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics.

A Chromosomal-level genome assembly and annotation of fat greenling (Hexagrammos otakii)

Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H. otakii, achieved using PacBio long-read sequencing and Hi-C technology. The assembly yielded a genome size of 682.43 Mb with a contig N50 size of 2.39 Mb and a scaffold N50 size of 27.83 Mb. The completeness of genome assessed by BUSCO is 96.99%. A total of 22,334 protein-coding genes were predicted, with 21,619 (96.80%) functionally annotated across various protein databases. This genomic resource is a step forward in supporting the breeding, germplasm conservation, and enhancement of H. otakii, facilitating genetic studies and the development of strategies for disease resistance and growth optimization in aquaculture.

Habitat Enrichment Causes Changes in Fish Behavioural Characteristics: A Case Study of Sparus latus

To better understand the habitat preferences and behavioural ecology of Sparus latus, we performed an experiment using box-shaped reefs as habitat enrichment materials, allowing us to determine the behavioural strategies and drivers involved in the response to different enrichment structures. The results showed that the first contact time of S. latus was negatively correlated (Pearson's correlation, p < 0.005) with the distribution rate in the artificial reef area. Enrichment structures affected the habitat preferences of S. latus, and there was a significant difference in the average distribution rate between the control and treatment groups (Adonis, p < 0.001). The opening ratio (Adonis, R2 = 0.36) explained the distribution difference of S. latus better than the opening shape (Adonis, R2 = 0.12). In the absence of an enrichment structure, S. latus remained more active during the daytime, exhibiting poor clustering, while in the presence of an enrichment structure, S. latus exhibited clustered movement at night. The opening ratio was negatively correlated with the average interindividual distance (Spearman's correlation, p < 0.01) and showed a significant positive correlation with the average distribution rate in the reef area (Spearman's correlation, p < 0.001), indicating that the reef opening ratio significantly affected the reef-tropism and clustering behaviours of S. latus. The light intensity was negatively correlated with the average distance moved, and the average speed (Spearman's correlation, p < 0.05) was significantly positively correlated with the reef first contact time (Spearman's correlation, p < 0.001), indicating that the light intensity affected the exploration and activity patterns of S. latus. These results provide a research basis for analysing the pattern and process of fish proliferation induced by artificial reef habitats.

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10-6 to 8.77 × 10-6, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

Response mechanism of meiofaunal communities to multi-type of artificial reef habitats from the perspective of high-throughput sequencing technology

Multiple types of artificial reefs have been widely deployed in the coast of northern Yellow Sea, which can enhance fishery resources, restore coastal habitats and improve the marine environment. Meiofauna plays important ecological roles in marine ecosystem, but the response mechanism of meiofaunal community to different types of artificial reef is still poorly understood. In this study, we characterized the meiofaunal communities of concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) and adjacent natural habitat (NH) using 18S rRNA gene high-throughput sequencing technology, and explored the relationship of community-environment. The results showed that the diversity and community structure of meiofauna differed significantly on both spatial and temporal scales. Spatial differences were mainly contributed to the flow field effects and biological effects generated by artificial habitats, while temporal differences were driven by temperature (T) and dissolved oxygen (DO). The dominant taxa of meiofauna included arthropods, annelids, platyhelminths and nematodes. Platyhelminths were mainly positively influenced by artificial habitats but annelids were the opposite. Co-occurrence network analysis revealed that NH was more sensitive to environmental change than artificial habitat, while the performance of CAR and SAR were more stable. These results indicated that meiofauna can respond accordingly to different types of artificial habitats, and could be superimposed over the normal seasonal effects. The current study could provide fundamental data for understanding the response mechanism of meiofaunal community to different types of artificial habitats and a reference for assessments of the impact of artificial reefs on the marine environment.

Evaluation of artificial reef habitats as reconstruction or enhancement tools of benthic fish communities in northern Yellow Sea

Artificial reefs have been widely deployed in the northern Yellow Sea. However, the differences in the ecological benefits on different types of artificial reef habitats are still poorly understood. In this study, the temporal and spatial differences on benthic fish communities were evaluated among concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) around Xiaoshi Island in northern Yellow Sea. The results indicated that all three types of artificial reef habitats can enhance the diversity variables of benthic fish communities, and fish abundance, species richness and Shannon-Wiener index of CAR were generally better than the other two. CAR and RAR hosted similar community composition of benthic fish, and all types of habitats showed significant differences in community composition between winter-spring and summer-autumn. Environmental factors, especially water temperature, can also affect the community composition by affecting the migration of temperature-preferred species. Overall, the enhancement effects of artificial habitats on fisheries productivity varied with fish species and reef types. This study will help to understand the ecological effects of different types of artificial reefs in northern Yellow Sea, and then could give an insight for scientific construction of artificial reefs in this region.

Comparison of Marine Ecosystems of Haizhou Bay and Lvsi Fishing Ground in China Based on the Ecopath Model

Recently, under the impacts of environmental shifts and human activities, marine ecosystem conservation and recovery have become increasingly important for the management and sustainable development of fishery resources. We construct two Ecopath models to describe and compare the similarities and differences in the structure and function of the ecosystems in Haizhou Bay (HZB) for 2020–2021 and Lvsi Fishing Ground (LSFG) for 2018–2019 in this study. Our results highlight the similarities of the two ecosystems in which plankton (e.g., zooplankton and phytoplankton) are important functional groups with bottom-up effect control and congers control the top-down effect. The differences between the two ecosystems indicate that the HZB ecosystem is relatively mature due to higher Finn’s cycling index (FCI), Finn’s mean path length (FMPL), Connectance Index (CI), System Omnivory Index (SOI), and Ascendency/capacity (A/C). However the food web structure in the LSFG is more diverse and stable with higher Overhead/capacity (O/C) and Overhead/capacity (H). The differences are possibly due to the low trophic level (TL) species composition in the two ecosystems. Therefore, we suggest that stock enhancement and release methods should be deployed to release high TL species into designated water areas to increase food web complexity and ecosystem maturity in HZB and LSFG. This study will help inform ecosystem and fishery regulations in different ways and facilitate discussion towards the establishment of strategic conservation planning and adaptive management.