Coreoperca whiteheadi is an economically important and ecologically significant freshwater fish distributed across southern China and northern Vietnam, yet genomic resources for this species remain limited. Here, we present a high-quality, chromosome-level genome assembly for C. whiteheadi generated using an integrated sequencing strategy combining PacBio HiFi long-read, MGI short-read, and Hi-C chromatin conformation data. The assembled genome spans 787.17 Mb, with 99.00% of sequences anchored to 24 pseudochromosomes, achieving a contig N50 of 24.26 Mb and a scaffold N50 of 33.57 Mb, with a 99.42% BUSCO completeness. A total of 22,288 protein-coding genes were predicted, of which 98.87% were supported by BUSCO analysis, and 99.45% were functionally annotated in at least one public database. Repetitive elements comprise 32.18% of the genome. This assembly represents the first high-quality chromosome-level genomic resource for the genus Coreoperca and will serve as a valuable reference for comparative genomics, population genetics, and evolutionary studies of Sinipercidae fishes.

Siniperca obscura is an economically valuable and ecologically significant species in China, yet the lack of comprehensive genomic resources has hindered genetic studies and breeding efforts. In this study, we present a high-quality, chromosome-level genome assembly for S. obscura, generated by integrating PacBio HiFi long-read sequencing with Hi-C scaffolding. The final assembly spans 734.12 Mb, with 99.85% of the assembled bases anchored and oriented onto 24 chromosomes. It achieves a contig N50 of 24.59 Mb and a scaffold N50 of 30.62 Mb, with high genome completeness further demonstrated by a BUSCO score of 99.37%. We predicted 23,225 protein-coding genes, with a 99.12% BUSCO completeness, and 98.50% of the genes were functionally annotated. Approximately 30.54% of the genome sequences were classified as repeat elements. This high-quality reference genome provides a valuable resource for advancing molecular breeding, comparative genomics, and evolutionary studies of S. obscura and closely related species.

Changes in lake shorelines can significantly impact its ecological environment and lead to the erosion of wetland soils. Accurate extraction and continuous monitoring of lake shorelines are critically important for protecting and managing these ecosystems. To characterize the evolution of Chaohu Lake shoreline from 2000 to 2020, we used Landsat remote sensing imagery in combination with the modified normalized difference water index (MNDWI) and the digital shoreline analysis system (DSAS). The spatiotemporal changes of the shoreline were quantified using the end point rate (EPR) and linear regression rate (LRR) metrics. Results indicate that between 2000 and 2020, the surface area of Chaohu Lake shrank by 2.38 km2 and its shoreline length decreased by 2.89 km, following a pattern of initial expansion followed by contraction. The most rapid shoreline retreat (6.63 km) occurred between 2005 and 2011. There was significant spatial variability in the shoreline change, especially in areas such as Hongshi Bay and Jindou Donglu, where the highest erosion and accretion rates were −22.09 m/a (EPR) and 20.72 m/a (LRR), respectively. Notably, the western part of the lake (near Hefei) experienced greater human disturbance and correspondingly higher annual shoreline change rates (EPR: 0.73 m/a; LRR: 0.91 m/a) than the eastern part (EPR: 0.60 m/a; LRR: 0.47 m/a). Overall, these findings provide a scientific basis for ecological restoration and sustainable shoreline management of Chaohu Lake.

Although the bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) has been extensively studied, there is no consensus on their trophic transfer in freshwater food webs. More importantly, data on bioaccumulation and trophic transfer of PAH derivatives remain scarce. To fill this knowledge gap, 79 polycyclic aromatic compounds (PACs), including PAHs, alkylated PAHs (Alk-PAHs), oxygenated PAHs (OPAHs), and heterocyclic aromatic hydrocarbons (HAHs), were quantified in 19 aquatic species from Lake Chaohu, China. Total concentrations of PACs ranged from 2.2 to 47 ng g-1 wet weight (median: 15 ng g-1). Notably, unlike lake sediments, Alk-PAHs replaced PAHs as the predominant component in organisms, demonstrating their strong bioaccumulation. Biota-sediment accumulation factor (BSAF) further indicated that methylation likely enhances the bioavailability and bioaccumulation of anthracene, phenanthrene, benzo[a]anthracene, and benzo[c]phenanthrene. In addition, ontogenetic shifts in diet and metabolism during growth also appeared to affect Alk-PAHs burdens in C. alburnus, H. molitrix, and C. carpio. Trophic magnification factors (TMFs) for PACs varied from 0.50 to 2.1. A comparison with data from a 2010 survey revealed a shift in trophic transfer of priority PAHs, from dominated-biodilution toward more frequent occurrences of TMFs > 1. Importantly, several PAH derivatives, including dibenzothiophene, 2-methylnaphthalene, 1,4-dimethylnaphthalene, 1,5-dimethylnaphthalene, 2-methylbenzo[c]phenanthrene, 9,10-anthraquinone, 9-fluorenone, and 6,8-dimethylbenzo[a]anthracene displayed higher TMFs than their corresponding parent PAHs or analogs, highlighting the necessity of enhancing the priority of their monitoring.

Plastics, combined with plasticizers, have been widely utilized worldwide. Microplastic fibers (MPFs) and dibutyl phthalate (DBP) account for the most predominant microplastics and plasticizers detected in freshwater ecosystem, with their joint toxicity being limited studied. In this study, we employed freshwater algae (Chlorella vulgaris) as toxicity test model organism to assess their growth, photosynthesis, metabolism, and oxidative response when exposing to different concentrations of polypropylene MPFs and the co-exposure of DBP. In addition, the toxic interaction between MPFs and DBP was assessed by combining the integrated toxicity value (Integrated Biomarker Response version 2, IBRv2) and the mixture toxicity index (Effect Addition Index, EAI). Our results demonstrated significant toxic effects of MPFs and DBP on C. vulgaris, and highlighted their dynamic interactions with C. vulgaris. Specifically, when combining with DBP, MPFs with high concentrations exhibited significantly increase in algae growth inhibition, photosynthetic pigment contents (Chl-a, Chl-b, and carotenoids), protein contents, and oxidative enzymes (SOD, CAT, and MDA). In terms of integrated toxicity values, higher IBRv2 values were recorded by the combined exposure of MPFs and DBP in contrast with the sole exposure groups, indicating that the combined exposure caused more severe damage to photosynthesis, oxidation and metabolism. In addition, our study recorded synergistic combined toxicity when MPFs were in high concentrations, whereas antagonistic combined toxicity when MPFs were in low concentrations. Our study highlights the MPFs concentration-dependent combined toxicity (synergistic or antagonistic) when exposing to microplastics and plasticizers in freshwater ecosystems.

This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.

The effect of different cooking methods on metal(loid) bioaccessibility in crayfish muscles has not been adequately addressed. In this study, trace metal(loid)s (Cr, Mn, Fe, Co, Cu, Zn, As, Se, Cd, Hg, Pb) in raw and cooked abdominal muscles of red swamp crayfish (Procambarus clarkii) were extracted using an in vitro gastrointestinal digestion model. The effect of cooking methods, specifically steaming, boiling, frying and high-pressure steam, on total concentration and bioaccessibility of trace metal(loid)s was investigated. Trace metal(loid)s were 100 % detected in raw and cooked crayfish muscles with levels met national standard limits. Cooking increased total concentrations of certain metal(loid)s (notably Cr, Cd, and Pb), yet generally reduced bioaccessibility. Methods employing higher temperatures combined with pressure exhibited more pronounced decrease in bioaccessibility. Health risk assessment adjusted by bioaccessibility demonstrated low health risk for crayfish consumers. This research provided a more precise estimation of metal(loid) exposure risk associated with crayfish consumption, thereby informing the development of more appropriate public health safety guidelines.

Potentially toxic metals pose threats to ecosystems through bioaccumulation, yet the traceability of metal bioaccumulation pathways and their induction of metabolic disorders in fish tissues remain poorly understood. Here, we present an integrative study combining multi-media metal analysis, lipidomics, and machine learning to decipher metal-lipid interactions in Chaohu Lake, China-a critical freshwater system facing industrial and agricultural pollution. Analyzing 16 metals across water, sediments, and four fish tissues (muscle, liver, gonad, brain) and profiled 297 lipid species specifically in these fish tissues, we developed a SHAP-BF (Shapley Additive Explanations-Bioaccumulation Factor) framework to quantify metal origins and tissue-specific lipid responses. Our framework revealed dual water-sediment sources for brain/gonad metals (e.g., Mn, Ni) versus predominant water-derived accumulation in muscle/liver (Ni, Be, Mn, Co). Lipid profiling identified glyceride dominance in muscle/liver/gonad (64.7-69.1 %) and phospholipid enrichment in brain (75.4 %), with muscle lipids exhibiting the highest sensitivity to aqueous metals. Machine learning further linked Ni and Mn to disrupted phospholipid homeostasis (e.g., PC 39:6, PE 32:1 et al.) in muscle, highlighting risks to nutritional quality and food safety. This work pioneers an AI-driven approach for tracing metal transfer dynamics and lipidomic disruptions, offering a transformative framework for ecological risk assessment and pollution mitigation strategies.

The small-scale yellowfin (Plagiognathops microlepis) is a highly valued species in East Asian aquaculture due to its adaptability and high yield. However, the lack of genomic data has impeded genetic research and breeding efforts. In this study, we utilize PacBio Hifi long-read sequencing and Hi-C technologies to construct a highly detailed genome of P. microlepis at the chromosomal level. The assembly encompasses 976.41 Mb, with an exceptional 99.84% distribution across 24 chromosomes. Notably, the contig N50 was 34.41 Mb and scaffold N50 was 38.38 Mb. The completeness of the P. microlepis genome assembly is underscored by a BUSCO score of 98.08%. A total of 25,389 protein-coding genes were identified, with a BUSCO score of 96.98%, and 99.85% of these genes were functionally annotated. Synteny relationships at the chromosome level with Danio rerio and Chanodichthys erythropterus genomes uncover small-scale chromosomal rearrangements. This high-fidelity genome assembly serves as a pivotal resource for forthcoming endeavors such as the genome structure, functional elements, comparative genomics, and evolutionary characteristics of P. microlepis and its relative species.

Environmental DNA (eDNA) metabarcoding has been widely used in freshwater systems, contributing to the advancements in the monitoring of fish diversity and community species composition. Nevertheless, the accuracy and reliability of eDNA metabarcoding in assessing functional structures and revealing the mechanisms underlying fish community assembly remain unclear. In this study, we combined a traditional survey method (electrofishing) and eDNA metabarcoding to conduct fish stock monitoring in the upper reaches of the Huishui stream. We assessed taxonomic and functional structures, as well as community assembly mechanisms, during dry and wet seasons. The results revealed that, compared with electrofishing surveys, eDNA metabarcoding detected a greater number of species and higher functional richness in both seasons. Despite significant differences in fish taxonomic composition between the seasons, both eDNA and traditional methods indicated that environmental filtering dominated the process of fish community assembly in both dry and wet seasons. We showed that eDNA metabarcoding is comparable to the electrofishing method in monitoring the community composition of stream fish and can accurately and reliably determine fish community assembly mechanisms. Combining functional traits and eDNA is a robust approach for monitoring stream fish community compared to taxonomic uncertainty.

The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

This study aimed to examine the bacterial communities present in the macrophyte- (MDZs) and algae-dominated zones (ADZs) of the Chengdong Lake, by utilizing high-throughput sequencing techniques. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the two lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The results obtained through the analysis of Shannon indices indicated that the biodiversity of water samples in the ADZs was greater compared to the MDZs. However, no statistically significant difference was observed in sediment samples across different regions of the lake. Our findings indicate that Cyanobacteria phylum abundance was highest in the ADZs, while the MDZs had Proteobacteria as the most abundant phylum, comprising over 30% of the bacterial community. The db-RDA analysis revealed that total nitrogen (TN) and total phosphorus (TP) in the water, as well as organic matter (OM) in the sediment, were the primary environmental factors influencing the variation in bacterial communities. This study contributes fundamental data towards comprehending the diversity variation of bacterial communities across different habitats within Chengdong Lake.

Strain FF17T, a Gram-negative, obligate aerobic, motile, pink-pigmented, and methylotrophic bacterium, was selected for a polyphasic taxonomic investigation due to its capacity for aggregation, or floc formation. The predominant respiratory quinone observed was Q-10, accounting for 83.36

When assessing microplastics (MPs) in freshwater ecosystems, previous studies have primarily focused on natural rivers and lakes, with limited attention to urban water source areas. Sediments, recording the steady process of MPs accumulation during a long period of time, can act as an important sink for MPs. In this study, we investigated the distribution, characteristics and pollution evaluation of MP contaminants in sediments of a water supply reservoir of Hefei City (the Dafangying Reservoir). Meanwhile, the differences of MP concentrations in sediments in rural and urban areas were also compared. Our results detected five shapes, seven colors and six polymer types of MPs in sediments of the Dafangying Reservoir. Polystyrene, polyethylene and polypropylene were the most abundance types of MPs identified. The average MPs abundance of sediments in rural areas was 83.20 +/- 32.99 n/100 g dry weight (d.w.), and 182.67 +/- 72.21 n/100 g (d.w.) in urban areas. The total MP concentrations were significantly higher in sediments of urban sites than that in rural sites, which can be ascribed to more complex and diverse MP sources triggered by intensive anthropogenic activity in cities. Specifically, we also demonstrated significantly higher microbead abundance in urban sites, which may result from the widespread use of microbead in personal care products. Given the complexity and diversity of MPs in urban areas, we exhibited a relatively higher abundance of MPs in the Dafangying Reservoir than that in other rural larger reservoirs. According to the index of geoaccumulation, the sedimentary MPs were assessed as moderately polluted. Our study enriches valuable data on the distribution of MPs contaminants in water supply reservoir, and provides theoretical references for MPs control and management in reservoir ecosystems.

The land-based container with recycling water aquaculture system (C-RAS) has gained popularity in China due to its water conservation and pollution reduction capabilities. However, there is a dearth of theoretical research on this subject. In this study, water from Koi-cultured container and three-stage eco-ponds was sampled over three seasons and then the bacterial communities were analyzed. The findings of this study indicate that the implementation of three-stage eco-ponds significantly enhances water quality. Specifically, during the summer season, eco-ponds exhibit the highest removal efficiencies of total nitrogen and total phosphorus in comparison to other seasons. During winter, the bacterial communities’ operational taxonomic units, diversity, and richness experience a substantial decline. The system was dominated by Proteobacteria, Bacteroidota, and Actinobacteriota phyla. The lower relative abundance of Actinobacteriota and Cyanobacteria elucidated the reason for the lower off-flavor compounds in container-cultured fish compared to pond-cultured fish. The bacterial community was significantly influenced by water temperature and pH, as revealed by canonical correspondence analysis. These findings establish a fundamental basis for the development of a healthy and sustainable C-RAS technology.

为研究巢湖中浮游甲壳动物功能群的时空变化特征及其主要影响因子,在巢湖的主要河口区以及敞水区共设置了 20个采样点,对浮游甲壳动物群落结构和水环境因子进行了调查和分析.结果表明:(1)巢湖河口区的8个采样点中共鉴定出枝角类10属21种,桡足类11属16种;敞水区12个点中鉴定出枝角类9属18种,桡足类12属13种;共22属39种.(2)巢湖河口区和敞水区浮游甲壳动物平均密度为530.8 ind·L-1和506.3 ind·L-1,平均生物量分别为14.7 ind·L-1和21.5 ind·L-1;浮游甲壳动物Shannon-Wiener多样性指数显示巢湖秋季河口区的污染程度高于敞水区.(3)巢湖浮游甲壳动物按照体型大小和食性可划分5个功能群,其中,河口区有SCF、LCF共2个优势功能群,敞水区有SCF、LCF、MCF共3个优势功能群,SCF在功能群中占绝对的优势地位.(4)水温是影响河口区和敞水区浮游甲壳动物功能群主要的环境理化因子;巢湖敞水区中浮游甲壳动物LCF功能群能显著影响SCF、MCC、LCC等功能群.巢湖河口区污染程度高于敞水区,巢湖的富营养化治理和藻类水华控制应侧重于河口区的外源污染治理;敞水区可以通过调整浮游甲壳动物功能群结构重建水生生态系统.

The genetic diversity of Taenioides cirratus was investigated on the basis of mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) gene sequences. A total of 159 specimens collected from the Chaohu Lake (CL), Nansihu Lake (NL), Taihu Lake (TL), Pearl River (PR), and Nandu River (NR) were sequenced. The total length of the sequence was 2485 bp with 412 polymorphic sites. A total of 73 haplotypes were identified, with Hap1 being the most widely distributed. The PR and NR populations showed high genetic diversity, while the CL population showed low genetic diversity. TL and NL showed high haplotype diversity but low nucleotide diversity. The analysis of molecular variance demonstrated that the sequence variations were mainly occurred among populations. T. cirratus populations are declining, and rare alleles are present at low frequencies, as analysed using a neutral test and a mismatched distribution analysis. There was a relatively high level of genetic differentiation among the populations of the Yangtze River basin (including NL), PR, and NR (Fst > 0.15). The two similar phylogenetic trees constructed by the maximum likelihood (ML) and Bayesian inference (BI) methods presented three major lineages, of which lineage II contains haplotypes from PR and NR, lineage III contains haplotypes from CL, NL, TL, and PR, whereas lineage I contains only a portion of haplotypes from NR. Based on the neutral test, mismatch analysis, and Bayesian Skyline Plot (BSP), geological and climatic events were inferred to have played an important role in the historical dynamics of T. cirratus population. Hap1, Hap25, and Hap58 were inferred as possible ancestral haplotypes by network analysis. Our study offers an essential foundation for resource preservation and additional taxonomic clarification of T. cirratus.

Dams are undoubtedly a primary threat to global freshwater fishes. However, how fish functional traits respond to dams at the global scale remains poorly understood, which hinders a general understanding of related ecological processes, conservation, and management. By synthesizing fish data from 4040 relevant publications, this study investigates the species compositional and functional differences before and after dam construction, aiming to obtain general fish response patterns to dams and to propose pertinent conservation suggestions. The mean values of body size and trophic level of the occurrence-increased (OI) fishes and occurrence-decreased (OD) fishes were found to be larger than those of global freshwater fishes obtained from FishBase, respectively. In terms of mouth orientation, most OI fishes have terminal mouths, while a large proportion of the OD fishes have inferior mouths. The sensitive functional traits that respond to dams are habitat preferences and reproductive traits because the OI fishes are mainly lentic-adapted, warm-water, non-migratory, and produce demersal eggs, while the majority of the OD fishes are lotic-adapted, cold-water, migratory, and produce floating eggs. These results indicate that functional trait-based evaluations are essential for predicting the impacts of dam development on fish assemblages and guiding global biodiversity conservation, management, and sustainability.

为了解须鳗虾虎鱼(Taenioides cirratus)线粒体基因组特征和系统发育状况,采用Illumina Hiseq高通量测序技术,测定了从南渡江口、珠江口、太湖、巢湖和南四湖中采集的12 尾须鳗虾虎鱼的线粒体全基因组,并下载近缘种线粒体全基因组序列进行系统发育分析.结果表明:须鳗虾虎鱼线粒体全基因组长为16 641～16 978 bp,包含13 个蛋白编码基因、22 个tRNA基因、2 个rRNA基因和1 个D-loop控制区,各样本的编码基因序列长度较一致,线粒体全基因组长度差异主要是由控制区长度(975～1 314 bp)差异造成的;基于 13 个蛋白编码基因和 2 个rRNA 基因序列构建系统发育树,须鳗虾虎鱼分为 3 个高支持率进化枝,与红狼牙虾虎鱼(Odontamblyopus rubicundus)、鲡形鳗虾虎鱼(Taenioides anguillaris)形成并系,太湖、巢湖和南四湖的须鳗虾虎鱼个体聚为 1 个进化枝,南渡江口和珠江口的须鳗虾虎鱼个体均分属 2 个进化枝.研究表明,青藏高原隆起和亚洲季风形成带来的中国水系格局变化,可能是须鳗虾虎鱼形成目前系统发育结构的重要原因,本研究结果可为进一步明确须鳗虾虎鱼的分类地位和资源保护提供重要依据.

Caizi Lake is an important lake connected to the Yangtze River in Anhui Province and a crucial connection for the Yangtze-to-Huaihe Water Diversion Project. There were marked differences in trophic status of the six sampling sites based on the physicochemical characterization. The Bacterial Eutrophic Index (BEI), used to quantify water quality, was well related to Carlson's trophic state index (TSI) (Spearman's rho = 0.829, P < 0.05). Mean TSI and BEI were 54 and 0.58, respectively, indicating that Caizi Lake was slightly eutrophic. Actinobacteriota were the predominant bacterial phylum in the water and Acidobacteriota in sediments. The diversity and composition of the bacterial community was markedly different between sites for water but not sediment samples. Unlike other Yangtze-connected freshwater lakes, the distance-based redundancy analysis revealed that dissolved oxygen affected the composition of the planktonic bacterial community (P < 0.001), while total phosphorus was the major factor in the sediments (P < 0.05). The water quality of Caizi Lake has significantly improved since a few years ago. These results contribute to the long-term monitoring of the ecological quality of the water environment along the Yangtze River to the Huaihe River. This is the first report of the water quality and microbial community composition across Caizi Lake, which is an important lake connected to the Yangtze River.