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Using unregulated tributaries to compensate fish habitat loss in dammed mainstreams has recently been suggested as a promising strategy for river ecological restoration. One critical prerequisite is to find potential tributaries as alternative habitat, which depends on precise fish community surveys. In this study, both eDNA metabarcoding and electrofishing were used to characterise fish community compositions in the dammed lower Jinsha river and its tributaries (Heishui, Pudu, and Xiaojiang rivers) in China. The fish community composition detected by eDNA metabarcoding was consistent with that detected by the conventional method. Besides, metabarcoding has the advantage of detecting the presence of rare species with relatively low abundances. The non-metric multidimensional scaling showed that there was no significant difference in fish community composition between the mainstream and the Heishui river, while there was large difference in the fish community composition between the mainstream and other tributaries. The effectiveness of using the Heishui river as alternative fish habitat was verified by comparing the changes in fish communities before and after the impoundment of the mainstream. Taken together, this study indicates that eDNA metabarcoding is a viable method to identify the suitable tributaries which at least partly compensate for fish habitat loss in the dammed mainstream. [ABSTRACT FROM AUTHOR]

Simple Summary: The water quality of reservoirs in water transfer projects is key as these reservoirs provide water directly to people. In general, the composition and structure of fish assemblage can reflect reservoir water quality and can also be regulated for its improving. We compared monitoring results of fish assemblages carried out by the traditional and environmental DNA methods in three-terminal reservoirs of the South-to-North Water Transfer project in China. The fish assemblages determined by both methods showed similar assemblage structure and patterns of diversity and spatial distribution; however, obvious differences in fish composition across the three reservoirs examined were found. Demersal and small fishes were the most common in all sites. Moreover, a strong association between water transfer distance and the distribution of non-native fish was found. Our findings highlight the importance of fish assemblage monitoring and the impact of water transfer distance on fish assemblage, providing valuable information that can be used in future water transfer projects. The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project. [ABSTRACT FROM AUTHOR]

Understanding the influence of environmental pollutants on the assembly mechanisms of estuarine fish communities is vital for addressing conservation challenges in these biodiverse ecosystems. Although significant research has explored the toxic impacts of pollutants such as petroleum, heavy metals, and eutrophication on individual species and populations, their effects on community assembly processes and the differential responses of native versus non-native fish at the meta-community level remain inadequately understood. This study utilized environmental DNA (eDNA) metabarcoding to analyze fish community diversity across 28 subtropical estuaries in China, assessing how these pollutants affect community composition and assembly mechanisms. Results indicated that eDNA was 2.54 times more effective than traditional methods in species identification, while also enabling the detection of a higher number of non-native fish species and more diverse functional guilds within estuarine ecosystems. A significant distance decay pattern (p < 0.05) was observed among native fish, whereas non-native species exhibited non-significant patterns. Neutral and null models showed that non-native species had significantly higher migration rates (0.005939 vs 0.001757) and a greater contribution of stochastic processes (82.38 % vs 70.59 %) compared to native species. Additionally, distance-based redundancy analysis (db-RDA), variance partitioning analysis (VPA), and correlation analyses revealed that native species were strongly constrained by environmental factors, particularly oil, Hg, Zn, Pb, Cr 6+ , and NH 4 + , while non - native species displayed notable resilience to these pollutants. These findings highlight the potential for non-native species to disproportionately influence community dynamics and assembly through unrestricted random dispersal amid environmental disturbances. This research clarifies the contrasting ecological responses of native and non-native fish communities to anthropogenic pressures in estuarine environments, offering essential insights into ecosystem resilience and informing biodiversity conservation strategies in rapidly changing coastal ecosystems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Fish diversity, an important indicator of aquatic ecosystem health, is declining due to water pollution, overfishing, climate change, and invasive species. Effective surveying and monitoring are required to protect fish diversity. Here, a high-sensitivity environmental DNA (eDNA) metabarcoding technique was used to investigate fish diversity in the Danjiang River, Shaanxi Province, China. In total, 59 species were identified in eight orders, 19 families, and 40 genera. Cypriniformes and Perciformes were the main groups in the survey area, while Cyprinidae accounted for 50.85% of the total fish species. Rhinogobius similis (19%), Hemibarbus umbrifer (11%), Gnathopogon herzensteini (10%), Triplophysa stewarti (8%), and Zacco platypus (7%) were the dominant species. Eight rare and two exotic fish species were identified. Combined with analysis of historical data, the richness of fish identified using eDNA metabarcoding was significantly higher than that of fish captured in ground cages. Temperature, pH, and oxidation-reduction potential are the main environmental factors that affect the spatial distribution of fish communities. These results suggest that eDNA metabarcoding could be a new tool with broad application prospects; however, local databases must be improved. This study provides theoretical data and a methodological reference for protecting and managing fish diversity in the Qinling Mountains., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

This study thoroughly examines three cetacean monitoring methods and assessing their advantages and limitations, establishing a foundational basis for comprehensive information on composition, distribution, and behavior. While real-time and non-invasive, visual surveys favor surface-active cetaceans and are weather-dependent. Local ecological knowledge supplements insights into group behavior. Environmental DNA (eDNA) analysis efficiently detects species like the narrow-ridged finless porpoise (Neophocaena asiaeorientalis) and common bottlenose dolphin (Tursiops truncatus), offering non-invasive, and spatially adept monitoring. Furthermore, eDNA provides prey species information, revealing the narrow-ridged finless porpoise's winter migration to deeper waters due to prey distribution. The study identifies prevalent prey species, like the Japanese Anchovy (Engraulis japonicus) and Osbeck's grenadier anchovy (Coilia mystus), offering insights into the porpoise's feeding ecology and adaptation to changing prey availability in winter. This study systematically compares diverse methodologies employed in cetacean surveys, thereby yielding a comprehensive understanding of cetacean distribution, behavior, and feeding ecology., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Aim: High‐throughput pipelines supported by eDNA metabarcoding have been applied in various freshwater ecosystems. Both eDNA in ethanol (EtOH) samples (ES‐eDNA) and in water samples (WS‐eDNA) can provide comprehensive classification lists with good taxonomic resolution and coverage for determining freshwater biodiversity and biomonitoring. But, the advantages of ES‐eDNA metabarcoding over WS‐eDNA metabarcoding remain unclear for routine assessments of diversity of benthic macroinvertebrates in streams. Location: Qiantang River Basin, China. Methods: Here, we compared ES‐eDNA and WS‐eDNA metabarcoding to evaluate the performance of two eDNA workflows in determining biodiversity and recovery of damaged macroinvertebrate communities. All eDNA samples from the environment and bulk specimen of macroinvertebrates were processed into available molecular operational taxonomic units (MOTUs) and identified to the level of genus. Results: WS‐eDNA detected more exact sequence variants (ESVs) (formerly referred to as operational taxonomic units; OTUs), than did ES‐eDNA (2,866 vs. 2,406), but fewer macroinvertebrate ESVs (381 vs. 481). Among sampling sites, the two eDNA workflows exhibited relatively large dissimilarity on inferred community composition (p <.001). Furthermore, ES‐eDNA metabarcoding exhibited more consistent with morphological identification approaches than did WS‐eDNA metabarcoding (24.24% vs. 17.63%, p =.002), especially for species identified by traditional morphology (morphotaxa). Main conclusions: Based on the attributes of ES‐eDNA and WS‐eDNA, it is suggested that ES‐eDNA metabarcoding performs better than does WS‐eDNA metabarcoding in detecting local biodiversity and was consistent with morphological results, while WS‐eDNA was more suitable for exploring biodiversity patterns on a broad scale, as it is the easiest and most convenient way to collect samples. Results of this study suggest ES‐eDNA metabarcoding could be an option in building molecular measurement biomonitoring programme based on EtOH sample used for preserving biological samples. [ABSTRACT FROM AUTHOR]

Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The Dongjiang River, a major tributary of the Pearl River system that supplies water to more than 40 million people in Guangdong Province and neighboring regions of China, harbors rich biodiversity, including many endemic and endangered species. However, human activities such as urbanization, agriculture, and industrialization have posed serious threats to its water quality and biodiversity. To assess the status and drivers of phytoplankton diversity, which is a key indicator of aquatic ecosystem health, this study used Environmental DNA (eDNA) metabarcoding combined with machine learning methods to explore spatial variations in the composition and structure of phytoplankton communities along the Dongjiang River, including its estuary. The results showed that phytoplankton diversity exhibited spatial distribution patterns, with higher community structure similarity and lower network complexity in the upstream than in the downstream regions. Environmental selection was the main mechanism shaping phytoplankton community composition, with natural factors driving the dominance of Pyrrophyta, Ochrophyta, and Cryptophyta in the upstream regions and estuaries. In contrast, the downstream regions was influenced by high concentrations of pollutants, resulting in increased abundance of Cryptophyta. The random forest model identified temperature, dissolved oxygen, chlorophyll a, NO 2 - as the main factors influencing the primary phytoplankton communities and could be used to predict changes during wet periods. This study provides valuable insights into the factors influencing phytoplankton diversity and community composition in the Dongjiang River, and demonstrates the application value of eDNA metabarcoding technique in large-scale, long-distance river biodiversity monitoring.4 + as the main factors influencing the primary phytoplankton communities and could be used to predict changes during wet periods. This study provides valuable insights into the factors influencing phytoplankton diversity and community composition in the Dongjiang River, and demonstrates the application value of eDNA metabarcoding technique in large-scale, long-distance river biodiversity monitoring., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Freshwater ecosystems face serious degeneration risks from anthropogenic activities, among which land use heterogeneity transformation is one of the main threats on aquatic biodiversity. However, the mechanisms by which land use heterogeneity affects fish community structure in aquatic ecosystems are still difficult to determine. The results of this study showed that we detected a total of 164 fish species during two seasons, with 97 fish species belonging to 15 orders, 31 families and 74 genera in dry season and 138 fish species belonging to 14 orders, 40 families and 98 genera in wet season. The intergroup differences between the upstream, midstream and downstream of the basin in dry season were smaller than those in wet season, and the species richness in wet season were higher than this in dry season. The values of β-diversity between the upstream and midstream regions was greater than downstream in dry season. The value of β-diversity between upstream and downstream regions was larger than in the midstream in wet season. It concluded that the β-diversity values were generally smaller in wet season than in dry season. Land use types on both sides of the Han River basin are mostly cropland, forest land and man-made surfaces. The results of calculating LUI and fish life history characteristics showed a greater correlation between K and M values in the dry water period and a greater correlation between PD50 and longevity in the rich water period. Moreover, we calculated the correlation between the land use index (LUI) and β-diversity NMDS values, respectively, showed a significant positive correlationship (0.712 in dry season; 0.742 in wet season). This research (a) obtained the spatial and temporal distribution of α-diversity and β-diversity data of fish in the whole basin using eDNA technology; (b) analyzed the relationship of land use heterogeneity on fish life history characteristics; and (c) revealed the correlation between land use index and β-diversity communities. Overall, this study can provide data support and theoretical basis for integrated watershed ecosystem management, and provide suggestions for environmental protection and management around the watershed. • obtained the spatial and temporal distribution of fish diversity data based on eDNA technology for the whole basin. • analyzed the relationship of land use heterogeneity on fish life history characteristics. • revealed the correlation between land use index and diversity communities. [ABSTRACT FROM AUTHOR]

[Display omitted] • The contents of Cr, Cu, Zn, As, Pb, Cd, Hg, V, Mn and Ni in the sediments of Xihe River were detected. • The potential ecological risk of heavy metals in Xihe River sediments is high, especially Cd and Hg. • Exposure to Xihe River sediment extracts caused phenotypic changes and oxidative stress in nematodes. • The content of heavy metals in sediments of Xihe River is correlated with the relative abundance of nematodes. Heavy metals have attracted much attention due to their irreversibility, persistence, concealment and bioaccumulation. Biomonitoring method combined chemical analysis can be well evaluate health risks of heavy metals in the environment. In this study, eleven sediments and water samples were collected along Xihe River, which was polluted by heavy metals in Shenyang city of China. The content of multiple heavy metals in these samples was determined by inductively coupled plasma mass spectrometry. 18S rRNA gene sequencing was performed to identify the composition and diversity of nematodes in fine River sediments. The biological toxicity of water-soluble extracts from the samples was further assessed by referring to different endpoints of Caenorhabditis Elegans. The results indicated that the risk of heavy metals in Xihe River was high (potential ecological risk index = 308.75), in which Hg and Cd are the main contributing factors. The relative abundance of nematodes complemented the chemical analysis result, Enoplida , Mononchida , Triplonchida, and Chromadorida nematodes presented a significant positive correlation with the concentration of heavy metals. Specially, Chromadorida nematodes were sensitive to changes in heavy metals in Xihe River, which was significant positively correlated with As, Pb and V. Therefore, nematodes such as Chromadorida can be applied in environmental monitoring to evaluate the health risks of heavy metals. [ABSTRACT FROM AUTHOR]

The South China Sea (SCS) is an important part of the Indo-Pacific convergence zone, with high biodiversity and abundant marine resources. Traditional methods are primarily used to monitor biodiversity. However, a few studies have used environmental DNA (eDNA) metabarcoding to research the assemblage structure of the SCS. This study used eDNA metabarcoding to survey the SCS assemblage and its relationship with environmental factors over a month-long time-series (August 30th to September 30th, 2020) of seawater samples from the central part of the SCS (9°–20°86′ N, 113°–118°47′ E). 32 stations were divided into six groups (A, B, C, D, E, F) according to longitude. We collected water samples, extracted eDNA, and amplified 18S rRNA gene V4 region (18S V4), 18S rRNA gene V9 region (18S V9), and 12S rRNA gene (12S). Krona diagrams were used to show species composition. We identified 192 phytoplankton, 104 invertebrate, and 61 fish species from 18S V4, 18S V9, and 12S, respectively. Generally, the three assemblage structures exhibited an increase in species diversity with increasing longitude. Group E had the highest fish diversity. Groups F and C had the highest phytoplankton and invertebrate diversity, respectively. Canonical correspondence analysis showed that four factors (chlorophyll a , depth, salinity, and temperature) were correlated with assemblage structure. Chlorophyll a was the main environmental factor that affected fish, phytoplankton, and invertebrate assemblage structures; salinity was strongly correlated with fish and invertebrate assemblage structures; temperature was a key factor that impacted fish and invertebrate assemblage structures; and depth was strongly correlated with invertebrate assemblage structure. Our results revealed that eDNA metabarcoding is a powerful tool for improving detection rate and using multiple markers is an effective approach for monitoring biodiversity. This study provided information that can be used to enhance biodiversity protection efforts in the SCS. • eDNA metabarcoding is sensitive to reveal biodiversity in the SCS. • Multiple trophic levels were identified effectively from one eDNA sample. • eDNA abundance reflected the assemblage variations across longitude. • Environmental factors were significantly correlated with assemblage structures. [ABSTRACT FROM AUTHOR]