Search Results (45)

Jingpo Lake in Northeast China is a vital aquatic ecosystem, yet it lacks baseline molecular data for its insects. Trichoptera (caddisflies) are excellent ecological bioindicators, but their accurate identification is often hindered by morphological similarities, life-stage limitations, and insufficient DNA barcode records. To address this gap, this study combined morphological identification with DNA barcoding to establish a local reference database. From 285 collected adult caddisflies, 105 representative specimens were selected for genetic analysis. The survey identified 22 species across 9 families, revealing four new records for China and six for Heilongjiang Province. Analyses confirmed the high efficacy of the COI marker, demonstrating low intraspecific genetic divergence (0.78%) and high interspecific divergence (17.80%), with a clear barcode gap separating all examined species. Species accumulation curves indicated robust sampling of the main genera, although expanded collection efforts could still uncover additional species. In conclusion, this study provides a valuable DNA barcode reference library for Trichoptera in the Jingpo Lake region. It establishes foundational data for regional biodiversity inventories and future ecological monitoring based on environmental DNA (eDNA) or metabarcoding approaches. Full article

Shansha Bay, southeastern China, is a typical semi-enclosed bay facing intense anthropogenic pressure, with mariculture production reaching approximately 660,000 tons annually, predominantly driven by the large yellow croaker (Larimichthys crocea) industry. To assess how these pressures influence biodiversity detection, we employed eDNA metabarcoding targeting the 12S rRNA gene to survey fish diversity across 10 sites, integrating both surface water and sediment matrices. A total of 40 species belonging to 16 orders, 27 families and 32 genera, were identified. Among them, L. crocea, Bostrychus sinensis, Clupanodon thrissa and Siganus fuscescens are the dominate species, which comprised over half of all OTUs. Comparison with historical trawl surveys revealed 30 newly recorded species, including the Japanese eel (Anguilla japonica) and oarfish (Regalecus glesne). Alpha diversity was low (Shannon: 0.69–1.93), with significant spatial disparities driven by freshwater runoff and hydrodynamics. While eDNA effectively captured the dominance of cultured species like L. crocea, the extreme biomass signal poses challenges for detecting wild populations. Our findings underscore that a multi-matrix eDNA approach is crucial for accurate biodiversity assessments in aquaculture-dominated coastal ecosystems, although distinguishing wild stocks from aquaculture-derived DNA remains a critical methodological hurdle. Full article

eDNA metabarcoding provides distinct benefits—including non-invasiveness, cost-effectiveness, and high detection sensitivity—that make it particularly appropriate for aquatic ecosystem conservation and fisheries management. An environmental DNA (eDNA) metabarcoding survey was performed in the Cuijiang River to assess the feasibility of this technique for fish diversity monitoring. Fish diversity was evaluated through water collection, eDNA extraction and purification, and subsequent bioinformatics analysis. Our results revealed that the surveyed river section harbours at least 36 fish species, belonging to 30 genera, 13 families, and 6 orders. The fish community was numerically dominated by Cypriniformes. Notably, invasive alien species represented a relatively high proportion (24.72%) of the total operational taxonomic units (OTUs). Alpha diversity indices showed spatial heterogeneity among the monitoring sites, which is likely influenced by anthropogenic activities, land-use patterns, and hydrological connectivity in the sampling areas. Overall, eDNA metabarcoding proves to be an effective approach for fish diversity assessment and can serve as a valuable supplementary tool to conventional methods, with particular utility for the early detection of elusive and invasive species. We therefore recommend its incorporation into ongoing and future aquatic monitoring and conservation frameworks to strengthen early detection, habitat management, and biodiversity protection, thereby offering essential baseline data for future conservation and management of local fish diversity. Full article

Environmental DNA (eDNA) metabarcoding is increasingly used as a complementary tool for coral biodiversity assessment, but its performance in subtropical, estuary-influenced reef systems remains insufficiently tested. This study combined seawater eDNA metabarcoding with concurrent underwater visual surveys and historical records to assess reef-building scleractinian corals in the Wanshan Archipelago, Pearl River Estuary. In June 2022, surface and bottom seawater samples were collected from seven sites, yielding 14 eDNA samples, and dive-based photographic surveys were conducted concurrently. A universal 18S rRNA assay was used for high-throughput sequencing, and eDNA detections were compared with visual and historical survey data at the genus level. eDNA detected 13 families and 21 genera, with Porites and Echinopora as dominant genera. eDNA recovered more genera than concurrent visual surveys in all five regional comparisons, although the two methods yielded overlapping but partly distinct genus inventories. Surface-water eDNA showed a slight, site-dependent advantage in genus recovery and overlap with concurrent visual surveys, whereas correspondence with historical records varied among regions; surface and bottom samples shared most genera but also contributed complementary layer-specific detections. Community composition showed spatial clustering broadly consistent with geographic proximity. These findings indicate that seawater eDNA provides complementary genus-level information and support paired surface- and bottom-water sampling for a more complete exploratory characterization of coral diversity in complex subtropical coastal reef systems. Full article

Water pollution and its ecological consequences have become central concerns in watershed governance and aquatic ecosystem conservation. Conventional ecotoxicological research on water pollution has long relied on physicochemical monitoring, laboratory-based single-species exposure tests, and morphology-based biological surveys. Although these approaches have provided essential support for pollutant identification, toxicity characterization, and environmental standard setting, they remain insufficient for resolving community-level responses, food-web perturbations, and ecosystem degradation under multiple-stressor conditions. Environmental DNA (eDNA) has emerged as a promising molecular tool because it is non-invasive, highly sensitive, high-throughput, and capable of detecting multiple taxa simultaneously. In aquatic systems, eDNA applications have expanded from biodiversity detection to pollution diagnosis, ecological health assessment, restoration monitoring, and early warning of ecological risk, while increasingly being integrated with eRNA, multi-omics approaches, machine learning, hydrological modeling, and ecological network analysis. However, several challenges still constrain its broader application, including incomplete methodological standardization, false-positive and false-negative detections, insufficient reference databases, limited quantitative capacity, scale mismatches caused by transport and mixing, and difficulties in causal attribution. This review synthesizes recent progress in the use of eDNA for water-pollution research, with emphasis on its technical workflow, major application domains, integrative analytical frameworks, and methodological boundaries. More specifically, three main points are highlighted: (1) eDNA is shifting water-pollution research from single-species toxicity characterization toward community- and ecosystem-level ecological interpretation; (2) its greatest value lies in its integrative role at the interface of biodiversity monitoring, ecological risk assessment, and management-oriented decision support; and (3) future progress will depend on improvements in standardization, quantitative inference, regional reference databases, and multi-source data integration. Overall, this review clarifies how eDNA can contribute to more robust, ecologically meaningful, and management-relevant assessment of water pollution. Full article

Coastal lagoons are crucial transitional zones connecting land and sea, and their ecological connectivity with adjacent open waters directly sustains regional biodiversity and ecosystem functions. However, how lagoon fish communities connect on a diurnal timescale remains poorly understood. In this study, we selected Xincun Lagoon on the southeastern coast of Hainan Island, China, as the study area. We established six sampling stations along an environmental gradient from the lagoon interior, through the tidal inlet, to the open sea, and conducted repeated diurnal sampling at six time points on 24 January 2024. Using eDNA metabarcoding, we analyzed the spatiotemporal dynamics of fish communities to examine spatial functional differentiation within the lagoon ecosystem and the potential corridor role of the tidal inlet. Our results showed clear spatial functional differentiation of fish communities along the environmental gradient. The lagoon inlet (XC4) exhibited the highest rate of community temporal change and the greatest amplitude of diversity fluctuation, with a peak change rate of 0.854 during the evening period (18:00–21:00). Its coefficient of variation for Shannon diversity was 6.2 times that of the mangrove creek (XC3). The mangrove creek area (XC3) had the highest Shannon diversity and the smallest fluctuations, functioning as a biodiversity hotspot and a region of relatively stable community structure. Within the lagoon interior, the temporal dynamics at the marginal zone (XC1) were substantially stronger than those in the central zone (XC2). Offshore stations indicated that the ecological influence of the lagoon extended to the 5 m isobath but weakened at the 10 m isobath. Furthermore, Clupeidae eDNA signals were strongest inside the lagoon during the day, at the tidal inlet in the evening, and in offshore waters at night. This study demonstrates the utility of eDNA metabarcoding for capturing fine-scale diel variation in fish community composition and distribution across the lagoon–inlet–offshore gradient, providing information that is difficult to obtain through conventional surveys. These patterns suggest, rather than confirm, that the tidal inlet may play an important role as a corridor linking lagoon and offshore habitats, and provide a reference case for using eDNA technology to study fine-scale connectivity in similar systems. Full article

Introduction: Mediterranean coastal wetlands are highly dynamic ecosystems that support diverse fish communities and are often of high conservation value. The Ebro Delta is one of the most important coastal wetlands in the Western Mediterranean, and knowledge of fish assemblages is essential for its effective conservation and management. Environmental DNA (eDNA) metabarcoding provides a non-invasive approach that can potentially complement conventional surveys for fish biodiversity monitoring. Objective: This study aimed to evaluate the potential of eDNA metabarcoding as a complementary tool to conventional fyke net surveys for fish biodiversity monitoring in the Mediterranean coastal wetlands. Methodology: In 2022, fish assemblages were surveyed across 12 areas of the Ebro Delta using eDNA metabarcoding (12S MiFish) and conventional fyke net sampling. Results were compared with a 22-year historical dataset. Results: A total of 27 fish taxa were detected, 13 of which were exclusive to eDNA, 11 were shared between methods, and three were recorded only by fyke nets. The reliability of eDNA metabarcoding was supported by the detection of endangered species, such as Anguilla anguilla and Apricaphanius iberus; ubiquitous taxa, such as Atherina boyeri and Pomatoschistus microps; and invasive species, such as Gambusia holbrooki and Cyprinus carpio. Detection of invasive species was maximized using eDNA. While eDNA revealed higher species richness than fyke nets, community composition differed significantly between methods, reflecting distinct detection patterns. eDNA preferentially detected non-benthic species, whereas fyke nets were more robust for benthic taxa detection. eDNA recovered most historically recorded species but failed to detect some taxa, such as Misgurnus anguillicaudatus and Sardina pilchardus. Despite richness differences, the two methods provided complementary views of fish assemblages, highlighting method-specific detection limitations and opportunities. Conclusions: eDNA does not fully replace conventional surveys and their combined use improves the detection of threatened and invasive species, better supporting conservation and management. Full article

The Con Dao archipelago hosts the oldest MPA in Vietnam and is recognized as a regional marine biodiversity hotspot. Here, we applied environmental DNA (eDNA) metabarcoding to assess coastal fish diversity across four major habitat types: coral reefs, seagrass beds, mangroves, and a harbour in the Con Dao archipelago. Using MiFish-U 12S primers at eight stations, we detected 282 operational taxonomic units, corresponding to 144 fish taxa. Fish assemblages exhibited strong habitat structuring: community composition differed markedly among habitats, with minimal overlap. Only three species were shared across all habitats. Multivariate analyses confirmed that habitat type, rather than spatial distance among sites, was the primary driver of community differentiation. Mangrove and seagrass supported distinct assemblages that were underrepresented in existing species checklists and MPA management frameworks. Notably, eDNA detected cryptic and non-commercial species overlooked by conventional survey methods. These results substantially expand the known fish diversity of the Con Dao Archipelago and highlight the need to incorporate habitat heterogeneity, particularly non-reef ecosystems, into MPA design and monitoring. Although eDNA metabarcoding is subject to amplification biases and limited taxonomic resolution in reference databases, it offers a powerful complement to traditional surveys for characterizing under-sampled habitats. Full article

Biological invasion is a major driver of biodiversity loss and ecosystem disruption, with non-native aquatic species threatening ecological integrity and economic stability. The Qinling Mountains, located in central China, serve as a crucial barrier between temperate and subtropical climate zones, and separate the Yellow and Yangtze River basins. This study investigates the role of these geographical barriers in regulating the distribution and invasion risk of non-native aquatic species. We identified 27 non-native species in Shaanxi Province based on occurrence records compiled from field survey conducted between 2012 and 2024 (and from 2019 to 2024 in the Yellow River mainstream of the Shanxi–Shaanxi Gorge), including 13 high-risk species, such as Trachemys scripta elegans, Procambarus clarkii, Sander lucioperca, and Hypomesus olidus. Using the Aquatic Species Invasiveness Screening Kit and species distribution models, we identified the Hanjiang River in the Yangtze basin and Weihe River estuary in the Yellow River basin as high-risk areas for these species. Mean annual temperature was the primary environmental factor influencing species distribution, with species adapted to cooler conditions predominantly found north of the Qinling Mountains, while those preferring warmer climates are more common in the south. Our findings highlight the Qinling Mountains as both a physical and climatic barrier, limiting cross-basin dispersal and creating distinct invasion patterns. However, human activities such as inter-basin water-transfer projects, damming, and aquaculture practices have gradually weakened the barrier’s effectiveness, facilitating the spread of invasive species. We recommend prioritizing monitoring efforts in cross-basin water-transfer regions, focusing on high-risk species adapted to both cooler and warmer climates, and incorporating environmental DNA (eDNA)-based monitoring in recipient areas of inter-basin water-transfer projects for early detection and control to minimize ecosystem damage. Full article

The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches—culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses—discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota. Full article

Hulun Lake, a UNESCO Biosphere Reserve, faces mounting threats from extreme climate events and anthropogenic pressures, highlighting the need for robust biodiversity monitoring. Environmental DNA (eDNA) has emerged as a promising tool for aquatic biomonitoring, yet different bioinformatic pipelines—such as Amplicon Sequence Variant (ASV) and Operational Taxonomic Unit (OTU) clustering—may yield divergent results. This study compares ASV and OTU clustering approaches in eDNA metabarcoding alongside traditional capture-based surveys to assess fish diversity in Hulun Lake. Across all methods, we identified 43 taxa (40 species), including the critically endangered Acheilognathus hypselonotus and vulnerable Choi’s spiny loach (Cobitis choii). While eDNA methods detected 2~3 times more species than in nets (13 species), strong methodological correlations (p < 0.001) were observed between net frequencies and eDNA-derived relative abundances (based on both ASV and OTU datasets using 4th-root and log transformations). Clustering analysis of capture-based data revealed four distinct ecological zones: the areas near tourist facilities, Wuerxun River inflow region, Wulan Nuoer Lake (connected via the Wuerxun River), and the Lake Centre. Significant spatial variation (p < 0.05) between these four zones was found in eDNA datasets, whereas nets captured more heterogeneous patterns, consistent with previous studies. Community structures were shaped by both generalists (e.g., Cyprinus carpio, Hemiculter bleekeri) and habitat specialists such as Amur catfish (Silurus asotus). The Lake Centre hosted a unique assemblage, likely due to reduced human disturbance. Overall, both eDNA clustering methods outperformed capture-based survey in detecting species richness and offered semi-quantitative insights. However, discrepancies between ASV and OTU approaches were evident in resolving fine-scale community differences. We recommend an integrated monitoring strategy that combines the sensitivity of eDNA with the abundance resolution of net captured to inform spatially targeted conservation and habitat protection in this vulnerable ecosystem. Full article

Environmental DNA (eDNA) metabarcoding has transformed marine biodiversity monitoring by allowing non-invasive, cost-effective detection of species with high resolution across diverse marine habitats. A systematic literature search was conducted using Google Scholar, Scopus, and the Qatar University Library databases. Relevant peer-reviewed publications were screened and selected based on predefined inclusion criteria to ensure comprehensive coverage of studies. This review synthesizes advances in global and regional eDNA applications, emphasizing the Middle East and North Africa (MENA) region, which faces unique environmental extremes, high endemism, and significant data gaps. eDNA metabarcoding often outperforms traditional methods under comparable sampling effort to traditional surveys in detecting rare, cryptic, and invasive taxa, but technical challenges like incomplete reference databases, primer biases, PCR inhibitors, and inconsistent methodologies limit their effectiveness, particularly in understudied areas such as MENA. Recent developments, including multi-marker approaches, autonomous samplers, and next-generation sequencing, are enhancing detection precision and enabling broader, real-time monitoring. In the MENA region, early studies have revealed eDNA’s potential for habitat distinction, biogeographic research, pollution assessment, and the early discovery of non-indigenous species, although progress is hindered by gaps in reference libraries, infrastructure, and regulation. This review underscores the urgent need for regional collaboration, standardized protocols, and capacity-building. By integrating eDNA with traditional methods and leveraging emerging technologies, the MENA region can establish itself as a leader in marine biomonitoring under extreme environmental conditions, providing actionable insights for conservation and sustainable management of its unique marine ecosystems. Full article

The waters surrounding the Five West Sea Islands of South Korea are ecologically important but challenging to survey due to their location within a strategic military zone, strong tidal currents, and significant tidal variation. To assess the fish community in this region, we conducted Korea’s first parallel investigation combining traditional bottom trawl surveys with environmental DNA (eDNA) metabarcoding. Sampling was performed at 10 stations in March, May, and August 2023, and the relationship between fish species occurrence and environmental variables (water temperature, salinity, and depth) was examined. Dominant trawl-caught species included Engraulis japonicus, Johnius grypotus, Coilia nasus, and Okamejei kenojei, each showing seasonal migration and spawning patterns associated with temperature changes. eDNA analysis detected nine additional species absent from trawl catches, such as Ilisha elongata and Thamnaconus modestus, demonstrating its sensitivity in identifying both migratory and sedentary taxa. Our findings confirm that eDNA surveys can complement traditional sampling, improving biodiversity assessment in regions with limited accessibility and complex oceanographic conditions. Full article

The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean are relatively well-documented, studies on pelagic zones remain sparse, especially for non-target species constituting fishery bycatch. Traditional biodiversity surveys rely on labor-intensive, inefficient trawling methods. To address these limitations, this study aims to apply environmental DNA (eDNA) metabarcoding for a species diversity survey in the Western Indian Ocean, offering a more reliable, efficient, and non-invasive alternative to traditional methods. The results will provide important insights into the region’s fish biodiversity, supporting sustainable management and conservation of fisheries resources in the area. Samples were collected from 130 stations in different water layers in the Western Indian Ocean, and species diversity was analyzed through 12S rRNA gene amplicon sequencing. The results showed that 98 fish species were detected from 176 seawater eDNA samples, belonging to two classes (Actinopteri and Chondrichthyes), 20 orders, 35 families, and 60 genera. Within a depth range of 300 m, there were no significant differences in species diversity parameters among samples from different depths. The orders with the highest relative abundance detected include Scombriformes, Aulopiformes, and Myctophiformes. The species with the highest relative abundance include Thunnus albacares, Alepisaurus ferox, Xiphias gladius, Diaphus fragilis, Decapterus macarellus, Thunnus maccoyii, and Platycephalus cultellatus. The species composition and relative abundance of economic species observed in this study showed, as expected, differences from fishery catch statistics. These results suggest that eDNA technology can not only monitor marine fish diversity more efficiently but also complement the lack of fisheries data. Integrating eDNA technology into routine monitoring in the Western Indian Ocean in the future could promote sustainable management of fisheries resources in the region. Full article

Assessing fish biodiversity is essential for freshwater ecosystem conservation. This study compares environmental DNA (eDNA) metabarcoding and traditional morphological surveys to investigate fish communities in the Gaya River, China. A total of 42 fish species were identified, with 13 detected only by eDNA, 7 exclusively by morphology, and 11 by both methods. A comparative analysis of species composition, functional diversity, and phylogenetic diversity revealed significant differences between the two approaches. Notably, eDNA data indicated higher phylogenetic diversity (PD), while morphological surveys captured greater functional evenness (FEve). Multivariate analyses indicated that total phosphorus (TP), total suspended solids (TSS), electrical conductivity (EC), temperature (T), and pH significantly influenced fish community composition, while dissolved oxygen (DO) was a key driver of species richness (SR), functional richness (FRic), and PD. These findings highlight the methodological differences and complementary strengths of eDNA and morphological approaches in biodiversity assessments. By providing comparative insights into fish diversity patterns, this study underscores the importance of using multi-method approaches to improve freshwater biodiversity monitoring and conservation strategies. Full article