Search Results (501)

Large-water fisheries are central to China’s freshwater aquaculture, but their sustainability is threatened by eutrophication from traditional high-density stocking. Polyculture of grass carp and crucian carp offers an ecologically sound alternative; nevertheless, its direct effects on plankton communities require further study. We conducted monthly sampling from July to December 2023 (over two seasons within a single aquaculture cycle) in polyculture ponds and used eDNA metabarcoding (18S V9) with high-throughput sequencing. We detected 288 planktonic taxa across 28 phyla and 290 genera based on eDNA sequence assignment. Alpha diversity (Chao1, Shannon, Simpson) peaked in autumn and was lowest in winter, with Chao1 showing greater seasonal variation. Beta diversity revealed season as the dominant factor (R² = 0.287, p = 0.012), with significant summer–winter divergence. Null-model analysis indicated stochastic processes (56.3%) slightly exceeded deterministic filtering (43.7%), and stochasticity was higher in summer (67.2%), suggesting fish bioturbation and grazing create heterogeneous microhabitats. Co-occurrence networks were dominated by positive links (87.3%), with Cryptomonas as a central hub, implying mutualism and niche complementarity. This study is the first to integrate eDNA metabarcoding with community assembly theory to elucidate seasonal succession and interactions in this polyculture. Our findings confirm that polyculture sustains diversity and stability via top-down (grazing) and bottom-up (nutrient release) effects, providing eDNA-based taxonomic evidence for management of large-water aquaculture. Full article

Hydrological seasonality is a major driver of microbial community dynamics in river ecosystems, yet how seasonal flow regimes regulate protistan diversity, community assembly, and functional organization remains poorly understood. In this study, environmental DNA metabarcoding targeting the 18S rRNA gene was employed to investigate seasonal variations in protistan communities across 17 sites along the Hongshuihe River, a subtropical tributary of the Pearl River, during flood and normal seasons. Flood events significantly altered environmental conditions and increased protistan alpha diversity, while community composition showed clear seasonal differentiation. Although dominant protistan lineages remained relatively stable, seasonal turnover was primarily associated with rare and low-abundance taxa, highlighting their critical role in maintaining biodiversity and driving community reassembly. Null model analyses revealed a seasonal shift in community assembly mechanisms, with deterministic processes, particularly heterogeneous selection, dominating during the flood season, whereas stochastic drift prevailed during the normal season. Distance–decay and variance partitioning analyses further demonstrated that environmental and spatial processes jointly regulated protistan community variation, with stronger environment–spatial coupling during flood periods. Functional trait analysis revealed an increased proportion of consumer taxa and a reduced contribution of phototrophic taxa during floods, suggesting a shift toward stronger heterotrophic pathways under hydrological disturbance. Collectively, our findings demonstrate that hydrological seasonality regulates riverine protistan communities through coordinated changes in rare taxa dynamics, assembly processes, and functional restructuring, emphasizing the importance of incorporating protistan diversity and functional traits into long-term river ecosystem monitoring. Full article

It is imperative that freshwater fish biodiversity research incorporates diverse components, encompassing taxonomy, phylogeny and function, alongside multifaceted facets, including richness, divergence and regularity. This comprehensive approach is essential to facilitate a more profound comprehension of freshwater ecosystem functions, to elucidate the mechanisms underpinning fish community assembly, and to accurately assess the impacts of anthropogenic disturbance. Consequently, this scientific understanding can inform the development of effective fish conservation and ecosystem management strategies. This study utilized environmental DNA metabarcoding to assess the diversity of fish across the entire Yangtze River, encompassing the upper reach (Upper), the Three Gorges Reservoir area (RES_SX), and the downstream reach (Down). The results indicated that 150 distinct fish species were detected, with the RES_SX area exhibiting a significantly lower taxonomic diversity and fish detection rate in comparison to the other two regions. Conversely, phylogenetic and functional diversity exhibited stability post-normalization by taxonomic richness. Furthermore, investigation of the divergence facet of alpha-diversity demonstrated a reduction in clustering and an improvement of overdispersion on the phylogenetic and functional diversity, respectively, in the RES_SX and Down regions. Beta-diversity analysis further revealed lower taxonomic beta-diversity but higher phylogenetic and functional beta-diversity in the RES_SX area. A substantial degree of geographic distance-dependent similarity was identified for all three components of beta-diversity in the Upper Reach. Conversely, these components were found to be disrupted in the Down Reach. Finally, an analysis of the assembly mechanism revealed stochastic processes, dispersal limitation and drift as the dominant factors shaping the fish communities, with reduced dispersal limitation in the RES_SX area. This study provides novel insights into the multidimensional diversity of fish populations in response to dam construction, emphasizing the necessity of integrating multiple facets of diversity for accurate impact assessment and supporting evidence-based conservation of fish species in the Yangtze River. Full article

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

Understanding seasonal dietary shifts in reintroduced herbivores is essential for conservation, yet detailed patterns for Milu (Elaphurus davidianus) in wetland habitats remain underexplored. This study applied high-throughput sequencing to fecal samples collected across four seasons in Tianjin Qilihai Wetland, identifying 43 plant species from 24 families. Significant seasonal differences were detected in relative read abundance. At the family level, Poaceae dominated spring, significantly exceeding all other seasons; Asteraceae and Cyperaceae were highest in summer, with Cyperaceae also surpassing winter and spring; Amaranthaceae peaked in autumn, higher than spring and summer; and Celastraceae prevailed in winter. At the species level, Phragmites australis was overwhelmingly consumed in spring; Lactuca indica and Bolboschoenus planiculmis peaked in summer; Euonymus japonicus dominated winter; and Suaeda salsa was highest in autumn, exceeding spring. These compositional shifts reveal a strategic transition from a specialized diet focused on high-quality resources in spring–summer to a broad-spectrum diet including woody plants, legumes, and cultivated species in autumn–winter. Overall, Milu exhibit substantial dietary plasticity, a key trait underpinning reintroduction success, and our findings provide empirical evidence to guide adaptive forage management in wetland reserves. 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

The Chilean flamingo (Phoenicopterus chilensis) is a widely distributed South American species inhabiting diverse wetland ecosystems from Ecuador and Peru south to Chile and Argentina, and east to Brazil, Uruguay, and Paraguay, ranging from sea level to high-altitude Andean salars. Despite its broad distribution, local populations are increasingly exposed to anthropogenic pressures, raising conservation concerns at regional scales. In this study, we generated mitogenomic resources and developed a molecular framework for species identification using non-invasive samples. We sequenced genomic DNA from P. chilensis and assembled its complete mitogenome, enabling the in silico evaluation of commonly used metabarcoding markers. Subsequently, we collected eight fecal samples from a feeding site in a high-Andean lagoon where P. chilensis co-occurs with Phoenicoparrus andinus and Phoenicoparrus jamesi. As a positive control, nine additional fecal samples were collected from the Zoológico Nacional, Santiago, Chile, where only P. chilensis is maintained. DNA was extracted and initially screened via Sanger sequencing. To robustly assign taxonomic identity, we implemented a probabilistic framework combining maximum likelihood and Bayesian inference to estimate the posterior probability of species membership based on observed genetic variants. This approach revealed the presence of two genetically distinct groups not attributable to P. chilensis, indicating the coexistence and detectability of other flamingo taxa through fecal DNA. Our results demonstrate the value of integrating mitogenomic resources, metabarcoding, and statistical inference for non-invasive species identification in mixed-species systems. This framework provides a scalable tool for biodiversity monitoring and has direct implications for conservation strategies and evidence-based policy development in fragile high-Andean ecosystems. 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

The Beagle Channel, located south of Tierra del Fuego (~54° S), is South America’s southernmost intracoastal ecosystem. Here, we applied environmental DNA metabarcoding using a partial sequence of the 12sRNA mitochondrial gene to evaluate the seasonal and spatial dynamics of marine vertebrate communities along the longitudinal gradient of the Beagle Channel. Water samples were collected across seasons and sites spanning the central and eastern sectors of the channel. Vertebrate DNA was amplified and analyzed against a custom reference database enriched with locally generated sequences. A total of 43 vertebrate taxa were detected, including 25 fish, 13 mammals, and 5 seabirds. Vertebrate assemblages were spatially structured along the longitudinal gradient of the Beagle Channel, with the central sector characterized by higher relative abundances of Fuegian sprat (Sprattus fuegensis), Southern elephant seal (Mirounga leonina), South American fur seal (Arctocephalus australis), and domestic species, whereas the eastern sector showed higher relative abundances of fish species including silversides (Odontesthes spp.), Magellanic rockcod (Paranotothenia magellanica), and striped rockcod (Trematomus hansoni), as well as mammals including southern sea lion (Otaria flavescens), North American beaver (Castor canadensis), and native grass mice (Abrothrix spp.). This spatial differentiation was associated with contrasting environmental conditions. No significant seasonal effect was detected. This study provides the first environmental DNA-based baseline of marine vertebrates on the Beagle Channel and validates this approach for ecosystem-scale biodiversity monitoring in subantarctic coastal environments. 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

Food products containing plant ingredients are particularly vulnerable to economically motivated adulteration (EMA), which poses risks to consumer trust and regulatory compliance. While traditional methods—such as microscopy, chemical profiling or targeted PCR—struggle to detect adulterants in processed food products or complex mixes, DNA metabarcoding offers a non-targeted, high-throughput alternative. This study presents a nanopore sequencing-based technique that is easy to implement, cost-effective and sufficiently sensitive to detect substitutions, with a focus on spices and herbal teas as model matrices. The method was evaluated using eight single-species reference samples and five commercial multi-ingredient products. It reliably detected undeclared contaminants (e.g., mint in oregano) and species substitutions. Compared to single-barcode approaches, the combination of ITS2 + matK + trnH-psbA markers achieved higher sensitivity. The proposed workflow requires minimal infrastructure and a 2–4-day turnaround time. However, factors such as DNA degradation in highly processed foods, database gaps, and biological diversity limited detection in some cases. These findings demonstrate the workflow’s potential as a first-line screening tool for food authenticity testing, aligning with requirements such as EU regulation 1169/2011 on food labelling or the FDA’s Economically Motivated Adulteration (EMA) program. Future work should validate the method against regulatory thresholds and expand testing to a broader variety of species and matrices. Full article

Urbanization-driven land use transitions, especially impervious surface expansion, profoundly affect aquatic ecosystems, yet the regulatory mechanisms of microbial assembly and disassembly remain unclear. Using environmental DNA metabarcoding, this study examined relationships between landscape patterns, environmental gradients, and microbial communities in the middle-lower Yangtze River. Impervious surfaces (source landscapes) increased from 10% (midstream) to 37% (downstream), disrupting source–sink balance, elevating nitrogen and phenolics, and worsening water quality. Eukaryotes exhibited higher α-diversity and more complex co-occurrence networks, showing greater responsiveness to disturbance. Stochastic processes dominated community assembly (>68%) for both eukaryotic and prokaryotic communities. Dispersal limitation led to higher total β-diversity and nestedness in eukaryotes; by contrast, land use intensified environmental filtering on prokaryotes, resulting in lower β-diversity but higher turnover contribution. Community disassembly simulation reveals a scenario in which impervious surface expansion is associated with non-random species loss, reducing predicted functional richness of both eukaryotic and prokaryotic microbes; the preferential loss of sensitive species is associated with a sharp decline in predicted functional richness, which may have implications for ecosystem stability. Our findings demonstrate that land use change is significantly associated with altered aquatic environments and affects ecosystem functions through biodiversity changes, providing theoretical support for ecosystem conservation. Full article

Mainland Portugal has a lichenological tradition spanning more than three centuries, yet it still lacks a modern, critically revised checklist of its lichen biota. This gap is particularly relevant given the increasing role of species checklists as authoritative references for DNA metabarcoding applications and the expansion of large biodiversity datasets, including those derived from citizen science initiatives. Here we present the first comprehensive checklist of lichens and lichenicolous fungi recorded from Mainland Portugal, based on the critical assessment of 43,718 bibliographic records drawn from 381 publications issued between 1788 and 2021. A total of 2012 species and infraspecific taxa are documented from a universe of 4440 taxonomic names, including synonyms. Nomenclature was updated in accordance with the ITALIC 8.0 database. Species distributions are provided by province, following the scheme adopted in Portuguese botanical floras, with additional information on substrates and altitudinal ranges where available. With over 2000 taxa recorded, Mainland Portugal can be considered a lichen-rich territory relative to its land area, comparing favourably with other European checklists. We discuss the factors underlying this diversity, with particular emphasis on the biogeographical position of Portugal at the south-western edge of the European continent. Full article

The influence of cover crop functional type on soil nematode feeding group structure, food web condition, and crop productivity in horticultural systems remains poorly understood. Using DNA metabarcoding targeting the V6–V8 region of the 18S rRNA gene, we characterized nematode community responses in soil samples collected from a carrot (Daucus carota L.) production system in Ontario, Canada. We evaluated the effects of alfalfa (Medicago sativa L.), sorghum (Sorghum bicolor), and their mixture under two nitrogen regimes. Bacterivores dominated all treatments (60.8%), whereby sampling time and cover crop identity jointly explained 33.5% of community variance. Nematode community ecological indices revealed highly significant temporal shifts in food web condition, including seasonal decline in maturity and structure indices and a rise in the channel index, indicating food web restructuring regardless of cover crop type. Individual cover-crop exhibited distinct trade-offs between nematode suppression and crop productivity, while sorghum drove a pronounced bacterivore-to-fungivore transition. The alfalfa–sorghum (legume–non-legume) mixture emerged as the most agronomically balanced treatment, uniquely combining plant-parasitic nematode suppression with the highest individual carrot weight and the most balanced soil food web structure. This study provides important insights into how cover crop functional type influences soil nematode communities and crop performance in carrot production systems. Future studies repeating this experiment across multiple locations and growing seasons would help determine the consistency of these responses under a broader range of environmental conditions. 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