Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China

Contrasting pollution responses of native and non-native fish communities in anthropogenically disturbed estuaries unveiled by eDNA metabarcoding

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, Cr6+, and NH4+, 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.

Application of Synchronous Evaluation-Diagnosis Model with Quantitative Stressor-Response Analysis (SED-QSR) to Urban Lake Ecological Status: A Proposed Multiple-Level System

Ecological integrity assessment and degradation diagnosis are used globally to evaluate the health of water bodies and pinpoint critical stressors. However, current studies mainly focus on separate evaluation or diagnosis, leading to an inadequate exploration of the relationship between stressors and responses. Here, based on multiple data sets in an urban lake system, a synchronous evaluation-diagnosis model with quantitative stressor-response analysis was advanced, aiming to improve the accuracy of evaluation and diagnosis. The weights for key physicochemical stressors were quantitatively determined in the sequence of NDAVIadj > CODMn > TP > NH4+-N by the combination of generalized additive model and structural equation modeling, clarifying the most significant effects of aquatic vegetation on the degradation of fish assemblages. Then, sensitive biological metrics were screened by considering the distinct contributions of four key stressors to alleviate the possible deviation caused by common methods. Finally, ecological integrity was evaluated by summing the key physicochemical stressors and sensitive biological metrics according to the model-deduced weights instead of empirical weights. Our system's diagnosis and evaluation results achieved an accuracy of over 80% when predicting anthropogenic stress and biological status, which highlights the great potential of our multiple-level system for ecosystem management.

Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities

Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging species on their potential impacts. However, little research has been conducted on quantifying actual impacts and assessing causes of species-specific vulnerabilities to particular IAS due to persistent methodological challenges. The underlying interspecific mechanisms driving species-specific vulnerabilities therefore remain poorly understood, even though they can substantially improve the accuracy of risk assessments. Given that interspecific interactions underlying ecological impacts of IAS are often shaped by phenological synchrony, we tested the hypothesis that temporal mismatches in breeding phenology between native species and IAS can mitigate their ecological impacts. Focusing on the invasive American bullfrog (Lithobates catesbeianus), we combined an environmental DNA (eDNA) quantitative barcoding and metabarcoding survey in Belgium with a global meta-analysis, and integrated citizen-science data on breeding phenology. We examined whether the presence of native amphibian species was negatively related to the presence or abundance of invasive bullfrogs and whether this relationship was affected by their phenological mismatches. The field study revealed a significant negative effect of increasing bullfrog eDNA concentrations on native amphibian species richness and community structure. These observations were shaped by species-specific vulnerabilities to invasive bullfrogs, with late spring- and summer-breeding species being strongly affected, while winter-breeding species remained unaffected. This trend was confirmed by the global meta-analysis. A significant negative relationship was observed between phenological mismatch and the impact of bullfrogs. Specifically, native amphibian species with breeding phenology differing by 6 weeks or less from invasive bullfrogs were more likely to be absent in the presence of bullfrogs than species whose phenology differed by more than 6 weeks with that of bullfrogs. Taken together, we present a novel method based on the combination of aqueous eDNA quantitative barcoding and metabarcoding to quantify the ecological impacts of biological invaders at the community level. We show that phenological mismatches between native and invasive species can be a strong predictor of invasion impact regardless of ecological or methodological context. Therefore, we advocate for the integration of temporal alignment between native and IAS's phenologies into invasion impact frameworks.

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Inland navigation and land use interact to impact European freshwater biodiversity

Inland navigation in Europe is proposed to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this would impact biodiversity at large scales and interact with existing stressors. Here we addressed this knowledge gap by analysing fish and macroinvertebrate community time series across large European rivers comprising 19,592 observations from 4,049 sampling sites spanning the past 32 years. We found ship traffic to be associated with biodiversity declines, that is, loss of fish and macroinvertebrate taxonomic richness, diversity and trait richness. Ship traffic was also associated with increases in taxonomic evenness, which, in concert with richness decreases, was attributed to losses in rare taxa. Ship traffic was especially harmful for benthic taxa and those preferring slow flows. These effects often depended on local land use and riparian degradation. In fish, negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was evident only when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian habitats and landscape characteristics could help to mitigate these impacts.

Effects of point and nonpoint source pollution on urban rivers: From the perspective of pollutant composition and toxicity

Wastewater discharge is considered to be one of the anthropogenic factors affecting the water quality of urban rivers. The source and composition of wastewater are complex and diverse, and it is difficult to evaluate its effect on water quality and ecological health of receiving waters. Environmental DNA method can determine all species living in waters by examining DNA sequences, reflecting the impact of water quality changes on aquatic systems. In this study, water samples from two urban rivers were collected in dry and wet seasons, and the composition of pollutants was investigated by nontarget screening. Based on the pollutant composition, compound toxicity prediction and concentration addition model were used to predict the toxicity changes of pollutants in the urban rivers. More than 1500 suspect organic pollutants were nontarget screened, and silafluofen was found to be a major toxicity contributor. Environmental DNA analysis was combined with water quality measure and pollutant toxicity prediction to reveal the effects of pollutants from different sources on aquatic ecosystems. Fish diversity was negatively correlated with the mixed toxicity of organic pollutants, suggesting potential ecological risk in these two urban rivers. Our study developed a water quality assessment method based on pollutant composition and toxicity, and the potential risk of nonpoint source pollutants on aquatic ecosystems should not be neglected.

Open riparian canopy and nutrient pollution interactively decrease trophic redundancy and allochthonous resource in streams

Riparian deforestation, which leads to increase in light intensity and excessive nutrient loading in waterways, are two pervasive environmental stressors in the stream ecosystems. Both have been found to alter basal resource availability and consequently stream food webs. However, their interactive effects on trophic structure in stream food webs are unclear. Here, we manipulated light intensity and nutrient availability in three headwater streams to evaluate their effects on consumer diet composition and food web characteristics (i.e., trophic diversity and redundancy) with stable isotope analysis. Dietary analysis revealed that the relative contribution of stream periphyton to the diets of macroinvertebrates increased, while that of allochthonous resources, specifically leaf litter from the terrestrial ecosystems in the catchment, decreased in response to open canopy and nutrient enrichment in the streams. The trophic diversity also increased with the elevated light intensity and nutrient availability, while the trophic redundancy decreased, suggesting a reduced ability of the stream ecosystems to resist environmental changes. Nutrient enrichment also increased the δ15N ratios of periphyton and macroinvertebrates, indicating potential δ15N enrichment of stream benthos by nitrogen pollution. Our results suggested that an increase in light intensity due to riparian canopy openness and stream water nutrient enrichment primarily from human activities have interactive effects on resource flow and trophic structure in stream food webs.