Holistic Impact Evaluation of Human Activities on the Coastal Fish Biodiversity in the Chinese Coastal Environment

Environmental DNA biomonitoring reveals the human impacts on native and non-native fish communities in subtropical river systems

Subtropical rivers are one of the hotspots of global biodiversity, facing increased risks of fish diversity changes and species extinction. However, until now, human impacts on native and non-native fish communities in subtropical rivers still lack sufficient effort. Here, we used the environmental DNA (eDNA) approach to investigate fish communities in the Dongjiang River of southeast China, a typical subtropical river, and explored the effects of regional land use and local water pollution on fish taxonomic and functional diversity. Our data showed that 90 species or genera of native fish and 15 species or genera of non-native fish were detected by the eDNA approach, and there was over 85% overlap between eDNA datasets and historical records. The taxonomic and functional diversity of all, native and non-native fish communities showed consistent spatial patterns, that is, the upstream of the tributary was significantly higher than that of the mainstream and downstream. Land use and water pollution such as COD and TP were the determinants in shaping the spatial structure of fish communities, and water pollution explained 31.56%, 29.88%, and 27.80% of the structural variation in all, native and non-native fish communities, respectively. The Shannon diversity and functional richness of native fish showed a significant downward trend driven by COD (pShannon = 0.0374; pfunctional = 0.0215) and land use (pShannon = 0.0159; pfunctional = 0.0441), but they did not have significant impacts on non-native fish communities. Overall, this study emphasizes the inconsistent response of native and non-native fish communities to human impacts in subtropical rivers, and managers need to develop strategies tailored to specific fish species to effectively protect water security and rivers.

Fishing eDNA in One of the World's Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze

The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.

Phytoplankton and Microzooplankton Community Structure and Assembly Mechanisms in Northwestern Pacific Ocean Estuaries with Environmental Heterogeneity and Geographic Segregation

Phytoplankton and microzooplankton are crucial players in marine ecosystems and first responders to environmental changes, but their community structures and how they are shaped by environmental conditions have rarely been studied simultaneously. In this study, we conducted an eDNA metabarcoding sequencing combined with multiple statistical methods to simultaneously analyze the phytoplankton and microzooplankton in Liaohe (LH) and Yalujiang (YLJ) estuaries. The major objective was to examine how plankton community structure and assembly mechanism may differ between two estuaries with similar latitudinal position and climate but geographical segregation and differential level of urbanization (more in LH). Clear differences in diversity and composition of phytoplankton and microzooplankton communities between LH and YLJ estuaries were observed. Richness of phytoplankton was significantly higher in LH than YLJ, while richness of microzooplankton was higher in YLJ. The magnitude of intrahabitat variations in phytoplankton communities was significantly stronger than that of microzooplankton. Some phytoplankton and microzooplankton taxa also showed interhabitat differences in their relative abundances. Phytoplankton showed a stronger geographic distance-decay of similarity than microzooplankton, while significant environmental distance-decay of similarity in microzooplankton was found in the less urbanized YLJ estuary. Community assembly of phytoplankton was, based on the neutral community models, driven primarily by stochastic processes, while deterministic processes contributed more for microzooplankton. Furthermore, we detected wider habitat niche breadths and stronger dispersal abilities in phytoplankton than in microzooplankton. These results suggest that passive dispersal shapes the phytoplankton community whereas environmental selection shapes the microzooplankton community. IMPORTANCE Understanding the underlying mechanisms shaping a metacommunity is useful to management for improving the ecosystem function. The research presented in the manuscript mainly tried to address the effects of habitat geography and environmental conditions on the phytoplankton and microzooplankton communities, and the underlying mechanisms of community assembly in temperate estuaries. In order to achieve this purpose, we developed a metabarcoding sequencing method based on 18S rRNA gene. The phytoplankton and microzooplankton communities from two estuaries with similar latitude and climatic conditions but obvious geographical segregation and significant environmental heterogeneity were investigated. The results of our study could lay a solid foundation for ascertaining phytoplankton and microzooplankton communities in estuaries with obvious environmental heterogeneity and geographic segregation and mechanisms underlying community assembly.