The species-area relationship is important for understanding species diversity patterns at spatial scales, but few studies have examined the relationship using environmental DNA (eDNA) techniques. We investigated amphibian diversity on 21 islands of the Zhoushan Archipelago and nearby mainland areas in China using the combination of eDNA metabarcoding and the traditional line transect method (TLTM) and identified the species-area relationship for amphibians on the islands. The mean detection probability of eDNA is 0.54, while the mean detection probability of TLTM is 0.24. The eDNA metabarcoding detected eight amphibian species on the islands and nine species in the mainland areas, compared with seven species on the islands and nine species in the mainland areas that were identified by TLTM. Amphibian richness on the islands increased with island area and habitat diversity. The species-area relationship for amphibians in the archipelago was formulated as the power function (S = 0.47A0.21) or exponential function (S = 2.59 + 2.41 (logA)). Our results suggested that eDNA metabarcoding is more sensitive for the detection of amphibian species. The combined use of eDNA metabarcoding and the traditional line transect method may optimize the survey results for amphibians.

As one of the nine primary non-ferrous metal smelting bases in China, Daye Lake basin was polluted due to diverse human activities. But so far the pollution status and related ecological risks of this region have not been detailly investigated. In current study, pollutants including heavy metals, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in eight sediment samples from Daye Lake were quantified. 18S rRNA gene sequencing was employed to profile the nematode community structure within these sediments. Model organism Caenorhabditis elegans (C. elegans) were further applied for a comprehensive ecological risk assessment of Daye Lake. Notably, Cadmium (Cd) was identified as a key driver of ecological risk, reaching an index of 1287.35. At sample point S4, OCPs particularly p,p\'-DDT, displayed an extreme ecological risk with a value of 23.19. Cephalobidae and Mononchida showed strong sensitivity to pollutant levels, reinforcing their suitability as robust bioindicators. The composite pollutants in sampled sediments caused oxidative stress in C. elegans, with gene Vit-2 and Mtl-1 as sensitive biomarkers. By employing the multiple analysis methods, our data can offer valuable contributions to environmental monitoring and health risk assessment for composite polluted areas.

Monitoring mollusk biodiversity is a great challenge due to their large diversity and broad distribution. Environmental DNA (eDNA) technology is increasingly applied for biodiversity monitoring, but relevant studies on marine mollusks are still limited. Although previous studies have developed several pairs of primers for mollusk eDNA analyses, most of them targeted only a small group of mollusks. In this study, seven primers were designed for the mollusk community and validated and compared with eight pairs of published primers to select the best candidates. After in silico test, MollCOI154 and MollCOI255 primers showed non-specific amplification, and same results were also obtained in published primers (COI204, Sepi, and veneroida). Moll12S100, Moll12S195 and Moll16S primers failed to amplify across all genomic DNA from selected mollusk. Except Moll16S, all developed and two published (unionoida and veneroida) primers were successfully amplified on four eDNA samples from Yangtze River estuary. After annotation of the amplified sequences, MollCOI253 showed higher annotation of the amplification results than the other primers. In conclusion, MollCOI253 had better performance in terms of amplification success and specificity, and can provide technical support for eDNA-based research, which will be beneficial for molluscan biodiversity investigation and conservation.

Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.

Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.

The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.

The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial \"technical tips\". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform\'s effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.

Heat stress and coral diseases are the predominant factors causing the degradation of coral reef ecosystems. Over recent years, Vibrio coralliilyticus was identified as a temperature-dependent pathogen causing tissue lysis in Pocillopora damicornis and one of the primary pathogens causing bleaching and mortality in other corals. Yet current detection techniques for V. coralliilyticus rely primarily on qPCR and ddPCR, which cannot meet the requirements for non-invasive and real-time detection. Herein, we developed an effective electrochemical biosensor modified by an Au-MoS2/rGO (AMG) nanocomposites and a specific capture probe to dynamically detect V. coralliilyticus environment DNA (eDNA) in aquarium experiments, with a lower limit of detection (0.28 fM) for synthetic DNA and a lower limit of quantification (9.8 fg/µL, ∼0.86 copies/µL) for genomic DNA. Its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). Notably, coral tissue started to lyse at only 29 °C when the concentration of V. coralliilyticus increased abruptly to 880 copies/µL, indicating the biosensor could reflect the types of pathogen and health risks of corals under heat stress. Overall, the novel and reliable electrochemical biosensing technology provides an efficient strategy for the on-site monitoring and early warning of coral health in the context of global warming.

Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.

Dispersal of infectious biofilms increases bacterial concentrations in blood. To prevent sepsis, the strength of a dispersant should be limited to allow the immune system to remove dispersed bacteria from blood, preferably without antibiotic administration. Biofilm bacteria are held together by extracellular polymeric substances that can be degraded by dispersants. Currently, comparison of the strength of dispersants is not possible by lack of a suitable comparison parameter. Here, a biofilm dispersal parameter is proposed that accounts for differences in initial biofilm properties, dispersant concentration and exposure time by using PBS as a control and normalizing outcomes with respect to concentration and time. The parameter yielded near-identical values based on dispersant-induced reductions in biomass or biofilm colony-forming-units and appeared strain-dependent across pathogens. The parameter as proposed is largely independent of experimental methods and conditions and suitable for comparing different dispersants with respect to different causative strains in particular types of infection.