eDNA biomonitoring revealed the ecological effects of water diversion projects between Yangtze River and Tai Lake

Assembly mechanism and stability of zooplankton communities affected by China's south-to-north water diversion project

Water diversion can effectively alleviate water resource shortages and improve water environmental conditions, while also causing unknown ecological consequences, in particular, the assembly mechanism of zooplankton communities in the affected areas will become more complex after long-term water transfer. Taking Nansi Lake, the second largest impounded lake along the eastern route of China's South to North Water Diversion Project (SNWDP), as an example, the composition and diversity of zooplankton communities in the lake area and estuaries during the water diversion period (WDP) and non-water diversion period (NWDP) were studied. The potential assembly process of zooplankton communities was further explored, and the stability of communities in different regions during different periods was compared. The related results indicated that the changes in water quality conditions induced by water diversion had a relatively weak impact on the zooplankton communities. In the assembly mechanism of zooplankton communities, stochastic process played a more important role during both WDP or NWDP, and the proportion of deterministic process was relatively higher during NWDP, which may be related to the greater role of total nitrogen (TN) in the assembly of the zooplankton communities. The network analysis and cohesion calculation results showed that the stability of the zooplankton communities in the lake area sites was higher than that in the estuary sites, and the stability during NWDP was higher than that during WDP. In sum, the stability of zooplankton communities displayed a degree of change affected by water diversion activities, but the community assembly was not significantly influenced by the water quality fluctuations after about relatively long-term water diversion. This study provides an in-depth understanding of the ecological effects of water diversion on the biological communities in the affected lake, which is beneficial to the management and regulation of long-term water diversion projects.

Effects of water replenishment on lake water quality and trophic status: An 11-year study in cold and arid regions

Water replenishment is an important measure for maintaining and improving the aquatic environmental quality of lakes. The problems of water quality deterioration and water shortage can be alleviated by introducing water of higher quality. However, the mechanism of water replenishment in the improvement of the water quality and trophic status of lakes remains unclear. This study investigated water replenishment in Wuliangsuhai Lake (WLSHL) from 2011 to 2021 by collecting seasonal water samples and conducting laboratory analyses. Water replenishment was found to be capable of significantly improving lake water quality and alleviating eutrophication. It is worth noting that single long-term water replenishment measures have limitations in improving the water quality and trophic status. The whole process was divided into three stages according to the water quality and trophic status, namely the buffer period, decline period, and stable period. During the buffer period, the water quality and trophic status showed only slight improvement because of the small amount of water replenishment and the low proportion of higher-quality water from the Yellow River. In the decline period, with increasing water replenishment, the proportion of higher-quality water from the Yellow River gradually increased, leading to the most significant and stable degree of improvement. In the stable period, increases in the amount of water replenishment had little effect on improving the water quality and trophic status, which is attributable to the balance between internal pollutants (lake water-sediment), and the balance between internal-external pollutants (lake water-irrigation return flow + Yellow River water). On the premise of stable water quality, with eutrophication control as the management goal, the optimal water replenishment would be approximately 10.58 ×108 m3. Further necessary measures for solving aquatic environmental problems include the combination of sediment dredging, optimization of the water replenishment route, and implementation of quality management in water replenishment.

Enhancing amphibian biomonitoring through eDNA metabarcoding

Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.

The dynamic changes in phytoplankton and environmental factors within Dongping Lake (China) before and after the South-to-North Water Diversion Project

Dongping Lake is one of the most important regulation and storage lakes along the eastern route of the South-to-North Water Diversion Project in China, the water quality condition of which directly influences the safety of water diverting, because it serves as a Yangtze River water redistribution control point. However, the changes in algae, and in environmental factors affecting their community structures, before and after the water diversion project are rarely reported. In this study, the temporal variations of phytoplankton abundance were examined based on monthly samples collected at three stations from May 2010 to April 2022. The total abundance of algae greatly decreased after the water diversion project was implemented, with a relatively stable biodiversity and evenness before and after the water translocation. Multiple statistical methods were used together with the water quality indices (WQIs) and the nutrient status index (TSIM) to evaluate overall water condition and analyse relationships among environmental factors. The WQIs demonstrated a general "Good" water quality with a seasonal differentiation, and that water conditions during water transfer periods were better than during non-water transfer periods, which may be ascribed to the improved hydraulic conditions and purified water environment during water transfer periods. Redundancy analysis showed that water temperature, ammonia nitrogen, water transparency, and total phosphorus were the most important environmental factors, with relatively decreased contribution rates towards phytoplankton communities after the water translocation. Importantly, some dominant phytoplankton genera of Chlorophyta, Bacillariophyceae, and Cyanophyceae were similarly affected by water transparency, and nitrogen and phosphorus nutrients in summer after the water translocation. These research findings helped us gain a comprehensive understanding of the changing patterns of water quality and microalgae and their relationships before and after the water diversion project, providing a guidance for future lake management in regulating hydraulic conditions and improving water quality of Dongping Lake.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

Ecological water diversion activity changes the fate of carbon in a eutrophic lake

Lake eutrophication mitigation measures have been implemented by ecological water diversion, however, the responses of carbon cycle to the human-derived hydrologic process still remains unclear. With a famous river-to-lake water diversion activity at eutrophic Lake Taihu, we attempted to fill the knowledge gap with integrative field measurements (2011-2017) of gas carbon (CO2 and CH4) flux, including CO2-equivalent, and dissolved carbon (DOC and DIC) at water-receiving zone and reference zone. Overall, results showed the artificial water diversion activity increased gas carbon emissions. At water-receiving zone, total gas carbon (expressed as CO2-equivalent) emissions increased significantly due to the occurring of water diversion, with CO2 flux increasing from 9.31 ± 16.28 to 18.16 ± 12.96 mmol C m-2 d-1. Meanwhile, CH4 emissions at water-receiving zone (0.06 ± 0.05 mmol C m-2 d-1) was double of that at reference zone. Water diversion decreased DOC but increased DIC especially at inflowing river mouth. Temporal variability of carbon emissions and dissolved carbon were linked to water temperature, chlorophyll a, and nutrient, but less or negligible dependency on these environment variables were found with diversion occurring. Water diversion may increase gas carbon production via stimulating DOC mineralization with nutrient enrichment, which potentially contribute to increasing carbon emissions and decreasing DOC at the same time and the significant correlation between CO2 flux and CH4 flux. Our study provided new insights into carbon biogeochemical processes, which may help to predict carbon fate under hydrologic changes of lakes.

Integrating impacts of climate change on aquatic environments in inter-basin water regulation: Establishing a critical threshold for best management practices

Inter-basin water diversion (IBWD) is a viable strategy to tackle water scarcity and quality degradation due to climate change and increasing water demand in headwaters regions. Nevertheless, the capacity of IBWD to mitigate the impacts of climate change on water quality has rarely been quantified, and the underlying processes are not well understood. Therefore, this study aims to elucidate how the IBWD manipulated total phosphorus (TP) loading dilution and conveying patterns under climate change and determine a critical threshold for the quantity of water entering downstream reservoirs (WIN) for operational scheduling. To resolve this issue, climate-driven hydrologic variability over a 60-year period was derived utilizing the least square fitting approach. Subsequently, six scenarios evaluating the response of in-lake TP concentrations (TPL) to increased temperatures and IBWDs of 50 %, 100 %, and 150 % from the baseline water volume in 2030 and 2050 were studied by employing a calibrated hydrological-water quality model (SWAT-YRWQM). In the next stage, three datasets derived from mathematical statistics based on the observed data, the Vollenweider formula, and modeled projections were integrated to formulate best management practices. The results revealed that elevated air temperatures would lead to reduced annual catchment runoff but increased IBWD. Additionally, our study quantified the IBWD potential for mitigating water quality degradation, indicating the adverse effects of climate change on TPL would be weakened by 4.2-14.4 %. A critical threshold for WIN was also quantified at 617 million m3, maintaining WIN at or near 617 million m3 through optimized operational scheduling of IBWD could effectively restrict external inflow TP loading to lower levels. This study clearly illustrates the intricate interactive effects of climate change and IBWD on aquatic environments. The methodology elucidated in this study for determining the critical threshold of WIN could be applied in water management for analogous watershed-receiving waterbody systems.

Trade-offs and synergies among ecosystem services in Inland River Basins under the influence of ecological water transfer project: A case study on the Tarim River basin

Ecosystem services (ESs) are the largest benefits that humans derive directly or indirectly from ecosystems. Inland river basins in arid zones have a variety of key ecosystem functions. At present, inland river basins are experiencing a decline in ESs, such as shrinking lakes, land degradation, and rapid biodiversity loss. In order to address these problems, several ecological restoration projects (ERPs) have been implemented. Therefore, this study selected the Tarim River Basin (TRB), which is highly affected by the ecological water transfer project (EWTP), as the study area, and quantified the differences in ESs caused by the implementation of the EWTP through different scenarios of simulation, and discussed the impact of the EWTP in changing the ESs of the basin. Compared to the pre-EWTP period (1990-1999), the major ESs within the basin showed varying degrees of improvement. Water yield increased by 18 %, carbon sequestration increased by 2 %, wind prevention and sand fixation increased by 13 %, habitat quality increased by 8 %, and food production increased by 35 %. EWTP has shown positive impacts by directly or indirectly affecting runoff, vegetation, evapotranspiration, and landscape patterns, which in turn improves the comprehensive benefits of ESs in the TRB. The implementation of EWTP plays an important role in restoring ESs in inland river basins, and this study provides a key reference for the restoration of ESs in inland river basins in arid zones.

Deep-reinforcement-learning-based water diversion strategy

Water diversion is a common strategy to enhance water quality in eutrophic lakes by increasing available water resources and accelerating nutrient circulation. Its effectiveness depends on changes in the source water and lake conditions. However, the challenge of optimizing water diversion remains because it is difficult to simultaneously improve lake water quality and minimize the amount of diverted water. Here, we propose a new approach called dynamic water diversion optimization (DWDO), which combines a comprehensive water quality model with a deep reinforcement learning algorithm. We applied DWDO to a region of Lake Dianchi, the largest eutrophic freshwater lake in China and validated it. Our results demonstrate that DWDO significantly reduced total nitrogen and total phosphorus concentrations in the lake by 7% and 6%, respectively, compared to previous operations. Additionally, annual water diversion decreased by an impressive 75%. Through interpretable machine learning, we identified the impact of meteorological indicators and the water quality of both the source water and the lake on optimal water diversion. We found that a single input variable could either increase or decrease water diversion, depending on its specific value, while multiple factors collectively influenced real-time adjustment of water diversion. Moreover, using well-designed hyperparameters, DWDO proved robust under different uncertainties in model parameters. The training time of the model is theoretically shorter than traditional simulation-optimization algorithms, highlighting its potential to support more effective decision-making in water quality management.

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.

Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects

Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.

Exploring invertebrate indicators of ecosystem health by focusing on the flow transitional zones in a large, shallow eutrophic lake

The river-lake transitional zone provides a unique environment for the biological community and can reduce pollution inputs in lake ecosystems from their catchments. To explore environmental conditions with high purification potential in Lake Taihu and indicator species, we examined the river-to-lake changes in water and sediment quality and benthic invertebrate communities in the transitional zone of four regions. The spatial variations in the environment and invertebrate community observed in this study followed the previously reported patterns in Taihu; the northern and western regions were characterized by higher nutrient concentrations in water, higher heavy metal concentrations in sediment, and higher total invertebrate density and biomass dominated by pollution-tolerant oligochaetes and chironomids. Although nutrient concentrations were low and transparency was high in the eastern region, the taxon richness was the lowest there, which disagreed with the previous findings and might be due to a poor cover of macrophytes in this study. The river-to-lake change was large in the southern region for water quality and the invertebrate community. Water circulation induced by strong wind-wave actions in the lake sites of the southern region is assumed to have promoted photosynthetic and nutrient uptake activities and favored invertebrates that require well-aerated conditions such as polychaetes and burrowing crustaceans. Invertebrates usually adapted to brackish and saline environments are suggested to be indicators of a well-circulated environment with active biogeochemical processes and a less eutrophic state in Taihu, and wind-wave actions are key to maintaining such a community and natural purifying processes.

Shift of phytoplankton assemblages in a temperate lake located on the eastern route of the South-to-North Water Diversion Project

There remains no consensus on the effects of changes in the environment factors under the action of water diversions on phytoplankton communities. Herein the changing rules applying to phytoplankton communities subject to water diversion were unveiled based on long-term (2011-2021) time-series observations on Luoma Lake, located on the eastern route of the South-to-North Water Diversion Project. We found that nitrogen decreased and then increased, while phosphorus increased after operation of the water transfer project. Algal density and diversity were not affected by water diversion, while the duration of high algal density was shorter after water diversion. Phytoplankton composition had dramatic differences before and after water transfer. The phytoplankton communities exhibited greater fragility when they first experienced a human-mediated disturbance, and then they gradually adapted to more interferences and acquired stronger stability. We furthermore found the niche of Cyanobacteria narrowed while that of Euglenozoa widened under the pressure of water diversion. In addition to WT and DO, the main environmental factor before water diversion was NH₄-N, whereas the effect of NO₃-N and TN on phytoplankton communities increased after water diversion. These findings fill the knowledge gap as to the consequence of water diversion on water environments and phytoplankton communities.

Abundance trade-offs and dominant taxa maintain the stability of the bacterioplankton community underlying Microcystis blooms

Microcystis blooms are an intractable global environmental problem that pollute water and compromise ecosystem functioning. Closed-lake management practices keep lakes free of sewage and harmful algae invasions and have succeeded in controlling local Microcystis blooms; however, there is little understanding of how the bacterioplankton communities associated with Microcystis have changed. Here, based on metagenomic sequencing, the phyla, genera, functional genes and metabolic functions of the bacterioplankton communities were compared between open lakes (underlying Microcystis blooms) and closed lakes (no Microcystis blooms). Water properties and zooplankton density were investigated and measured as factors influencing blooms. The results showed that (1) the water quality of closed lakes was improved, and the nitrogen and phosphorus concentrations were significantly reduced. (2) The stability of open vs. closed-managed lakes differed notably at the species and genus levels (p < 0.01), but no significant variations were identified at the phylum and functional genes levels (p > 0.05). (3) The relative abundance of Microcystis (Cyanobacteria) increased dramatically in the open lakes (proportions from 1.44 to 41.76%), whereas the relative abundance of several other dominant genera of Cyanobacteria experienced a trade-off and decreased with increasing Microcystis relative abundance. (4) The main functions of the bacterioplankton communities were primarily related to dominant genera of Proteobacteria and had no significant relationship with Microcystis. Overall, the closed-lake management practices significantly reduced nutrients and prevented Microcystis blooms, but the taxonomic and functional structures of bacterioplankton communities remained stable overall.

Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China

The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project.

Environmental DNA metabarcoding revealed the impacts of anthropogenic activities on phytoplankton diversity in Dianchi Lake and its three inflow rivers

Phytoplankton diversity is closely related to environmental variables and has been widely used in ecological health assessment of rivers and lakes. Combining advantages of DNA-based identification and high-throughput sequencing technology, environmental DNA (eDNA) metabarcoding permits a new measurement for biodiversity monitoring in aquatic ecosystems. However, it had rarely been used to explore the variability and similarity of phytoplankton diversity between lake and its inflow rivers and the effects of environmental variables on phytoplankton. This study utilized eDNA metabarcoding to investigate the spatial distribution of phytoplankton and the impacts of environmental variables on the phytoplankton diversity in Dianchi Lake (one of the most polluted urban lakes in China) and its main inflow rivers (Panlong River, Baoxiang River, and Chai River). A total of 243 distinct phytoplankton taxa were detected, covering 9 phyla, 30 classes, 84 orders, and 132 families, and the taxonomic richness of rivers was higher than that of Dianchi Lake. Distinct biodiversity patterns (e.g., community structure, dominant taxon, ɑ-diversity) were exhibited among Dianchi Lake and its three inflow rivers, but similar biodiversity patterns were also observed in Dianchi Lake and the estuarine sites. The patterns of phytoplankton diversity were closely related to environmental variables, which were associated with pollution sources from different anthropogenic activities (e.g., urbanization, water diversion, industrial and agricultural activities). The primary environmental variables correlated with phytoplankton diversity varied in different habitats. The total phosphorus (TP) and chemical oxygen demand (COD) positively correlated with the phytoplankton community structures in Dianchi Lake, whereas negatively correlated in Panlong River and Baoxiang River. The total nitrogen (TN) positively correlated with the phytoplankton community structures in Baoxiang River and Chai River but negatively correlated in Dianchi Lake. Overall, this study provides insights on the phytoplankton diversity monitoring and the conservation of its diversity and healthy management of Dianchi Lake.

Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa

The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.

Inter-basin water diversion homogenizes microbial communities mainly through stochastic assembly processes

Inter-basin water transfer is an effective manner to achieve the optimal allocation of water resources, while accompanied by some ecological effects. The responses of microorganisms to water diversion and the ecological processes in regulating the community assembly are still unclear. Taking the eastern route of South-to-North Water Diversion Project as the study area, we investigated the microbial community patterns and the underlying assemblage processes in habitats with different hydrological connectivity, including isolated lakes, connected lakes and man-made canal. The results showed that microbial communities in the canal had higher diversity, lower dissimilarity, weaker compositional variation, and stronger co-occurrence patterns compared with that in the connected and isolated lakes. These findings suggested that the increase of connectivity among natural aquatic habitats due to water diversion can homogenize microbial communities and reduce microbial heterogeneity. The neutral and null models demonstrated the importance of stochastic processes in shaping microbial community assembly. Dispersal limitation and variable selection were the predominant mechanisms structuring microbial communities in the isolated lakes. Due to the homogenized environmental condition and the enhanced hydrologic connectivity in the canal and the connected lakes, microbial communities had higher dispersal capability and ecological drift occurred more frequently in these lotic habitats. The variations in microbial community structure were mainly driven by biotic ecological succession than abiotic factors, with positive and negative cohesion explained 63% and 25% of variability, respectively. Six taxa were considered as the potential introduced microorganisms, which may favor the nutrient biogeochemical cycling and the organic matter degradation, but may also bring ecological risks. Overall, this study provides a deeper understanding of the ecological consequences of inter-basin water diversion, and helps the regulation and management of these projects.

Environmental DNA metabarcoding reveals the impact of different land use on multitrophic biodiversity in riverine systems

Human-induced changes in land use drive an alarming decline in river biodiversity and related ecosystem services worldwide. However, how different land use shapes aquatic multitrophic communities is still not well understood. Here, we used the biodiversity dataset from bacteria to fish captured by the environmental DNA (eDNA) approach in the four riverine systems with spatially different land use (i.e., Slightly disturbed group, Upstream disturbed group, Downstream disturbed group, and Strongly disturbed group) to reveal the changes in multitrophic biodiversity in relation to human land use. Firstly, our data showed that spatially different land use determined the pollutant loads of the riverine systems, most pollutants (e.g., TN and NH₃-N) had significant differences among the four riverine systems. Secondly, taxonomic α diversity across multitrophic levels did not necessarily change significantly, yet the change in community structure can be considered as a more sensitive indicator to reflect different land use, because different land use shaped the unique structure of multitrophic communities, and the dissimilarity of community structure was closely associated with land use gradient (e.g., positive relationships in the Slightly disturbed group, negative relationships in the Strongly disturbed group). Thirdly, different land use induced the shifts of key taxa, resulting in the variation of community structure and the change of co-occurrence network. Overall, these findings suggest that spatially different land use plays a critical role in shaping aquatic multitrophic communities, and an in-depth understanding of the interdependences between biodiversity and land use is a critical prerequisite for formulating river management strategies.

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

Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO₃^--N, algal spatial differentiation with TN, and macroinvertebrate and fish with NH₄⁺-N. Further partial least-squares path model confirmed more important effect of environmental variables on the relative abundance of bacteria and algae, while macroinvertebrate and fish communities were directly driven by the algae-mediated pathway in the food web. Our study highlighted the necessity of integrated consideration of multitrophic biodiversity for riverine pollution management, and emphasized the importance of controlling nitrogen inputs targeting a healthy ecosystem.

Environmental DNA Biomonitoring Reveals the Interactive Effects of Dams and Nutrient Enrichment on Aquatic Multitrophic Communities

Dam construction and nutrient enrichment are two pervasive stressors in rivers worldwide, which trigger a sharp decline in biodiversity and ecosystem services. However, the interactive effects of both stressors on multitrophic taxonomic groups remain largely unclear. Here, we used the multitrophic datasets captured by the environmental DNA (eDNA) approach to reveal the interactions between dams and nutrient enrichment on aquatic communities from the aspects of taxonomic α diversity, β diversity, and food webs. First, our data showed that dams and nutrient enrichment jointly shaped a unique spatial pattern of aquatic communities across the four river systems, and the dissimilarity of community structure significantly declined (i.e., structural homogenization) under both stressors. Second, dams and nutrients together explained 40-50% of the variations in aquatic communities, and dams had a stronger impact on fish, aquatic insects, and bacteria, yet nutrients had a stronger power to drive protozoa, fungi, and eukaryotic algae. Finally, we found that additive, synergistic, and antagonistic interactions of dams and nutrient enrichment were common and coexisted in river systems and led to significantly simplified aquatic food webs, with decreases in modularity (synergistic) and robustness (additive) and an increase in coherence (synergistic). Overall, our study highlights that eDNA-based datasets can provide multitrophic perspectives for fostering the understanding of the interactive effects of multiple stressors on rivers.

Patterns of microbial communities and their relationships with water quality in a large-scale water transfer system

Revealing the patterns and their mechanisms of microbial community in water transfer projects, especially in inter-basin water transfer projects, is the premise of biohazard warning, water quality monitoring and sustainable management of water resources. Using a river and impounded lakes from the eastern route of South-to-North Water Transfer project as a model system, we studied the diversity and assembly patterns of bacterial communities in artificially connected ecosystems and their influencing factors. Our results showed that water quality improved during the water transfer period (WTP). Further, the latitudinal pattern of bacterioplankton was reversed, which was mainly due to the change of evenness caused by water transfer and had no significant correlation with water quality parameters. Importantly, the spatial heterogeneity of the bacterial communities decreased during the WTP, and the differences in the communities between the impounded lakes and river was more significant in the non-water transfer period (NWTP) than in the WTP, which was the result of water transfer and water quality. Overall, bacterial community was largely shaped by stochastic processes. The bacterial communities had a higher migration rate during the WTP than during the NWTP. We believe that the water transfer increased the risk of biological homogenization while improving water quality. Combined, our work systematically discusses the microbial community pattern and mechanism in the inter-basin water transfer project, providing theoretical support for inter-basin water transfer project planning management and ecological environment protection.

Phytoplankton community variation and ecological health assessment for impounded lakes along the eastern route of China's South-to-North Water Diversion Project

Interbasin water diversion projects have been proven to effectively alleviate water resource shortages in areas along water diversion lines, but few studies have focused on ecological health in impounded lakes compared with research on water quality and pollutants. Herein, monitoring data were collected during the nonwater diversion period (NWDP) and the water diversion period (WDP) from 2018 to 2019, and the index of biological integrity (IBI) method based on phytoplankton communities was used to evaluate the ecological health of the impounded lakes (Nansi Lake and Dongping Lake) along the eastern route of the South-to-North Water Diversion Project. The results demonstrated that water diversion improved the water quality of the impounded lakes during the WDP, especially total nitrogen and ammonia nitrogen. Meanwhile, the water diversion affected the phytoplankton community structure and diversity, and network analysis further revealed water diversion could be beneficial to the ecological health of impounded lakes. Furthermore, the P-IBI showed that the overall ecological health assessment was "good" during the WDP. Water diversion substantially improved the ecological health status and stability of the impounded lakes during the dry season. Finally, the direct correlations between the water quality parameters and the P-IBI were weak, and water quality parameters could indirectly affect the P-IBI by changing the phytoplankton community structure. These findings will enhance our understanding of the ecological health of the impounded lakes of the South-to-North Water Diversion Project. Furthermore, this study will provide a reference to support the ecosystem security of impounded lakes in other large water diversion projects.

DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems

Simple Summary

Environmental DNA metabarcoding (eDNA) has strong potential in the assessment of biodiversity in aquatic ecosystems. The incompleteness of DNA barcode reference libraries represents a current limit to unveiling the whole biodiversity of an aquatic ecosystem. Therefore, barcode gap analyses at species level are of great significance, in particular at local/regional level, for the advancement of eDNA metabarcoding application to aquatic ecosystems surveillance and future biodiversity assessment.

Abstract

The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21–39.68%, 60.12–65.19% for the 16S marker gene, and 72.44–80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring.