Development of a bacteria-based index of biotic integrity (Ba-IBI) for assessing ecological health of the Three Gorges Reservoir in different operation periods

A bacteria-based index of biotic integrity assesses aquatic ecosystems effectively in rewetted long-term dry river channel after water replenishment

Climate-induced droughts exert a significant influence on the connectivity of river systems. It is estimated that about 25% of the world's rivers ran dry before reaching the ocean due to climate change and human activities. Ecological water replenishment is an effective measure for restoring aquatic ecosystems damaged by drought. It is urgently needed to quantitatively assess the aquatic ecosystems in rewetted dry river channels after water replenishment. This study investigated the variations in phytoplankton, zooplankton, benthic macroinvertebrates, and benthic bacterial communities in the rewetted dry river channel of Yongding River after water replenishment. In comparison with the water column communities, the benthic macroinvertebrates were identified as limiting factors for ecological restoration in rewetted dry river channels. In the absence of a certain recovery time for benthic macroinvertebrates, the benthic bacterial-based index of biological integrity, especially calculated based on their intrinsic properties, can properly assess aquatic ecosystems in rewetted dry river channels.

Supervised machine learning improves general applicability of eDNA metabarcoding for reservoir health monitoring

Effective and standardized monitoring methodologies are vital for successful reservoir restoration and management. Environmental DNA (eDNA) metabarcoding sequencing offers a promising alternative for biomonitoring and can overcome many limitations of traditional morphological bioassessment. Recent attempts have even shown that supervised machine learning (SML) can directly infer biotic indices (BI) from eDNA metabarcoding data, bypassing the cumbersome calculation process of BI regardless of the taxonomic assignment of eDNA sequences. However, questions surrounding the general applicability of this taxonomy-free approach to monitoring reservoir health remain unclear, including model stability, feature selection, algorithm choice, and multi-season biomonitoring. Here, we firstly developed a novel biological integrity index (Me-IBI) that integrates multitrophic interactions and environmental information, based on taxonomy-assigned eDNA metabarcoding data. The Me-IBI can better distinguish the actual health status of the Three Gorges Reservoir (TGR) than physicochemical assessments and have a clear response to human activity. Then, taking this reliable Me-IBI as a supervised label, we compared the impact of selecting different numbers of features and SML algorithms on the stability and predictive performance of the model for predicting ecological conditions in multiple seasons using taxonomy-free eDNA metabarcoding data. We discovered that even with a small number of features, different SML algorithms can establish a stable model and obtain excellent predictive performance. Finally, we proposed a four-step strategy for standardized routine biomonitoring using SML tools. Our study firstly explores the general applicability problem of the taxonomy-free eDNA-SML approach and establishes a solid foundation for the large-scale and standardized biomonitoring application.

Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI)

Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.

Microbial community composition in urban riverbank sediments: response to municipal effluents over spatial gradient

Municipal effluents have adverse impacts on the aquatic ecosystem and especially the microbial community. This study described the compositions of sediment bacterial communities in the urban riverbank over the spatial gradient. Sediments were collected from seven sampling sites of the Macha River. The physicochemical parameters of sediment samples were determined. The bacterial communities in sediments were analyzed by 16S rRNA gene sequencing. The results showed that these sites were affected by different types of effluents, leading to regional variations in the bacterial community. The higher microbial richness and biodiversity at SM2 and SD1 sites were correlated with the levels of NH₄⁺-N, organic matter, effective sulphur, electrical conductivity, and total dissolved solids (p < 0.01). Organic matter, total nitrogen, NH₄⁺-N, NO₃-N, pH, and effective sulphur were identified to be important drivers for bacterial community distribution. At the phylum level, Proteobacteria (32.8-71.7%) was predominant in sediments, and at the genus level, Serratia appeared at all sampling sites and accounted for the dominant genus. Sulphate-reducing bacteria, nitrifiers, and denitrifiers were detected and closely related to contaminants. This study expanded our understanding of municipal effluents on microbial communities in riverbank sediments, and also provided valuable information for further exploration of microbial community functions.

Evaluation and comparison of the benthic and microbial indices of biotic integrity for urban lakes based on environmental DNA and its management implications

With the intensification of human disturbance in urban lakes, the loss of eukaryotic biodiversity (macroinvertebrates, etc.) reduces the accuracy of the index of biotic integrity (IBI) assessment. Therefore, how to accurately evaluate the ecological status of urban lakes based on IBI has become an important issue. In this study, 17 sampling sites from four lakes in Wuhan City, China were selected to analyze the composition and diversity characteristics of benthic and microbial communities and their relationship with environmental factors based on eDNA high-throughput sequencing, and compare the application effects of the benthic index of biotic integrity (B-IBI) and the microbial index of biotic integrity (M-IBI). Canonical correspondence analysis showed that the key environmental factors affecting benthic family/genus composition were temperature, conductivity, total phosphorus (TP), and total nitrogen (TN). Redundancy analysis showed that pH, TP, conductivity, and ammonia nitrogen had the greatest impact on microbial phyla/genera. After screening, four and six core metrics were determined from candidate parameters to establish B-IBI and M-IBI. The B-IBI evaluation results showed that healthy, sub-heathy, and poor accounted for 58.8%, 35.3%, and 5.9%, respectively, in the sites. The results of the M-IBI evaluation showed that 29.4% of the sites were healthy, 47.1% were sub-healthy, and 23.5% were common. M-IBI was positively correlated with water quality (r = 0.74, P < 0.001), whereas B-IBI was not. Further results showed that M-IBI was negatively correlated with the relative abundance of bloom-forming cyanobacteria Planktothrix (r = -0.54, P < 0.05). Therefore, M-IBI is more sensitive than B-IBI and can better reflect the actual water pollution status. This study can provide a new perspective for ecological assessment and management of urban lakes strongly disturbed by human activities.

Ecological health evaluation of rivers based on phytoplankton biological integrity index and water quality index on the impact of anthropogenic pollution: A case of Ashi River Basin

Based on the phytoplankton community matrices in the Ashi River Basin (ASRB), Harbin city, we developed an evaluation method using the phytoplankton index of biotic integrity (P-IBI) to evaluate ecological health while investigating the response of P-IBI to anthropogenic activities. We compared the effectiveness of P-IBI with that of the water quality index (WQI) in assessing ecological health. Between April and October 2019, phytoplankton and water samples were collected at 17 sampling sites in the ASRB on a seasonal basis. Our results showed that seven phyla were identified, comprising 137 phytoplankton species. From a pool of 35 candidate indices, five critical ecological indices (Shannon–Wiener index, total biomass, percentage of motile diatoms, percentage of stipitate diatom, and diatom quotient) were selected to evaluate the biological integrity of phytoplankton in the ASRB. The ecological status of the ASRB as measured by the P-IBI and WQI exhibited a similar spatial pattern. It showed a spatial decline in ecological status in accordance with the flow of the river. These results highlighted that P-IBI was a reliable tool to indicate the interaction between habitat conditions and environmental factors in the ASRB. Our findings contribute to the ecological monitoring and protection of rivers impacted by anthropogenic pollution.

Predicting bend-induced heterogeneity in sediment microbial communities by integrating bacteria-based index of biotic integrity and supervised learning algorithms

Prioritizing the relationship between heterogeneity of sediment habitats and river bends is critical when planning and reconstructing urban rivers. However, the exact relationship between ecological heterogeneity and river bends remains ambiguous. Therefore, this research proposed a new approach to quantify and predict bend-induced ecological heterogeneity, incorporating the bacteria-based index of biotic integrity (Ba-IBI), path model, and random forest regression model. The developed Ba-IBI quantified heterogeneity in sediment microbial communities, ranging from low (1.40) to high (3.97). A path model was developed and validated in order to further investigate the relative contributions of environmental factors to the Ba-IBI. The established path model, which was considered acceptable with a CMIN/df = 1.949 < 4, suggested that primary environmental factors affecting the sediment bacterial communities were flow velocity and ammonium concentration in sediment. To further characterize the relationship between environmental factors and the Ba-IBI, a function was constructed using the random forest regression model that predicts the responses of sediment bacterial communities to environmental factors with R² = 0.6126. The proposed approach and prediction tools will provide knowledge to improve natural channel design and post-project evaluations in river restoration projects.

Assessing the effects of cascade dams on river ecological status using multi-species interaction-based index of biotic integrity (Mt-IBI)

Cascade dams have exerted significant effects on river ecosystems. To quantitatively assess dam-induced effects on river ecological status, a novel multi-species interaction-based index of biotic integrity (Mt-IBI) was developed. Benthic microbiota was selected as a bio-indicator for its sensitivity to the environmental disturbance. An environmental DNA metabarcoding tool was used to identify microbiota (bacteria, protozoan, and metazoan). The Mt-IBI was applied to assess the ecological status of the Hanjiang River, a representative dam-affected river in China. Fifteen sampling sites along the Hanjiang River were sampled in June 2018. Seven core metrics were screened from a total of 364 candidate metrics to calculate the value of the Mt-IBI. The Mt-IBI of the Hanjiang River ranged from 1.90 to 6.39, with a mean value of 4.02. The mean values of Mt-IBI at the reservoir and riverine side of dams were 2.11 and 3.81, respectively. The downstream reach without dam constructions had the highest mean Mt-IBI (5.79). Thus, the continuity of the river was strongly related to the Mt-IBI. Structural equation models (SEMs) were further established to identify the dominant environmental variables in the dam-affected river. The SEMs indicated that flow velocity (coefficient 0.749) was the most important determinant of ecological status in the Hanjiang River. Water organic matter also played a vital role in determining the ecological status of the Hanjiang River, and exerted the strongest direct effect (P < 0.001, r = 0.712). The reliability of SEMs was verified by building a support vector regression model (R² = 0.8141). This study can provide new tools for ecological assessment and diagnosis, and provide a new perspective for the management of cascade dams.

Toxic effects of shale gas fracturing flowback fluid on microbial communities in polluted soil

A large amount of shale gas fracturing flowback fluid (FFBF) from the process of shale gas exploitation causes obvious ecological harm to health of soil and water. However, biological hazard of soil microbial populations by fracturing flowback fluid remains rarely reported. In this study, the microbiological compositions were assessed via analyzing diversity of microbial populations. The results showed significant differences between polluted soil by fracturing flowback fluid and unpolluted soil in different pH and temperature conditions. And then, the microbe-index of biological integrity (M-IBI) was used to evaluate the toxicity of the fracturing flowback fluid based on analysis of microbial integrity. The results showed that polluted soil lacks key microbial species known to be beneficial to soil health, including denitrifying bacteria and cellulose-decomposing bacteria, and 35 °C is a critical value for estimating poor and sub-healthy level of damage to microbial integrity by fracturing flowback fluid. Our results provide a valuable reference for the evaluation of soil damage by fracturing flowback fluid.

Developing a statistical-weighted index of biotic integrity for large-river ecological evaluations

The efficiency, accuracy and universality of ecological assessment methods comprise an important foundation for comprehensive assessment and restoration of large river ecological health at the watershed scale. New evaluation metrics and methods are urgently needed to be developed to adapt the characteristics of large rivers, including geographical differences in surface runoff, regional ecological complexity, and seasonal changes. In this study, a bacteria-weighted index of biotic integrity was developed to assess the ecological health of large rivers (lrBW-IBI) based on compositional and functional characteristics of sediment bacterial communities from 33 sections of the lower mainstream of Yangtze River. Five key metrics were determined by range, responsiveness, and redundancy tests. Principal component analysis (PCA), entropy method, criteria importance through intercriteria correlation and random forest were applied to calculate weighted coefficients of key metrics. The optimal lrBW-IBI was observed through the sum of PCA weighted-metrics: the relative abundance of Latescibacteria (0.234), Gemmatimonadaceae (0.149), Nitrospira spp. (0.234), Rhizobiales (0.228), and nitrogenase NifH (0.156). According to PCA based lrBW-IBI, 12.12%, 24.24%, 39.39%, and 24.24% of river sections were labeled excellent, good, moderate, and relatively poor, respectively. The ecological status of the lower mainstream of the Yangtze River did not change significantly across seasons but declined gradually from upstream to downstream. This study provides a new assessment tool for the ecological health of large rivers and highlights the importance of microbial ecological index in river ecology.

Full Implementation of the River Chief System in China: Outcome and Weakness

Despite having explored various modes of water management over the past three decades, the water crisis persists and the Chinese government has been required to revolutionize river management from the top down. The River Chief System (RCS), which evolved from small scale, local efforts to manage rivers starting in 2007, is an innovative system that coordinates between existing ‘fragmented’ river/lake management and pollution control systems, to clearly define the responsibilities of all concerned departments. The system was promoted from an emergent policy to nationwide action in 2016, and ever since, has undergone steady development. We have analyzed recent developments in the system from the perspectives of functional expansion, implementation strategies, legislative processes, and public outreach after the full implementation of the RCS. By collecting data over the past several years, the changes in the water quality of representative watersheds in China were evaluated to assess the outcomes of RCS implementation. Finally, a summary of the weaknesses and outstanding problems of the system is presented, putting forward a multi-channel strategy for the long-term stability and effectiveness of river/lake chiefs, and promoting the RCS as a suitable solution to the collaborative and jurisdictional issues in water management in China.

Effects of hydropower dam construction on sulfur distribution and sulfate-reducing prokaryotes assemblage

River damming is significant for hydropower production, but also alters the ecological conditions, and especially affects the microbial community. Sulfate-reducing prokaryotes (SRPs) make vital contributions to biogeochemical sulfur cycle, but the information on the effects of dam construction on the SRPs assemblage are unclear. Here, a comprehensive survey was conducted by collecting water and sediment samples along horizontal and vertical profiles from six sites at the Xiaowan Reservoir on the Lancang River, China. We used 16S rRNA gene amplicon sequencing and qPCR assay with dsrB gene to study the composition and activity of SRPs. The results indicated that river damming accumulated nutrients in the middle layer of the reservoir, and the impoundment provided an anaerobic and high nutrient available environment, which is beneficial for the survival of SRPs. The abundance and diversity of SRPs in water and sediments at the bottom of the reservoir were higher than those in the other sites. The network analyses revealed a synergistic effect between SRPs and other dominant bacteria in water column, which was more complex than in sediments. Moreover, a relatively higher sulfate reduction activity was found in the middle and lower layers of the water profile according to dsrB gene analysis.

Identifying key environmental factors for enhancing the pollutant removal potential at a river confluence

The confluence area of river networks is a hot spot for pollutant removal. As an essential part of the river ecosystem, sediment bacterial communities played a crucial role in the removal of pollutants. However, how the potential of sediment bacterial communities can be enhanced toward the removal of pollutants remains unclear. Therefore, this study provides a new approach for the identification of key environmental factors that enhance the pollutant removal potential at a river confluence, integrating the bacteria-based index of biotic integrity (Ba-IBI), path model, support vector regression (SVR) model, and sensitivity analysis. The developed Ba-IBI could quantitatively evaluate the differences of both structure and function of bacterial communities before and after the confluence, with a range from 1.52 to 2.78. The flow regime, which was represented by the Froude number, exerted an indirect effect on Ba-IBI mediated through water nutrients and sediment nutrients according to path model results. Sediment nutrients and water nutrients were considered as the main environmental factors that directly affected sediment bacterial communities. A function that could predict the response of sediment bacterial communities to environmental factors in the best possible way was found through SVR modeling, with R² = 0.8357. The results of the sensitivity analysis indicated that the total phosphorus in water and ammonia nitrogen in sediments were key environmental factors for enhancing the pollutant removal potential at the river confluence. The established approach aids the improvement of the bioremediation potential of river confluence area, and might provide a theoretical basis for watershed restoration.

Changes to soil conservation in the Three Gorges Reservoir Area between 1982 and 2015

Soil erosion is a major threat in the Three Gorges Reservoir Area (TGRA) of China. Since 1990, the Chinese government has launched a series of ecological restoration projects to promote soil conservation in the TGRA. To understand the effects of ecological restoration on soil conservation in the TGRA, we used the abrupt change analysis of soil mass from 1982 to 2015 and its drivers; soil mass was obtained with the universal soil loss equation at continental scale. We found that soil conservation and annual rainfall decreased in the TGRA over the study period. Abrupt change points of soil conservation occurred in 1984 and 2007. Soil conservation in the TGRA showed a dramatic decrease before 1984, a slow increase after 1984 as a result of climate, and a rapid increase after 2007 due to an increase in vegetation cover. From 1982 to 2015, climate change played a primary role in soil conservation changes and was more influential than topography and vegetation. However, ecological restoration was an important factor affecting soil conservation in the TGRA, and it needs to be promoted.

The Fish Community Index: A Practical Management Tool for Monitoring and Reporting Estuarine Ecological Condition

Indicators of ecological health based on biological communities, including numerous multimetric indices, are used worldwide to assess and report the condition of aquatic ecosystems such as estuaries. Yet, these tools have rarely been applied to support estuary management in Australia. We present a case study of one such multimetric indicator, the Fish Community Index (FCI), which was developed and applied to quantify the ecological condition of estuaries in southwestern Australia (SWA). We outline the rationale, development, and implementation of the FCI for annual monitoring and reporting of the ecological condition of a highly urbanized estuary, highlighting the key research and management outcomes that it has delivered, and evaluating its potential future applications to support estuary management more broadly, both across Australia and internationally. The FCI is founded upon a conceptually simple and scientifically robust rationale and is sensitive to the ecological stressors that affect many estuaries across the region (e.g., hypoxia, algal blooms). Together with an accompanying annual fish monitoring regime, the FCI provides managers with a consistent, robust basis for quantifying and reporting spatiotemporal changes in estuary condition, with easily comprehensible outputs that facilitate communication with stakeholders, ranging from politicians to the general public. We attribute the successful implementation of this management tool to several characteristics, namely 1) support from a long-term, collaborative partnership between managers and researchers; 2) comprehensive testing and validation of the index prior to implementation; 3) a robust, standardized monitoring regime; and 4) sustained resourcing from managers to implement the index as part of a reporting framework. The FCI has also been applied to other SWA estuaries and could provide a platform for more coordinated assessment and reporting of estuarine condition at the bioregional scale, thereby helping to improve the gap in reporting on the biotic integrity of Australian estuaries. Integr Environ Assess Manag 2019;15:726-738. © 2019 SETAC.