Reduction of bacterial integrity associated with dam construction: A quantitative assessment using an index of biotic integrity improved by stability analysis

From disruption to adaptation: Response of phytoplankton communities in representative impounded lakes to China's South-to-North Water Diversion Project

Impounded lakes are often interconnected in large-scale water diversion projects to form a coordinated system for water allocation and regulation. The alternating runoff and transferred water can significantly impact local ecosystems, which are initially reflected in the sensitive phytoplankton. Nonetheless, limited information is available on the temporal dynamics and assembly patterns of phytoplankton community in impounded lakes responding to continuous and periodic water diversion. Herein, a long-term monitoring from 2013 to 2020 were conducted to systematically investigate the response of phytoplankton community, including its characteristics, stability, and the ecological processes governing community assembly, in representative impounded lakes to the South-to-North Water Diversion Project (SNWDP) in China. In the initial stage of the SNWDP, the phytoplankton diversity indices experienced a decrease during both non-water diversion periods (8.5 %∼21.2 %) and water diversion periods (5.6 %∼12.2 %), implying a disruption in the aquatic ecosystem. But the regular delivery of high-quality water from the Yangtze River gradually increased phytoplankton diversity and mediated ecological assembly processes shifting from stochastic to deterministic. Meanwhile, reduced nutrients restricted the growth of phytoplankton, pushing species to interact more closely to maintain the functionality and stability of the co-occurrence network. The partial least squares path model revealed that ecological process (path coefficient = 0.525, p < 0.01) and interspecies interactions in networks (path coefficient = -0.806, p < 0.01) jointly influenced the keystone and dominant species, ultimately resulting in an improvement in stability (path coefficient = 0.878, p < 0.01). Overall, the phytoplankton communities experienced an evolutionary process from short-term disruption to long-term adaptation, demonstrating resilience and adaptability in response to the challenges posed by the SNWDP. This study revealed the response and adaptation mechanism of phytoplankton communities in impounded lakes to water diversion projects, which is helpful for maintaining the lake ecological health and formulating rational water management strategies.

Digitalizing river aquatic ecosystems

Traditional river health assessment relies on limited water quality indices and representative organism activity, but does not comprehensively obtain biotic and abiotic information of the ecosystem. Here, we propose a new approach to evaluate the ecological and health risks of river aquatic ecosystems. First, detailed physicochemical and biological characterization of a river ecosystem can be obtained through pollutant determination (especially emerging pollutants) and DNA/RNA sequencing. Second, supervised machine learning can be applied to perform classification analysis of characterization data and ascertain river ecosystem ecology and health. Our proposed methodology transforms river ecosystem health assessment and can be applied in river management.

Decoupling the heterogeneity of sediment microbial communities along the urbanization gradients: A Bayesian-based approach

Comprehending the response of microbial communities in rivers along urbanization gradients to hydrologic characteristics and pollution sources is critical for effective watershed management. However, the effects of complex factors on riverine microbial communities remain poorly understood. Thus, we established a bacteria-based index of biotic integrity (Ba-IBI) to evaluate the microbial community heterogeneity of rivers along an urbanization gradient. To examine the response of Ba-IBI to multiple stressors, we employed a Bayesian network based on structural equation modeling (SEM-BN) and revealed the key control factors influencing Ba-IBI at different levels of urbanization. Our findings highlight that waterborne nutrients have the most significant direct impact on Ba-IBI (r = -0.563), with a particular emphasis on ammonia nitrogen, which emerged as the primary driver of microbial community heterogeneity in the Liuyang River basin. In addition, our study confirmed the substantial adverse effects of urbanization on river ecology, as urban land use had the greatest indirect effect on Ba-IBI (r = -0.460). Specifically, the discharge load from wastewater treatment plants (WWTP) was found to significantly negatively affect the Ba-IBI of the entire watershed. In the low urbanized watersheds, rice cultivation (RC) and concentrated animal feeding operations (CAFO) are key control factors, and an increase in their emissions can lead to a sharp decrease in Ba-IBI. In moderately urbanized watersheds, the Ba-IBI tended to decrease as the level of RC emissions increased, while in those with moderate RC emissions, an increase in point source emissions mitigated the negative impact of RC on Ba-IBI. In highly urbanized watersheds, Ba-IBI was not sensitive to changes in stressors. Overall, our study presents a novel approach by integrating Ba-IBI with multi-scenario analysis tools to assess the effects of multiple stressors on microbial communities in river sediments, providing valuable insights for more refined environmental decision-making.

Development and testing of a planktonic index of biotic integrity (P-IBI) for Lake Fuxian, China

Lake Fuxian has the largest reserves of high-quality water resources in China, and understanding its ecological health status is the basis of its environmental protection. Based on a seasonal field investigation of the plankton community, we established a planktonic index of biotic integrity (P-IBI) evaluation system to assess the lake's ecosystem health. The biological integrity of Lake Fuxian was relatively good during winter and spring, but gradually deteriorated from summer to autumn. Areas with poor biological integrity were mainly distributed near tourist attractions along the lake's west coast. Redundancy analysis (RDA) was performed to explore the relationships between the P-IBI, its selected indicators, and the environmental variables. Water temperature (WT), pH, ammonia nitrogen (NH3-N), and dissolved oxygen (DO) significantly influenced the P-IBI and its selected indicators. NH3-N and DO were significantly positively correlated with the P-IBI, indicating that it could be used as a water quality indicator to indirectly reflect lake biological integrity. We demonstrated that the P-IBI can effectively reflect temporal and spatial variations of biological integrity and could be used as a potential tool to evaluate Lake Fuxian ecosystem health.

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.

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.

Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship

Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.

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.

Determination of the direct and indirect effects of bend on the urban river ecological heterogeneity

The ecological heterogeneity created by river bends benefits the diversity of microorganisms, which is vital for the pollutant degradation and overall river health. However, quantitative tools capable of determining the interactions among different trophic levels and species are lacking, and research regarding ecological heterogeneity has been limited to a few species. By integrating the multi-species-based index of biotic integrity (Mt-IBI) and the structure equation model (SEM), an interactions-based prediction modeling framework was established. Based on DNA metabarcoding, a multi-species (i.e., bacteria, protozoans, and metazoans) based index of biotic integrity including 309 candidate metrics was developed. After a three-step screening process, eight core metrics were obtained to assess the ecological heterogeneity, quantitatively. The Mt-IBI value, which ranged from 2.08 to 7.17, was calculated as the sum of each single core metric value. The Mt-IBI revealed that the ecological heterogeneity of concave banks was higher than other sites. According to the result of the SEM, D₉₀ was the controlling factor (r = -0.779) of the ecological heterogeneity under the influence of the river bends. The bend-induced redistribution of sediment particle further influenced the concentrations of carbon, nitrogen, and sulphur. The nitrogen group (r = 0.668) also played an essential role in determining the ecological heterogeneity, follow by carbon group (r = 0.455). Furthermore, the alteration of niches would make a difference on the ecological heterogeneity. This multi-species interactions-based prediction modeling framework proposed a novel method to quantify ecological heterogeneity and provided insight into the enhancement of ecological heterogeneity in river bends.

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.

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.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

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.