Microbial community day-to-day dynamics during a spring algal bloom event in a tributary of Three Gorges Reservoir

Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems

Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.

Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance

Introduction

In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

Methods

Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

Results and discussion

This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.

How water stability relates with timing, size, and community successions of harmful algal blooms: A case study in the Three Gorges Reservoir

Effective management of Harmful Algal Blooms (HABs) requires understanding factors influencing their occurrence. This study explores these dynamics in the Pengxi River, a tributary of the Three Gorges Reservoir, focusing on nutrient stratification and algal blooms. We hypothesized that nutrient levels in eutrophic waters with stable stratification correlate with HAB magnitude and that disruption of stratification triggers blooms due to nutrient shifts. A 38-day sampling campaign in Gaoyang Lake (April 16-May 23, 2022) revealed that consistent weather between April 26 and May 16 led to a surface density layer, restricting nutrient transfer and causing a bloom with 173.0 μg L-1 Chl-a on May 1. After a heavy rain on May 18, a peak bloom on May 20, dominated by Ceratium hirundinella, showed 533 μg L-1 Chl-a. There was a significant negative correlation between Cyanobacteria and C. hirundinella biomasses (r = -0.296, P < 0.01), highlighting nutrient availability and physical stability's roles in regulating HABs.

Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes

Microcystis, a type of cyanobacteria known for producing microcystins (MCs), is experiencing a global increase in blooms. They have been recently recognized as potential contributors to the widespread of antibiotic resistance genes (ARGs). By reviewing approximately 150 pieces of recent studies, a hypothesis has been formulated suggesting that significant fluctuations in MCs concentrations and microbial community structure during Microcystis blooms could influence the dynamics of waterborne ARGs. Among all MCs, microcystin-LR (MC-LR) is the most widely distributed worldwide, notably abundant in reservoirs during summer. MCs inhibit protein phosphatases or increase reactive oxygen species (ROS), inducing oxidative stresses, enhancing membrane permeability, and causing DNA damage. This further enhances selective pressures and horizontal gene transfer (HGT) chances of ARGs. The mechanisms by which Microcystis regulates ARG dissemination have been systematically organized for the first time, focusing on the secretion of MCs and the alterations of bacterial community structure. However, several knowledge gaps remain, particularly concerning how MCs interfere with the electron transport chain and how Microcystis facilitates HGT of ARGs. Concurrently, the predominance of Microcystis forming the algal microbial aggregates is considered a hotspot for preserving and transferring ARGs. Yet, Microcystis can deplete the nutrients from other taxa within these aggregates, thereby reducing the density of ARG-carrying bacteria. Therefore, further studies are needed to explore the 'symbiotic - competitive' relationships between Microcystis and ARG-hosting bacteria under varied nutrient conditions. Addressing these knowledge gaps is crucial to understand the impacts of the algal aggregates on dynamics of waterborne antibiotic resistome, and underscores the need for effective control of Microcystis to curb the spread of antibiotic resistance. Constructed wetlands and photocatalysis represent advantageous strategies for halting the spread of ARGs from the perspective of Microcystis blooms, as they can effectively control Microcystis and MCs while maintaining the stability of aquatic ecosystem.

Reservoir regulation-induced variations in water level impacts cyanobacterial bloom by the changing physiochemical conditions

Gaining insight into the impact of reservoir regulation on algal blooms is essential for comprehending the dynamic changes and response mechanisms in the reservoir ecosystem. In this study, we conducted a comprehensive field investigation linking physiochemical parameters, and phytoplankton community to different water regimes in the Three Gorges Reservoir. Our aim was to explore the effects of reservoir regulation on the extinction of cyanobacterial blooms. The results showed that during the four regulatory events, the water levels decreased by 2.02-4.33 m, and the average water velocity increased 68 % compared to before. The average total phosphorus and total nitrogen concentrations reduced by up to 20 %, and the cyanobacterial biomass correspondingly declined dramatically, between 66.94 % and 75.17 %. As the change of water level decline increasing, there was a significant increase of algal diversity and a notable decrease of algal cell density. Additionally, a shift in the dominant phytoplankton community from Cyanobacteria to Chlorophyceae was observed. Our analysis indicated that water level fluctuations had a pronounced effect on cyanobacterial extinction, with hydrodynamic changes resulting in a reduction of cyanobacterial biomass. This research underlined the potential for employing hydrodynamic management as a viable strategy to mitigate the adverse ecological impacts of cyanobacterial blooms, providing a solution for reservoir's eco-environmental management.

Assembly mechanism of microbial community under different seasons in Shantou sea area

Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.

Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.

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.

Flow backward alleviated the river algal blooms

Mechanistic understanding and prediction of river algal blooms remain challenging. It is generally believed that these blooms are formed by the slowdown of water dynamics in tributaries due to the support of the main stream. However, few studies have investigated the impact of flow backward caused by the difference in water dynamics between the main stream and tributaries. Here, we focus on the eutrophication issue in the middle-lower reaches of the Han River, which is affected by the Middle Route of the South-to-North Water Diversion Project (SNWDP), the largest inter-basin water transfer project in Asia. We discover that the reversal of the Yangtze River water level could effectively alleviate the occurrence of Han River water blooms. The Yangtze River frequently back flows into the lower reaches of the Han River, with the probability of such events increasing as it nears the confluence (20 km from the Yangtze: 9.5 %, 10 km: 19.0 %, 8 km: 28.6 %). This flow backward carries nutrients that reduce the nitrogen to phosphorus ration (N:P), leading to a shift in the nutrient structure of the Han River. This change is concomitant with a significant decline in algae biomass (Chlorophyll-a = 11.19 µg·L-1 and algae density = 0.41×107 cells·L-1 under natural flow, Chlorophyll-a = 5.19 µg·L-1 and algae density = 0.18×107 cells·L-1 under flow backward), as well as a weakening of the correlation (R) between diatom density and chlorophyll-a concentration, i.e., R = 0.38 (p>0.05) under flow backward conditions versus R = 0.72 (p<0.01) under natural flow conditions. As phosphorus limitation typically suppresses algae growth, the correlation between diatom density and chlorophyll-a concentration can help to reveal the dominance of diatoms, with stronger correlations indicating greater diatom dominance. Consequently, our study provides evidence that the flow backward can alleviate river algal blooms by weakening the growth advantage of diatoms. This study could prove valuable in investigating the eutrophication mechanism within the complex hydrodynamic conditions of rivers. SYNOPSIS: Flow backward caused by the water level difference between the main streams and tributary alleviated the occurrence of river algal blooms in the confluence area.

Ecosystem anthropogenic enrichments enhance Chroococcus abundance and suppress Anabaena during cyanobacterial-dominated spring blooms in the Pengxi River, Three Gorges Reservoir, China

Taxa-specific responses to the increasing anthropogenic eutrophication offer promising insights for mitigating harmful algal blooms (HABs) in freshwaters. The present study evaluated the HABs species dynamics in response to the ecosystem anthropogenic enrichment during cyanobacterial-dominated spring HABs in the Pengxi River, Three Gorges Reservoir, China. Results show significant cyanobacterial dominance with a relative abundance (RA = 76.54 %). The ecosystem enrichments triggered shifts in the HABs community structure from Anabaena to Chroococcus, especially in the culture involving iron (Fe) addition (RA = 66.16 %). While P-alone enrichment caused a dramatic increase in the aggregate cell density (2.45 × 10⁸ cells L^-1), the multiple enrichment (NPFe) led to maximum biomass production (as chl-a = 39.62 ± 2.33 μgL^-1), indicating that nutrient in conjunction with the HABs taxonomic characteristics e.g., tendency to possess high cell pigment contents rather than cell density can potentially determine massive biomass accumulations during HABs. The stimulation of growth as biomass production demonstrated by both P-alone and the multiple enrichments, NPFe indicates that although P exclusive control is feasible in the Pengxi ecosystem, it can only guarantee a short-term reduction in HABs magnitude and duration, thus a lasting HABs mitigation measure must consider a policy recommendation involving multiple nutrient management, especially N and P dual control strategy. The present study would adequately complement the concerted effort in developing a rational predictive framework for freshwater eutrophication management and HABs mitigations in the TGR and elsewhere with similar anthropogenic stressors.

Novel insights in seasonal dynamics and co-existence patterns of phytoplankton and micro-eukaryotes in drinking water reservoir, Northwest China: DNA data and ecological model

Although associations between phytoplankton and micro-eukaryotes have been studied in aquatic ecosystems, there are still knowledge gaps in comprehending their dynamics and interactions in drinking water reservoirs. Here, the seasonal dynamics of phytoplankton and micro-eukaryotic diversities and their co-existence patterns were studied in a drinking water reservoir, Northwest China. The highest phytoplankton diversity was observed in summer, and Chlorella sp. that belongs to Chlorophyta was the most abundant genus. The highest eukaryotic diversity was also detected in summer, and Rimostrombidium sp. that belongs to Ciliophora was the most dominant genus. Mantel test showed that the phytoplankton diversity was significantly correlated with ammonia nitrogen (r = 0.561, p = 0.001) and dissolved organic carbon (r = 0.267, p = 0.017), while the eukaryotic diversity was significantly associated with ammonia nitrogen (r = 0.265, p = 0.034) and temperature (r = 0.208, p = 0.046). PLS-PM (Partial Least Squares Path Modeling) further revealed that nutrients (P < 0.01) significantly affected the phytoplankton diversity, while nutrients (P < 0.01) and temperature (P < 0.01) significantly influenced the eukaryotic diversity. Co-occurrence network displayed the primarily positive interactions (77.66% positive and 22.34% negative) between phytoplankton and micro-eukaryotes. These findings could deepen our understanding of interactions between phytoplankton and micro-eukaryotes and their driving factors under changing aquatic environments of drinking water reservoirs.

Determining Critical Thresholds of Environmental Flow Restoration Based on Planktonic Index of Biotic Integrity (P-IBI): A Case Study in the Typical Tributaries of Poyang Lake

Hydropower construction and climate change have aggravated river hydrological changes, which have reduced the water flow regime in the Ruhe River Basin. The reduced flow of the river seriously affected the water supply of nearby residents and the operation of the river ecosystem. Therefore, in order to alleviate the contradiction between water use for hydropower facilities and environmental water use, the urgent need is to explore the ecological flow-threshold of rivers. This study took the Fuhe River Basin as the research object, and summarized the monitoring data of eight hydrological stations from recent decades. Based on this, we explored the response law of P-IBI and flow, a tool to quickly measure the health of the ecosystem. Through the response relationship between alterations in environmental factors of the river and phytoplankton index of biotic integrity (P-IBI), it was determined that environmental flow was the dominant influencing factor of P-IBI. According to P-IBI, the threshold of environmental discharge in the Fuhe River was limited to 273~826.8 m³/s. This study established a regulatory framework for the river flow of large rivers by constructing P-IBI and determining the critical thresholds of environmental flow by constraining the constitution. These results provide a theoretical basis for better planning and improvement of river ecosystem restoration and river utilization.