Microbial compositions, ecological networks, and metabolomics in sediments of black-odour water in Dongguan, China

Dispersal limitation determines the ecological processes that regulate the seasonal assembly of bacterial communities in a subtropical river

Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems.

High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments

The tailwater from wastewater treatment plants serves as an important water resource in arid regions, alleviating the conflict between supply and demand. However, the effects of different tailwater discharge proportions on microbial community dynamics remain unclear. In this study, we investigated the effects of different tailwater discharge proportions on the water quality and microbial community characteristics of sediments in receiving water bodies under controlled conditions (WF-1, WF-2, WF-3, WF-4, and WF-5, containing 0% tailwater + 100% natural water, 25% tailwater + 75% natural water, 50% tailwater + 50% natural water, 75% tailwater + 25% natural water, and 100% tailwater + 0% natural water, respectively). Microbial co-occurrence networks and structural equation model were used to unveil the relationship between microbial communities and their shaping factors. Results showed that distinct microbial community compositions were found in the sediments with low- (< 50%) and high- (> 50%) proportions of tailwater. Specifically, WCHB1-41 and g_4-29-1, which are involved in organic degradation-related functions, were the key genera in the high-proportion cluster. A total of 21 taxa were more abundant in the low-proportion (< 50%) cluster than that in high-proportion (> 50%). Moreover, higher modularity was observed in the low-proportion. Total phosphorus directly affected while ammonia nitrogen indirectly affected the microbial community structure. Our findings support the distinct heterogeneity of microbial communities driven by tailwater discharge in receiving water bodies, and further confirmed that high-proportion tailwater depletes sensitive microbial communities, which may be avoided through scientific management.

Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan

Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.

A review of the formation conditions and assessment methods of black and odorous water

Black and odorous water is an extreme pollution phenomenon. This article reviews the formation process, formation conditions, and evaluation methods of black and odorous water. The results indicate that N, P, and TOC are the key nutrients inducing black and odorous water while S, Fe, and Mn are key elements forming blackening and odorizing pollutants. In addition, Cyanobacteria, Proteobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and Actinobacteria participate in the biogeochemistry cycles of key elements and play important roles in the blackening and odorizing process of water. The black and odorous thresholds that need further verification are as follows: 1.0 g/L of organic matrix, 2.0-8.0 mg/L of NH3-N, 0.6-1.2 mg/L of TP, 0.05 mg/L of Fe2+, 0.3 mg/L of Mn2+, 1.2-2.0 mg/L of DO, and -50 to 50 mV of the ORP. In order to propose a universal assessment method, it is suggested that NH3-N, DO, COD, BOD, and TP serve as the assessment indicators, and the levels of pollutions are I (not black odor), II (mild black odor), III (moderate black odor), IV (severe black odor), and inferior IV (extremely black odor).

Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China

Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R2 = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.

Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution

Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.

Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses

Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.

Response of microbial interactions in activated sludge to chlortetracycline

Chlortetracycline (CTC) has attracted increasing attention due to its potential environmental risks. However, its effects on bacterial communities and microbial interactions in activated sludge systems remain unclear. To verify these issues, a lab-scale sequencing batch reactor (SBR) exposed to different concentrations of CTC (0, 0.05, 0.5, 1 mg/L) was carried out for 106 days. The results showed that the removal efficiencies of COD, TN, and TP were negatively affected, and the system functions could gradually recover at low CTC concentrations (≤0.05 mg/L), but high CTC concentrations (≥0.5 mg/L) caused irreversible damage. CTC significantly altered bacterial diversity and the overall bacterial community structure, and stimulated the emergence of many taxa with antibiotic resistance. Molecular ecological network analysis showed that low concentrations of CTC increased network complexity and enhanced microbial interactions, while high concentrations of CTC had the opposite effect. Sub-networks analysis of dominant phyla (Bacteriodota, Proteobacteria, and Actionobacteriota) and dominant genera (Propioniciclava, a genus from the family Pleomorphomonadaceae and WCHB1-32) also showed the same pattern. In addition, keystone species identified by Z-P analysis had low relative abundance, but they were important in maintaining the stable performance of the system. In summary, low concentrations of CTC enhanced the complexity and stability of the activated sludge system. While high CTC concentrations destabilized the stability of the overall network and then caused effluent water quality deterioration. This study provides insights into our understanding of response in the bacteria community and their network interactions under tetracycline antibiotics in activated sludge system.

An Analysis of the Colony Structure of Prokaryotes in the Jialing River Waters in Chongqing

At present, research on the influence of human activities (especially urbanization) on the microbial diversity, structural composition, and spatial distribution of rivers is limited. In this paper, to explore the prokaryotic community structure and the relationship between the community and environmental factors in the Jialing River Basin of Chongqing, so as to provide a basis for monitoring microorganisms in the watershed. The V3–V4 region of the 16 S rRNA gene was analyzed by high-throughput sequencing and the microbial community of the waters of the Jialing River was analyzed for the diversity and composition of the prokaryotic community as well as the species difference of four samples and correlations with environmental factors. The main results of this study were as follows: (1) The diversity index showed that there were significant differences in the biodiversity among the four regions. At the genus level, Limnohabitans, unclassified_f_Comamonadaceae, and Hgcl_clade were the main dominant flora with a high abundance and evenness. (2) A Kruskal–Wallis H test was used to analyze the differences of species composition among the communities and the following conclusions were drawn: each group contained a relatively high abundance of Limnohabitans; the Shapingba District had a higher abundance of Limnohabitans, the Hechuan District had a wide range of unclassified_f_Comamonadaceae, and the Beibei District had a higher Hgcl_clade. (3) Through the determination of the physical and chemical indicators of the water—namely, total nitrogen, total phosphorus, chemical oxygen demand, chlorophyll A, and an analysis by an RDA diagram, the results demonstrated that the distribution of microbial colonies was significantly affected by the environmental factors of the water. Chemical oxygen demand and ammonia nitrogen had a significant influence on the distribution of the colonies. Different biological colonies were also affected by different environmental factors.