Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China

Differences of bacterioplankton communities between the source and upstream regions of the Yangtze River: microbial structure, co-occurrence pattern, and environmental influencing factors

The source area of the Yangtze River is located in the hinterland of the Qinghai-Tibet Plateau, which is known as the "Earth's third pole." It is the water conservation area and the natural barrier of the ecosystem of the Yangtze River basin. It is also the most sensitive area of the natural ecosystem, and the ecological environment is very fragile. Microorganisms play key roles in the biogeochemical processes of water. In this paper, the bacterioplankton communities in the source and upstream regions of the Yangtze River were studied based on 16S rRNA high-throughput sequencing, and their environmental influencing factors were further analyzed. Results showed that the upstream region had higher richness and diversity than the source region. The predominant bacterial phyla in the source and upstream regions were Proteobacteria, Firmicutes, and Actinobacteriota. The bacterial phyla associated with municipal pollution and opportunistic pathogen, such as Firmicutes and Actinobacteriota, were more abundant in the upstream. By contrast, distinct planktonic bacterial genera associated with mining pollution, such as Acidiphilium and Acidithiobacillus, were more abundant in the source region. The co-occurrence network showed that the interaction of bacterioplankton community is more frequent in the upstream. The bacterioplankton community compositions, richness, and functional profiles were affected by the spatial heterogeneity. Moreover, variation partitioning analysis further confirmed that the amount of variation in the source region independently explained by variables of altitude was the largest, followed by water nutrient. This paper revealed the spatial distribution of planktonic bacterial communities in the source and upstream regions of the Yangtze River and its correlation with environmental factors, providing information support for ensuring the health and safety of aquatic ecosystems in the Yangtze River Basin.

Effects of coal-fired power plants on soil microbial diversity and community structures

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.

Alternations of antibiotic resistance genes and microbial community dynamics on shared bicycles before and after pandemic lockdown

The prevalence of shared bicycles has raised concerns over their potential to transmit pathogens and microbes harboring antibiotic resistance genes (ARGs), which pose significant human health risks. This study investigated the impact of anthropogenic activities on the composition of ARGs and microbial communities on shared bicycles during the COVID-19 pandemic and subsequent lockdown when shared bicycle usage was altered. A total of 600 swab samples from shared bicycle surfaces were collected in Shanghai before and during COVID-19 lockdown periods. Even during lockdown, 12 out of 14 initially detected ARG subtypes persisted, indicating their tenacity in the face of reduced anthropogenic activities. These ARGs displayed significantly higher absolute and relative abundance levels before the lockdown. In addition, the percentage of potential pathogens in the total microbial abundance remained at 0.029 % during the lockdown, which was lower than the pre-lockdown percentage of 0.035 % and suggested that these risks persist within shared bicycle systems. Interestingly, although microbial abundance decreased without the consecutive use of shared bicycles during lockdown, the microbial diversity increased under the impact of restricted anthropogenic activities (p < 0.001). This emphasizes the need for continuous monitoring and research to comprehend microbial community behaviors in various environments. This study uncovered the underlying impacts of the COVID-19 lockdown on the microbial and ARG communities of shared bicycles, providing comprehensive insights into the health management of shared transportation. Although lockdown can decrease the abundance of ARGs and potential pathogens, additional interventions are needed to prevent their continued spread.

Metals and microorganisms in a Maar lake sediment core indicating the anthropogenic impact over last 800 years

A closed Maar lake, receiving mostly atmospheric deposition, offers a unique setting for investigating the impact of human activities on the environment. In this study, we aimed to investigate the historical record of metals in core sediments of Maar Lake in Huguangyan (HGY), Southeast China, and elucidate the possible microbial responses to anthropogenic metal stress. Five stages were divided according to the historical record of metals and corresponding distribution of microbial community, among which Pb and Sn showed a peak value around 1760 CE, indicating the ancient mining and smelting activities. Since the 1980s, a substantial enrichment of metals such as Zn, As, Mo, Cd, Sn, Sb, and Pb was observed, due to the rapid industrial growth in China. In terms of microorganisms, Chloroflexi phylum, particularly dominated by Anaerolineales, showed significant correlations with Pb and Sn, and could potentially serve as indicator species for mining and smelting-related contamination. Desulfarculales and Desulfobacterales were found to be more prevalent in recent period and exhibited positive correlations with anthropogenic metals. Moreover, according to the multivariate regression modeling and variance decomposition analysis, Pb and Sn could regulate Anaerolineales and further pose impact on the carbon cycle; while sulfate-reducing bacteria (SRB) could response to anthropogenic metals and influence sulfur cycle. These findings provide new insights into the interaction between metals and microbial communities over human history.

New insights into the sustainable use of co-pyrolyzed dredged sediment for the in situ remediation of Cd polluted sediments in coastal rivers

The remediation of Cd-polluted sediment in coastal rivers is essential because of its potential hazards to river and marine ecosystems. Herein, a co-pyrolysis product of contaminated dredged sediment (S@BC) was innovatively applied to cap and immobilize Cd-contaminated sediment in coastal rivers in situ, and their remediation efficiencies, mechanisms, and microbial responses were explored based on a 360 d incubation experiment. The results showed that although S@BC immobilization and capping restrained sediment Cd release to the overlying water, S@BC capping presented a high inhibitory efficiency (66.0% vs. 95.3% at 360 d). Fraction analysis indicated that labile Cd was partially transformed to stable fraction after remediation, with decreases of 0.5%- 32.7% in the acid-soluble fraction and increases of 5.0%- 182.8% in the residual fraction. S@BC immobilization and capping had minor influences on the sediment bacterial community structure compared to the control. S@BC could directly adsorb sediment mobile Cd (precipitation and complexation) to inhibit Cd release and change sediment properties (e.g., pH and cation exchange capacity) to indirectly reduce Cd release. Particularly, S@BC capping also promoted Cd stabilization by enhancing the sediment sulfate reduction process. Comparatively, S@BC capping was a priority approach for Cd-polluted sediment remediation. This study provides new insights into the remediation of Cd-contaminated sediments in coastal rivers.

Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea

In this study, we reported a Gram-stain-negative, rod-shaped, atrichous, and aerobic bacterial strain named YMD87T, which was isolated from the intertidal zone sediment of Chinese Yellow Sea. Growth of strain YMD87T occurred at 10.0-40.0 °C (optimum, 25-30 °C), pH 4.0-12.0 (optimum, 8.0) and with 0-6.0% (w/v) NaCl (optimum, 0.0-2.0%). Phylogenetic tree analysis based on 16S rRNA gene sequence indicated that strain YMD87T belonged to the genus Tropicibacter and was closely related to Tropicibacter alexandrii LMIT003T (97.2% sequence similarity). Genomic analysis indicated that strain YMD87T contains a circular chromosome of 3,932,460 bp with G + C content of 63.8% and three circular plasmids of 116,492 bp, 49,209 bp and 49,673 bp, with G + C content of 64.3%. Genomic functional analysis revealed that strain YMD87T is potential a novel sulfur-metabolizing bacteria. The predominant respiratory quinone of YMD87T was ubiquinone-10 (Q-10). The major polar lipids of YMD87T contained phosphatidylglycerol, phosphatidylethanolamine, five unidentified lipids, five unidentified phospholipids, phosphatidylcholine, unidentified glycolipid and five unidentified aminolipids. The major fatty acids of strain YMD87T contained C12:1 3-OH, C16:0, and summed feature 8 (C18:1 ω7c or/and C18:1 ω6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD87T represents a novel species of the genus Tropicibacter, and the name Tropicibacter oceani sp. nov is proposed. The type strain is YMD87T (= MCCC 1K08473T = KCTC 92856 T).

Assessing the Ecotoxicity of Eight Widely Used Antibiotics on River Microbial Communities

Global prevalence of antibiotic residues (ABX) in rivers requires ecotoxicological impact assessment. River microbial communities serve as effective bioindicators for this purpose. We quantified the effects of eight commonly used ABXs on a freshwater river microbial community using Biolog EcoPlates™, enabling the assessment of growth and physiological profile changes. Microbial community characterization involved 16S rRNA gene sequencing. The river community structure was representative of aquatic ecosystems, with the prevalence of Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings reveal that all ABXs at 100 µg/mL reduced microbial community growth and metabolic capacity, particularly for polymers, carbohydrates, carboxylic, and ketonic acids. Chloramphenicol, erythromycin, and gentamicin exhibited the highest toxicity, with chloramphenicol notably impairing the metabolism of all studied metabolite groups. At lower concentrations (1 µg/mL), some ABXs slightly enhanced growth and the capacity to metabolize substrates, such as carbohydrates, carboxylic, and ketonic acids, and amines, except for amoxicillin, which decreased the metabolic capacity across all metabolites. We explored potential correlations between physicochemical parameters and drug mechanisms to understand drug bioavailability. Acute toxicity effects at the river-detected low concentrations (ng/L) are unlikely. However, they may disrupt microbial communities in aquatic ecosystems. The utilization of a wide array of genetically characterized microbial communities, as opposed to a single species, enables a better understanding of the impact of ABXs on complex river ecosystems.

Reclaimed water influences bacterioplankton and bacteriobenthos communities differently in river networks

Reclaimed water reuse is a promising strategy for addressing water scarcity; however, its potential ecological impact remains largely unknown. In particular, the differential effects of reclaimed water on microbial communities in various habitats remain poorly understood. Here, we aimed to elucidate the distinct effects of reclaimed water on bacterioplankton and bacteriobenthos communities in reclaimed water-receiving river networks from multiple perspectives, including community structure, co-occurrence patterns, assembly mechanisms, and nitrogen cycle function. Significant differences in microbial composition were observed between the plankton and benthic habitats, and the average numbers of amplicon sequence variants (ASVs) that originated from the wastewater treatment plants (WWTP) sites were 310.0 and 613.3, respectively, indicating a stronger association between WWTP and benthic habitats. Random forest and network co-occurrence analyses identified the genus Clostridium_sensu_stricto as a biomarker and key module hub. The assembly of bacteriobenthos communities was driven primarily by deterministic processes (58.74% for River-S and 58.94% for WWTP-S), whereas for bacterioplankton communities, this proportion was reduced to 18.02% (River-W) and 19.09% (WWTP-W). The qPCR revealed a large difference in abundance between the N cycling related genes of bacteriobenthos (average 2.47 × 106 copies/ng) and bacterioplankton (average 3.11 × 103 copies/ng) communities, and different interaction patterns with functional genes. Variance partitioning analysis (VPA) indicated that nitrogen was the most important pollutant, affecting the structure and ecological functions of microbial communities. Moreover, pathway analysis suggested that the reuse of reclaimed water may have enhanced the N-cycling functions of microbial communities and the emission of nitrous oxide.

A systematic analysis of residue and risk of cyantraniliprole in the water-sediment system: Does metabolism reduce its environmental risk?

As a representative variety of diamide insecticides, cyantraniliprole has broad application prospects. In this study, the fate and risk of cyantraniliprole and its main metabolite J9Z38 in a water-sediment system were investigated. The present result showed that more J9Z38 was adsorbed in the sediment at the end of exposure. However, the bioaccumulation capacity of cyantraniliprole in zebrafish was higher than that of J9Z38. Cyantraniliprole had stronger influence on the antioxidant system and detoxification system of zebrafish than J9Z38. Moreover, cyantraniliprole induced more significant oxidative stress effect and more differentially expressed genes (DEGs) in zebrafish. Cyantraniliprole had significantly influence on the expression of RyR-receptor-related genes, which was confirmed by resolving their binding modes with key receptor proteins using AlphaFold2 and molecular docking techniques. In the sediment, both cyantraniliprole and J9Z38 had inhibitory effects on microbial community structure diversity and metabolic function, especially cyantraniliprole. The methane metabolism pathway, mediated by methanogens such as Methanolinea, Methanoregula, and Methanosaeta, may be the main pathway of degradation of cyantraniliprole and J9Z38 in sediments. The present results demonstrated that metabolism can reduce the environmental risk of cyantraniliprole in water-sediment system to a certain extent.

Remediation of Cr(VI) contaminated soil by chitosan stabilized FeS composite and the changes in microorganism community

In-suit immobilization is one of the major strategies to remediate heavy metals contaminated soil with the effectiveness largely depends on the characteristics of the added chemical reagents/materials. In this study, chitosan stabilized FeS composite (CS-FeS) was prepared to evaluate the performance of remediating the high and toxic hexavalent chromium contaminated soil from the effectiveness and microbial response aspects. The characterization analysis confirmed the successful preparation of composite, and the introduction of chitosan successfully stabilized FeS to protect it from rapid oxidation as compared to bare FeS particles. With the addition dosage at 0.1%, about 85.6% and 81.3% of Cr(VI) was reduced in 3 d based on toxicity characteristic leaching procedure (TCLP) and CaCl₂ extraction, and the reduction efficiency increased to 96.6% and 94.8% in 7 d, respectively. The Cr(VI) was non-detected in the TCLP leachates with increase the CS-FeS composites to 0.5%. The percentages of HOAc-extractable Cr decreased from 25.17% to 6.12% accompanied with the increase in the residual Cr from 4.26% to 13.77% and improvement of soil enzyme activity under CS-FeS composites addition. Cr(VI) contamination reduced the diversity of microbial community in soil. Three dominate prokaryotic microorganisms, namely Proteobacteria, Actinobacteria and Firmicutes, were observed in Cr-contaminated soil. The addition of CS-FeS composites increased the microbial diversity especially for that in relative lower abundance. The relative abundance of Proteobacteria and Firmicute related to Cr-tolerance and reduction increased in CS-FeS composites added soils. Taking together, these results demonstrated the potential and promising of using the CS-FeS composites for Cr(VI) polluted soil remediation.

Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments

The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (C_org/N_org and δ¹³C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.

Effect of nitrite on hydrolysis-acidification, biogas production and microbial community in semi-continuous two-phase anaerobic digestion of sewage sludge

Previous study found that the pre-treatment of sewage sludge with nitrite improves the biogas production during the mono/two-phase anaerobic digestion (AD) using batch biochemical methane potential tests. In this study, the effects of nitrite on hydrolysis-acidification, biogas production, volatile solids destruction and microbial composition in semi-continuous two-phase AD of sewage sludge were investigated. The addition of nitrite promotes sludge organic matter solubilization (+484%) and VFAs production (+98.9%), and causes an increase in the VS degradation rate during the AD process (+8.7%). The comparison of biogas production from the acidogenic and methanogenic reactors with or without the addition of nitrite implies that the nitrite has no significant effect on the overall biogas production of two-phase sludge AD process. High-throughput sequencing analysis shows that the microbial communities of bacteria and archaea in two-phase AD reactors significantly changes after the addition of nitrite. Vulcanibacillus (bacteria) and Candidatus Methanofastidiosum (archaea) become the dominant genera in the acidogenic and methanogenic reactors with the nitrite respectively. These findings provide new insights about using nitrite to promote the organic matter degradation of sewage sludge in a semi-continuous two-phase AD system.

Land-Water Transport and Sources of Nitrogen Pollution Affecting the Structure and Function of Riverine Microbial Communities

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Soil and Water Assessment Tool alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant variations in microbial communities were observed in sub-basins with distinct land-water pollution transport modes. Point source-dominated areas (PSDAs) exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. The negative relative deviations (-3.38) between the measured and simulated nitrate concentrations in PSDAs indicated that nitrate removal was more effective in PSDAs. Pollution sources were also closely associated with microbiota. Effluents from concentrated animal feeding operations were the primary factors relating to the microbiota compositions in PSDAs and balanced areas. In nonpoint source-dominated areas, contaminants from septic tanks become the most relevant sources to microbial community structures. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

Microbial indicators along a metallic contamination gradient in tropical coastal sediments

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.

Exploring the impacts of physicochemical characteristics and heavy metals fractions on bacterial communities in four rivers

Heavy metals contamination in sediment poses serious threats to bacterial communities that play critical roles in sediment biogeochemical processes. However, the physicochemical factors and the major heavy metals fractions that affect sediment bacterial communities are still unclear. Here, we performed heatmap and redundancy analyses to examine the effects of physico-chemical characteristics and heavy metals fractions on the sediment bacterial community from rivers in the UK (River Tyne and Ouseburn) and India (River Ganga and Yamuna). The results revealed that physicochemical characteristics and heavy metals fractions altered the diversity, richness, and structures of the bacterial community. Moreover, the fractions of Co, Zn, Pb, Cr, and Cu played significant roles in shaping the bacterial community structure, and physicochemical variables, particularly NH₄⁺-N and NO₂^--N, also influenced the bacterial diversity and structure. Firmicutes showed strong associations with both physicochemical factors and heavy metals fractions. Chloroflexi and Actinobacteriota can be used as biomarkers for Zn contamination. Overall, our study identified the significance of sediment chemical characteristics and heavy metals fractions in determining the bacterial community structure as well as bioremediation and environmental management of metals contaminated sites.

Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

Long-term study of ecological restoration in a typical shallow urban lake

We investigated the long-term effects (6 years) of sediment improvement and submerged plant restoration of a subtropical shallow urban lake, Hangzhou West Lake China. To reveal the lake ecosystems variations, we analyzed the sediment properties, submerged macrophyte characteristics, sediment microorganisms, and benthic macroinvertebrate communities from 2015 to 2020. The ecological restoration project decreased sediment TP and OM, increased submerged macrophyte biomass and sediment microbial diversity, and improved the benthic macroinvertebrate communities in the restored area. The sediment TP decreased from 2.94 mg/g in 2015 to 1.33 mg/g in 2020. The sediment OM of the restored area decreased from 27.44 % in 2015 to 8.08 % in 2020. Principal component analysis (PCA) confirmed that the restoration improved the sediment conditions, making it suitable for the growth of submerged macrophytes, and then sped up the restoration and reconstruction of the lake ecosystem. These results have significant implications on the ecological management of shallow lakes.

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

Development of Microbial Indicators in Ecological Systems

Indicators can monitor ecological environment changes and help maintain ecological balance. Bioindicators are divided into animal, plant, and microbial indicators, of which animal and plant indicators have previously been the most researched, but microbial indicators have drawn attention recently owing to their high sensitivity to the environment and their potential for use in monitoring environmental changes. To date, reviews of studies of animals and plants as indicator species have frequently been conducted, but reviews of research on microorganisms as indicator species have been rare. In this review, we summarize and analyze studies using microorganisms as indicator species in a variety of ecosystems, such as forests, deserts, aquatic and plateau ecosystems, and artificial ecosystems, which are contained in wetlands, farmlands, and mining ecosystems. This review provides useful information for the further use of microorganisms as indicators to reflect the changes in different environmental ecosystems.

Microbial community structure and shift pattern of industry brine after a long-term static storage in closed tank

Brine from Dingyuan Salt Mine (Anhui, China), an athalassohaline hypersaline environment formed in the early tertiary Oligocene, is used to produce table salt for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. Here, we employed cultivation and high-throughput sequencing strategies to uncover the microbial community and its shift after a long-term storage in the brine collected from Dingyuan Salt Mine. High-throughput sequencing showed (1) in the fresh brine (2021), Cyanobium_stocktickerPCC-6307 spp. (8.46%), Aeromonas spp. (6.91%) and Pseudomonas spp. (4.71%) are the dominant species in bacteria while Natronomonas spp. (18.89%), Halapricum spp. (13.73%), and Halomicrobium spp. (12.35%) in archaea; (2) after a 3-year-storage, Salinibacter spp. (30.01%) and Alcanivorax spp. (14.96%) surpassed Cyanobium_stocktickerPCC-6307 spp. (8.46%) becoming the dominant species in bacteria; Natronomonas spp. are still the dominant species, while Halorientalis spp. (14.80%) outnumbered Halapricum spp. becoming the dominant species in archaea; (3) Alcanivorax spp. and Halorientalis spp. two hydrocarbons degrading microorganisms were enriched in the brine containing hydrocarbons. Cultivation using hypersaline nutrient medium (20% NaCl) combined with high-throughput 16S rRNA gene sequencing showed that (1) the biomass significantly increased while the species diversity sharply declined after a 3-year-storage; (2) Halorubrum spp. scarcely detected from the environment total stocktickerDNA were flourishing after cultivation using AS-168 or NOM medium; (3) twelve possible new species were revealed based on almost full-length 16S rRNA gene sequence similarity search. This study generally uncovered the microbial community and the dominant halophiles in this inland athalassohaline salt mine, and provided a new insight on the shift pattern of dominant halophiles during a long-term storage, which illustrated the shaping of microorganisms in the unique environment, and the adaptation of microbe to the specific environment.

Microbial community assembly and co-occurrence relationship in sediments of the river-dominated estuary and the adjacent shelf in the wet season

In the estuarine ecosystem, microbial community plays a vital role in controlling biogeochemical processes. However, there is currently limited comprehensive study on the deterministic and stochastic processes that drive the microbial community assembly in the estuaries and adjacent shelves. In this study, we systematically investigated the co-occurrence relationship and microbial community assembly in the sediments along a large river-dominated estuary to shelf in the northern South China Sea during the wet season. The sampling sites were divided into estuary, transection, and shelf sections based on their salinity values. The microbial co-occurrence networks, hierarchical partitioning-based canonical analysis, null model, neutral community model, and the Mantel test were used to investigate the community assembly. Results suggested that microbial community in the estuary section exhibited more interactions and a higher positive interaction ratio than those in the transition and shelf sections. Stochastic processes dominated community assembly in the study, with homogenizing dispersal contributing the most. The estuary exhibited a higher degree of heterogeneous selection than the transition and shelf sections, whereas homogeneous selection showed an opposite trend. Only the estuary section showed dispersal limitation and undominated processes. The river inflow and the resulting environmental heterogeneity were believed to be the key regulators of the community assembly in the studied area. Our study improved the understanding of how microbial community assembly in estuaries and adjacent shelves.

Response and contribution of bacterial and archaeal communities to eutrophication in urban river sediments

Excessive loading of nitrogen (N) and phosphorus (P) that leads to eutrophication mutually interacts with sediment microbial community. To unravel the microbial community structures and interaction networks in the urban river sediments with the disturbance of N and P loadings, we used high-throughput sequencing analysis and ecological co-occurrence network methods to investigate the responses of diversity and community composition of bacteria and archaea and identify the keystone species in river sediments. The alpha-diversity of archaea significantly decreased with the increased total nitrogen (TN), whereas the operational taxonomic unit (OTU) number of bacteria increased with the increase of available phosphorus (AP). The beta-diversity of archaea and bacteria was more sensitive to N content than P content. The relative abundance of predominant bacterial and archaeal taxa varied differently in terms of different N and P contents. Complexity and connectivity of bacteria and archaea interaction networks showed significant variations with eutrophication, and competition between bacteria became more significant with the increase of N content. The sensitive and the highest connective species (keystone species) were identified for different N and P loadings. Total carbon (TC), water content (WC), microbial alpha-diversity and interaction networks played pivotal roles in the N and P transformation in urban river sediments.

Characterization of physicochemical parameters and bioavailable heavy metals and their interactions with microbial community in arsenic-contaminated soils and sediments

Mobility and toxicity of heavy metal contamination in the environment are highly dependent on its bioavailability. Most of previous studies focused on total heavy metal contents and their influence on microbial community in soils and sediments. Little were concerned about bioavailable fractions. In the current study, soil and sediment samples were collected near an abandoned realgar mine in Shimen County, China. Bioavailable heavy metals including Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Cd, Sb, and Pb in the samples were extracted using three-step sequential extraction method. Interactions among physicochemical parameters, total and bioavailable heavy metals, and microbial community in the collected samples were investigated. The study area has been severely contaminated by As with a concentration up to 2158 mg·kg-1 detected. The result of principal component analysis showed that the abundance of operational taxonomic units (OTUs) in the soils were obviously different from those in the sediments. In the soil samples, pH made a dominant contribution on the OTU abundance of microbial community. Correlation analyses revealed that the alpha diversity indices and microbial taxon were most correlated with bioavailable fractions of heavy metals in all the samples. That means bioavailable heavy metals rather than total heavy metals or physicochemical parameters played a more important role on richness and diversity of microbial community. Little connections were observed between microbial community and As no matter total concentration or bioavailable fraction. However, bioavailable Fe and Mn were recognized as the major driving force shaping the taxonomic structure of microbial community due to their relatively high concentrations and high affinity to other heavy metal contamination in soils and sediments.

How microorganisms tell the truth of potentially toxic elements pollution in environment

Potentially toxic elements (PTEs) posed a major hazard to microbial community in river sediments, but the way how different kinds of microorganisms responses to elements pollution has not been clearly understood. The target of this research was to discriminate the apposite indicators for diagnosing elements pollution based on the sensitivity of microbial abundance, biodiversity, predicted metabolic functions to PTEs (Cu, Cd, Cr, Ni, Pb, Zn, As and Hg). Considering Huaihe River Basin as the main subject, sediment samples were gathered from 135 sites. Ni, Zn and Cd significantly influenced the microbial communities and predicted functions. In general, the microbial sensitivity to PTEs was bacteria > archaea. Geo-accumulation index and potential ecological risk (PER) index suggested Hg and Cd were the significant contaminates and posed the most serious ecological risk in sediments. Structural Equation Model identified the bioindicators 1/nitrate reduction and rara taxa (Azoarcus) as reflect and speculate Hg and Cd pollution, respectively. PER was predicted by 1/nitrate reduction and rare taxa (Phaeodactylibacter and Illumatobacter). Results elucidated the rather role of rare taxa in indicating PTEs pollution. The findings contributed to provide useful reference for bioremediation of contaminated sediments under PTEs stress.

Omics-based ecosurveillance uncovers the influence of estuarine macrophytes on sediment microbial function and metabolic redundancy in a tropical ecosystem

Vertical zonation within estuarine ecosystems can strongly influence microbial diversity and function by regulating competition, predation, and environmental stability. The degree to which microbial communities exhibit horizontal patterns through an estuary has received comparatively less attention. Here, we take a multi-omics ecosurveillance approach to study environmental gradients created by the transition between dominant vegetation types along a near pristine tropical river system (Wenlock River, Far North Queensland, Australia). The study sites included intertidal mudflats fringed by saltmarsh, mangrove or mixed soft substrata habitats. Collected sediments were analyzed for eukaryotes and prokaryotes using small sub-unit (SSU) rRNA gene amplicons to profile the relative taxonomic composition. Central carbon metabolism metabolites and other associated organic polar metabolites were analyzed using established metabolomics-based approaches, coupled with total heavy metals analysis. Eukaryotic taxonomic information was found to be more informative of habitat type. Bacterial taxonomy and community composition also showed habitat-specificity, with phyla Proteobacteria and Cyanobacteria strongly linked to mangroves and saltmarshes, respectively. In contrast, metabolite profiling was critical for understanding the biochemical pathways and expressed functional outputs in these systems that were tied to predicted microbial gene function (16S rRNA). A high degree of metabolic redundancy was observed in the bacterial communities, with the metabolomics data suggesting varying degrees of metabolic criticality based on habitat type. The predicted functions of the bacterial taxa combined with annotated metabolites accounted for the conservative perspective of microbial community redundancy against the putative metabolic pathway impacts in the metabolomics data. Coupling these data demonstrates that habitat-mediated estuarine gradients drive patterns of community diversity and metabolic function and highlights the real redundancy potential of habitat microbiomes. This information is useful as a point of comparison for these sensitive ecosystems and provides a framework for identifying potentially vulnerable or at-risk systems before they are significantly degraded.

Heavy metals in a typical city-river-reservoir system of East China: Multi-phase distribution, microbial response and ecological risk

The rapid construction of artificial reservoirs in metropolises has promoted the emergence of city-river-reservoir systems worldwide. This study investigated the environmental behaviors and risks of heavy metals in the aquatic environment of a typical system composed of main watersheds in Suzhou and Jinze Reservoir in Shanghai. Results shown that Mn, Zn and Cu were the dominant metals detected in multiple phases. Cd, Mn and Zn were mainly presented in exchangeable fraction and exhibited high bioavailability. Great proportion and high mobility of metals were found in suspended particulate matter (SPM), suggesting that SPM can greatly affect metal multi-phase distribution process. Spatially, city system (CiS) exhibited more serious metal pollution and higher ecological risk than river system (RiS) and reservoir system (ReS) owing to the diverse emission sources. CiS and ReS were regarded as critical pollution source and sink, respectively, while RiS was a vital transportation aisle. Microbial community in sediments exhibited evident spatial variation and obviously modified by exchangeable metals and nutrients. In particular, Bacteroidetes and Firmicutes presented significant positive correlations with most exchangeable metals. Risk assessment implied that As, Sb and Ni in water may pose potential carcinogenic risk to human health. Nevertheless, ReS was in a fairly safe state. Hg was the main risk contributor in SPM, while Cu, Zn, Ni and Sb showed moderate risk in sediments. Overall, Hg, Sb and CiS were screened out as priority metals and system, respectively. More attention should be paid to these priority issues to promote the sustainable development of the watershed.

Risk assessments of emerging contaminants in various waters and changes of microbial diversity in sediments from Yangtze River chemical contiguous zone, Eastern China

Over recent decades, increasing chemical contamination has greatly affected aquatic life and human health, even though most contaminants are present at low concentrations. The large-scale chemical industrial parks (CIPs) concentrated in the Yangtze River Delta account for over half of the total in China, and Jiangsu Province occupies one fifth of the Yangtze River Delta. Inevitably, the ecosystems could be affected by these CIPs. In this study, we collected 35 water and 12 sediment samples from the Yangtze River (Taizhou section) surrounding waters adjacent to concentrated CIPs and determined their cumulative chemical levels to be 0.2 to 28.4 μg/L and cumulative detections to be 11 to 39 contaminants with a median of 20 contaminants. 61 out of 153 screened chemicals were detected from at least one sampling site, and 6 contaminants, mostly semi-volatile organic compounds, appeared at all sites. Among these detected chemicals, di-n-octyl phthalate and dibutyl phthalate were at the highest levels. Ecological assessment revealed that 4-chloroaniline, phenol and dibutyl phthalate possibly would induce adverse effects on Yangtze River (Taizhou) ecosystems. Further aided with an evaluation of integrated biomarker response (IBR) index, it was found that site W06 (downstream of Binjiang CIP wastewater inlet) was the location in greatest need of urgent action. As a result, the microbial diversity of sediments in the Yangtze River mainstream was significantly higher than that of tributaries, where CIPs wastewater entered.

Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality

The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.

Interactions among heavy metal bioaccessibility, soil properties and microbial community in phyto-remediated soils nearby an abandoned realgar mine

Soil samples were collected from a representative arsenic (As) contaminated region under phytoremediation of hyperaccumulation plants. Relative abundance and diversity of microbial communities in the soil samples were characterized via 16S rRNA genes sequencing. At the phylum level, Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Firmicutes shows the highest abundance, accounting for more than 90 % of the classified sequences in the soil samples. Physicochemical parameters including pH, total organic carbon (TOC), cation exchange capacity (CEC), and electrical conductivity (EC), and heavy metal concentrations including total and bioaccessible contents in the soil samples were determined to investigate potential relationships between the microbial communities and the environmental factors. Principal component analysis (PCA) based on the operational taxonomic units (OTUs) matrix revealed distinct separation among the samples. The soil pH was confirmed as the dominant force to discriminate the soil samples with similar land use type and heavy metal contamination. There was little relevance between the total concentrations of heavy metals and the microbial communities. However, the bioaccessible concentrations of heavy metals were associated with the physicochemical parameters and relative abundances of bacterial genera according to correlation analyses. Although the soil samples were considerably contaminated by As, the abundances of bacterial phyla linked with As were lower than 1.0 % in most of the soil samples. The results indicated that the abundances of microbial communities in the soils were the consequence of concerted effects from all the environmental factors.

Impact of anthropogenic organic matter on bacterial community distribution in the continental shelf sediments of southeastern Arabian Sea

The objective of this study was to understand the influence of anthropogenic organic matter on the spatial distribution microbial community in the continental shelf sediments of the Southeastern Arabian Sea (SEAS). The sediment samples were taken from the inner shelf (30 m depths) and outer shelf (100-200 m). The C:N_molar ratio of the sediment displayed a significant variation between the inner and outer shelf and a higher terrestrial organic input in the inner shelf. Microbial community composition also showed a significant variation between the inner and outer shelf (p ≤ 0.05). Proteobacteria was the dominant phylum in the outer shelf sediments (42.5%), whereas Desulfobacterota (21.9%) was the dominant phylum in the inner shelf. Complex terrestrial organic matter degrading bacteria dominated the inner shelf, whereas oligophilic microbial community and autochthonous organic matter utilizing bacteria dominated the outer shelf. Thus the source of organic matter controlled the microbial distribution in the SEAS.

Impact of different types of anthropogenic pollution on bacterial community and metabolic genes in urban river sediments

Sediment bacterial communities play a crucial role in the biogeochemical cycle of nutrient elements in urban river. However, the distribution of nitrogen cycle genes on bacterial communities in urban rivers sediments is largely unknown. Here, 16S rRNA amplicon sequencing was used to analyze the composition, co-occurrence patterns and nitrogen cycle process of bacterial communities in urban river sediments under the influence of different exogenous pollution. The results revealed that bacterial communities had significant spatial heterogeneity in river sediments of different polluted areas, and the input of different exogenous pollutants shaped the abundance and distribution of nitrogen cycle-related genes in the sediments. In addition, denitrification process played a leading role in the nitrogen cycle of river sediments, and the genes associated with the nitrification process were rarely observed in all samples. The important bacterial taxonomic biomarkers of nitrogen cycling-related genes screened by random forest algorithm were Synergistia, WS6_Dojkabacteria and Caldisericia. Meanwhile, different co-occurrence patterns observed in different types of polluted areas clarified the impact of environmental filtration and niche differentiation on bacterial communities. In conclusion, this study reveals the nitrogen cycle process and the distribution of related genes mediated by bacterial communities under the impact of different anthropogenic contamination, and provides novel insights for the assembly of bacterial communities in urban river sediments.

Human activities can drive sulfate-reducing bacteria community in Chinese intertidal sediments by affecting metal distribution

Sulfate-reducing bacteria (SRB), which are ubiquitous in intertidal sediments, play an important role in global sulfur and carbon cycles, and in the bioremediation of toxic metalloids/metals. Pollution from human activities is now a major challenge to the sustainable development of the intertidal zone, but little is known about how and to what extent various anthropic and/or natural factors affect the SRB community. In the current study, based on the dsrB gene, we investigated the SRB community in intertidal sediment along China's coastline. The results showed that dsrB gene abundances varied among different sampling sites, with the highest average abundance of SRB at XHR (near the Bohai Sea). The SRB community structures showed obvious spatial distribution patterns with latitude along the coastal areas of China, with Desulfobulbus generally being the dominant genus. Correlation analysis and redundancy discriminant analysis revealed that total organic carbon (TOC) and pH were significantly correlated with the richness of the SRB community, and salinity, pH, sulfate and climatic parameters could be the important natural factors influencing the composition of the SRB community. Moreover, metals, especially bioavailable metals, could regulate the diversity and composition of the SRB communities. Importantly, according to structural equation model (SEM) analysis, anthropic factors (e.g., population, economy and industrial activities) could drive SRB community diversity directly or by significantly affecting the concentrations of metals. This study provides the first comprehensive investigation of the direct and indirect anthropic factors on the SRB community in intertidal sediments on a continental scale.

Response of Fungal Diversity, Community Composition, and Functions to Nutrients Management in Red Soil

Soil fungi play a critical role in plant performance and soil nutrient cycling. However, the understanding of soil fungal community composition and functions in response to different nutrients management practices in red soils remains largely unknown. Here, we investigated the responses of soil fungal communities and functions under conventional farmer fertilization practice (FFP) and different nutrient management practices, i.e., optimization of NPK fertilizer (O) with soil conditioner (O + C), with lime and mushroom residue (O + L + M), and with lime and magnesium fertilizer (O + L + Mg). Illumina high-throughput sequencing was used for fungal identification, while the functional groups were inferred with FUNGuild. Nutrient management practices significantly raised the soil pH to 4.79–5.31 compared with FFP (3.69), and soil pH had the most significant effect (0.989 ***) on fungal communities. Predominant phyla, including Ascomycota, Basidiomycota, and Mortierellomycota were identified in all treatments and accounted for 94% of all fungal communities. The alpha diversity indices significantly increased under nutrients management practices compared with FFP. Co-occurrence network analysis revealed the keystone fungal species in the red soil, i.e., Ascomycota (54.04%), Basidiomycota (7.58%), Rozellomycota (4.55%), and Chytridiomycota (4.04%). FUNGuild showed that the relative abundance of arbuscular mycorrhizal fungi and ectomycorrhizal fungi was higher, while pathogenic fungi were lower under nutrient management practices compared with FFP. Our findings have important implications for the understanding of improvement of acidic soils that could significantly improve the soil fungal diversity and functioning in acidic soils.

Effect of copper ions on glucose fermentation pathways in bioelectrochemical system

Toxic metal ions were previously found to be effective removed by anodic biofilms under the coexistence of organics in bioelectrochemical system (BES). However, the effect of toxic metal ions on the organics fermentation pathways remains unclear. To investigate the pathway systematically, the glucose fermentation pathways were discussed under different Cu²⁺ concentrations. After introducing Cu²⁺, more acetate and less propionate were observed, implying that the metabolic reaction of glucose fermentation altered from mixed acid type to acetogenesis type. This pattern produced more "food" (acetate or hydrogen) for methanogens, thus, the methane content increased by 19.67%, 39.51%, and 27.71% in the presence of 0.1, 1, and 7 mg L^-1 Cu²⁺ compared to the blank, respectively. Increased Cu²⁺ concentrations resulted in the decrease of current production, which was associated with the decrease of electricigen (Geobacter). Consistent with the change of fermentation type, the fermenters (Klebsiella and norank_f__norank_o__Bacteroidales) that related to the production of acetate increased, while the dominant methanogens (Methaospirillum) didn't decrease until the Cu²⁺ concentration reached 7 mg L^-1.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.

Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle

Due to the geographical circumstances, the Yangtze River Estuary (YRE) and the adjacent East China Sea are extensively influenced by both anthropogenic activities and environmental factors. To reveal the responses of microbes in surface sediment to environmental factors and their contributions to the biogeochemical cycle in this area, surface sediment and overlying water samples were collected at 21 stations from the estuary to the coastal region. Water and sediment parameters were determined, and 16S rRNA genes of microbes in sediment samples were sequenced using high throughput sequencing technology. The results indicated that ocean currents, sediment density (SD), nutrients, sulfate (SO₄^2-), and salinity were the key factors shaping the microbial communities. Coastal microbes were affected mainly by SD, whereas anthropogenic discharge might have been responsible for a decrease in indigenous microbial diversity in the ocean. Due to the anthropogenic discharge, the most representative bacteria in the nearshore were aerobic and chemoheterotrophic bacteria, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and polyphosphate accumulating organisms. In the offshore, anaerobic bacteria, thermophilic bacteria, halophilic bacteria, sulfate-reducing bacteria, and sulfide oxidizing bacteria were the dominant bacteria, and these were characterized by strong solidarity and cooperative properties within the malnourished environment. In summary, these results provide a new perspective for revealing the biogeochemical significance of the bacterial lineages in the YRE, as well as constructive guidance for the management of the marginal sea ecosystems in distinct regions.

The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments

This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.

Effects of heavy metals on microbial communities in sediments and establishment of bioindicators based on microbial taxa and function for environmental monitoring and management

Heavy metals have always been a research hotspot due to their persistence, hazard and bioaccumulation. Microorganisms are highly sensitive to heavy metal pollution and play an important role in the material cycling and energy flow of the ecosystem. In order to further explore the influence of heavy metals on the diversity, composition, and function of microbial communities in the wetland sediment ecosystem, and to find suitable indicators to reflect heavy metal pollution status, we collected sediments from Huangjinxia nature reserve and determined the physicochemical properties, heavy metal (Cu, Cr, Ni, Pb, Zn, and Mn) concentrations, and microbial information. We found that: the contamination status of the study area stood at a moderate level evaluated by the pollution load index (PLI); heavy metals explained more of microbial community variation than the sediment physicochemical properties; in particular, Cr and Mn negatively affected microbial α-diversity; heavy metals significantly affected the structure of microbial communities, elements Cr, Pb, and Zn showed uniformly negative associations with the relative abundance of bacteria Nitrospirae (including class Nitrospira and order Nitrospirales), Bacteroidetes (including class Bacteroidia), and Verrucomicrobia; moreover, heavy metals affected predicted functions of microbial communities, including metabolic functions, genetic information processes, and functions related to the carbon cycle and the nitrogen cycle. Based on the relative abundance of sensitive microbial taxa and predicted functions, bioindicators [Bacteroidia], 1/[Nitrospira], 1/[Nitrification], and 1/[Aerobic nitrite oxidation] were established to reflect and predict the contamination status of heavy metals in sediments. Our in-depth research on the effects of heavy metals on microorganisms and the establishment of bioindicators provide references and new perspectives for environmental monitoring and management.

Metagenomic Analysis Revealed that the Terrestrial Pollutants Override the Effects of Seasonal Variation on Microbiome in River Sediments

Researching the structure and function of sediment microbiome contribute to understanding the response of microbiome to external disturbances. However, seasonal changes in sediment microbiome with different terrestrial pollutants input have not yet been clearly understood. Metagenomic sequencing was used to evaluate the effects of seasonal variations and different land use types on sediment microbiome. Results showed that the differences in structure and functions of sediment microbiome among different land use types were obviously greater than different seasons. This indicated that the terrestrial pollutants weakened the effects of seasonal variations on shaping the sediment microbiome. The significant differences in sediment properties under the input of different terrestrial pollutants was observed, but no obvious differences between seasons, which may be the reason why terrestrial pollutants override the effects of seasonal variation on the sediment microbiome. Overall, the results extended our understanding of the impacts of seasonal variation and terrestrial pollutants on river sediment microbiome.

Antibiotic resistance genes in biofilms on plastic wastes in an estuarine environment

Plastic wastes are ubiquitous in aquatic environment. Biofilms, which are often formed on the surface of plastic waste, may contain antibiotic resistance genes (ARGs). This study focused on the occurrence and distribution of ARGs, metal resistance genes (MRGs) and their associated microbial communities in biofilms formed on different types of plastic, in comparison to associated sediment and water samples taken from the Yangtze Estuary. The results showed that polypropylene (PP) and polyethylene (PE) with visible biofilms were highly abundant, and the average absolute abundance of most tested ARGs in the biofilms was higher than that in the sediment and water, indicating that biofilms on plastics can act as a reservoir for ARGs. Moreover, the biofilms on PE had a higher relative abundance of ARGs, compared to those on other plastics, and Firmicutes on PE may be potential hosts for these ARGs. Furthermore, Bacillus, Mycobacterium and Pseudomonas may be multi-resistance genera on plastics, and tetA and tetW may have more potential hosts on PET and PP. Metals, total phosphorus and salinity may be the major environmental factors regulating ARGs in biofilms formed on plastics. The results provide new insights into evaluating the risks caused by plastic wastes and ARGs in biofilms formed on plastics in estuarine environment.

Characteristics of spatial and seasonal bacterial community structures in a river under anthropogenic disturbances

In this study, the seasonal characteristics of microbial community compositions at different sites in a river under anthropogenic disturbances (Maozhou River) were analyzed using Illumina HiSeq sequencing. Taxonomic analysis revealed that Proteobacteria was the most abundant phylum in all sites, followed by Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Firmicutes. The variations of the community diversities and compositions between the seasons were not significant. However, significant differences between sites as well as water and sediment samples were observed. These results indicated that sites under different levels of anthropogenic disturbances have selected distinct bacterial communities. pH, dissolved oxygen (DO), concentrations of total nitrogen (TN) and heavy metals were the main factors that influence the diversity and the composition of bacterial community. Specifically, the relative abundance of Proteobacteria was negatively correlated with pH and DO and positively correlated with TN, while Actinobacteria and Verrucomicrobia showed the opposite pattern. Moreover, positive correlations between the relative abundances of Firmicutes and Bacteroidetes and the concentration of heavy metals were also found. Results of functional prediction analysis showed no significant differences of the carbon, nitrogen and phosphorus metabolism across the sites and seasons. Potential pathogens such as Vibrio, Arcobacter, Acinetobacter and Pseudomonas were found in these samples, which may pose potential risks for environment and human health. This study reveals the effect of anthropogenic activities on the riverine bacterial community compositions and provides new insights into the relationships between the environmental factors and the bacterial community distributions in a freshwater ecosystem under anthropogenic disturbances.

Impact of long-term industrial contamination on the bacterial communities in urban river sediments

BACKGROUND

The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.

RESULTS

The overall community composition and abundance of individual bacterial groups differed between samples. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P < 0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.

CONCLUSIONS

Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

Wastewater treatment plant upgrade induces the receiving river retaining bioavailable nitrogen sources

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature

In this study, a spatial model has been developed to investigate the role of water temperature to the distribution of bacteria over the selected regions in the Bay of Bengal, located in the southern region of Bangladesh using next-generation sequencing. Bacterial concentration, quantitative polymerase chain reactions, and sequencing were performed on water samples and identified Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The spatial model tessellated the parts of the Bay of Bengal with hexagons and analyzed the relationship between the distribution of bacteria and water temperature. A geographically weighted regression was used to observe whether water temperature contributed strongly or weakly to the distribution of bacteria. The residuals were examined to assess the model’s fitness. The spatial model has the potential to predict the bacterial diversity in the selected regions of Bangladesh.

Time-dependent effects of ZnO nanoparticles on bacteria in an estuarine aquatic environment

Many studies have examined the acute toxicity of nanoparticles (NPs) towards model bacteria. In this study, we report the time-dependent effects of ZnO NPs on native, selected Zn-resistant and dominant bacteria in estuarine waters. An initial inhibition of bacterial growth followed by a recovery at 24 h was observed, and this rebound phenomenon was particularly notable when the raw water samples were treated with relatively high ZnO NP concentrations (1 and 10 mg/L).By comparing the groups treated with Zn²⁺, Zn²⁺ was shown to largely explain the acute cytotoxic effect of ZnO NPs on bacteria in raw waters. Furthermore, similar to the native bacteria, especially the dominant bacteria, the viability of Escherichia coli (E. coli) decreased with the increasing treatments time and the concentrations of ZnO NPs in water with different salinities. Moreover, the expression of Zn-resistance genes including zntA and zntR in E. coli suggested that the Zn-resistance system in E. coli can be activated to defend against the stress of Zn²⁺ released from ZnO NPs, and salinity may promote this process in estuarine aquatic systems. Thus, the effect of ZnO NPs on bacteria in estuarine water bodies is likely determined by the synergistic effect of environmental salinity and dissolved Zn ions. As such, our findings are of high relevance and importance for understanding the ecological disturbances caused by anthropogenic NPs in estuarine environments.

The responses of bacterial community and N2O emission to nitrogen input in lake sediment: Estrogen as a co-pollutant

Excessive nitrogen (N) input is one of the most important causative factors of lake eutrophication, which has aroused increasing public attention in past decades. Estrogen contamination is also an increasing environmental problem in aquatic systems around the world. Although both substances usually co-exist in aquatic ecosystems, many researches have only investigated the influences of either N or estrogen individually on sediment bacterial community and nitrous oxide (N₂O) emission. Knowledge regarding the combined effects of N and estrogen is still very limited. In this study, a 30-day laboratory incubation experiment was performed to examine the impacts of different N sources (ammonium and nitrate) combined with 17β-estradiol (E2) on sediment bacterial community. High-throughput 16S rRNA gene sequencing technique was used and N₂O emission was measured. The results revealed that the relative abundances of Proteobacteria and Bacteroidetes were higher in nitrate treatment than ammonium treatment. Compared to N treatments, N and E2 combined treatments showed higher relative abundances of Proteobacteria, Bacteroidetes, and Firmicutes, but lower relative abundances of Chloroflexi, Acidobacteria, and Actinobacteria over entire incubation period. At the genus level, the relative abundances of genera Flavobacterium, Pseudomonas, Arenimonas, Novosphingobium, Massilia, Aquabacterium, and Bacillus were enhanced by N treatments and especially N and E2 combined treatments, compared to sediment without addition of N and E2. However, the relative abundances of Sporacetigenium, Gaiella, Desulfatiglans, Nitrospira, and Haliangium were decreased in N treatments. Apart from the changes in bacterial community structure, N₂O emission was also influenced by different treatments. Nitrate exerted a more significant positive effect on N₂O emission than ammonium, and the cumulative emission of N₂O was highest in nitrate and E2 combined treatment. Very low abundances of ammonia monooxygenase (amoA) gene and hydroxylamine oxidase (hao) gene were observed in sediments compared to other genes involved in N cycles (such as nitrate reductase (narG and napA) genes, nitrite reductase (nirB, nirK, and nrfA) genes, and nitric oxide reductase (norB) gene), implying that denitrification rather than nitrification played an important role in sediments. The abundances of napA, nirK, and norB were higher in N and E2 combined treatments, indicating that E2 might provide a carbon source for denitrifiers. Moreover, decrease in the abundance of nitrous oxide reductase (nosZ) gene during the denitrifying process in N and E2 combined treatment might be an important reason for increases of N₂O emission. These results indicated that alterations of the bacterial community structure due to the co-existence of N and E2 could also change the abundances of genes involved in N cycle.

Long-term effect of water diversion and CSOs on the remediation of heavy metals and microbial community in river sediments

Untreated combined sewer overflows (CSOs) cause serious water pollution problems. In this study, the effects of CSO-induced heavy metals and the remediation practice of installation of a long-term water diversion (LTWD) on the microbial environment in river sediments were analyzed in an inland river. The Zn, Cd, Cr, and Cu contents in sediments and water were analyzed. DNA extraction and polymerase chain reaction analysis were conducted based on the Illumina MiSeq platform. The results showed that CSOs have a significant adverse impact on the diversity of microbial populations in river sediments. The LTWD is helpful in improving the richness of microorganisms and the proportion of Gram -ves, but it is challenging to reduce the accumulation of heavy metals in the sediment. The correlation analysis shows a strong relationship between some metabolic pathways and Zn and Cd accumulation in river sediments. Some detoxification compound metabolisms are also promoted at these sites. Thus, chronic exposure to environmental heavy metals from CSOs decreases the river microbial community, and further affects the ecological environment of the river. Therefore, without eliminating CSOs or reducing overflow frequency, it is difficult to alleviate the accumulation of heavy metals in river sediments and improve river ecology via water diversion alone.

Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia

Tonle Sap Lake, the largest freshwater body in Southeast Asia, plays an important role in lives and environment. The lake is reportedly under anthropogenic pressure and suffers from eutrophication. The floating villagers suffer from waterborne diseases. However, the shift in bacterial community due to human activities in this great lake has not yet been reported. We aimed to determine the dynamics of the bacterial community and their concentration in the lake using 67 surface waters, 53 sub-layer waters and 59 sediment samples by Next Generation Sequencing (NGS). The bacterial communities in the surface water and sub-layer water were similar but they differed from the sediment; however, their abundance showed spatiotemporal variations. The bacterial diversity reached the highest value in the dry season but lowest value in the rainy season in the surface water and sediment. Their diversity in the sub-layer water was highest in the transition from dry to rainy season. The total 16S rRNA gene copy number in the sediment were >100 times higher than that measured in the water. The Cyanobacteria, Actinobacteria, and Proteobacteria concentrations in the lake water increased in the dry season and reached a peak in the transition from dry to rainy season. The concentrations of Proteobacteria and Firmicutes elevated in the lake water and sediment, respectively, in the floating villages which were >10 times higher than the places with non-point sources. The bacterial concentration and its diversity in the Tonle Sap Lake changed based on the lake water volume between rainy and dry season. The bacterial concentration in the Tonle Sap Lake diluted with the water inflow from Mekong River and its tributaries in the rainy season. As influenced by the fecal waste, the bacterial community in the floating villages differed from the places with non-point source.