Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland)

Loss of submerged macrophytes in shallow lakes alters bacterial and archaeal community structures, and reduces their co-occurrence networks connectivity and complexity

Introduction

Bacteria and archaea are important components in shallow lake ecosystems and are crucial for biogeochemical cycling. While the submerged macrophyte loss is widespread in shallow lakes, the effect on the bacteria and archaea in the sediment and water is not yet widely understood.

Methods

In this study, 16S rRNA gene sequencing was used to explore the bacteria and archaea in samples taken from the sediment and water in the submerged macrophyte abundant (MA) and submerged macrophyte loss (ML) areas of Caohai Lake, Guizhou, China.

Results

The results showed that the dominant bacterial phyla were Proteobacteria and Chloroflexi in the sediment; the dominant phyla were Proteobacteria, Actinobacteriota, and Bacteroidota in the water. The dominant archaea in sediment and water were the same, in the order of Crenarchaeota, Thermoplasmatota, and Halobacterota. Non-metric multidimensional scaling (NMDS) analyses showed that bacterial and archaeal community structures in the water were significantly affected by the loss of submerged macrophytes, but not by significant changes in the sediment. This suggests that the loss of submerged macrophytes has a stronger effect on the bacterial and archaeal community structures in water than in sediment. Furthermore, plant biomass (PB) was the key factor significantly influencing the bacterial community structure in water, while total nitrogen (TN) was the main factor significantly influencing the archaeal community structure in water. The loss of submerged macrophytes did not significantly affect the alpha diversity of the bacterial and archaeal communities in either the sediment or water. Based on network analyses, we found that the loss of submerged macrophytes reduced the connectivity and complexity of bacterial patterns in sediment and water. For archaea, network associations were stronger for MA network than for ML network in sediment, but network complexity for archaea in water was not significantly different between the two areas.

Discussion

This study assesses the impacts of submerged macrophyte loss on bacteria and archaea in lakes from microbial perspective, which can help to provide further theoretical basis for microbiological research and submerged macrophytes restoration in shallow lakes.

Temporal patterns of bacterial communities in the Billings Reservoir system

In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4-2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.

Organic enrichment reduces sediment bacterial and archaeal diversity, composition, and functional profile independent of bioturbator activity

Eutrophication is a worldwide issue that can disrupt ecosystem processes in sediments. Studies have shown that macrofauna influences sediment processes by engineering environments that constrain microbial communities. Here, we explored the effect of different sizes of the Sydney cockle (Anadara trapezia), on bacterial and archaeal communities in natural and experimentally enriched sediments. A mesocosm experiment was conducted with two enrichment conditions (natural or enriched) and 5 cockle treatments (small, medium, large, mixed sizes and a control). This study was unable to detect A. trapezia effects on microbial communities irrespective of body size. However, a substantial decrease of bacterial richness, diversity, and structural and functional shifts, were seen with organic enrichment of sediments. Archaea were similarly changed although the magnitude of effect was less than for bacteria. Overall, we found evidence to suggest that A. trapezia had limited capacity to affect sediment microbial communities and mitigate the effects of organic enrichment.

Analysis of bacterial community distribution characteristics in the downstream section of a cross confluence in a polluted urban channel

Channel confluences are common in urban rivers and caused complex hydrodynamic conditions in the downstream section, significantly influencing the distribution of pollutants and the microbial community. So far, the principles of bacterial community assembly and their linkages with environmental factors are poorly understood. In the present study, the hydrodynamic and pollution conditions were investigated in a typical channel confluence of an urban river in the Yangtze River delta area, China, and their impacts on the bacterial community structure in the water and sediment were characterized using 16S rRNA gene high-throughput sequencing technology. Based on the results, the flow velocity was the crucial factor influencing the dispersal of nutrients, organic compounds, and bacterial communities in the river water. Moreover, the sediments exhibited higher α-diversity and bacterial richness for nitrogen and sulfur cycling than the water. In addition to flow velocity, the contents of total organic carbon, total phosphorus, and heavy metals determined the sediment bacterial communities at varying depths. The predictive analysis of functional gene category indicated differences between the water and sediment communities in metabolic potentials and pathogen risk and provided guidance for water pollution control and the eco-remediation of urban rivers.

Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China

Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.

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

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

Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors

Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.

Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments

Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe²⁺ showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe²⁺ . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.

Effects of lead pollution on bacterial communities in biofilm attached to submerged plants

Submerged plants and biofilms have significant advantages in hydro-ecology rehabilitation, but their tolerance and physiological responses to heavy metal stress have thus far been under-investigated. This study investigated the influence of lead on physiological and biochemical responses, as well as variation in bacterial communities and functional characteristics of submerged plant biofilms. The results showed that chlorophyll a content of two submerged plants decreased with increased lead concentration. The concentration of malondialdehyde of both submerged plants was higher under high lead concentrations than under low lead concentrations, and the concentrations of malondialdehyde and hydrogen peroxide in Vallisneria natans were more stable. The antioxidant enzyme systems of the two plants played protective roles against lead stress. High lead concentration can inhibit the bacterial community and lead to decreased diversity. The most abundant bacterial phyla were Proteobacteria (40.9%), Cyanobacteria (21.5%), and Bacteroidetes (14.3%). Proteobacteria abundance decreased with increased lead concentration, while Cyanobacteria abundance increased. The lead concentration in plants (19.7%, P < 0.01) and the lead concentration in aquatic environment (17.7%, P < 0.01) were significantly correlated with variation in bacterial communities. High lead concentration inhibits the activity of these bacteria related to the conversion of nitrogen and sulfur.

Bacterial community composition and indicators of water quality in Caizi lake, a typical Yangtze-connected freshwater lake

Caizi Lake is an important lake connected to the Yangtze River in Anhui Province and a crucial connection for the Yangtze-to-Huaihe Water Diversion Project (YHWD). There were marked differences in trophic status of the six sampling sites based on the physicochemical characterization. The Bacterial Eutrophic Index (BEI), used to quantify water quality, was well related to Carlson's trophic state index (TSI) (Spearman's ρ = 0.829, P < 0.05). Mean TSI and BEI were 54 and 0.58, respectively, indicating that Caizi Lake was slightly eutrophic. Actinobacteriota were the predominant bacterial phylum in the water and Acidobacteriota in sediments. The diversity and composition of the bacterial community was markedly different between sites for water but not sediment samples. Unlike other Yangtze-connected freshwater lakes, the distance-based redundancy analysis (db-RDA) revealed that dissolved oxygen (DO) affected the composition of the planktonic bacterial community (P < 0.001) while total phosphorus (TP) was the major factor in the sediments (P < 0.05). Water quality of Caizi Lake significantly improved since a few years ago. These results contribute to the long-term monitoring of the ecological quality of the water environment along the Yangtze River to the Huaihe River.

Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community

Archaea are important participants in biogeochemical cycles of metal(loid)-polluted ecosystems, whereas archaeal structure and function in response to metal(loid) contamination remain poorly understood. Here, the effects of multiple metal(loid) pollution on the structure and function of archaeal communities were investigated in three zones within an abandoned sewage reservoir. We found that the high-contamination zone (Zone I) had higher archaeal diversity but a lower habitat niche breadth, relative to the mid-contamination zone (Zone II) and low-contamination zone (Zone III). Particularly, metal-resistant species represented by potential methanogens were markedly enriched in Zone I (cumulative relative abundance: 32.24%) compared to Zone II (1.93%) and Zone III (0.10%), and closer inter-taxon connections and higher network complexity (based on node number, edge number, and degree) were also observed compared to other zones. Meanwhile, the higher abundances of potential metal-resistant and methanogenic functions in Zone I (0.24% and 9.24%, respectively) than in Zone II (0.08% and 7.52%) and Zone III (0.01% and 1.03%) suggested archaeal functional adaptation to complex metal(loid) contamination. More importantly, six bioavailable metal(loid)s (titanium, tin, nickel, chromium, cobalt, and zinc) were the main contributors to archaeal community variations, and metal(loid) pollution reinforced the role of deterministic processes, particularly homogeneous selection, in the archaeal community assembly. Overall, this study provides the first integrated insight into the survival strategies of archaeal communities under multiple metal(loid) contamination, which will be of significant guidance for future bioremediation and environmental governance of metal(loid)-contaminated environments.

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.

Effect of different washing solutions on soil enzyme activity and microbial community in agricultural soil severely contaminated with cadmium

Soil enzyme activities and microbial communities have a good response to the remediation effect of heavy metal-contaminated soils. To evaluate the effect of three commonly used washing agents, ferric chloride (FC), ethylenediaminetetraacetic acid (EDTA) and ethylenediamine-tetra-methylenephosphonic acid (EDTMP) on soil enzyme activities and microbial community in cadmium (Cd)-contaminated agricultural soil were collected from farmland near a non-ferrous metal smelter. The soil enzyme activities, microbial community, chemical forms of Cd and some physicochemical properties of the soil washed with different washing solutions were determined. The results showed that the three washing solutions had moderate removal efficiencies for Cd in the tested soil and the breakdown product of EDTMP has a certain stabilizing effect on Cd. The geometric mean and the integrated total enzyme activity index showed that soil washing with FC and EDTA was more beneficial to the restoration of biochemical functions than that with EDTMP. After soil washing, the Chao1 index of bacteria increased, and the microbial community structure changed. Pearson correlation analysis and redundancy analysis (RDA) indicated that the three washing solutions affected soil enzyme activities and microbial community by altering soil nutrient, total Cd concentration and Cd fractions in soils.

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.

Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs

Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.

Simultaneous elimination of black-odor and stabilization of heavy metals in contaminated sediment using calcium peroxide/hydroxyapatite: Microbial responses and ecotoxicological effects

In this study, laboratory-scale experiments were conducted to investigate the feasibility of the combined use of calcium peroxide and hydroxyapatite (CaO₂/HAP) for simultaneous black-odor sediment remediation and heavy metal stabilization. The ecotoxicological effects of remediated sediment were also evaluated based on biological toxicity. Results showed that CaO₂/HAP effectively eliminated the black-odor and simultaneously stabilized heavy metals in the sediment. Under the optimal dosage ratio of CaO₂/HAP (1:2), the acid volatile sulfides decreased to approximately 20 mg/kg (dry weight, dw) and oxidation-reduction potential increased from - 165 mV to approximately - 90 mV. The leaching of heavy metals meets the strictest standards (Level I) of the "Technical Specification for Output Disposal of Contaminated Sediment Treatment Plant of River and Lake" (SZDB/Z 236-2017). The indigenous microbial community succession occurred (p < 0.01), Proteobacteria and Firmicutes accounting for 75.54% and 20.19%, respectively, were the predominant bacteria in the remediated sediment. Additionally, CaO₂/HAP remediated sediments were safer and more environmentally friendly than raw sediments, and were not biotoxic to the benthic environment (p < 0.01). This study provides new insights into the combined use of the beneficial amendments remediating heavy metal-contaminated black-odor river sediment.

Effects of Nutrient Levels on Microbial Diversity in Sediments of a Eutrophic Shallow Lake

Microorganisms can both indicate the water quality characteristics and the health of the aquatic environment, which have an important influence on the cycling of organic carbon, nitrogen (N), and phosphorus (P) in nature. In this study, we took Taihu Lake, a typical eutrophic lake in China, as the research object, and monitored the northern (Changzhou City) and southern (Changxing County) regions of Taihu Lake for three consecutive years (2019–2021), respectively. We also analyzed the microbial diversity in sediments, and then summarized the effects of different nutrient environments on microorganisms in the aquatic environment. The results showed that the pollution level in the northern part of Taihu Lake was higher than that in the southern region of Taihu Lake, where the pollution was mainly in summer (June–July). The pollution in the southern region of Taihu Lake is relatively stable between 2019 and 2021; the changes in the northern part of Taihu Lake are relatively significant. Microbial diversity in the study area was negatively correlated with the degree of eutrophication of water bodies; microbial abundance was positively correlated with nutrient levels. The functional difference analysis indicated that the microorganisms in the sediments of Taihu Lake in the study area were involved in the nutrient transport and transformation, and played an important role in the purification of the lake water body. This study reveals the relationship between water eutrophication and microbial diversity, and then provides a theoretical basis for the management of eutrophic lakes.

Heavy metals speciation and distribution of microbial communities in sediments from the abandoned Mo-Ni polymetallic mines, southwest of China

Chemical fractions of heavy metals (Mo, Ni, Cu, Zn, Fe, Mn, Pb, Cd, and Cr) and compositions of bacteria and fungi in surface sediments from the Mo-Ni polymetallic mine area were analyzed. The results indicated that the mean concentrations of Mo, Ni, Cu, Zn, and Cd were higher than their background values. The mean percentage of Cr in residual fraction was much higher than that of other heavy metals. Mo, Cu, Zn, Fe, and Pb were mainly associated with oxidizable fraction. The dominant proportions of Mn and Cd were found in exchangeable fraction with mean percentages of 93.46% and 54.50%, respectively. According to RAC classification and potential ecological risk index (PERI), the Cd with high bioavailability had a very high environmental risk. The MisSeq sequencing results of bacteria and fungi revealed that microbial communities discrepantly respond to different sampling sites. The most abundant phylum of bacteria and fungi were Proteobacteria and Ascomycota, respectively. The bioavailable heavy metals including Mo-B, Pb-B, and Cd-B were recognized to have important influences on both dominant bacterial and fungal communities. The present study manifested that the bioavailability of heavy metal is very important to assess the potential environmental risk and plays a key role in shaping microbial structure.

Occurrence of toxic metals and their selective pressure for antibiotic-resistant clinically relevant bacteria and antibiotic-resistant genes in river receiving systems under tropical conditions

The co-occurrence of heavy metals, antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) from hospital effluents spreading into the river receiving systems and evaluating associated risks are topics of scientific interest and still under-studied in developing countries under tropical conditions. To understand the selectors of the ARGs, we examined the occurrence of heavy metals (Cr, Co, Ni, Cu, Cd, Pb and Zn), associated ARB (β-lactam-resistant Escherichia coli, β-lactam-resistant Enterobacteriaceae, and carbapenem-resistant Enterobacteriaceae) and ARGs (bla_OXA, bla_CTX-M, bla_IMP, bla_TEM) in water and sediments from two sub-urban rivers receiving urban and hospital effluent waters in the Democratic Republic of the Congo (DRC). High abundances of ARB and ARGs were observed in all sediment samples. All the metal contents correlated negatively with grain size (- 0.94 ≤ r ≤  - 0.54, p < 0.05) except for Ni and positively with organic matter content and total copies of 16 s rRNA (0.42 ≤ r ≤ 0.79, p < 0.05), except for Ni and Zn. The metals had a significant positive correlation with the faecal indicator Enterococcus except for Ni and Cd (0.43 ≤ r ≤ 0.67, p < 0.05). Carbapenem-resistant Enterobacteriaceae correlated negatively with Zn (r =  - 0.44, p < 0.05) and positively with all the rest of toxic metals (0.58 ≤ r ≤ 1.0, p < 0.05). These results suggested that some metals had a great influence on the persistence of ARB and ARGs in sediments. Overall, this study strongly recommends the managing urban wastewater to preserve water resources used for human and agricultural purposes. Additionally, we recommend the utilizing biological indicators (faecal indicator bacteria, ARB, ARGs) when investigating urban wastewater pollutions.

Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake

The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.

Effect of elemental composition assigned to antrotopic pollution on the quality of the water and sediment of the Marrecas river (PR, Brazil) as highlighted by multivariate statistical analyses

In recent years, several environmental pollutants have been monitored in surface waters and sediments. However, few studies apply multivariate statistics to identify the main components and correlate them temporally and spatially. In this sense, the present study sought to monitor the quality of water and sediments in the Rio Marrecas/Brazil, through the analysis of physicochemical parameters and trace elements, as well as to identifying sources of contamination, using multivariate statistics. For this purpose, sampling was carried out in nine locations for a period of 12 months. The Total Reflection X-ray Fluorescence (TXRF) technique was used to quantify the 15 elements identified in water and sediment samples. Through multivariate statistical analyses, the most significant elements, their correlations and possible pollutant sources were defined, and the pollution index (HPI) and assessment index (HEI) of heavy metals were applied. The parameters pH and BOD₅ do not comply with Brazilian legislation. Based on PCA and Spearman correlation, there was strong evidence of contamination of the water naturally, composed of the elements Ti, V, Mn, Fe, and of anthropogenic origin composed of the elements Ca, Ni, Cu, Zn. These findings provide insights to determine the impacts of heavy metals on human health and the environment.

Response of microorganisms to phosphate nanoparticles in Pb polluted sediment: Implications of Pb bioavailability, enzyme activities and bacterial community

In recent years, various phosphate nanoparticles (PNPs) have been synthesized and applied for in situ Pb remediation in laboratory investigations. Here, three kinds of PNPs, CMC-nClAP (carboxymethyl cellulose stabilized nano-chlorapatite), SDS-nClAP (sodium dodecyl sulfate stabilized nano-chlorapatite) and Rha-nClAP (rhamnolipid stabilized nano-chlorapatite) were used to investigate the influence of PNPs on Pb bioavailability, enzyme activities and bacterial community in Pb polluted sediment. Pb bioavailability can be reduced by the application of CMC-nClAP, SDS-nClAP and Rha-nClAP with the maximum increases of residual fraction to 57.2 %, 58.3 % and 61.4 %, respectively. Alternatively, catalase activity, urease activity and protease activity also changed with the remediation of PNPs. Microbes responded quickly to PNPs in different ways: bacterial richness was all increased while bacterial diversity was only increased with the application of SDS-nClAP. Three dominant species, Proteobacteria, Firmicutes and Bacteroidetes were redistributed differentially during the treatment of PNPs. Interestingly, PNPs didn't significantly change the bacterial community structure in treated samples and CMC-nClAP induced fewer changes in microbial activity and community as compared with SDS-nClAP and Rha-nClAP. Overall, our findings suggested that long-term exposure to PNPs would decrease Pb bioavailability, regulate enzyme activities and affect bacterial community in sediments. The Pb bioavailability, physical-chemical properties of PNPs and properties of chemical/bio-surfactant may determine the response of microorganisms to PNPs in Pb polluted sediment.

Longitudinal patterns in sediment type and quality during daily flow regimes and following natural hazards in an urban estuary: a Hurricane Harvey retrospective

Understanding the transport of sediments in urban estuaries and their effects on water quality and microorganisms is a convergent challenge that has yet to be addressed especially as a result of natural hazards that affect the hydrodynamics of estuarine systems. This study provides a holistic view of the longitudinal nature and character of sediment in an urban estuary, the Galveston Bay Estuary System (GBES), under daily and extreme flow regimes and presents the results of water and sediment sampling after Hurricane Harvey. The sediment sampling quantified total suspended sediment (TSS) concentrations, metal concentrations, and the diversity of microbial communities. The results revealed the impact of the substantial sediment loads that were transported into the GBES in terms of sediment grain type, the spatial distribution of trace metals, and the diversity of microbial communities. A measurable shift in the percentage of silt relative to historical norms was noted in the GBES after Hurricane Harvey. Not only did sediment metal data confirms this shift and its ensuing impact on metal concentrations; microbial data provided ample evidence of the effect of leaks and spills from wastewater treatment plants, superfund sites, and industrial runoff on microbial diversity. The research demonstrates the importance of understanding longitudinal sediment transport and deposition in estuarine systems under daily flow regimes but more critically, following natural hazard events to ensure sustainability and resilience of systems such as the GBES that encounter numerous acute and chronic stresses.

Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination

Lake sediments are natural receptors for a wide range of anthropogenic contaminants including organic matter and toxicants such as trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls that accumulate over time. This contamination can impact benthic communities, including microorganisms which play a crucial role in biogeochemical cycling and food-webs. The present survey aimed at exploring whether anthropogenic contamination, at a large lake scale, can influence the diversity, structure and functions of microbial communities associated to surface sediment, as well as their genetic potential for resistance to metals and antibiotics. Changes in the characteristics of these communities were assessed in surface sediments collected in Lake Geneva from eight sampling sites in October 2017 and May 2018. These sampling sites were characterized by a large concentration range of metal and organic compound contamination. Variation between the two sampling periods were very limited for all sampling sites and measured microbial parameters. In contrast, spatial variations were observed, with two sites being distinct from each other, and from the other six sites. Benthic communities from the most contaminated sampling site (Vidy Bay, near the city of Lausanne) were characterized by the lowest bacterial and archaeal diversity, a distinct community composition, the highest abundance of antibiotic resistance genes and functional (respiration, denitrification, methanogenesis, phosphatase, and beta-glucosidase) activity levels. The second sampling site which is highly influenced by inputs from the Rhône River, exhibited low levels of diversity, a distinct community composition, high abundance of antibiotic resistance genes and the highest bacterial abundance. Overall, our results suggest that local anthropogenic contamination, including organic matter and toxicants, is a major driver of the diversity and functioning of sediment-microbial communities in Lake Geneva. This highlights the need to consider benthic microbial communities and a suite of complementary ecotoxicological endpoints for more effective environmental risk assessments of contaminants in lake sediments.

Denitrifier abundance and community composition linked to denitrification potential in river sediments

Denitrification in river sediments plays a very important role in removing nitrogen in aquatic ecosystem. To gain insight into the key factors driving denitrification at large spatial scales, a total of 135 sediment samples were collected from Huaihe River and its branches located in the northern of Anhui province. Bacterial community composition and denitrifying functional genes (nirS, nirK, and nosZ) were measured by high-throughput sequencing and real-time PCR approaches. Potential denitrification rate (PDR) was measured by acetylene inhibition method, which varied from 0.01 to 15.69 μg N g^-1 h^-1. The sequencing results based on 16S rRNA gene found that the main denitrification bacterial taxa included Bacillus, Thiobacillus, Acinetobacter, Halomonas, Denitratisoma, Pseudomonas, Rhodanobacter, and Thauera. Therein, Thiobacillus might play key roles in the denitrification. Total nitrogen and N:P ratio were the only chemical factors related with all denitrification genes. Furthermore, nirS gene abundance could be more susceptible to environmental parameters compared with nirK and nosZ genes. Canonical correspondence analysis indicated that NO₃^-, NO₂^-, NH₄⁺ and IP had the significant impacts on the nirS-encoding bacterial community and spatial distributions. There was a significantly positive correlation between Thiobacillus and nirS gene. We considered that higher numbers of nosZ appeared in nutrient rich sediments. More strikingly, PDR was positively correlated with the abundance of three functional genes. Random forest analysis showed that NH₄⁺ was the most powerful predictor of PDR. These findings can yield practical and important reference for the bioremediation or evaluation of wetland systems.

Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France)

Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.

Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China

Fe(III) reducing bacteria (FeRB) play a vital role in the biogeochemical cycle of Fe, C and N in nature. The volcanic lake can be considered as an ideal habitat for FeRB. Here, we investigated the diversity and spatial distribution of FeRB in sediments of Wenbo lake in Wudalianchi volcano based on culture-dependent and independent methods. A total of 28 isolates affiliated with the genera of Enterobacter, Bacillus, Pseudomonas and Clostridium were obtained from 18 sediment samples. We detected 783 operational taxonomic units (OTUs) belonged to FeRB using high high-throughput sequencing, and the dominant phyla were Proteobacteria (3.65%), Acidobacteria (0.29%), Firmicutes (10.78%). The representative FeRB genera such as Geobacter, Pseudomonas, Thiobacillus and Acinetobacter distributed widely in Wenbo lake. Results showed that the diversity and abundance of FeRB declined along the water-flow direction from Libo to Jingbo. In contrast, the FeRB diversity decreased and the FeRB abundance increased along with depth transect of sediments. It was found that the dominant phylum changed from Firmicutes to Proteobacteria along the water-flow direction, while changed from Proteobacteria to Firmicutes along with the depth of sediments. RDA indicated that the FeRB distribution were driven by soluble total iron, total organic carbon, Fe(II) and Fe(III). These will provide information for understanding the role of FeRB in the elements geochemical cycles in the volcanic environment.

Efficiency of Fez WWTP: multi-parameter evaluation of water and sediment quality

In order to assess the impact of the proper functioning of wastewater treatment plants (WWTPs) and sanitation networks on the quality of water and surface sediments of the Oued Fez River and its tributaries, and ultimately their outlet in the Sebou River, physico-chemical, geochemical and mineralogical analyses were performed. The components were studied in high- and low-water regimes at eight sites. Seven heavy metals (As, Cd, Cr, Cu, Ni, Pb and Zn) were investigated in the sediments, with a decreasing trend being identified as Zn > Cu > Pb > Cr > As > Ni > Cd, and a mobility sequence as Cu > Pb > Zn > Ni > Cr. A comparison of the total heavy metal concentrations in the Oued Fez and Sebou River sediments with those of previous studies indicated a reduction in the harmful and polluting contribution of the Oued Fez to the Sebou River. The heavy metal assessment was achieved using environmental indices and sediment quality guidelines. The obtained results indicate that the presence of heavy metals in the sediment mainly comes from anthropogenic activities. Based on these results and their comparison with those from previous studies, the contribution of WWTPs and sanitation networks to improving the water quality of the middle Sebou River is clearly noteworthy.

Stabilization of lead in polluted sediment based on an eco-friendly amendment strategy: Microenvironment response mechanism

Stabilization is the most important remediation mechanisms for sediment polluted heavy metals. However, little research has been done on the identification of microenvironmental response and internal correlation, as well as synergistic mechanisms during heavy metal remediation. This study aims to investigate the inner response mechanisms of microenvironment after the lead (Pb) are gradually stabilized in sediment. An eco-friendly amendment strategy which firstly used 100% biodegradable sophorolipids (SOP) to modify chlorapatite (ClAP) for the fabrication of SOP@nClAP was applied in this study. The stabilization efficiency of Pb was significantly improved by SOP@nClAP compared with ClAP. Most importantly, the high-throughput sequencing showed that the dominant species in the sediment changed with the stabilization of Pb. The decrease of Proteobacteria and increase of Firmicutes, especially the Sedimentibacter within the phylum Firmicute directly suggested that large amounts of Pb were stabilized. This research is not only devoted to stabilize Pb in sediment by eco-friendly amendment strategy, but also keep a watchful eye on microenvironment response mechanisms during the Pb stabilization in sediment. Therefore, this study lays a foundation for the future application of more heavy metal amendment strategies in the sediment environment and improves the possibility of large-scale site amendment.

Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing

Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.

Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China

The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.

Remediation of Cd-Contaminated Soil by Modified Nanoscale Zero-Valent Iron: Role of Plant Root Exudates and Inner Mechanisms

In this study, the role of exogenous root exudates and microorganisms was investigated in the application of modified nanoscale zero-valent iron (nZVI) for the remediation of cadmium (Cd)-contaminated soil. In this experiment, citric acid (CA) was used to simulate root exudates, which were then added to water and soil to simulate the pore water and rhizosphere environment. In detail, the experiment in water demonstrated that low concentration of CA facilitated Cd removal by nZVI, while the high concentration achieved the opposite. Among them, CA can promote the adsorption of Cd not only by direct complexation with heavy metal ions, but also by indirect effect to promote the production of iron hydroxyl oxides which has excellent heavy metal adsorption properties. Additionally, the H⁺ dissociated from CA posed a great influence on Cd removal. The situation in soil was similar to that in water, where low concentrations of CA contributed to the immobilization of Cd by nZVI, while high concentrations promoted the desorption of Cd and the generation of CA–Cd complexes which facilitated the uptake of Cd by plants. As the reaction progressed, the soil pH and cation exchange capacity (CEC) increased, while organic matter (OM) decreased. Meanwhile, the soil microbial community structure and diversity were investigated by high-throughput sequencing after incubation with CA and nZVI. It was found that a high concentration of CA was not conducive to the growth of microorganisms, while CMC had the effect of alleviating the biological toxicity of nZVI.

Community Composition and Function of Bacteria in Activated Sludge of Municipal Wastewater Treatment Plants

Municipal wastewater treatment plants (WWTPs) use functional microorganisms in activated sludge (AS) to reduce the environmental threat posed by wastewater. In this study, Illumina NovaSeq sequencing of 16S rRNA genes was performed to explore the microbial communities of AS at different stages of the two WWTP projects in Shenzhen, China. Results showed that Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, and Nitrospirae were the dominant phyla in all the samples, with Proteobacteria being the most abundant and reaching a maximum proportion of 59.63%. There was no significant difference in biodiversity between the two water plants, but Stage 1 and Stage 2 were significantly different. The Mantel test indicated that nitrate, total nitrogen (TN), chemical oxygen demand (COD), and nutrients were essential factors affecting the bacterial community structure. FAPROTAX analysis emphasized that the leading functional gene families include nitrification, aerobic nitrite oxidation, human pathogens, and phototrophy. This study reveals changes in the community structure of AS in different treatment units of Banxuegang WWTP, which can help engineers to optimize the wastewater treatment process.

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.

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China

Bacterial communities are sensitive to environmental fluctuations, and a better understanding of the relationships between bacterial community distribution and complex environmental conditions is important for the remediation of lake ecosystems. In this study, bacterial communities from 7 water and 7 sediment samples in 3 different regions (east, the hydrophyte-dominated region; north, the transitional region; west, the highly polluted region) of Lake Taihu were investigated via high-throughput sequencing. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the three lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The Shannon and Simpson values indicated that the diversity of bacterial communities in water was the highest in the eastern region, followed by the northern and western regions, while there was no significant difference in the bacterial community characteristics in sediments among lake regions. We found that the western lake region had the highest Cyanobacteria concentration (34.71%), suggesting that Cyanobacteria may have competitive advantages over the other bacterioplankton in water columns without plants. The abundances of Chlorobi detected in the water samples in the east (2.69%) and north (6.66%) were higher than those in the west because the high turbidity in the western lake region was unsuitable for the growth of Chlorobi. Nitrospirae (average 6.36%) and Chloroflexi (average 11.62%) were more common in the sediments than in the water of Lake Taihu, suggesting that the nutrient level of Lake Taihu sediment was higher than that of water bodies. Welch's t test revealed that there were significant differences in species abundance (such as Microcystis, Synechococcus, Flavobacterium, and hgcI_clade) among the different regions, except that the east was relatively similar to the north. Canonical correspondence analysis demonstrated that TN, TP, and DO showed significant effects on the relative abundance of the dominant bacterial genera in water, while TOC, TP, and TN were positively correlated with TOC, TP and TN. This study provides useful information for understanding the variation in the diversity of bacterial communities in different habitats of Lake Taihu.

How does the microenvironment change during the stabilization of cadmium in exogenous remediation sediment?

The pollution degree of heavy metals is closely related to the sediment microenvironment. This study aims to give a comprehensive account of the changes of microenvironment in sediment during the stabilization of cadmium (Cd) by the sodium lignosulphonate (SLS) modified chlorapatites (SLS@nClAP). Chemical speciation change demonstrated that SLS@nClAP possessed better stabilizing capacity (65.84 %-76.66 %) for Cd than unmodified chlorapatites (ClAP) (45.88 %). It might be since that the surface of SLS@nClAP presented a more dispersive thin sheet structure with sulfonate groups compared with the aggregate block structure of ClAP. High-throughput sequencing results displayed that succession of microbial community occurred after remediation in sediment. Most importantly, the dominant genus changed from massilia to phosphate-solubilizing bacterium-pseudomonas which might be due to the remediation of chlorapatites and the stabilization of Cd. Moreover, enzyme activity changes showed that the activity of catalase and urease were highly influenced by the stability and bioavailability of Cd during the incubation. This study not only provided a novel remediation technology for Cd-polluted sediment but also confirmed that the change of microenvironment was closely related to the stability and bioavailability of Cd in sediment.

Sediment Bacterial Community Structure Under the Influence of Different Domestic Sewage Types

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial cooccurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake

The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria, Nitrospirae, Chloroflexi, Firmicutes and Ignavibacteriae. The dominant groups of archaea consisted of Euryarchaeota, Woesearchaeota DHVEG-6, Bathyarchaeota and WSA2. Lastly, the meta-analysis results highlighted that the low TOC (LT) prokaryotic community structure is larger and more complex compared to moderate TOC (MT). On the whole, the prokaryotic community structure is obviously distinct among groups with different TOC levels, and LT communities may interact with each other strongly in the Dianchi Lake sediment. This study can provide more insights into prokaryotic assemblages in eutrophic lake sediment and provide suggestions for the restoration and maintenance of sediment ecosystems.

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.

Reliance and effect of sediment bulking on the physicochemical properties of sediments in aquatic environments

Sediment bulking is intently related to the occurrence of black water agglomerate, sediment resuspension and erosion in aquatic environments. In this study, five different lake sediments were sampled to study effects of sediment characteristics on sediment bulking and then investigate how sediment bulking affected in turn sediment physicochemical properties. Within 30 days of experiments, the sediment properties showed an obvious influence on variation in sediment height (VSH) ranging from only 0.03 to 1.26 cm for five sediment samples. It was found that labile nutrients were closely related to the VSH (P < 0.05) during sediment bulking. In addition, the high-throughput sequencing revealed that the microbial communities in sediments associated with degradation of organic matter and anaerobic environments, were also related to sediment bulking. Through comparing sediments with and without bulking, it was found that sediment bulking would clearly increase the proportion of air around 2.14 times, and reduce the critical shear stress of sediment with a decrease by 67.33% after 30 days, which favored sediment resuspension and erosion. Thus, this study could provide a deep insight in the key factors and the environmental effects of sediment bulking, and then be helpful in protecting the aquatic environments against ecological disasters.

Heavy metals and persistent organic pollutants contamination in river, estuary, and marine sediments from Atlantic Coast of Democratic Republic of the Congo

The pollution assessment and the evaluation of potential risks in the Atlantic Coastal Region of the Democratic Republic of the Congo are still very limited. Consequently, the present study investigates for the first time the concentrations of heavy metals and persistent organic pollutants (organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and polycyclic aromatic hydrocarbons (PAHs)) in river, estuary, and marine sediments from this area. The results highlighted high concentrations of Cr, Zn, As, and Pb exceeding the probable effect level (PEL) on aquatic life. Zn was the most dominant element detected at a range of 180-480 mg kg^-1 in marine sediment, 132-382 mg kg^-1 in estuary sediment, and 121-687 mg kg^-1 in river sediment. Total PCBs (∑7 × 4.3) ranged from 1995 to 20,156 μg kg^-1, 2013-12,058 μg kg^-1, and 1861-36,417 μg kg^-1 in marine, estuary, and river sediments, respectively. Total PCBs (∑7 × 4.3) were above PEL for all sediments, suggesting potential adverse effects on benthic organisms. The OCP, PBDE, and PAH levels were low to moderate for all sediments. Taking into consideration, the concentrations of Zn, Pb, PCBs, and DDTs, probable environmental risks, are present.

Real-time monitoring of sediment bulking through a multi-anode sediment microbial fuel cell as reliable biosensor

Sediment bulking was closely related to the occurrence of black water agglomerate in anoxic aquatic sediments. Real-time monitoring of sediment bulking can be labor intensive and technically difficult, especially in dynamic environments where a record of variation in height over time is desired. In this study, a vertically distributed multi-anodes sediment microbial fuel cell (SMFC) as biosensor was developed for monitoring the changes in sediment height. According to the principle of sediment microbial fuel cell (SMFC), the voltage of SMFC would increase when the anode embedded into the sediment. The results showed that when the anode buried in the sediment, the biosensing system delivered voltage can increase to 40 mV, where the power density of SMFC exceeded 10 mW m^-2 with overshoot of power density appeared. However, for the anodes above the water-sediment interface, the voltages and power densities kept at around 0. The redundancy analysis further indicated that the labile carbon pool-I of sediment was a key factor for sediment bulking, which led to drastic changes in sediment characteristics. The results from this study can provide a simple strategy for identifying sediment bulking in shallow lakes.

Using flow cytometry for bacterioplankton community analysis as a complementary tool to Water Framework Directive to signal putatively impacted sites

Metal contamination, as well as pesticides, organic matter and nutrient input are main factors leading to freshwater ecosystems degradation. The Water Framework Directive (WFD) was implemented within the European Union with the ultimate goal of promoting a good ecological status in all European waterbodies. However, the broad implementation of the bioassessment behind WFD is costly and time-consuming and the search for complementary methodologies has been given significant attention. In this context, the main goal of this study was to evaluate whether flow cytometry (FCM) and denaturing gradient gel electrophoresis (DGGE) can be used as cellular/molecular tools to efficiently assess riverine bacterioplankton communities and relevantly inform on the ecological quality of these ecosystems. Caima river was chosen as case study using three sampling sites reflecting different levels and types of contamination (point-source organic and metal input). Both bacterioplankton community assessment approaches (DGGE and FCM), as well as macroinvertebrate and periphyton communities were consistent in signaling organic contamination. The putatively metal-loaded site bears some contradictory results depending on the community focused, possibly due to the overall low levels of metals actually found and seasonality. When comparing the two bacterioplankton community analysis tools, DGGE and FCM, the results obtained were essentially coherent, with FCM being simpler, faster and still accurate for screening bacteria communities via quantification of bacteria of high and low DNA content. This highlights the suitability of the FCM approach for prioritization of contaminated sampling sites and reinforces the suitability of using bacterioplankton communities as the focus of rapid tools to complement bioassessment sensu the WFD methodology, e.g. assisting the prioritization of potentially impacted areas.

Phytoremediation of cadmium-contaminated soil by Sorghum bicolor and the variation of microbial community

In this paper, the growth of S. bicolor in Cd-polluted sandy clay loam soil in north China, Cd accumulation in plant and the corresponding soil microbial community were characterized when the plant matured (140 d of growth). Cadmium promoted the growth of mature S. bicolor with higher height and heavier dry mass, especially at the spiked level of 1 mg kg^-1 soil (P < 0.05). The higher microbial diversity was found under Cd stress at the spiked level of 15 mg kg^-1, which basically corresponded with its influence on the plant growth. High-throughput sequencing data demonstrated that the predominant bacterial phyla include Proteobacteria (35.99% for Cd-polluted soil and 35.22% for the control soil), Chloroflexi (21.33% and 20.58%), Actinobacteria (12.00% and 12.89%), Acidobacteria (7.47% and 11.14%), Bacteroidetes (7.37% and 6.96%), Gemmatimonadetes (5.60% and 6.65%), Firmicutes (2.82% and 1.86%), Planctomycetes (2.47% and 0.95%), Saccharibacteria (1.26% and 1.11%). The predominant fungal phyla was Ascomycota, with the relative abundance of 89.96% for the control soil and 86.2% for the Cd-polluted soil. S. bicolor could grow well in sandy clay loam soil in northern China at low Cd lvel, but it could not accumulate cadmium at higher cadmium level. S. bicolor could be used for phytoextraction of cadmium from the lightly Cd-polluted soil.

Composition of bacterial communities in municipal wastewater treatment plant

Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.

Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea

The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China

Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.

Occurrence of Bacterial Markers and Antibiotic Resistance Genes in Sub-Saharan Rivers Receiving Animal Farm Wastewaters

Antibiotic resistant bacteria and genes which confer resistance to antibiotics from human/animal sources are currently considered a serious environmental and a public health concern. This problem is still little investigated in aquatic environment of developing countries according to the different climatic conditions. In this research, the total bacterial load, the abundance of relevant bacteria (Escherichia coli (E. coli), Enterococcus (Ent), and Pseudomonas), and antibiotic resistance genes (ARGs: bla_OXA-48, bla_CTX-M, sul1, sul2, sul3, and tet(B)) were quantified using Quantitative Polymerase Chain Reaction (qPCR) in sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo. Human and pig host-specific markers were exploited to examine the sources of contamination. The total bacterial load correlated with relevant bacteria and genes bla_OXA-48, sul3, and tet(B) (P value < 0.01). E. coli strongly correlated with 16s rDNA, Enterococcus, Pseudomonas spp., bla_OXA-48, sul3, and tet(B) (P value < 0.01) and with bla_CTX-M, sul1, and sul2 at a lower magnitude (P value < 0.05). The most abundant and most commonly detected ARGs were sul1, and sul2. Our findings confirmed at least two sources of contamination originating from pigs and anthropogenic activities and that animal farm wastewaters didn’t exclusively contribute to antibiotic resistance profile. Moreover, our analysis sheds the light on developing countries where less than adequate infrastructure or lack of it adds to the complexity of antibiotic resistance proliferation with potential risks to the human exposure and aquatic living organisms. This research presents useful tools for the evaluation of emerging microbial contaminants in aquatic ecosystems which can be applied in the similar environment.

The spatial and seasonal variations of bacterial community structure and influencing factors in river sediments

Studying the composition and structure of bacterial communities in sediments helps to understand the contribution of bacteria to environmental changes and the role of feedback in response to disturbances. However, seasonal changes in bacterial communities of river sediments with different pollution levels and sources have not been clear yet. In this study, we collected sediment samples during the dry season, wet season and level season from 40 sites with various pollution sources in three inflow rivers (Fengle-Hangbu River, Nanfei River and Zhegao River) of Chaohu Lake. Bacterial community compositions were determined based on high-throughput sequencing. The 'Bioenv' in the R package 'Vegan' and redundancy analysis was used to explore the influence of environmental factors on the bacterial community in the river sediments. Results showed that a significant deviation in bacterial communities was found among seasons and rivers. In addition, seasonal dynamics had a greater impact on shaping bacterial communities than rivers with different pollution sources. A higher diversity was found in the wet season as compared to the other seasons. The bacterial diversity was negatively correlated with nutrients (OM, TN, NH₄⁺, IP, OP and TP) and metals (Cu and Zn). Bacterial communities were more sensitive to heavy metals pressure than nutrients. We also concluded that heavy metals (Cu and Cd) were the key contributing factors in explaining variations in bacterial communities. This study provided a valuable reference for assessing ecological stress.

Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia

Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.