Mercury induced community tolerance in microbial biofilms is related to pollution gradients in a long-term polluted river

Unravelling the Portuguese Coastal and Transitional Waters' Microbial Resistome as a Biomarker of Differential Anthropogenic Impact

Portugal mainland and Atlantic archipelagos (Madeira and Azores) provide a wide array of coastal ecosystems with varying typology and degrees of human pressure, which shape the microbial communities thriving in these habitats, leading to the development of microbial resistance traits. The samples collected on the Portuguese northeast Atlantic coast waters show an unequivocal prevalence of Bacteria over Archaea with a high prevalence of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several taxa, such as the Vibrio genus, showed significant correlations with anthropogenic pollution. These anthropogenic pressures, along with the differences in species diversity among the surveyed sites, lead to observed differences in the presence and resistance-related sequences' abundance (set of all metal and antibiotic resistant genes and their precursors in pathogenic and non-pathogenic bacteria). Gene ontology terms such as antibiotic resistance, redox regulation and oxidative stress response were prevalent. A higher number of significant correlations were found between the abundance of resistance-related sequences and pollution, inorganic pressures and density of nearby population centres when compared to the number of significant correlations between taxa abundance at different phylogenetic levels and the same environmental traits. This points towards predominance of the environmental conditions over the sequence abundance rather than the taxa abundance. Our data suggest that the whole resistome profile can provide more relevant or integrative answers in terms of anthropogenic disturbance of the environment, either as a whole or grouped in gene ontology groups, appearing as a promising tool for impact assessment studies which, due to the ubiquity of the sequences across microbes, can be surveyed independently of the taxa present in the samples.

Research trends and hotspots of aquatic biofilms in freshwater environment during the last three decades: a critical review and bibliometric analysis

Freshwater periphytic biofilms (FPBs), existing widely in various aquatic environments, have attracted extensive attention for many years. In the present study, a bibliometric analysis based on Web of Science Core Collection (WoSCC) was used to understand the research progress, trends, and hot topics of FPBs qualitatively and quantitatively. The results indicated that publications on FPBs have increased from 1991 to 2020 rapidly, and researchers have focused more on the areas of environmental sciences, microbiology, and marine freshwater biology. The most influential countries were mainly the USA, Spain, France, and Germany. Cooperation network analysis reflected that the USA and its affiliated institutions played crucial roles in the research of FPB cooperation, but the collaboration between core author groups still fell short. Based on the analysis of top 20 high-cited FPB documents over the last 30 years, research hotspots mainly included micro-observation and assembly mechanisms of FPBs; interactions of FPBs and pollutants including heavy metals, antibiotic resistance genes, pathogens, organic pollutants, and nanoparticles; and the role of FPBs for biogeochemical cycling, especially nitrogen cycling. Additionally, future research directions were proposed. Overall, this study provides a comprehensive and systematic overview of FPBs, which is useful for research development and researchers who are interested in this area.

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.

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.

Contaminants of Emerging Concern in the Seine River Basin: Overview of Recent Research

For over 30 years, the sources and the transfer dynamics of micropollutants have been investigated in the PIREN-Seine programme. Recent works included a wide range of chemicals and biological contaminants of emerging concern (i.e. contaminants whose occurrence, fate and impact are scarcely documented). This chapter presents a brief overview of research recently conducted on contaminants as diverse as macro- and microplastics, poly- and perfluoroalkyl substances (PFASs), pathogenic protozoa, antibiotics and the associated antibiotic resistance. The multiscalar study of plastics and PFASs at a large spatial scale is rare; the results produced in recent years on the Seine River catchment have provided an original contribution to the investigation of the dynamics of these contaminants in urban environments. The results also highlighted that pathogenic protozoa are ubiquitous in the Seine River basin and that the contamination of bivalves such as Dreissena polymorpha could reflect the ambient biological contamination of watercourses. The widespread occurrence of antibiotics in the Seine River was demonstrated, and it was shown that the resistome of biofilms in highly urbanised rivers constitutes a microenvironment where genetic support for antibiotic resistance (clinical integrons) and resistance genes for trace metals are concentrated.

The Impact of Metal-Rich Sediments Derived from Mining on Freshwater Stream Life

Metal-rich sediments have the potential to impair life in freshwater streams and rivers and, thereby, to inhibit recovery of ecological conditions after any remediation of mine water discharges. Sediments remain metal-rich over long time periods and have long-term potential ecotoxicological interactions with local biota, unless the sediments themselves are physically removed or replaced by less metal-rich sediment. Laboratory-derived environmental quality standards are difficult to apply to the field situation, as many complicating factors exist in the real world. Therefore, there is a strong case to consider other, field-relevant, measures of toxic effects as alternatives to laboratory-derived standards and to seek better biological tools to detect, diagnose and ideally predict community-level ecotoxicological impairment. Hence, this review concentrated on field measures of toxic effects of metal-rich sediment in freshwater streams, with less emphasis on laboratory-based toxicity testing approaches. To this end, this review provides an overview of the impact of metal-rich sediments on freshwater stream life, focusing on biological impacts linked to metal contamination.

Simultaneous mercury oxidation and NO reduction in a membrane biofilm reactor

This work demonstrates bacterial oxidation of mercury (Hg⁰) coupled to nitric oxide (NO) reduction in a denitrifying membrane biofilm reactor (MBfR). In 93 days' operation, Hg⁰ and NO removal efficiency attained 90.7% and 74.1%, respectively. Thauera, Pseudomonas, Paracoccus and Pannonibacter played dual roles as Hg⁰ oxidizers and denitrifiers simultaneously. Denitrifying bacteria and the potential mercury resistant bacteria dominated the bacterial community. Denitrification-related genes (norB, norC, norD, norE, norQ and norV) and enzymatic Hg⁰ oxidation-related genes (katG, katE) were responsible for bacterial oxidation of Hg⁰ and NO reduction, as shown by metagenomic sequencing. XPS, HPLC-ICP-MS and SEM-EDS indicated the formation of a stable mercuric species (Hg²⁺) reasulting from Hg⁰ oxidation in the biofilm. Bacterial oxidation of Hg⁰ was coupled to NO reduction in which Hg⁰ served as the initial electron donor while NO served as the terminal electron acceptor and thereby redox between Hg⁰ and NO was formed. MBfR was capable of both Hg⁰ bio-oxidation and denitrifying NO reduction. This research opens up new possibilities for application of MBfR to simultaneous flue gas demercuration and denitration.

Mercury bioavailability, transformations, and effects on freshwater biofilms

Mercury (Hg) compounds represent an important risk to aquatic ecosystems because of their persistence, bioaccumulation, and biomagnification potential. In the present review, we critically examine state-of-the-art studies on the interactions of Hg compounds with freshwater biofilms, with an emphasis on Hg accumulation, transformations, and effects. Freshwater biofilms contain both primary producers (e.g., algae) and decomposers (e.g., bacteria and fungi), which contribute to both aquatic food webs and the microbial loop. Hence they play a central role in shallow water and streams, and also contribute to Hg trophic transfer through their consumption. Both inorganic and methylated mercury compounds accumulate in biofilms, which could transform them mainly by methylation, demethylation, and reduction. Accumulated Hg compounds could induce diverse metabolic and physiological perturbations in the microorganisms embedded in the biofilm matrix and affect their community composition. The bioavailability of Hg compounds, their transformations, and their effects depend on their concentrations and speciation, ambient water characteristics, biofilm matrix composition, and microorganism-specific characteristics. The basic processes governing the interactions of Hg compounds with biofilm constituents are understudied. The development of novel conceptual and methodological approaches allowing an understanding of the chemo- and biodynamic aspects is necessary to improve the knowledge on Hg cycling in shallow water as well as to enable improved use of freshwater biofilms as potential indicators of water quality and to support better informed risk assessment. Environ Toxicol Chem 2017;36:3194-3205. © 2017 SETAC.

Biofilm composition in the Olt River (Romania) reservoirs impacted by a chlor-alkali production plant

Freshwater biofilms can be useful indicators of water quality and offer the possibility to assess contaminant effects at the community level. The present field study examines the effects of chlor-alkali plant effluents on the community composition of biofilms grown in the Olt River (Romania) reservoirs. The relationship between ambient water quality variables and community composition alterations was explored. Amplicon sequencing revealed a significant modification of the composition of microalgal, bacterial and fungal communities in the biofilms collected in the impacted reservoirs in comparison with those living in the uncontaminated control reservoir. The abundance corrected Simpson index showed lower richness and diversity in biofilms collected in the impacted reservoirs than in the control reservoir. The biofilm bacterial communities of the impacted reservoirs were characterized by the contaminant-tolerant Cyanobacteria and Bacteroidetes, whereas microalgal communities were predominantly composed of Bacillariophyta and fungal communities of Lecanoromycetes and Paraglomycetes. A principal component analysis revealed that major contaminants present in the waste water of the chlor-alkali production plant, i.e. Na⁺, Ca²⁺, Cl^- and Hg, were correlated with the alteration of biofilm community composition in the impacted reservoirs. However, the biofilm composition was also influenced by water quality variables such as NO₃^-, SO₄^2-, DOC and Zn from unknown sources. The results of the present study imply that, even when below the environmental quality standards, typical contaminants of chlor-alkali plant releases may affect biofilm composition and that their impacts on the microbial biodiversity might be currently overlooked.

Influence of chemical speciation and biofilm composition on mercury accumulation by freshwater biofilms

Mercury (Hg) is a pollutant of high concern for aquatic systems due to the biomagnification of its methylated form along the food chain. However, in contrast to other metals, gaining knowledge of its bioavailable forms for aquatic microorganisms remains challenging, making Hg risk assessment difficult. Ubiquitous and sessile freshwater biofilms are well known to accumulate and to transform Hg present in their ambient environment. The present study thus aims to evaluate whether non-extractable (proxy of intracellular) Hg accumulated by biofilms could be a good indicator of Hg bioavailability for microorganisms in freshwater. To that end, the link between Hg concentration and speciation, as well as biofilm composition (percentage of abiotic, biotic, chlorophyll and phycocyanin-fractions and abundance of dsrA, gcs, merA and hgcA bacterial genes) and biofilm Hg accumulation was examined. The studied biofilms were grown on artificial substrata in four reservoirs along the Olt River (Romania), which was contaminated by Hg coming from chlor-alkali plant effluents. The 0.45 μm-filterable Hg concentrations in ambient waters were measured and inorganic IHg speciation was modelled. Biofilms were analyzed for their non-extractable IHg and methylmercury (MeHg) contents as well as for their composition. The non-extractable IHg content was related, but not significantly, to the concentration of total IHg (r² = 0.88, p = 0.061) whereas a significant correlation was found with the predicted IHg concentration that is not bound to dissolved organic matter (r² = 0.95, p = 0.027), despite its extremely low concentrations (10^-25 M), showing a limitation of the thermodynamic Hg modelling to predict Hg bioavailability. The studied biofilms were different in biomass and composition and a principal component analysis showed that the non-extractable IHg content correlated with the abundance of the merA and hgcA genes, while MeHg accumulation was only linked with the abundance of the rRNA 16S gene. The present study suggests that non-extractable IHg concentrations in biofilms are a useful proxy of IHg bioavailable forms in waters whereas the hgcA and merA genes are good biomarkers of both biofilm IHg exposure and bioavailability.

Diversity change of microbial communities responding to zinc and arsenic pollution in a river of northeastern China

Pollution discharge disturbs the natural functions of water systems. The environmental microbial community composition and diversity are sensitive key indicators to the impact of water pollutant on the microbial ecology system over time. It is meaningful to develop a way to identify the microbial diversity related to heavy metal effects in evaluating river pollution. Water and sediment samples were collected from eight sections along the Tiaozi River where wastewater and sewage were discharged from Siping City in northeastern China. The main pollutants contents and microbial communities were analyzed. As the primary metal pollutants, zinc (Zn) and arsenic (As) were recorded at the maximum concentrations of 420 and 5.72 μg/L in the water, and 1704 and 1.92 mg/kg in the sediment, respectively. These pollutants posed a threat to the microbial community diversity as only a few species of bacteria and eukaryotes with strong resistance were detected through denaturing gradient gel electrophoresis (DGGE). Acinetobacter johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii were the dominant bacteria in the severely polluted areas. The massive reproduction of Limnodrilus hoffmeisteri almost depleted the dissolved oxygen (DO) and resulted in the decline of the aerobic bacteria. It was noted that the pollution reduced the microbial diversity but the L. hoffmeisteri mass increased as the dominant community, which led to the overconsuming of DO and anaerobic stinking water bodies. Water quality, concentrations of heavy metals, and the spatial distribution of microbial populations have obvious consistencies, which mean that the heavy metals in the river pose a serious stress on the microorganisms.

Development of magnetic separation and quantum dots labeled immunoassay for the detection of mercury in biological samples

A rapid and sensitive immunoassays of mercury (Hg) in biological samples was developed using quantum dots (QDs) and magnetic beads (MBs) as fluorescent and separated probes, respectively. A monoclonal antibody (mAb) that recognizes an Hg detection antigen (BSA-DTPA-Hg) complex was produced by the injection of BALB/c mice with an Hg immunizing antigen (KLH-DTPA-Hg). Then the ascites monoclonal antibodies were purified. The Hg monoclonal antibody (Hg-mAb) is conjugated with MBs to separate Hg from biological samples, and the other antibody, which is associated with QDs, is used to detect the fluorescence. The Hg in biological samples can be quantified using the relationship between the QDs fluorescence intensity and the concentration of Hg in biological samples following magnetic separation. In this method, the detection linear range is 1-1000ng/mL, and the minimum detection limit is 1ng/mL. The standard addition recovery rate was 94.70-101.18%. The relative standard deviation values were 2.76-7.56%. Furthermore, the Hg concentration can be detected in less than 30min, the significant interference of other heavy metals can be avoided, and the simultaneous testing of 96 samples can be performed. These results indicate that the method could be used for rapid monitoring Hg in the body.