Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks

Microbial diversity and abundance of Hg related genes from water, sediment and soil the Colombian amazon ecosystems impacted by artisanal and small-scale gold mining

The Amazon region abounds in precious mineral resources including gold, copper, iron, and coltan. Artisanal and small-scale gold mining (ASGM) poses a severe risk in this area due to considerable mercury release into the surrounding ecosystems. Nonetheless, the impact of mercury on both the overall microbiota and the microbial populations involved in mercury transformation is not well understood. In this study we evaluated microbial diversity in samples of soil, sediment and water potentially associated with mercury contamination in two localities (Taraira and Tarapacá) in the Colombian Amazon Forest. To this end, we characterized the bacterial community structure and mercury-related functions in samples from sites with a chronic history of mercury contamination which today have different levels of total mercury content. We also determined mercury bioavailability and mobility in the samples with the highest THg and MeHg levels (up to 43.34 and 0.049 mg kg-1, respectively, in Taraira). Our analysis of mercury speciation showed that the immobile form of mercury predominated in soils and sediments, probably rendering it unavailable to microorganisms. Despite its long-term presence, mercury did not appear to alter the microbial community structure or composition, which was primarily shaped by environmental and physicochemical factors. However, an increase in the relative abundance of merA genes was detected in polluted sediments from Taraira. Several Hg-responsive taxa in soil and sediments were detected in sites with high levels of THg, including members of the Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi phyla. The results suggest that mercury contamination at the two locations sampled may select mercury-adapted bacteria carrying the merA gene that could be used in bioremediation processes for the region.

Magnetite-equipped algal-rich sediments for microbial fuel cells: Remediation of sediment organic matter pollution and mechanisms of remote electron transfer

Using the bio-electrochemical methods for the restoration of high algae sediments is full of potential and challenges. How to promote extracellular electron transfer (EET) process in microbial fuel cells (MFC) is the key bottleneck. The study had explored the potential application of magnetite on accelerating electron transfer for improving the output of MFC and sediment pollution remediation. The results indicated that the organic matter degradation rate showed a remarkable increase of 27.45 %, and the voltage output was approximately 1.68 times higher compared to the MFC configured with regular sediment. Abundant electroactive bacteria (EABs), such as Geobacter and Burkholderiaceae, and fermentative bacteria were responsible for these results, accompanied by the enhanced fluorescence of humic substances (HS), increased concentration and activity of cytochrome C (25.05 % and 21.12 %), as well as elevated extracellular polymeric substance content. Moreover, the intrinsic EET mechanisms among Fe-oxides, HS, and EABs were explored. According to the electrochemical analysis and substance transformation, the EET process involved four stages: magnetite-enhanced direct electron transfer via strong conductivity, iron respiration mediating electron transfer to the electrode, the model quinone substance acting as an electron shuttle facilitating EET and iron reduction, and iron cycling mediating electron transfer. This study provides an effective strategy for pollution remediation in algal-rich sediment, which was beneficial for the harmless treatment and resource utilization of both algae and sediment, simultaneously.

Remobilization of Cd caused by iron oxide phase transformation and Mn2+ competition after stabilization by nano zero valent iron

Stabilization techniques are vital in controlling Cd soil pollution. Nano zero valent iron (nZVI) has been extensively utilized for Cd remediation owing to its robust adsorption and reactivity. However, the environmental stress-induced stability of Cd after nZVI addition remains unclear. A pot experiment was conducted to evaluate the Cd bioavailability in continuously flooded (130 d) soil after stabilization with nZVI. The findings indicated that nZVI application did not result in a decline in Cd concentration in rice, as compared to the no-nZVI control. Additionally, nZVI simultaneously increased the available Cd concentration, iron-manganese oxide-bound (OX) Mn fraction, and relative abundance of Fe(III)-reducing bacteria, but it decreased OX-Cd and Mn availability in soil. Cadmium in rice tissues was positively correlated with the available Cd in soil. The results of subsequent adsorption tests demonstrated that CdO was the product of Cd adsorption by the nZVI aging products. Conversely, Mn2+ decreased the adsorption capacity of Cd-containing solutions. These results underscore the crucial role of both biotic and abiotic factors in undermining the stabilization of nZVI under continuous flooding conditions. This study offers novel insights into the regulation of nZVI-mediated Cd stabilization efficiency in conjunction with biological inhibitors and functional modification techniques.

Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes

Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.

Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center

The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.

Fractionation analysis and risk assessment of potential toxic elements in reservoir sediments in central China

The pollution of potential toxic elements (PTEs) in the environment is a persistent issue and draws public attention constantly. However, there is no study comprehensively assessing the PTE pollution of water supply reservoirs in central China. This study determined the total contents and fractions of seven PTEs in 10 water supply reservoirs of central China, and evaluated PTE pollution risks by adopting various models. The results indicated that PTE pollution in water supply reservoirs was lower comparing that in estuary or river sediments, and Mn (manganese) was the predominant PTE in central China reservoirs. Fractionation analysis revealed that for B1 fraction (exchangeable/acid-soluble fraction) of Mn, Zn (zinc) and B2 fraction (reducible fraction) of Pb (lead) was high, while the effective state portion of Cr (chromium) was small. The monomial potential ecological risk indices and Igeo values were low among most samples, indicating overall modest PTE pollution. However, the results of the individual contamination factor (ICF) suggested that Pb might lead to potential health risks to human beings.

A new insight to explore toxic Cd(II) affecting denitrification: Reaction kinetic, electron behavior and microbial community

Denitrification process is a crucial step in nitrogen removal and is more vulnerable to external shocks due to the fact that anoxic process is always located before aerobic process in conventional sewage treatment. This study aims to elaborate the nitrogen conversion characteristics by investigating denitrification kinetics, electron behavior and microbial community under Cd(II) shock. Reaction kinetics showed that 10 mg/L of Cd(II) accelerated nitrate reduction rate by 52.29% but 80 mg/L of Cd(II) severely decelerated it by 95.41% with the accumulation of nitrite. High concentration of COD (C/N = 10.4) in the system caused by Cd(II) disrupting the integrity of cell membrane (lactate dehydrogenase increased by 328.7%) was proved to induce occurrence of Dissimilatory Nitrate Reduction to Ammonia (DNRA). The electron transport system activity (ETSA), electron consumption and electron distribution were combined to reveal the electron behavior regulated by Cd(II). The electron ratio of nitrate reductase to nitrite reductase increased from 1.48 (control) to 3.91 and 3.52 (40 and 80 mg/L of Cd(II)) indicated the electrons allocating tendency and further explained the nitrite accumulation. High concentration of Cd(II) also decreased ETSA by weakening the physiological activities of flavin adenine dinucleotide, flavin mononucleotide and cytochrome c or hindered the microbes to secrete these electron carriers. Furthermore, Cd(II) inhibited dominant bacteria genera containing napA gene (Azospirillum and Thauera) and nirS gene (unclassified_c_Betaproteobacteria). Enterobacteriaceae family was found to dominate the DNRA process.

Metagenome-Assembled Genomes from Monte Cristo Cave (Diamantina, Brazil) Reveal Prokaryotic Lineages As Functional Models for Life on Mars

Microbial communities have been explored in various terrestrial subsurface ecosystems, showing metabolic potentials that could generate noteworthy morphological and molecular biosignatures. Recent advancements in bioinformatic tools have allowed for descriptions of novel and yet-to-be cultivated microbial lineages in different ecosystems due to the genome reconstruction approach from metagenomic data. Using shotgun metagenomic data, we obtained metagenome-assembled genomes related to cultivated and yet-to-be cultivated prokaryotic lineages from a silica and iron-rich cave (Monte Cristo) in Minas Gerais State, Brazil. The Monte Cristo Cave has been shown to possess a high diversity of genes involved with different biogeochemical cycles, including reductive and oxidative pathways related to carbon, sulfur, nitrogen, and iron. Three genomes were selected for pangenomic analysis, assigned as Truepera sp., Ca. Methylomirabilis sp., and Ca. Koribacter sp. based on their lifestyles (radiation resistance, anaerobic methane oxidation, and potential iron oxidation). These bacteria exhibit genes involved with multiple DNA repair strategies, starvation, and stress response. Because these groups have few reference genomes deposited in databases, our study adds important genomic information about these lineages. The combination of techniques applied in this study allowed us to unveil the potential relationships between microbial genomes and their ecological processes with the cave mineralogy and highlight the lineages involved with anaerobic methane oxidation, iron oxidation, and radiation resistance as functional models for the search for extant life-forms outside our planet in silica- and iron-rich environments and potentially on Mars.

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

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

A comprehensive exploration on distribution, risk assessment, and source quantification of heavy metals in the multi-media environment from Shaying River Basin, China

Comprehensively understand the distribution of pollutants in the multi-media environment at basin scale is of major importance to the ecological risk assessment and pollution control. In this study, multi-media contamination characteristics of eight heavy metals in the water, soil, and sediment from the Shaying River Basin of China have been analyzed to probe their ecological risks and potential sources. Results revealed that heavy metal concentrations in pore water were higher than those in surface water. While the mean concentrations of most heavy metals increased follow the order of bankside soil (BS)<water-level-fluctuating zone soil (WLFZS)<sediment. The WLFZ was an important transition zone between the BS and sediment for pollutant exchange. The mean heavy metal concentrations in surface water were all below their corresponding water quality standards except Hg. Whereas the mean concentrations of Cr, Ni, Zn, Cd, and Hg in BS, WLFZS, and sediment exceeded their corresponding background values. The assessment results of pollution and risks indicated that Hg and Cd posed the highest potential risks in each medium. Furthermore, according to the factor analysis and PMF model, six potential sources were identified, in which agricultural, fuel combustion, and industrial sources were the dominant anthropogenic sources, accounting for 23.84%, 17.43%, and 14.25% of the total contribution.

Spatiotemporal dynamics of the resistome and virulome of riverine microbiomes disturbed by a mining mud tsunami

Aquatic ecosystems are highly vulnerable to anthropogenic activities. However, it remains unclear how the microbiome responds to press disturbance events in these ecosystems. We examined the impact of the world's largest mining disaster (Brazil, 2015) on sediment microbiomes in two disturbed rivers compared to an undisturbed river during 390 days post-disturbance. The diversity and structure of the virulome and microbiome, and of antibiotic and metal resistomes, consistently differed between the disturbed and undisturbed rivers, particularly at day 7 post-disturbance. 684 different ARGs were predicted, 38% were exclusive to the disturbed rivers. Critical antibiotic resistance genes (ARGs), e.g., mcr and ereA2, were significantly more common in the disturbed microbiomes. 401 different ARGs were associated with mobile genetic elements (MGEs), 95% occurred in the disturbed rivers. While plasmids were the most common MGEs with a broad spectrum of ARGs, spanning 16 antibiotic classes, integrative conjugative elements (ICEs) and integrons disseminated ARGs associated with aminoglycoside and tetracycline, and aminoglycoside and beta-lactam, respectively. A significant increase in the relative abundance of class 1 integrons, ICEs, and pathogens was identified at day 7 in the disturbed microbiomes, 72-, 14- and 3- fold higher, respectively, compared with the undisturbed river. Mobile ARGs associated with ESKAPEE group pathogens, while metal resistance genes and virulence factor genes in nonpathogenic hosts predominated in all microbiomes. Network analysis showed highly interconnected ARGs in the disturbed communities, including genes targeting antibiotics of last resort. Interactions between copper and beta-lactam/aminoglycoside/macrolide resistance genes, mostly mobile and critical, were also uncovered. We conclude that the mud tsunami resulted in resistome expansion, enrichment of pathogens, and increases in promiscuous and mobile ARGs. From a One Health perspective, mining companies need to move toward more environmentally friendly and socially responsible mining practices to reduce risks associated with pathogens and critical and mobile ARGs.

Stable immobilization of uranium in iron containing environments with microbial consortia enriched via two steps accumulation method

The stable stabilization of uranium (U) in iron (Fe) containing environments is restricted by the reoxidation of UO₂. In the current study, based on air reoxidation tests, we propose a novel two steps accumulation method to enrich microbial consortia from paddy soil. The constructed microbial consortia, denoted as the Fe-U bacteria, can co-precipitate U and Fe to form stable Fe-U solids. Column experiments running for 4 months demonstrated the production of U(IV)-O-Fe(II) precipitates containing maximum of 39.51% uranium in the presence of Fe-U bacteria. The reoxidation experiments revealed the U(IV)-O-Fe(II) precipitates were more stable than UO₂. 16S rDNA high throughput sequencing analysis demonstrated that Acinetobacter and Stenotrophomonas were responsible for Fe and U precipitation, while, Caulobacteraceae and Aminobacter were crucial for the formation of U(VI)-PO₄ chemicals. The proposed two steps accumulation method has an extraordinary application potential in stable immobilization of uranium in iron containing environments.

The interaction of acidophiles driving community functional responses to the re-inoculated chalcopyrite bioleaching process

Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe³⁺ coupling with S⁰ oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or sulfur oxidizers (SO) were inoculated to chalcopyrite microcosm, then they were crossly re-inoculated again to characterize the interspecific interaction patterns. The results showed that the dominant species in Fe groups were Acidithiobacillus ferrooxidans, while A. thiooxidans predominated in S groups. Introducing FeO resulted in a great disturbance by shifting the community diversity and evenness significantly (p < 0.05). In comparison, the communities intensified by SO maintained the original composition and structures. Microbial networks were constructed positively and modularly. The networks intensified by FeO were less connected and complex with less nodes and edges, but showed faster responses to the re-inoculation disturbance reflected by shorter average path length. Interestingly, the genus Leptospirillum were identified as keystones in S groups, playing critical roles in iron-oxidizing with lots of sulfur oxidizers. The introduced sulfur oxidizers enhanced microbial cooperation, formed robust community with strong bio-dissolution capability, and harbored the highest bioleaching efficiency. These findings improved our understanding about the acidophiles interactions, which drive community functional responses to the re-inoculated bioleaching process.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Improved enrichment factor model for correcting and predicting the evaluation of heavy metals in sediments

As the most widely used method for evaluating heavy metals (HMs) in soil or sediment, the enrichment factor (EF) is prone to bias and even yields misleading assessment results for HM pollution due to data uncertainties, lack of local background values and a failure to assess the comprehensive pollution of multiple HMs. Here, we developed an improved EF model integrating stochastic mathematical methods and geochemical baselines (GBs). First, GBs were obtained using the relative cumulative frequency distribution method. The probability that each HM belongs to each enrichment degree was then quantified based on the probability density function deduced from the maximum entropy method. Furthermore, we defined a synthetic index to reveal the probability that multiple HMs belongs to comprehensive enrichment degree considering the weight of each HM. Finally, the enrichment category for each HM and multiple HMs were determined following the first-order moment principle. The improved EF model was successfully applied to evaluate and predict the HM pollution in sediments collected from Poyang Lake, the largest freshwater lake in China. Slight enrichment (1.88) of multiple HMs was found in sediments from Poyang Lake, characterized by a pronounced probability (0.35) to deteriorate to the "moderate enrichment" category. Among the different HMs, Cd requires more attention considering its dominant contribution (0.51) to the comprehensive pollution and high probability (0.65) for deterioration. Otherwise, assessment results employing the improved EF model agree with the spatial patterns of HM concentrations based on spatial autocorrelation analysis and source apportionment using Pb isotopic signatures and principal component analysis. Compared with the conventional EF method, the assessment results of the improved EF model were more accurate, comprehensive and reliable. In conclusion, the improved EF model has a better capability of evaluating and predicting HM enrichment in sediments and can be helpful for optimizing control measures for HM pollution.

Combined heterotrophic and autotrophic system for advanced denitrification of municipal secondary effluent in full-scale plant and bacterial community analysis

Total nitrogen (TN) removal is the major technical challenge for wastewater treatment plants to meet the more stringent discharge standard. In this study, lab- (0.05 m³/d), pilot- (1000 m³/d) and full-scale (10,000 m³/d) combined heterotrophic and autotrophic denitrification reactors (HARs) were designed and operated to treat municipal secondary effluent. During the 110-day stable operation, the effluent TN was reduced below 2.5 mg/L without secondary pollution causing by the excessive addition of organics, close to Class IV of Environmental Quality Standards for Surface Water. The bacterial richness and diversity increased with the expansion of reactor scale. Denitrifying bacteria (DB) dominated in all reactors, however, Thiomonas (12.42%), Methylotenera (6.35%), Thiobacillus (20.62%), Methyloverstatilis (5.44%) and Thauera (8.21%) were the main genera in lab-, pilot- and full-scale reactors respectively. The denitrification efficiency temporarily deteriorated at the later stage, and redundancy analysis (RDA) indicated the obviously increased sulfate reducing bacteria (SRB) and sulfide were main contributors. Sludge supplement rapidly recovered the reactors performance in five days. This study suggests that HARs could be a promising technique for advanced denitrification of the municipal secondary effluent.

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences (p < 0.05) in the concentrations of total VFA and the proportions of acetate and butyrate in the rumen fluid among the three groups, whereas the proportions of propionate and the acetate/propionate ratio did not differ substantially. Alpha diversity of the rumen bacterial and archaeal populations in the GR and SF kids was significantly higher (p < 0.05) than that in the IF goat kids, and significant differences (p < 0.05) in similarity were observed in the comparisons of GR vs. IF and SF vs. IF. The most predominant bacterial phyla were Bacteroidetes and Firmicutes across the three groups, and the archaeal community was mainly composed of Euryarchaeota. At the genus and species levels, the cellulose-degrading bacteria, including Lachnospiraceae, Ruminococcaceae and Butyrivibrio fibrisolvens, were abundant in the GR and SF groups. Furthermore, 27 bacterial and 11 unique archaeal taxa, such as Lachnospiraceae, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium, were identified as biomarkers, and showed significantly different (p < 0.05) abundances among the three groups. Significant Spearman correlations (p < 0.05), between the abundances of several microbial biomarkers and the concentrations of VFAs, were further observed. In summary, our results demonstrated that the adaptation to grazing required more rumen bacterial populations due to complex forage types in shrub-grassland, although the rumen fermentation pattern did not change substantially among the three feeding systems. Some microbial taxa could be used as biomarkers for different feeding systems, particularly cellulose-degrading bacteria associated with grazing.

Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments

For a century, the MetalEurop foundry released metals into the river "La Deûle". Previous work revealed higher microbial diversity in metal impacted sediments, and horizontal gene transfer mediated by conjugative plasmids was suggested to drive the community adaptation to metals. We used an integrative state-of-the-art molecular approach coupling quantitative PCR, conjugation assays, flow cytometry, fluorescence activated cell sorting and 16S rRNA gene amplicon sequencing to investigate the presence of conjugative plasmids and their propagation patterns in sediment microbiomes. We highlighted the existence of a native broad-host range IncP conjugative plasmid population in polluted sediments, confirming their ecological importance for microbial adaptation. However, despite incompatibilities and decreased transfer frequencies with our own alien IncP plasmid, we evidenced that a wide diversity of bacterial members was still prone to uptake the plasmid, indicating that sediment microbial communities are still inclined to receive conjugative plasmids from the same group. We observed that metal pollution favoured exogenous plasmid transfer to specific metal-selected bacteria, which are likely coming from upstream sources (e.g. wastewater treatment plant, farms…). Altogether, our results suggest that MetalEurop sediments are hotspots for gene transfer via plasmids, acting as an "environmental reservoir" for microbes and mobile elements released by human activities.

Cadmium (II) alters the microbial community structure and molecular ecological network in activated sludge system

Cadmium (II) can potentially alter the microbial community structure and molecular ecological network in activated sludge systems. In this study, we used Illumina sequencing combined with an RMT-based network approach to show the response of the microbial community and its network structure to Cd (II) in activated sludge systems. The results demonstrated that 1 mg/L Cd (II) did not have chronic negative effects on chemical oxygen demand (COD) reduction and denitrification processes, but negatively affected the nitrification process and phosphorus removal. In contrast, 10 mg/L Cd (II) adversely affected both COD and nutrient removal, and reduced the microbial diversity and changed the overall microbial community structure. The relative abundances of Nitrosomonadaceae, Nitrospira, Accumulibacter and Acinetobacter, which are involved in nitrogen removal, significantly decreased with increases in the Cd (II) concentration. In addition, molecular ecological network analysis showed that the networks sizes in the presence of higher levels of Cd (II) were smaller than in the control, but the nodes were more closely connected with neighbors. These shifts in bacterial abundance and the bacterial network structure may be responsible for the deterioration of COD and nutrient removal. Overall, this study provides new insights into the effects of Cd (II) on the bacterial community and its interactions in activated sludge systems.

A meta-taxonomic investigation of the prokaryotic diversity of water bodies impacted by acid mine drainage from the São Domingos mine in southern Portugal

The prokaryotic communities of water bodies contaminated by acid mine drainage from the São Domingos mining area in southern Portugal were analyzed using a meta-taxonomics approach with 16S rRNA gene sequences. Samples were collected in two seasonal sampling campaigns (summer and winter of 2017) from the most contaminated sites from where the water flows downstream to the freshwater reservoir of the river Chança. The physicochemical data indicate a trend of decreasing acid mine drainage contamination downstream of the mining area to the Chança's reservoir. The most contaminated sites (pH = 2.3-3.1) are distinguished by prokaryotic diversity with high abundances of operational taxonomics units related to acidophiles (genera Metallibacterium, Acidibacter, Leptospirillum, Acidobacterium, Thiomonas, Acidicapsa, Acidocella, Acidiphilium; family Acidobacteriaceae, order CPla-3 termite group). Likewise, in the transition zone in the mouth of the contaminated water flow into the Chança´s reservoir (pH = 6.4), a specific prokaryotic flora exists with some acidophiles, but notably with a cyanobacteria bloom and a high abundance of the genus Sediminibacterium (family I; order Subsection III). Moreover, the strong correlation between the abundance of acidophiles and characteristic physiochemical parameters (metals, acidity, and sulfate) confirm their potential as biomarkers of acid mine drainage pollution.

Adaption and restoration of anammox biomass to Cd(II) stress: Performance, extracellular polymeric substance and microbial community

Cadmium (Cd) can cause the deterioration of biological systems through inhibiting the enzymes activity and disturbing the microbial metabolism. Although the influence of Cd on conventional wastewater treatment process has been studied, the response of anammox to Cd exposure still remains unclear. This study firstly investigated the adaption and restoration of anammox biomass to Cd(II) stress. Results showed that long-term exposure of anammox bacteria to 2 mg L^-1 Cd(II) was beneficial for the reactor performance, while 5 mg L^-1 Cd(II) would cause the decline of SAA, extracellular polymeric substance content and relative abundance of Candidatus kuenenia by 40%, 25% and 31%, respectively. Furthermore, these indexes could approximately recover to the initial status after withdrawing Cd(II) from the influent. Overall, the anammox biomass exhibited a certain adaption and restoration ability to the suppression of Cd(II). This study may provide key valuable information for the biological treatment of wastewater containing Cd(II).

Chitin as a substrate for the biostimulation of sulfate-reducing bacteria in the treatment of mine-impacted water (MIW)

This study aims to know the basis of sulfate-reducing bacteria (SRB) and chitin source relationship for the development of a biotreatment system for mine-impacted water (MIW). The MIW consists of river water impacted by coal acid mine drainage (AMD), an extremely acid effluent, rich in sulfate and dissolved metal ions, with a high pollutant potential. Chitin was used as metal ion sorbent and biostimulant of SRB, whose anaerobic dissimilatory metabolism reduces sulfate to sulfide. Microcosms were built in an oxygen-free atmosphere using chitin from two different sources: commercial chitin and shrimp shell waste, which contains calcium carbonate, an acidity removal agent, in addition to chitin. The results indicate that the shrimp shell performs best in removing sulfate (99.75%), iron (99.04%), aluminum (98.47%), and manganese (100%) ions. The iron ion sorption kinetics of the sediments were also studied; pseudo-second order behavior was observed. High-throughput sequencing analysis revealed the present bacterial community and its abundance in the microcosms after 11 and 30 treatment days: SRB were detected but were not the majority. Thus, this research aims to contribute to the sustainable treatment MIW through the employment of an abundant and low-cost biomaterial.

Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions

Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China

Sediment is the one of most important storage of heavy metal. Microbiotas in sediment can be used as the effective indicators of heavy metals. The goal of this study was to understand the bacterial communities responding to heavy metal enrichment in sediments and prioritize some factors that affected significantly to bacterial community. Sediments were sampled from five river-lake systems in the Poyang Lake in dry season, and the bacterial community was analyzed using Illumina high-throughput sequencing. Relationships between sediment environment and the diversity and structure of bacterial communities were determined by correlation analysis and redundancy analysis (RDA). The result indicated that Cd and Sb were identified as the heavy metals of the great risk in sediments. Sediments from five river-lake systems shared 31.83% core operational taxonomic units (OTUs) of bacterial communities. Proteobacteria (33.54% of total sequences) and Actinobacteria (15.04%) were the dominant phyla across all sites. High enrichment of heavy metals (MRI and mC_d) resulted in low diversity of bacterial communities (Simpson index). The RDA revealed pH, OC, mCd, and Efs of As, Pb, Cd were major factors related to bacterial community structure changes. The dominant phylum Actinobacteria was regarded as tolerant bacteria, while the dominant phylum Proteobacteria was named as resistant bacteria in sediment with high anthropogenic Cd enrichment.

Arsenic mitigation in paddy soils by using microbial fuel cells

Arsenic (As) behavior in paddy soils couples with the redox process of iron (Fe) minerals. When soil is flooded, Fe oxides are transformed to soluble ferrous ions by accepting the electrons from Fe reducers. This process can significantly affect the fate of As in paddy fields. In this study, we show a novel technique to manipulate the Fe redox processes in paddy soils by deploying soil microbial fuel cells (sMFC). The results showed that the sMFC bioanode can significantly decrease the release of Fe and As into soil porewater. Iron and As contents around sMFC anode were 65.0% and 47.0% of the control respectively at day 50. The observed phenomenon would be explained by a competition for organic substrate between sMFC bioanode and the iron- and arsenic-reducing bacteria in the soils. In the vicinity of bioanode, organic matter removal efficiencies were 10.3% and 14.0% higher than the control for lost on ignition carbon and total organic carbon respectively. Sequencing of the 16S rRNA genes suggested that the influence of bioanodes on bulk soil bacterial community structure was minimal. Moreover, during the experiment a maximum current and power density of 0.31 mA and 12.0 mWm^-2 were obtained, respectively. This study shows a novel way to limit the release of Fe and As in soils porewater and simultaneously generate electricity.

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.

Phosphate enhanced abiotic and biotic arsenic mobilization in the wetland rhizosphere

Although abiotic process of competitive sorption between phosphate (P) and arsenate (As(V)), especially onto iron oxides, are well understood, P-mediated biotic processes of Fe and As redox transformation contributing to As mobilization and speciation in wetlands remain poorly defined. To gain new insights into the effects of P on As mobility, speciation, and bioavailability in wetlands, well-controlled greenhouse experiments were conducted. As expected, increased P levels contributed to more As desorption, but more interestingly the interactions between P and wetland plants played a synergistic role in the microbially-mediated As mobilization and enhanced As uptake by plants. High levels of P promoted plant growth and the exudation of labile organic carbon from roots, enhancing the growth of heterotrophic bacteria, including As and Fe reducers. This in turn resulted in both, more As desorption into solution due to reductive iron dissolution, and a higher fraction of the dissolved As in the form of As(III) due to the higher number of As(V) reducers. Consistent with the dissolved As results, arsenic-XANES spectra from solid medium samples demonstrated that more As was sequestered in the rhizosphere as As(III) in the presence of high P levels than for low P levels. Hence, increased P loading to wetlands stimulates both abiotic and biotic processes in the wetland rhizosphere, resulting in more As mobilization, more As reduction, as well as more As uptake by plants. These interactions are important to be taken into account in As fate and transport models in wetlands and management of wetlands containing As.

Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment

Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.