Dynamics of Bacterial Communities Mediating the Treatment of an As-Rich Acid Mine Drainage in a Field Pilot

Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection

Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.

Towards an understanding of the factors controlling bacterial diversity and activity in semi-passive Fe- and As-oxidizing bioreactors treating arsenic-rich acid mine drainage

Semi-passive bioreactors based on iron and arsenic oxidation and coprecipitation are promising for the treatment of As-rich acid mine drainages. However, their performance in the field remains variable and unpredictable. Two bioreactors filled with distinct biomass carriers (plastic or a mix of wood and pozzolana) were monitored during 1 year. We characterized the dynamic of the bacterial communities in these bioreactors, and explored the influence of environmental and operational drivers on their diversity and activity. Bacterial diversity was analyzed by 16S rRNA gene metabarcoding. The aioA genes and transcripts were quantified by qPCR and RT-qPCR. Bacterial communities were dominated by several iron-oxidizing genera. Shifts in the communities were attributed to operational and physiochemical parameters including the nature of the biomass carrier, the water pH, temperature, arsenic, and iron concentrations. The bioreactor filled with wood and pozzolana showed a better resilience to disturbances, related to a higher bacterial alpha diversity. We evidenced for the first time aioA expression in a treatment system, associated with the presence of active Thiomonas spp. This confirmed the contribution of biological arsenite oxidation to arsenic removal. The resilience and the functional redundancy of the communities developed in the bioreactors conferred robustness and stability to the treatment systems.

Changes in the prokaryotic diversity in response to hydrochemical variations during an acid mine drainage passive treatment

Acid mine drainage (AMD) causes major environmental problems and consequently, several treatments are proposed, favoring the passive systems because of their many advantages. The main goal of these procedures is the neutralization and removal of potentially toxic elements (PTE), yet little is known about the changes in the microbial assemblages in response to the hydrochemical variations during the treatments. Therefore, the main objective of this research was to determine the changes in the diversity and structure of the prokaryotic assemblages in a hybrid abiotic and biological (wetland) passive treatment system. The 16S rRNA gene survey showed that the AMD coming from the mine (pH 2.6) was mainly composed of acidophilic genera such as Acidithiobacillus, Leptospirillum, Ferritrophicum, and Cuniculiplasma (up to 76 % relative abundance). In the abiotic treatment, Acidiphilium was dominant in the sections with limestone filters (pH 2.2-4.8), followed by Limnobacter in the subsequent dolomite/limestone and phosphoric rock filters (pH 5.2-5.8). In these abiotic passive treatment sections, the microbial assemblage showed a limited diversity and richness. However, when the treated AMD reached the two final wetlands (pH ~6.8), the microbial diversity and richness increased, suggesting that further bioattenuation mechanisms might be occurring. Limnobacter and Novosphingobium were the main bacterial genera in the water samples of the wetland sections (Arundo donax). These changes in the composition of the microbial assemblages were highly correlated with the pH and Eh values during the treatment (p-value <0.001); however, the concentration of metal(loid)s such as Al, Cd, Fe, Mn, Ni, and Zn were also significantly related (p-value <0.05). In conclusion, the studied passive AMD treatment system enhanced the chemical quality of the treated AMD, showing high removal efficiencies for Al and Fe (> 99 %), and increasing the microbial diversity and richness in the effluent.

Start-Up and Performance of a Full Scale Passive System In-Cluding Biofilters for the Treatment of Fe, as and Mn in a Neutral Mine Drainage

Passive mine drainage treatment plants are the scene of many chemical and biological reactions. Here, the establishment of iron (Fe), arsenic (As), and manganese (Mn) removal was monitored immediately after the commissioning of the Lopérec (Brittany, France) passive water treatment plant, composed of aeration cascades and settling ponds followed by pozzolana biofilters. Iron and As were almost completely removed immediately after commissioning, while Mn removal took more than 28 days to reach its maximum performance. Investigations were performed during two periods presenting strong variations in feeding flow-rates: from 2.8 m3.h−1 to 8.6 m3.h−1 and from 13.2 m3.h−1 to 31.3 m3.h−1. Design flow rate was reached during the first week of the second period. Dissolved Fe and As were not affected by the decrease in residence time while Mn was only slightly affected. Microbial communities in biofilter presented similarities with those of the pond sludge, and genera including Mn-oxidizing species were detected. Proportion of bacteria carrying the aioA gene encoding for As(III)-oxidase enzyme increased in communities during the second period. Results suggest Mn removal is mainly associated with bio-oxidation whereas removal of Fe and As could be mainly attributed to chemical oxidation and precipitation of Fe, possibly helped by As(III) bio-oxidation.

Seasonal effects of natural attenuation on drainage contamination from artisanal gold mining, Cambodia: Implication for passive treatment

In Mondulkiri province, Cambodia, artisanal gold miners dump tailings and wastewater from gold processing into a tributary of the Prek Te River. In the rainy season, heavy metal concentrations in the tributary decrease below the WHO drinking water standard levels through natural attenuation; however, this does not occur in the dry season. To further understand the natural attenuation mechanism, detailed analyses of the wastewater from tailing and tributary water, tributary sediments, waste rock, and ore minerals were undertaken in both seasons. The high concentration of dissolved Fe in the contaminated tributary plays a significant role in As removal during the rainy season, whereas other elements such as Ni, Se, and Cu concentration decrease due to dilution. Schwertmannite formation, controlled by iron-oxidizing bacteria, was only found at the bottom of the tributary during the rainy season. In the dry season, As, Ni, Se, and Cu concentrations remained at their original levels because there was no formation of schwertmannite or dilution by rainwater. The existing schwertmannite also starts to dissolve as the pH decreases. Seasonal dynamics cause the failure of natural attenuation; thus, methods for maintaining its effectiveness in the dry season are needed. In addition, geochemical modeling was conducted to determine the significant roles of schwertmannite formation and dilution of rainwater in the tributary. Schwertmannite is a potential adsorbent for As removal from drainage. However, dilution provided indirect and direct impacts on the tributary, such as increasing the pH and diluting the concentration of toxic elements.

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3)

The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO₄²⁻, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg²⁺ and SO₄²⁻ were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg²⁺ and SO₄²⁻, Ca²⁺, temperature, and Fe²⁺, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg²⁺ and SO₄²⁻ concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.

Integrating sulfur, iron(II), and fixed organic carbon for mixotrophic denitrification in a composite filter bed reactor for decentralized wastewater treatment: Performance and microbial community

Decentralized wastewater treatment in rural areas is an imperative challenge around the world, particularly in developing countries. The composite filter bed reactor is viable for decentralized wastewater treatment, but its performance on nitrogen removal often fluctuates with the unstable influent characteristics and loadings. Here, a composite filter bed reactor integrating sulfur, iron(II), and fixed organic carbon (shaddock peel) was developed and continuously operated under different conditions. The fixed organic carbon source promoted nitrogen removal with an efficiency higher than 90% and reduced effluent sulfate level by 40%, indicating that the integrated electron donors could improve the resistance and stability of the reactor. Moreover, sulfur-oxidizing bacteria (Thiomonas, Sulfuriferula, and Acidithiobacillus), iron-oxidizing bacteria (Ferritrophicum), and denitrifiers (Simplicispira and Hydrogenophaga) were identified in the anoxic/anaerobic layer of the reactor, suggesting that mixotrophic denitrification was stimulated by sulfur, iron(II), and fixed organic carbon. The findings of this study indicate that the developed reactor with the integrated electron donors could be reliable for carbon, nitrogen, and phosphorus removal and promising for the application of decentralized wastewater treatment.

A watershed impacted by anthropogenic activities: Microbial community alterations and reservoir of antimicrobial resistance genes

Water is the main resource for maintaining life. Anthropic activities influence the microbial epidemiological chain in watersheds, which can act as ways of disseminating microorganisms resistant to antimicrobial drugs, with impacts on human, animal, and environmental health. Here, we characterized aquatic microbial communities and their resistomes in samples collected along Rio das Ostras watershed during two seasons. Surface water samples were collected at eleven sites from the Jundiá, Iriry, and Rio das Ostras rivers in two seasons (dry and wet season). Microbial DNA was extracted, high-throughput sequenced and screened for antimicrobial resistance genetic (ARG) markers. The physicochemical characteristics and the microbiota data confirmed that Rio das Ostras watershed can be divided into three well defined portions: rural, urban, and marine. Rural areas were enriched by bacteria typically found in limnic environments and Patescibacteria phyla. The urban portion was characterized by sites with low pH and groups associated with iron oxidation. Some genera of clinical relevance were also identified, though in relatively low abundance. The marine site was enriched mainly by Cyanobacteria and bacteria that showed strong correlation with conductivity, salinity, and chloride. Twenty-six ARG markers were identified on the resistome, being found most frequently in the urban area, despite being present in rural sites. Among them were some related to classes of great clinical concern, such as genes coding for extended-spectrum beta-lactamase (bla_CTX-M and bla_TEM), resistance to carbapenems (bla_KPC) and to methicillin by Staphylococcus aureus (mecA). These results broaden our understanding of the microbial community of a watershed impacted by anthropogenic actions. The large number of ARGs detected along the Rio das Ostras watershed contrasts with the small number of microorganisms of clinical relevance observed, suggesting that antimicrobial resistance has arisen from non-clinical environments and microbes. Our results corroborate that freshwater acts as a reservoir of antimicrobial resistance genes.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

Mixotrophic Iron-Oxidizing Thiomonas Isolates from an Acid Mine Drainage-Affected Creek

Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: Thiomonas ferrovorans FB-6 and Thiomonas metallidurans FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments. These strains precipitated amorphous iron oxides, lepidocrocite, goethite, and magnetite or maghemite and grew at a pH optimum of 5.5. While Thiomonas spp. are known as mixotrophic sulfur oxidizers and As oxidizers, the FB strains oxidized Fe, which suggests they can efficiently remove Fe and other metals via coprecipitation. Previous evidence for Thiomonas sp. Fe oxidation is largely ambiguous, possibly because of difficulty demonstrating Fe oxidation in heterotrophic/mixotrophic organisms. Therefore, we also conducted a genomic analysis to identify genetic mechanisms of Fe oxidation, other metal transformations, and additional adaptations, comparing the two FB strain genomes with 12 other Thiomonas genomes. The FB strains fall within a relatively novel group of Thiomonas strains that includes another strain (b6) with solid evidence of Fe oxidation. Most Thiomonas isolates, including the FB strains, have the putative iron oxidation gene cyc2, but only the two FB strains possess the putative Fe oxidase genes mtoAB The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known Thiomonas genetic potential. Our results revealed that the FB strains are two distinct novel species of Thiomonas with the genetic potential for bioremediation of AMD via iron oxidation.IMPORTANCE As AMD moves through the environment, it impacts aquatic ecosystems, but at the same time, these ecosystems can naturally attenuate contaminated waters via acid neutralization and catalyzing metal precipitation. This is the case in the former Ronneburg uranium-mining district, where AMD impacts creek sediments. We isolated and characterized two iron-oxidizing Thiomonas species that are mildly acidophilic to neutrophilic and that have two genetic pathways for iron oxidation. These Thiomonas species are well positioned to naturally attenuate AMD as it discharges across the landscape.

Effect of neutralizing agents on the type of As co-precipitates formed by in situ Fe oxides synthesis and its impact on the bioaccessibility of As in soil

The bioaccessibility of heavy metals in soil is closely related to their potential risk. Therefore, developing techniques for reducing it needs considerable attention. In this study, we aimed to co-precipitate soil As(V) through an in situ formation of Fe oxides, thereby reducing its bioaccessibility. Soil As(V) was co-precipitated by introducing 2% Fe-nitrate (w/w) and 30% water (v/w) into soil at pH ~7. Two different neutralizing agents (NaOH and CaO) were used to induce the precipitation of Fe oxides, and their effects on the speciation of As were investigated. In all the stabilized soils, the exchangeable As fraction decreased, and the fraction of As bound to amorphous Fe oxides increased by a factor of more than 1.4. In contrast, a marked decrease in bioaccessibility of As was achieved using NaOH (40% to 7%). X-ray absorption spectroscopy analysis demonstrated that highly bioaccessible forms of calcium iron arsenate (yukonite and arseniosiderite) could be generated in CaO-stabilized soil. Our study found that neutralizing agents may play an important role in stabilizing As(V) and lowering its bioaccessibility through determining the type of formed Fe oxides in soil.

Functional redundancy imparts process stability to acidic Fe(II)-oxidizing microbial reactors

In previous work, lab-scale reactors designed to study microbial Fe(II) oxidation rates at low pH were found to have stable rates under a wide range of pH and Fe(II) concentrations. Since the stirred reactor environment eliminates many of the temporal and spatial variations that promote high diversity among microbial populations in nature, we were surprised that the reactors supported multiple taxa presumed to be autotrophic Fe(II) oxidizers based on their phylogeny. Metagenomic analyses of the reactor communities revealed differences in the metabolic potential of these taxa with respect to Fe(II) oxidation and carbon fixation pathways, acquisition of potentially growth-limiting substrates and the ability to form biofilms. Our findings support the hypothesis that the long-term co-existence of multiple autotrophic Fe(II)-oxidizing populations in the reactors are due to distinct metabolic potential that supports differential growth in response to limiting resources such as nitrogen, phosphorus and oxygen. Our data also highlight the role of biofilms in creating spatially distinct geochemical niches that enable the co-existence of multiple taxa that occupy the same apparent metabolic niche when the system is viewed in bulk. The distribution of key metabolic functions across different co-existing taxa supported functional redundancy and imparted process stability to these reactors.

Mine drainage: Treatment technologies and rare earth elements

The recent research and development on mine drainage published in 2018 was summarized in this annual review. In particular, this review was focused on two main aspects of mine drainage: (a) advances in treatment technologies and (b) rare earth elements in mine drainage and its recovery. The first section covers passive treatment technologies and active treatment options, including physiochemical treatment and biological treatment. The second section includes the characterization of rare earth elements in mine drainage and recovery technologies. Due to the importance of rare earth elements and the growing interest in their recovery from mine drainage, rare earth elements are reported as a separate section for the first time in this review. PRACTITIONER POINTS: Advances in treatment technologies for mine drainage are reviewed. Rare earth elements in mine drainage and its recovery are summarized. Reviewed technologies include passive, active, advanced and novel processes.

Sulfur-siderite autotrophic denitrification system for simultaneous nitrate and phosphate removal: From feasibility to pilot experiments

Siderite (FeCO₃) is one kind of abundant and cheap carbonate minerals, but it has never been used as inorganic carbon sources and pH buffer in the sulfur autotrophic denitrification before. In this study, sulfur-siderite autotrophic denitrification (SSAD) system was formed. Batch, column and pilot experiments of the SSAD system showed that siderite could provide inorganic sources and pH buffer for sulfur autotrophic denitrification. The optimal volume ratio of sulfur and siderite was 1:3 for the SSAD system. Siderite could not be used as an electron donor by the sulfur autotrophic denitrifiers. The SSAD column removed 28 mg/L NO₃^--N and 3.1 mg/L PO₄^3--P completely at 12 h HRT. The SSAD pilot biofilter during treating secondary effluent obtained stable NO₃^- and PO₄^3- removal, and controlled effluent NO₃^--N and PO₄^3--P around 4 and 0.2 mg/L, respectively, at 4 h HRT, and no blocking occurred in operation of 401 days. In the SSAD system, the main bacteria were Thiobacillus (67.8%), Sulfurimonas (20.0%), and Simplicispira (3.5%); and Sulfurimonas (29.4%), Ferritrophicum (15.2%), and Thiobacillus (10.3%) during treating synthetic wastewater and secondary effluent, respectively. PO₄^3- was removed through iron phosphate precipitate. The SSAD system was a promising way to remove NO₃^- and PO₄^3- simultaneously from wastewater lack of organic carbon sources.