Microbial communities in acid mine drainage

Influence of Extremophiles on the Generation of Acid Mine Drainage at the Abandoned Pan de Azúcar Mine (Argentina)

The risk of generation of acid drainages in the tailings of the Pan de Azúcar mine that closed its activities more than three decades ago, was evaluated through biooxidation studies using iron- and sulfur-oxidizing extremophilic leaching consortia. Most of tailings showed a high potential for generating acid drainage, in agreement with the results from net acid generation (NAG) assays. In addition, molecular analysis of the microbial consortia obtained by enrichment of the samples, demonstrated that native leaching microorganisms are ubiquitous in the area and they seemed to be more efficient in the biooxidation of the tailings than the collection microorganisms. The acid drainages detected at the site and those formed by oxidation of the tailings, produced a significant ecotoxicological effect demonstrated by a bioassay. These drainages, even at high dilutions, could seriously affect a nearby Ramsar site (Laguna de Pozuelos) that is connected to the Pan de Azúcar mine through a hydrological route (Cincel River).

Acid mine drainage at the Bahia Gold Belt (Brazil): microbial isolation and characterization

Acid mine drainage occurs due to the chemical and microbiological oxidation of sulfide minerals and can be a source of potentially toxic elements contamination of groundwater and surface water. The objective of this study was to identify microorganisms involved in sulfide oxidation in the tailings of a Bahia Gold Belt mine (Brazil). Samples of solids and water were collected at the mine tailings dam and characterized. The microorganisms were isolated after enrichment and subsequent purification. The major constituents of the tailings are Si, Fe, Al, S, and K. The sulfur content of the tailings is 0.98%. The major phases are quartz, muscovite, and clinochlore. Gravity concentrates of the tailings show several particles of pyrite, that is, the major sulfide phase. Molecular analysis identified the microorganisms isolated in the acid mine drainage process in this region. Five bacterium species were found: Acidithiobacillus spp., Acidithiobacillus ferrooxidans, Acidiphilium spp., Leptospirillum type II, and Sulfobacillus spp. No organisms of the archaea or eukaryote domains were found. The isolate was used in the bioleaching of copper sulfide ore, and the copper extraction was about 60% in 60 days for ground ore.

Quorum Sensing Signaling Molecules Positively Regulate c-di-GMP Effector PelD Encoding Gene and PEL Exopolysaccharide Biosynthesis in Extremophile Bacterium Acidithiobacillus thiooxidans

Acidithiobacillus species are fundamental players in biofilm formation by acidophile bioleaching communities. It has been previously reported that Acidithiobacillus ferrooxidans possesses a functional quorum sensing mediated by acyl-homoserine lactones (AHL), involved in biofilm formation, and AHLs naturally produced by Acidithiobacillus species also induce biofilm formation in Acidithiobacillus thiooxidans. A c-di-GMP pathway has been characterized in Acidithiobacillus species but it has been pointed out that the c-di-GMP effector PelD and pel-like operon are only present in the sulfur oxidizers such as A. thiooxidans. PEL exopolysaccharide has been recently involved in biofilm formation in this Acidithiobacillus species. Here, by comparing wild type and ΔpelD strains through mechanical analysis of biofilm-cells detachment, fluorescence microscopy and qPCR experiments, the structural role of PEL exopolysaccharide and the molecular network involved for its biosynthesis by A. thiooxidans were tackled. Besides, the effect of AHLs on PEL exopolysaccharide production was assessed. Mechanical resistance experiments indicated that the loss of PEL exopolysaccharide produces fragile A. thiooxidans biofilms. qRT-PCR analysis established that AHLs induce the transcription of pelA and pelD genes while epifluorescence microscopy studies revealed that PEL exopolysaccharide was required for the development of AHL-induced biofilms. Altogether these results reveal for the first time that AHLs positively regulate pel genes and participate in the molecular network for PEL exopolysaccharide biosynthesis by A. thiooxidans.

Recovering iron and sulfate in the form of mineral from acid mine drainage by a bacteria-driven cyclic biomineralization system

Acid mine drainage (AMD) is recognized as a challenge encountered by mining industries globally. Cyclic mineralization method, namely Fe²⁺ oxidation/mineralization-residual Fe³⁺ reduction-resultant Fe²⁺ oxidation/mineralization, could precipitate Fe and SO₄^2- present in AMD into iron hydroxysulfate minerals and greatly improve the efficiency of subsequent lime neutralization, but the current Fe⁰-mediated reduction approach increased the mineralization cycles. This study constructed a bacteria-driven biomineralization system based on the reactions of Acidithiobacillus ferrooxidans-mediated Fe²⁺ oxidation and Acidiphilium multivorum-controlled Fe³⁺ reduction, and utilized water-dropping aeration and biofilm technology to satisfy the requirement of practical application. The resultant biofilms showed stable activity for Fe conversion: the efficiency of Fe²⁺-oxidation, Fe-precipitation, and Fe³⁺-reduction maintained at 98%, 32%, and 87%, respectively. Dissolved oxygen for Fe-oxidizing bacteria growth was continuously replenished by water-dropping aeration (4.2-7.2 mg/L), and the added organic carbon was mainly metabolized by Fe-reducing bacteria. About 89% Fe and 60% SO₄^2- were precipitated into jarosite mineral after five biomineralization cycles. Fe was removed via forming secondary mineral precipitates, while SO₄^2- was coprecipitated into mineral within the initial three biomineralization cycles, and then mainly precipitated with Ca²⁺ afterwards. Fe concentration in AMD was proven to directly correlate with subsequent lime neutralization efficiency. Biomineralization for five cycles drastically reduced the amount of required lime and neutralized sludge by 75% and 77%, respectively. The results in this study provided theoretical guidance for practical AMD treatment based on biomineralization technology.

Acidophilic microorganisms enhancing geochemical dynamics in an acidic drainage system, Amarillo river in La Rioja, Argentina

The Amarillo River in La Rioja, Argentina, is a natural acidic environment that is influenced by an abandoned mine. The river is characterized by extremely low pH and high concentrations of metals and metalloids. Fe(III)-bearing neoformed precipitated minerals are widespread along the hydrological basin. This work reports the presence of different species of iron-oxidizing bacteria and demonstrates that their action has a significant role in geochemical processes of the Amarillo River, mainly by catalyzing Fe²⁺ oxidation and intensifying the Fe(III)-bearing mineral precipitation. Various iron oxidizers (i.e. Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans, Ferrimicrobium acidophilum, Alicyclobacillus cycloheptanicus) were detected in enrichment cultures at different temperatures. Moreover, this is the first report confirming that Acidithiobacillus ferrivorans is able to grow at 4 °C. Other acidophilic bacteria (i.e., Acidiphilium iwatensii) and fungi (e.g., Fodinomyces uranophilus, Coniochaeta fodinicola, Acidea extrema, Penicillium sp. and Cladosporium pseudocladosporioides) were also detected. In vitro laboratory studies recreating natural Fe(III)-bearing mineral formation showed that mineral precipitation rate was higher than 350 mg L^-1 day^-1 in the presence of microorganisms whereas it was about 15 mg L^-1 day^-1 under abiotic conditions. Jarosite was the only mineral detected in the precipitates generated by microbial action and it was also identified in the Amarillo River bed sediments. Biological Fe²⁺ oxidation rates depend on temperature which range from 8 to 32 mM day^-1 at 4 and 30 °C, respectively. Finally, a conceptual model recognizing the significant microbial role is proposed to gain a better understanding of the biogeochemistry dynamics of the Amarillo River.

Sulfate-reducing bacterial community shifts in response to acid mine drainage in the sediment of the Hengshi watershed, South China

Sulfate-reducing bacteria (SRB) are an attractive option for treating acid mine drainage (AMD) and are considered to be of great significance in the natural attenuation of AMD, but the available information regarding the highly diverse SRB community in AMD sites is not comprehensive. The Hengshi River, which is continually contaminated by AMD from upstream mining areas, was selected as a study site for investigation of the distribution, diversity, and abundance of SRB. Overall, high-throughput sequencing of the 16S rRNA and dsrB genes revealed the high diversity, richness, and OTU numbers of SRB communities, suggesting the existence of active sulfate reduction in the study area. Further analysis demonstrated that AMD contamination decreased the richness and diversity of the microbial community and SRB community, and led to spatiotemporal shifts in the overall composition and structure of sediment microbial and SRB communities along the Hengshi watershed. However, the sulfate reduction activity was high in the midstream, even though AMD pollution remained heavy in this area. Spatial distributions of SRB community indicated that species of Clostridia may be more tolerant of AMD contamination than other species, because of their predominance in the SRB communities. In addition, the results of CCA revealed that environmental parameters, such as pH, TS content, and Fe content, can significantly influence total microbial and SRB community structure, and dissolved organic carbon was another important factor structuring the SRB community. This study extends our knowledge of the distribution of indigenous SRB communities and their potential roles in natural AMD attenuation.

MONITORAMENTO E REMOÇÃO DE METAIS EM UM REATOR ANAERÓBIO APLICADO AO TRATAMENTO DE DRENAGEM ÁCIDA DE MINA

Uma forma eficiente de tratar efluentes provindos de drenagem ácida de mina (DAM), frente aos tratamentos convencionais de neutralização da acidez, é por meio da aplicação de processos biológicos anaeróbios que utilizam bactérias redutoras de sulfato (BRS) apresentando remoção de sulfato, alcalinização do meio e precipitação de metais. O presente trabalho teve como objetivo o monitoramento da concentração total dos metais Co, Cu, Fe, Mn, Mo, Ni, Se, V, W e Zn e a avaliação das respectivas eficiências de remoção destes metais em um reator de leito fixo-estruturado e fluxo descendente (DFSBR), utilizado para tratar efluentes oriundos de DAM sintética rica em sulfato. A digestão anaeróbia empregada para o tratamento de DAM obteve um elevado desempenho com eficiências médias de remoção, nas Fases de II a IV, de 92 ± 4, 87 ± 8, 71 ± 21, 61 ± 24, 92 ± 4 e 86 ± 8 para Co, Cu, Fe, Mn, Ni e Zn, respectivamente. O tratamento anaeróbico de DAM pelo reator DFSBR revela-se como uma alternativa promissora para a remoção de metais, além da redução de sulfato e elevação do pH, de acordo com as condições descritas neste estudo, e uma opção promissora e complementar para a remoção de manganês, comumente considerado de difícil remoção em DAMs reais, empregando processos físico-químicos convencionais.

Hypergraph Clustering Based on Game-Theory for Mining Microbial High-Order Interaction Module

Microbial community is ubiquitous in nature, which has a great impact on the living environment and human health. All these effects of microbial communities on the environment and their hosts are often referred to as the functions of these communities, which depend largely on the composition of the communities. The study of microbial higher-order module can help us understand the dynamic development and evolution process of microbial community and explore community function. Considering that traditional clustering methods depend on the number of clusters or the influence of data that does not belong to any cluster, this paper proposes a hypergraph clustering algorithm based on game theory to mine the microbial high-order interaction module (HCGI), and the hypergraph clustering problem naturally turns into a clustering game problem, the partition of network modules is transformed into finding the critical point of evolutionary stability strategy (ESS). The experimental results show HCGI does not depend on the number of classes, and can get more conservative and better quality microbial clustering module, which provides reference for researchers and saves time and cost. The source code of HCGI in this paper can be downloaded from https://github.com/ylm0505/HCGI.

Co-Disposal of Coal Gangue and Red Mud for Prevention of Acid Mine Drainage Generation from Self-Heating Gangue Dumps

The seepage and diffusion of acid mine drainage (AMD) generated from self-heating coal gangue tailings caused acid pollution to the surrounding soil and groundwater. Red mud derived from the alumina smelting process has a high alkali content. To explore the feasibility of co-disposal of coal gangue and red mud for prevention of AMD, coal gangue and red mud were sampled from Yangquan (Shanxi Province, China), and dynamic leaching tests were carried out through the automatic temperature-controlled leaching system under the conditions of different temperatures, mass ratios, and storage methods. Our findings indicated that the heating temperature had a significant effect on the release characteristics of acidic pollutants derived from coal gangue, and that the fastest rate of acid production corresponding to temperature was 150 °C. The co-disposal dynamic leaching tests indicated that red mud not only significantly alleviated the release of AMD but also that it had a long-term effect on the treatment of acid pollution. The mass ratio and stacking method were selected to be 12:1 (coal gangue: red mud) and one layer was alternated (coal gangue covered with red mud), respectively, to ensure that the acid-base pollution indices of leachate reached the WHO drinking-water quality for long-term discharge. The results of this study provided a theoretical basis and data support for the industrial field application of solid waste co-treatment.

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.

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond

Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m² of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m² for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Metabolic Diversity and Evolutionary History of the Archaeal Phylum "Candidatus Micrarchaeota" Uncovered from a Freshwater Lake Metagenome

Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum "Candidatus Micrarchaeota" have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse "Ca Micrarchaeota" are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of "Ca Micrarchaeota" from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of "Ca Micrarchaeota" Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN "Ca Micrarchaeota," the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of "Ca Micrarchaeota" genomes representing different order-level divisions indicated that evolution of the "Ca Micrarchaeota" from a free-living "Candidatus Diapherotrites"-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the "Ca Micrarchaeota" in terms of metabolic potential.IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, "Ca Micrarchaeota," comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, "Ca Micrarchaeota" include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of "Ca Micrarchaeota" from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of "Ca Micrarchaeota."

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L^-1, iron ~ 35-61 mg L^-1 (waters), and ~ 8-293 g kg^-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L^-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

Source identification and component characterization of dissolved organic matter in an acid mine drainage reservoir

Acid mine drainage (AMD) is one of the most serious environmental problems and extreme environments on the earth, with high concentrations of sulphate and dissolved metals. A comprehensive description of dissolved organic matter (DOM) in these reservoirs is lacking, and it can play an important role in AMD pollution treatment and ecosystem. Thus, the source, composition and property of DOM in an AMD reservoir in Ma'an shan, China were studied using Fourier transform ion cyclotron resonance mass spectrometry and three-dimension excitation emission matrix fluorescence spectroscopy. The results suggested that the autochthonous algal metabolites significantly contributed to the DOM pool in the AMD reservoir. Bioavailable substances with lower oxidation, unsaturation and aromaticity such as lipids and carbohydrates were lacking in the AMD reservoir especially in the deeper layers. In addition, the proportion of sulfur compounds was significantly higher than that in other waters, suggesting the potential formation of organic matter with sulfur atom in a sulfur-rich environment. These findings underscore that the investigation of DOM in AMD reservoirs may offer references for the AMD treatment with addition of organic matter and broaden the understanding of special carbon cycling in the extreme environment of AMD.

Contributions of Microbial “Contact Leaching” to Pyrite Oxidation under Different Controlled Redox Potentials

The function of microbial contact leaching to pyrite oxidation was investigated by analyzing the differences of residue morphologies, leaching rates, surface products, and microbial consortia under different conditions in this study. This was achieved by novel equipment that can control the redox potential of the solution and isolate pyrite from microbial contact oxidation. The morphology of residues showed that the corrosions were a little bit severer in the presence of attached microbes under 750 mV and 850 mV (vs. SHE). At 650 mV, the oxidation of pyrite was undetectable even in the presence of attached microbes. The pyrite dissolution rate was higher with attached microbes than that without attached microbes at 750 mV and 850 mV. The elemental sulfur on the surface of pyrite residues with sessile microorganisms was much less than that without attached microbes at 750 mV and 850 mV, showing that sessile acidophiles may accelerate pyrite leaching by reducing the elemental sulfur inhibition. Many more sulfur-oxidizers were found in the sessile microbial consortium which also supported the idea. The results suggest that the microbial “contact leaching” to pyrite oxidation is limited and relies on the elimination of elemental sulfur passivation by attached sulfur-oxidizing microbes rather than the contact oxidation by EPS-Fe.

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa

Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.

Effect of Sodium Chloride on Pyrite Bioleaching and Initial Attachment by Sulfobacillus thermosulfidooxidans

Biomining applies microorganisms to extract valuable metals from usually sulfidic ores. However, acidophilic iron (Fe)-oxidizing bacteria tend to be sensitive to chloride ions which may be present in biomining operations. This study investigates the bioleaching of pyrite (FeS2), as well as the attachment to FeS2 by Sulfobacillus thermosulfidooxidans DSM 9293T in the presence of elevated sodium chloride (NaCl) concentrations. The bacteria were still able to oxidize iron in the presence of up to 0.6M NaCl (35 g/L), and the addition of NaCl in concentrations up to 0.2M (~12 g/L) did not inhibit iron oxidation and growth of S. thermosulfidooxidans in leaching cultures within the first 7 days. However, after approximately 7 days of incubation, ferrous iron (Fe2+) concentrations were gradually increased in leaching assays with NaCl, indicating that iron oxidation activity over time was reduced in those assays. Although the inhibition by 0.1M NaCl (~6 g/L) of bacterial growth and iron oxidation activity was not evident at the beginning of the experiment, over extended leaching duration NaCl was likely to have an inhibitory effect. Thus, after 36 days of the experiment, bioleaching of FeS2 with 0.1M NaCl was reduced significantly in comparison to control assays without NaCl. Pyrite dissolution decreased with the increase of NaCl. Nevertheless, pyrite bioleaching by S. thermosulfidooxidans was still possible at NaCl concentrations as high as 0.4M (~23 g/L NaCl). Besides, cell attachment in the presence of different concentrations of NaCl was investigated. Cells of S. thermosulfidooxidans attached heterogeneously on pyrite surfaces regardless of NaCl concentration. Noticeably, bacteria were able to adhere to pyrite surfaces in the presence of NaCl as high as 0.4M. Although NaCl addition inhibited iron oxidation activity and bioleaching of FeS2, the presence of 0.2M seemed to enhance bacterial attachment of S. thermosulfidooxidans on pyrite surfaces in comparison to attachment without NaCl.

Host age is not a consistent predictor of microbial diversity in the coral Porites lutea

Corals harbour diverse microbial communities that can change in composition as the host grows in age and size. Larger and older colonies have been shown to host a higher diversity of microbial taxa and this has been suggested to be a consequence of their more numerous, complex and varied micro-niches available. However, the effects of host age on community structure and diversity of microbial associates remain equivocal in the few studies performed to date. To test this relationship more robustly, we use established techniques to accurately determine coral host age by quantifying annual skeletal banding patterns, and utilise high-throughput sequencing to comprehensively characterise the microbiome of the common reef-building coral, Porites lutea. Our results indicate no clear link between coral age and microbial diversity or richness. Different sites display distinct age-dependent diversity patterns, with more anthropogenically impacted reefs appearing to show a winnowing of microbial diversity with host age, possibly a consequence of corals adapting to degraded environments. Less impacted sites do not show a signature of winnowing, and we observe increases in microbial richness and diversity as the host ages. Furthermore, we demonstrate that corals of a similar age from the same reef can show very different microbial richness and diversity.

Stromatolitic digitate sinters form under wide-ranging physicochemical conditions with diverse hot spring microbial communities

Digitate siliceous hot spring deposits are a form of biomediated sinter that is relatively common in the Taupo Volcanic Zone (TVZ), New Zealand, and elsewhere on Earth. Such deposits have gained prominence recently because of their morphological similarity to opaline silica rocks of likely hot spring origin found by the Spirit rover on Mars and the consequent implications for potential biosignatures there. Here, we investigate the possible relationship between microbial community composition and morphological diversity among digitate structures from actively forming siliceous hot spring sinters depositing subaerially in shallow discharge channels and around pool rims at several physicochemically distinct geothermal fields in the TVZ. The TVZ digitate sinters range in morphologic subtype from knobby to spicular, and are shown to be microstromatolites that grow under varied pH ranges, temperatures, and water chemistries. Scanning electron microscopy and molecular analyses revealed that TVZ digitate sinters are intimately associated with a diverse array of bacterial, archaeal and eukaryotic micro-organisms, and for most digitate structures the diversity and quantity of prokaryotes was higher than that of eukaryotes. However, microbial community composition was not correlated with morphologic subtypes of digitate sinter, and observations provided limited evidence that pH (acidic versus alkali) affects morphology. Instead, results suggest hydrodynamics may be an important factor influencing variations in morphology, while water chemistry, pH, and temperature are strong drivers of microbial composition and diversity.

Edaphic factors influencing vegetation colonization and encroachment on arsenical gold mine tailings near Sudbury, Ontario

Mine tailings are found worldwide and can have significant impacts on ecosystem and human health. In this study, natural vegetation patterns on arsenical (As) gold (Au) mine tailings located in Sudbury, Ontario were assessed using transects located at the edge of the tailings and on the tailings. Vegetation communities were significantly different between the edge and open tailings areas of the site. Arsenic concentrations in both areas were extremely variable (from 285-17,567 mg/kg) but were not significantly correlated with vegetation diversity at the site. Nutrients (carbon (C), phosphorus (P)) and organic matter concentrations were associated with higher diversity and with the presence of climax vegetation on the tailings, but there were no significant relationships between tailings chemistry and vegetation indices on the edge. Encroachment onto the tailings from the edge occurred in conventional succession patterns, with a clear gradient from grasses (Agrostis gigantea) to trees such as Picea glauca. On the tailings, a nucleation pattern was visible, distinct from conventional succession. Trees and shrubs such as Betula papyrifera and Diervilla lonicera were associated with higher diversity and higher nutrient concentrations in the underlying tailings, whereas grasses such as A. gigantea were not. We concluded that at all areas of the site, vegetation - particularly trees - was facilitating amelioration of the underlying tailings. Despite high concentrations of As, nutrients appeared to have a greater influence than metals on vegetation diversity.

Crab shell amendments enhance the abundance and diversity of key microbial groups in sulfate-reducing columns treating acid mine drainage

Substrate amendments composed of crab shell (CS) waste materials have been shown to significantly improve the longevity and performance of acid mine drainage (AMD) treatment systems containing spent mushroom compost (SMC), yet the development of key microbial populations within these systems has not been investigated. To better understand the effects of CS on microbial dynamics in these systems, clone libraries and real-time quantitative PCR (qPCR) were performed on materials from a laboratory-scale AMD treatment system containing SMC and 0 to 100% CS substrate after receiving a continuous flow of AMD for 148 days (428 pore volumes). The proportion of CS in the substrate positively correlated with the diversity of sulfate-reducing bacteria (SRB) and archaeal clones, but negatively correlated with fungal diversity. CS also impacted microbial community structure, as revealed in Unifrac significance and principal coordinate analysis tests. The column containing 100% CS substrate supported 7 different genera of SRB-the most ever observed in an AMD treatment system. Moreover, the copy numbers of functional genes representing fermenters, sulfate reducers, and chitin degraders increased with increasing proportions of CS. These observations agree well with the chemical performance data, further validating that by supporting more abundant key microbial groups, chitinous substrates may provide benefits for improving both the longevity and performance of AMD treatment systems, and may provide similar benefits for the treatment of other environmental contaminants that are amenable to anaerobic bioremediation.Key points• Crab shell improves the longevity and performance of acid mine drainage treatment.• The diversity of sulfate-reducing bacteria is enhanced with crab shell amendments.• Crab shell supports more abundant key microbial groups than spent mushroom compost.

Effect of Bactericides on Control of Acidification Pollution and Spontaneous Combustion of Coal Gangue Dumps in China and Its Mechanism

Oxidation of pyrite in the coal gangue dumps usually results in acidification and spontaneous combustion, causing many environmental problems such as air, soil, and water pollution. The oxidizing bacteria exacerbate problems such as acidification, spontaneous combustion, and explosions. The bacterium Acidithiobacillus ferrooxidans was first separated and isolated from coal gangue samples. Bactericides such as Triclosan, Kathon (isothiazolinones), and sodium dodecyl sulfate (SDS) were selected for our study. Our findings indicated that the addition of bactericide effectively inhibited the oxidation of Fe2+, preventing pH decreases and oxidation-reduction potential increases. We also investigated the bactericidal mechanisms employed by the three bactericides against A. ferrooxidans by conducting a protein flocculation test, scanning electron microscopy, and time-of-flight mass spectrometry. We found that the specific inhibitory activities of the three bactericides differed. Kathon treatment caused A. ferrooxidans to release small amounts of proteins and lipids. A. ferrooxidans treated with Triclosan released small amounts of lipids and large amounts of plasmas. SDS caused the bacteria to release a large amount of proteins and lipids and degraded the surface structure of the cells, resulting in altered cell morphology.

Mine Waste Rock: Insights for Sustainable Hydrogeochemical Management

Mismanagement of mine waste rock can mobilize acidity, metal (loid)s, and other contaminants, and thereby negatively affect downstream environments. Hence, strategic long-term planning is required to prevent and mitigate deleterious environmental impacts. Technical frameworks to support waste-rock management have existed for decades and typically combine static and kinetic testing, field-scale experiments, and sometimes reactive-transport models. Yet, the design and implementation of robust long-term solutions remains challenging to date, due to site-specificity in the generated waste rock and local weathering conditions, physicochemical heterogeneity in large-scale systems, and the intricate coupling between chemical kinetics and mass- and heat-transfer processes. This work reviews recent advances in our understanding of the hydrogeochemical behavior of mine waste rock, including improved laboratory testing procedures, innovative analytical techniques, multi-scale field investigations, and reactive-transport modeling. Remaining knowledge-gaps pertaining to the processes involved in mine waste weathering and their parameterization are identified. Practical and sustainable waste-rock management decisions can to a large extent be informed by evidence-based simplification of complex waste-rock systems and through targeted quantification of a limited number of physicochemical parameters. Future research on the key (bio)geochemical processes and transport dynamics in waste-rock piles is essential to further optimize management and minimize potential negative environmental impacts.

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.

Taking insights into phenomics of microbe-mineral interaction in bioleaching and acid mine drainage: Concepts and methodology

Phenomics is originally a biological concept. In the most recent years, the studies of plant and human phenomics have started, and show a strong momentum and trend of development. In this paper, based on the related research on bioleaching/acid mine drainage (AMD), we put forward the relevant concepts and methodology of phenomics of microbe-mineral interaction (MMI) in bioleaching/AMD environments. It refers to the systematic study on phenotypes of MMI on both levels of microbiome and mineralome under various environmental conditions, by which it gives the relationship between microbial/mineral genome and phenome of MMI responding to the varying environmental conditions. The pertinent methodology is of mainly (meta)-omics, synchrotron radiation-based techniques and supercomputing-based density function theory (DFT) calculation.

Digitalization in microbiology - Paving the path to sustainable circular bioeconomy

The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.

Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs

Geothermal systems emit substantial amounts of aqueous, gaseous, and methylated mercury, but little is known about microbial influences on mercury speciation. Here, we report results from genome-resolved metagenomics and mercury speciation analysis of acidic warm springs in the Ngawha Geothermal Field (<55°C, pH <4.5), Northland Region, Aotearoa New Zealand. Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250 to 16,000 ng liter^-1 and 0.5 to 13.9 ng liter^-1, respectively). Total solid mercury concentrations in spring sediments ranged from 1,274 to 7,000 μg g^-1 In the context of such ultrahigh mercury levels, the geothermal microbiome was unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. By integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry.IMPORTANCE Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illustrates environmental factors that influence mercury cycling in acidic springs, including transitions between solid (mineral) and aqueous phases of mercury, as well as the interconnections among mercury, sulfur, and iron cycles. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where they are mobilized in spring waters that mix with surface or groundwaters. Furthermore, in the context of thermophilic origins for microbial mercury volatilization, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.

Isolation and characterization of an acid and metal tolerant Enterobacter cloacae NZS strain from former mining lake in Selangor, Malaysia

Background

Metal polluted environments have been found to harbor acid and metal tolerant bacterial communities. Metal oxidizing bacteria in particular are industrially important microorganisms that can be utilized for potential applications in biomining and bioremediation. However, some well-characterized strains are not readily culturable as they are obligate and fastidious chemolithotrophs requiring special techniques for their cultivation. Hence, this study was aimed at isolating, identifying, and characterizing indigenous metal tolerant heterotroph(s) from abandoned mines that can potentially be used for biomining or bioremediation processes in the future.

Results

Seventeen bacteria from former mining lakes were isolated and identified using 16S rRNA. Minimal inhibition concentration (MIC) and growth study of isolated bacteria carried out in Luria-Bertani media containing three different metals ions, zinc (II), copper (II), and iron (II), showed that a particular isolate termed Enterobacter cloacae NZS was found to exhibit better growth and tolerance for copper (up to 90 mM), zinc (up to 200 mM), and iron (up to 170 mM). Growth of the strain was notably well in the presence of iron (II). Compared to all the isolates, only E. cloacae NZS was able to be enumerated at pH lower than 5 while other strains were culturable only at pH 7. Its capability in iron (II) oxidation was preliminary assessed based on the pH, cell count, glucose consumption, and amount of iron oxidized throughout incubation in 9K media. E. cloacae NZS strain was found to be capable of oxidizing iron (II) supplied in 9K media to iron (III).

Conclusion

As preliminary investigation showed that E. cloacae NZS was able to oxidize iron (II) in 9K media at pH2, further optimization on the strain, medium, and culture conditions in future may be able to provide a better insight on this strain to be possibly used as an iron oxidizer for various applications.

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage

Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation. A terrace with sharp geochemical gradients caused by AMD flooding were selected to study the microbial response to changes in environmental parameters related to AMD contamination. AMD intrusion reduced soil microbial community diversity and further changed phylogenetic clustering patterns along the terrace gradient. We observed several genera seldom reported in AMD-related environments (i.e., Corynebacterium, Ochrobactrum, Natronomonas), suggesting flexible survival strategies such as nitrogen fixation, despite the poor nutritional environment. A co-occurrence network of heavily-contaminated fields was densely connected. The phyla Proteobacteria, Acidobacteria, Chloroflexi, and Euryarchaeota were all highly interconnected members, which may affect the formation of AMD. Detailed microbial response to different soil characterizations were highlighted by random forest model. Results revealed the top three parameters influencing the microbial diversity and interactions were pH, Fe(III), and sulfate. Various acidophilic Fe- and S-metabolizing bacteria were enriched in the lower fields, which were heavily contaminated by AMD, and more neutrophiles prevailed in the less-contaminated upper fields. Many indicator species in the lower fields were identified, including Desulfosporosinus, Thermogymnomonas, Corynebacterium, Shewanella, Acidiphilium, Ochrobactrum, Leptospirillum, and Allobaculum, representing acid-tolerant bacteria community in relevant environment. The detection of one known sulfate-reducing bacteria (i.e., Desulfosporosinus) suggested that biotic sulfate reduction may occur in acidic samples, which offers multiple advantages to AMD contamination treatment. Collectively, results suggested that the geochemical gradients substantially altered the soil microbiota and enriched the relevant microorganisms adapted to the different conditions. These findings provide mechanistic insights into the effects of contamination on the soil microbiota and establish a basis for in situ AMD bioremediation strategies.

Impact of acid mine drainage chemistry and microbiology on the development of efficient Fe removal activities

Coal mine derived acid mine drainage (AMD) is formed when oxygenated water infiltrates mine voids and oxidizes FeS phases, generating acidic fluid rich in heavy metals, polluting thousands of miles of streams. Existing remediation options are cost-prohibitive and difficult to sustain. In some cases, AMD flows over previously pristine soil in thin sheets over terrestrial surface, enhancing AMD aeration and Fe(II) oxidizing activities, leading to oxidative Fe(II) precipitation from AMD, without any human intervention. Since robust Fe(II) biooxidation occurs in the mixture of intruding AMD and pristine soil, understanding the effects of chemically variant AMD can be exploited for effective Fe(II) removal. We hypothesized that chemistry and microbiology of AMD intruding pristine soil on surface would influence the development of Fe(II) oxidizing capabilities. Therefore, to investigate the response of pristine soil to the addition of AMD varying in chemical and microbial characteristics, we mixed soil with a near-neutral and moderately acidic AMD, in separate incubations. Incubations with near-neutral AMD developed microbial Fe(II) oxidation activities after 10 days. However, Fe(II) oxidation in moderately acidic AMD incubations was mostly abiotic. 16S rRNA gene sequences and metabolic functional prediction (Tax4Fun) analysis of near-neutral AMD and soil mixture indicated development of taxonomically different communities capable of activities similar to microorganisms in a mine void. In conclusion, results indicate that AMD chemistry and microbiology affects development of Fe(II) biooxidation. Therefore, understanding of the effect of AMD chemistry on the development of FeOB activities in soil can be exploited to design site-specific and sustainable solutions.

Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic

Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.

Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum

The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001-0.005 fmol%) proteins for polypeptides' hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures.

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site

BACKGROUND

Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY.

RESULTS

Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis.

CONCLUSIONS

Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.

Comparative characterization of microbial communities that inhabit arsenic-rich and antimony-rich contaminated sites: Responses to two different contamination conditions

Due to extensive mining and industrial activities, arsenic (As) and antimony (Sb) contaminations are becoming a global environmental concern. Both As and Sb are toxic and carcinogenic metalloids from the group 15 in the periodic table. Since As and Sb share many similar geochemical properties, it is often assumed that they exert similar environmental pressure on the native microbial communities. This hypothesis, however, still requires further confirmation. In the current study, a systematic comparison of microbial responses to As and Sb contamination were conducted. The results suggested that regular geochemical parameters, such as pH, nitrate, and TOC, were the driving forces for shaping the microbial community. In correspondence, two heavily contaminated groups showed similar microbial community compositions and the same microbial populations were enriched. The interactions between the contaminant fractions (As and Sb related fractions) and the individual OTUs, however, suggested the different and more diverse impacts of As comparing to Sb fractions, with more taxa significantly impacted by As species comparing to Sb species. The identification of the keystone taxa in the heavily contaminated samples revealed a group of microbial populations that could survive in both As and Sb heavily contaminated conditions and may providing critical environmental services to the community. Further investigation of these key microbial populations may provide valuable insights on employing these microorganisms for remediation applications.

Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance

A unique terrace with sharp gradient of environmental conditions was selected to study the microbial response and survival strategies to the extreme environments introduced by acid mine drainage (AMD) contamination. A combination of geochemical analyses, metagenomic sequencing, ex-situ microcosm setups, and statistical analyses were used to investigate the environment-microbe interactions. The microbial communities and metabolic potentials along the terrace were studied by focusing on the genes associated with important biogeochemical processes (i.e., C, N, S cycling and metal resistance). Results show that the variations of geochemical parameters substantially shaped the indigenous microbial communities. Sharp environmental gradients also impacted the microbial metabolic potentials, especially for C, N, and S cycling. Although the relative abundances of carbon fixing genes did not significantly vary along the environmental gradients, the taxa for carbon fixation varied significantly in more contaminated fields versus less contaminated fields, indicating the effects of AMD contamination on the autotrophic microbial communities. AMD input also influenced the N cycling, especially for nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). In addition, ex situ experiments were undertaken to evaluate the effects of AMD contamination on nitrogen fixation rates. Random Forest (RF) analysis indicated that nitrate, pH, total N, TOC exhibited positive correlations with the rates of nitrogen fixation while total Fe, Fe(III), and sulfate showed negative effects. Two co-occurrence networks at taxonomic and genomic levels indicated that geochemical parameters such as pH, TOC, total N, total S, and total Fe substantially influenced the innate microbial communities and their metabolic potentials. The current study provides an understanding for microbial response to AMD contamination and lays the foundation for future potential AMD bioremediation.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation.

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

Performance of a Geosynthetic-Clay-Liner Cover System at a Cu/Zn Mine Tailings Impoundment

The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic-clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen and to mitigate sulfide oxidation. The cover system includes a vegetated uppermost soil layer underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste rock-capillary break layer installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were characterized by high sulfur and low carbon content. The bulk pH of the tailings pore water was circumneutral (∼5.5 to 7.3). Total genomic DNA was extracted from 36 samples recovered from the constituent layers of the cover system and the underlying tailings and was analyzed in triplicates using high-throughput amplicon sequencing of 16S rRNA genes. Iron-oxidizing, sulfur-oxidizing, sulfate-reducing, and aerobic heterotrophic microorganisms were enumerated by use of most probable number enumeration, which identified heterotrophs as the most numerous group of culturable microorganisms throughout the depth profile. Low relative abundances and viable counts of microorganisms that catalyze transformations of iron and sulfur in the covered tailings, compared to previous studies on unreclaimed tailings, indicate that sulfide oxidation rates have decreased due to the presence of the GCL. Characterization of the microbial community can provide a sensitive indicator for assessing the performance of remediation systems.IMPORTANCE Mining activities are accompanied by significant environmental and financial liabilities, including the release of acid mine drainage (AMD). AMD is caused by accelerated chemical and biological oxidation of sulfide minerals in mine wastes and is characterized by low pH and high concentrations of sulfate and metal(loid)s. Microorganisms assume important roles in the catalysis of redox reactions. Our research elucidates linkages among the biogeochemistry of mine wastes and remediation systems and microbial community and activity. This study assesses the performance and utility of geosynthetic-clay-liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system.

Effect of Introduction of Exogenous Strain Acidithiobacillus thiooxidans A01 on Structure and Function of Adsorbed and Planktonic Microbial Consortia During Bioleaching of Low-Grade Copper Sulfide

The introduction of Acidithiobacillus thiooxidans A01 strengthens the positive interactions between physiologically distinct microorganisms and enhances the bioleaching ability of the consortium. However, the effect of introducing an exogenous strain, A. thiooxidans A01 on the structure and function of the adsorbed and planktonic microbial consortia during bioleaching of low-grade copper sulfide remains unclear. In this study, A. thiooxidans A01 was introduced into an indigenous leaching microbial community on the 0th (group B), 24th (group C), and 36th day (group D). Results revealed that the copper leaching efficiency was highest in group D, in which the Cu2+ concentration in the solution reached 251.5 mg/L on day 48, which was 18.5% higher than that of the control (group A, no addition of A. thiooxidans A01). Restriction fragment length polymorphism (RFLP) analysis of the microbial community in group D revealed the presence of Leptospirillum ferriphilum, Acidithiobacillus ferrooxidans, Acidithiobacillus caldus, Sulfobacillus sp., Acidiphilium spp., and Acidithiobacillus albertensis before introduction of A. thiooxidans A01 on the 36th or 48th day; however, A. albertensis was absent on day 48 in group A. Further, the proportion of dominant A. caldus, L. ferriphilum, and A. ferrooxidans became altered. The results of real-time PCR in group D showed that A. thiooxidans A01 was primarily adsorbed on the surface of the ore, with the adsorption reaching the maxima on day 42; while the free A. thiooxidans A01 in solution grew slowly, reaching its maximum concentration on day 45. Compared with that in the control group, the abundance of both free and attached A. caldus and Sulfobacillus sp. decreased following the introduction of A. thiooxidans A01, while that of L ferriphilum, A. ferrooxidans, and Acidiphilium sp. increased. Functional gene arrays data indicated that the abundance of genes involved in sulfide and iron oxidation in L. ferriphilum and A. ferrooxidans, as well as that of the metal (loid) resistance genes of A. ferrooxidans, L. ferriphilum, and Acidiphilium sp. increased, while the abundance of genes involved in sulfur metabolism in A. caldus and Sulfolobus spp. decreased. Taken together, these results provide useful information for application of bioleaching of copper sulfide in industry.

Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang

Thallium (Tl) is a toxic element, but little is known about microbial communities' response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.

Tailings microbial community profile and prediction of its functionality in basins of tungsten mine

In a circular economy concept, where more than 300 million tons of mining and quarrying wastes are produced annually, those are valuable resources, supplying metals that are extracted today by other processes, if innovative methods and processes for efficient extraction of these elements are applied. This work aims to assess microbiological and chemical spatial distribution within two tailing basins from a tungsten mine, using a MiSeq approach targeting the 16S rRNA gene, to relate microbial composition and function with chemical variability, thus, providing information to enhance the efficiency of the exploitation of these secondary sources. The tailings sediments core microbiome comprised members of family Anaerolineacea and genera Acinetobacter, Bacillus, Cellulomonas, Pseudomonas, Streptococcus and Rothia, despite marked differences in tailings physicochemical properties. The higher contents of Al and K shaped the community of Basin 1, while As-S-Fe contents were correlated with the microbiome composition of Basin 2. The predicted metabolic functions of the microbiome were rich in genes related to metabolism pathways and environmental information processing pathways. An in-depth understanding of the tailings microbiome and its metabolic capabilities can provide a direction for the management of tailings disposal sites and maximize their potential as secondary resources.

Diversity, Ecology, and Prevalence of Antimicrobials in Nature

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.

Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek

Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis

This study surveyed physicochemical properties and bacterial community structure of water and sediments from an acid mine drainage (AMD) dam in South Africa. High-throughput sequence analysis revealed low diversity bacterial communities affiliated within 8 dominant phyla; Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Proteobacteria, Saccharibacteria, and ca. TM6_(Dependentiae). Acidiphilium spp. which are common AMD inhabitants but rarely occur as dominant taxa, were the most abundant in both AMD water and sediments. Other groups making up the community are less common AMD inhabitants; Acidibacillus, Acidibacter, Acidobacterium, Acidothermus, Legionella, Metallibacterium, Mycobacterium, as well as elusive taxa (Saccharibacteria, ca. TM6_(Dependentiae) and ca. JG37-AG-4). Although most of the taxa are shared between sediment and water communities, alpha diversity indices indicate a higher species richness in the sediments. From canonical correspondence analysis, DOC, Mn, Cu, Cr, Al, Fe, Ca were identified as important determinants of community structure in water, compared to DOC, Ca, Cu, Fe, Zn, Mg, K, Mn, Al, sulfates, and nitrates in sediments. Predictive functional profiling recovered genes associated with bacterial growth and those related to survival and adaptation to the harsh environmental conditions. Overall, the study reports on a distinct AMD bacterial community and highlights sediments as microhabitats with higher species richness than water.

Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.