Microbial diversity and metabolic networks in acid mine drainage habitats

Oxyplasma meridianum gen. nov., sp. nov., an extremely acidophilic organotrophic member of the order Thermoplasmatales

A mesophilic, hyperacidophilic archaeon, strain M1T, was isolated from a rock sample from Vulcano Island, Italy. Cells of this organism were cocci with an average diameter of 1 µm. Some cells possessed filaments. The strain grew in the range of temperatures between 15 and 52 °C and pH 0.5-4.0 with growth optima at 40 °C and pH 1.0. Strain M1T was aerobic and chemoorganotrophic, growing on complex substrates, such as casamino acids, trypticase, tryptone, yeast and beef extracts. No growth at expenses of oxidation of elemental sulphur or reduced sulphur compounds, pyrite, or ferrous sulphate was observed. The core lipids were glycerol dibiphytanyl glycerol tetraether lipids (membrane spanning) with 0 to 4 cyclopentane moieties and archaeol, with trace amounts of hydroxy archaeol. The dominant quinone was MK-7 : 7. The genome size of M1T was 1.67 Mbp with a G+C content of 39.76 mol%, and both characteristics were well within the common range for Thermoplasmatales. The phylogenetic analysis based on 16S rRNA gene sequence placed the strain M1T within the order Thermoplasmatales with sequence identities of 90.9, 90.3 and 90.5% to the closest SSU rRNA gene sequences from organisms with validly published names, Thermoplasma acidophilum, Thermoplasma volcanium and Thermogymnomonas acidicola, respectively. Based on the results of our genomic, phylogenetic, physiological and chemotaxonomic studies, we propose that strain M1T (=DSM 116605T=JCM 36570T) represents a new genus and species, Oxyplasma meridianum gen. nov., sp. nov., within the order Thermoplasmatales.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities

The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.

Formic acid enhances whole-plant mulberry silage fermentation by boosting lactic acid production and inhibiting harmful bacteria

Mulberry has also been regarded as a valuable source of forage for ruminants. This study was developed to investigate the impact of four additives and combinations thereof on fermentation quality and bacterial communities associated with whole-plant mulberry silage. Control fresh material (FM) was left untreated, while other groups were treated with glucose (G, 20 g/kg FM), a mixture of Lactobacillus plantarum and L. buchneri (L, 106 CFU/g FM), formic acid (A, 5 mL/kg FM), salts including sodium benzoate and potassium sorbate (S, 1.5 g/kg FM), a combination of G and L (GL), a combination of G and A (GA), or a combination of G and S (GS), followed by ensiling for 90 days. Dry matter content in the A, S, GA, and GS groups was elevated relative to the other groups (p < 0.01). Relative to the C group, all additives and combinations thereof were associated with reductions in pH and NH3-N content (p < 0.01). The A groups exhibited the lowest pH and NH3-N content at 4.23 and 3.27 g/kg DM, respectively (p < 0.01), whereas the C groups demonstrated the highest values at 4.43 and 4.44 g/kg DM, respectively (p < 0.01). The highest levels of lactic acid were observed in the GA and A groups (70.99 and 69.14 g/kg DM, respectively; p < 0.01), followed by the GL, L, and GS groups (66.88, 64.17 and 63.68 g/kg DM, respectively), with all of these values being higher than those for the C group (53.27 g/kg DM; p < 0.01). Lactobacillus were the predominant bacteria associated with each of these samples, but the overall composition of the bacterial community was significantly impacted by different additives. For example, Lactobacillus levels were higher in the G, A, and GA groups (p < 0.01), while those of Weissella levels were raised in the L, GL, and GS groups (p < 0.01), Pediococcus levels were higher in the A and GA groups (p < 0.01), Enterococcus levels were higher in the G and S groups (p < 0.01), and Lactococcus levels were raised in the S group (p < 0.01). Relative to the C group, a reduction in the levels of undesirable Enterobacter was evident in all groups treated with additives (p < 0.01), with the greatest reductions being evident in the A, S, GA, and GS groups. The additives utilized in this study can thus improve the quality of whole-plant mulberry silage to varying extents through the modification of the associated bacterial community, with A and GA addition achieving the most efficient reductions in pH together with increases in lactic acid content and the suppression of undesirable bacterial growth.

Sustainable utilization of residual grass: effect of anaerobic storage days on chemical composition, fermentation performance, microbial community, and functional profiles of Pennisetum giganteum

The seasonal surplus and putrefactive property of moist forages inevitably increase the pressure on environmental protection and residual grass disposal. In the current work, the anaerobic fermentation approach was adopted to assist the sustainable recycling of leftover Pennisetum giganteum (LP), and its chemical composition, fermentation performance, bacterial community and functional profiles during anaerobic fermentation were studied. Fresh LP was spontaneously fermented for up to 60 d. At the end of anaerobic fermentation, fermented LP (FLP) displayed homolactic fermentation with low pH value, ethanol, and ammonia nitrogen concentrations but high lactic acid concentration. Weissella was dominant in 3-day FLP, yet Lactobacillus was the overwhelming genus (92.6%) in 60-day FLP. The anaerobic fermentation process promoted (P < 0.05) the metabolism of carbohydrate and nucleotide while suppressing (P < 0.05) that of lipid, cofactors, vitamins, energy, and amino acid. The results showed that the residual grass with LP as an example could be successfully fermented even if no additives were added, without signs of clostridial and fungal contamination.

Effect of Regulation of Whole-Plant Corn Silage Inoculated with Lactobacillus buchneri or Bacillus licheniformis Regarding the Dynamics of Bacterial and Fungal Communities on Aerobic Stability

Enhancing the aerobic stability of whole-plant corn silage is essential for producing high-quality silage. Our research assessed the effect of inoculation with Lactobacillus buchneri or Bacillus licheniformis and its modulation of the bacterial and fungal microbial community structure in an aerobic stage of whole-plant corn silage. Following treatment with a distilled sterile water control, Lactobacillus buchneri, and Bacillus licheniformis (2 × 105 cfu/g), whole-plant corn was ensiled for 60 days. Samples were taken on days 0, 3, and 7 of aerobic exposure, and the results showed that inoculation with Lactobacillus buchneri or Bacillus licheniformis improved the aerobic stability of silage when compared to the effect of the control (p < 0.05). Inoculation with Bacillus licheniformis attenuated the increase in pH value and the decrease in lactic acid in the aerobic stage (p < 0.05), reducing the filamentous fungal counts. On the other hand, inoculation with Lactobacillus buchneri or Bacillus licheniformis increased the diversity of the fungal communities (p < 0.05), complicating the correlation between bacteria or fungi, reducing the relative abundance of Acetobacter and Paenibacillus in bacterial communities, and inhibiting the tendency of Monascus to replace Issatchenkia in fungal communities, thus delaying the aerobic spoilage process. Due to the prevention of the development of aerobic spoilage microorganisms, the silage injected with Lactobacillus buchneri or Bacillus licheniformis exhibited improved aerobic stability.

Effects of Dried Tea Residues of Different Processing Techniques on the Nutritional Parameters, Fermentation Quality, and Bacterial Structure of Silaged Alfalfa

The effects of dried tea residues on the nutritional parameters and fermentation quality, microbial community, and in vitro digestibility of alfalfa silage were investigated. In this study, dried tea residues generated from five different processing techniques (green tea, G; black tea, B; white tea, W; Pu'er raw tea, Z; Pu'er ripe tea, D) were added at two addition levels (5% and 10% fresh weight (FW)) to alfalfa and fermented for 90 days. The results showed that the tea residues increased the crude protein (CP) content (Z10: 23.85%), true protein nitrogen (TPN) content, DPPH, and ABST radical scavenging capacity, total antioxidant capacity (T-AOC), and in vitro dry matter digestibility (IVDMD) of the alfalfa silage. Moreover, the pH, ammonia-N (NH3-N) content, and acetic acid (AA) content decreased (p < 0.05). The effects of tea residues were promoted on these indicators with increasing tea residue addition. In addition, this study revealed that the influence of dried tea residues on the nutritional quality of alfalfa silage was greater than that on fermentation quality. Based on the nutrient composition, the addition of B or G to alfalfa silage can improve its silage quality, and these tea byproducts have the potential to be used as silage additives.

Effects of inoculation and dry matter content on microbiome dynamics and metabolome profiling of sorghum silage

Sorghum forage was ensiled for 90 days at two dry matter (DM) contents (27 vs. 39%) without or with Lactiplantibacillus plantarum inoculation. On day 90 of fermentation, silages were sampled to assess the microbial community dynamics and metabolome profile. L. plantarum inoculation improved silage quality, as shown by a lower pH and greater acetic acid concentration. Loss of DM remained unaffected by L. plantarum inoculation but was greater in low- vs. high-DM sorghum silages (14.4 vs. 6.62%). The microbiome analysis revealed that Pseudomonas congelans represented the dominant species of the epiphytic microbiota in both low- and high-DM sorghum forage before ensiling. However, L. buchneri represented the dominant species at the end of ensiling. Ensiling fermentation resulted in distinct metabolic changes in silages with varying DM content. In low-DM silages, ensiling fermentation led to the accumulation of 24 metabolites and a reduction in the relative concentration of 13 metabolites. In high-DM silages, ensiling fermentation resulted in an increase in the relative concentration of 26 metabolites but a decrease in the concentration of 8 metabolites. Compared to non-inoculated silages, L. plantarum inoculation resulted in an increased concentration of 3 metabolites and a reduced concentration of 5 metabolites in low-DM silages. Similarly, in high-DM silages, there was an elevation in the relative concentration of 3 metabolites, while a decrease in 7 other metabolites. Ten metabolites with bio-functional activity were identified, including chrysoeriol, isorhamnetin, petunidin 3-glucoside, apigenin, caffeic acid, gallic acid, p-coumaric acid, trans-cinnamic acid, herniarin, and 3,4-dihydroxy-trans-cinnamate. This study presents a comprehensive analysis of microbiome and metabolome profiling of sorghum forage during ensiling as a function of DM content and L. plantarum inoculation, with a particular emphasis on identifying metabolites that may possess bio-functional properties. KEY POINTS: • DM loss was not different by L. plantarum but higher in low- vs. high-DM silage. • L. buchneri dominated ensiling, regardless of DM level. • 10 metabolites with bio-functional activity were identified.

Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy

The Ansanto Valley's Mefite, one of the Earth's largest non-volcanic CO2 gas emissions, is distinguished by its cold natural carbon dioxide springs. These emissions originate from the intricate tectonics and geodynamics of the southern Apennines in Italy. Known for over two millennia for its lethal concentration of CO2 and other harmful gases, the Mefite has a reputation for being toxic and dangerous. Despite its historical significance and unique geological features, there is a lack of information on the microbial diversity associated with the Mefite's gas emissions. This study presents an integrated exploration of the microbial diversity in the mud soil, using high-throughput sequencing of 16S rRNA (Prokaryotes) and ITS2 (Fungi), alongside a geochemical site characterisation. Our findings reveal that the Mefite's unique environment imposes a significant bottleneck on microbial diversity, favouring a select few microbial groups such as Actinobacteria and Firmicutes for Prokaryotes, and Basidiomycota for Fungi.

The First Description of the Microbial Diversity in the Amarillo River (La Rioja, Argentina), a Natural Extreme Environment Where the Whole Microbial Community Paints the Landscape Yellow

The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river's natural acidity is influenced by environmental factors beyond mineralogy, where microbial species have a crucial role. Although iron-oxidising bacteria have been identified, a comprehensive analysis of the entire microbial community in this extreme environment has not yet been conducted. In this study, we employ high-throughput sequencing to explore the bacterial and fungal diversity in the Amarillo River and Cueva de Pérez terraces, considered prehistoric analogues of the current river basin. Fe(II)-enrichment cultures mimicking different environmental conditions of the river were also analysed to better understand the roles of prokaryotes and fungi in iron oxidation processes. Additionally, we investigate the ecological relationships between bacteria and fungi using co-occurrence and network analysis. Our findings reveal a diverse bacterial community in the river and terraces, including uncultured species affiliated with Acidimicrobiia, part of an uncharacterised universal microbial acidic diversity. Acidophiles such as Acidithiobacillus ferrivorans, the main iron oxidiser of the system, and Acidiphilium, which is unable to catalyse Fe(II) oxidation but has a great metabolic flexibility,, are part of the core of the microbial community, showing significant involvement in intraspecies interactions. Alicyclobacillus, which is the main Fe(II) oxidiser in the enrichment culture at 30 °C and is detected all over the system, highlights its flexibility towards the iron cycle. The prevalence of key microorganisms in both rivers and terraces implies their enduring contribution to the iron cycle as well as in shaping the iconic yellow landscape of the Amarillo River. In conclusion, this study enhances our understanding of microbial involvement in iron mineral precipitation, emphasising the collaborative efforts of bacteria and fungi as fundamental geological agents in the Amarillo River.

Microbial processes with the potential to mobilize As from a circumneutral-pH mixture of flotation and roaster tailings

The Northwest Tailings Containment Area at the inactive Giant Mine (Canada) contains a complex mixture of arsenic-containing substances, including flotation tailings (84.8 wt%; with 0.4 wt% residual S), roaster calcine wastes (14.4 wt% Fe oxides), and arsenic trioxide (0.8 wt%) derived from an electrostatic precipitator as well as As-containing water (21.3 ± 4.1 mg L-1 As) derived from the underground mine workings. In the vadose zone the tailings pore water has a pH of 7.6 and contains elevated metal(loid)s (2.37 ± 5.90 mg L-1 As); mineral oxidizers account for 2.5% of total 16S rRNA reads in solid samples. In the underlying saturated tailings, dissolved Fe and As concentrations increase with depth (up to 72 and 20 mg L-1, respectively), and the mean relative abundance of Fe(III)-reducers is 0.54% of total reads. The potential for As mobilization via both reductive and oxidative (bio)processes should be considered in Giant Mine remediation activities. The current remediation plan includes installation of an engineered cover that incorporates a geosynthetic barrier layer.

Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil)

Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.

Challenges and Approaches of Culturing the Unculturable Archaea

Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.

Global trends and future prospects of acid mine drainage research

The uncontrolled release of acid mine drainage (AMD) results in the ongoing deterioration of groundwater and surface water, along with harmful impacts on aquatic ecosystems and surrounding habitats. This study employed a bibliometric analysis to examine research activities and trends related to AMD from 1991 to 2021. The analysis demonstrated a consistent growth in AMD research over the years, with a notable surge in the number of publications starting from 2014. Applied Geochemistry and Science of the Total Environment emerged as the top two extensively published journals in the field of AMD research. The USA held a prominent position, achieving the highest h-index (96) and central value (0.36) among 111 countries/territories, with China and Spain following closely behind. The author keyword analysis provides an overview of the main focuses in AMD research. Furthermore, the co-citation reference analysis reveals four primary domains of AMD research. Moreover, the prevention and remediation of AMD, including source prevention and migration control, as well as the hazards posed by heavy metals/metalloids and the mechanisms and techniques employed for their removal, are discussed in detail.

Silage preparation and sustainable livestock production of natural woody plant

As the global population increases and the economy grows rapidly, the demand for livestock products such as meat, egg and milk continue to increase. The shortage of feed in livestock production is a worldwide problem restricting the development of the animal industry. Natural woody plants are widely distributed and have a huge biomass yield. The fresh leaves and branches of some woody plants are rich in nutrients such as proteins, amino acids, vitamins and minerals and can be used to produce storage feed such as silage for livestock. Therefore, the development and utilization of natural woody plants for clean fermented feed is important for the sustainable production of livestock product. This paper presents a comprehensive review of the research progress, current status and development prospects of forageable natural woody plant feed resources. The nutritional composition and uses of natural woody plants, the main factors affecting the fermentation of woody plant silage and the interaction mechanism between microbial co-occurrence network and secondary metabolite are reviewed. Various preparation technologies for clean fermentation of woody plant silage were summarized comprehensively, which provided a sustainable production mode for improving the production efficiency of livestock and producing high-quality livestock product. Therefore, woody plants play an increasingly important role as a potential natural feed resource in alleviating feed shortage and promoting sustainable development of livestock product.

Evolutionary patterns of archaea predominant in acidic environment

BACKGROUND

Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.

RESULTS

Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.

CONCLUSIONS

This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.

Dynamics of Phyllosphere Microbiota and Chemical Parameters at Various Growth Stages and Their Contribution to Anaerobic Fermentation of Pennisetum giganteum

This work evaluated the dynamic changes of phyllosphere microbiota and chemical parameters at various growth stages of Pennisetum giganteum and their effects on the bacterial community, cooccurrence networks, and functional properties during anaerobic fermentation. P. giganteum was collected at two growth stages (early vegetative stage [PA] and late vegetative stage [PB]) and was naturally fermented (NPA and NPB) for 1, 3, 7, 15, 30, and 60 days, respectively. At each time point, NPA or NPB was randomly sampled for the analysis of chemical composition, fermentation parameter, and microbial number. In addition, the fresh, 3-day, and 60-day NPA and NPB were subjected to high-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction analyses. Growth stage obviously affected the phyllosphere microbiota and chemical parameters of P. giganteum. After 60 days of fermentation, NPB had a higher lactic acid concentration and ratio of lactic acid to acetic acid but a lower pH value and ammonia nitrogen concentration than NPA. Weissella and Enterobacter were dominant in 3-day NPA and Weissella was dominant in 3-day NPB, while Lactobacillus was the most abundant genus in both 60-day NPA and NPB. The complexity of bacterial cooccurrence networks in the phyllosphere decreased with P. giganteum growth. The ensiling process further decreased the complexity of bacterial networks, with the simplest bacterial correlation structures in NPB. There were great differences in the KEGG functional profiles of PA and PB. Ensiling promoted the metabolism of lipid, cofactors, vitamins, energy, and amino acids but suppressed the metabolism of carbohydrates and nucleotides. Storage time had a greater influence than growth stage on bacterial community diversity, cooccurrence networks, and functional profiles of P. giganteum silage. Differences in bacterial diversity and functionality of P. giganteum silage caused by growth stage appear to be offset by long-term storage. IMPORTANCE The phyllosphere microbiota consists of various and complex microbes, including bacteria with crucial relevance to the quality and safety of fermented food and feed. It initially derives from soil and becomes specific to its host after interaction with plants and climate. Bacteria associated with the phyllosphere are highly abundant and diverse, but we know little about their succession. Here, the phyllospheric microbiota structure was analyzed within the growth of P. giganteum. We also evaluated the effects of phyllosphere microbiota and chemical parameter changes on the anaerobic fermentation of P. giganteum. We observed remarkable differences in bacterial diversity, cooccurrence, and functionality of P. giganteum at various growth stages and storage times. The obtained results are important for understanding the fermentation mechanism and may contribute to high-efficient production without additional cost.

Culturable heterotrophic bacterial diversity study from an Indian lignite mine habitat

Diversity lifts the productivity of any ecosystem as all the species have a vital role to play that is present within the ecosystem. The characterization is essential to delve into the ecological functions of microbial communities and discover the type of microorganisms present within the ecosystem. As microbial diversity in ecosystems responds to environmental disturbances, it functions as a marker to indicate the change in such ecosystems. Mine ecology differs significantly from other habitats due to the presence of acidic runoff. This paper provides insight into the diversity of cultivable bacteria isolated from lignite mines located in south Gujarat. A total of 67 heterotrophic isolates were successfully cultivated from the collected solid and water samples of the Rajpardi and Tadkeshwar Lignite mine sites. The isolates were characterized morphologically and biochemically, and intra- and extracellular enzyme synthesis were studied. Moreover, the relative density and frequency of cultivated isolates from the samples were calculated. The similarity and evenness of the heterotrophic isolated were studied by calculating diversity indices such as Shannon and Simpson. Alpha diversity was calculated in PAST software to analyse the similarity between the selected two mine sites. This research also explored the relationship between the variance in heterotrophic microbial diversity and substrate utilization richness of the studied lignite mines of Gujarat.

Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions

Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.

Characteristics of groundwater microbial communities and the correlation with the environmental factors in a decommissioned acid in-situ uranium mine

Microorganisms play an important role in the bioremediation process for the decommissioned acid in-situ leaching uranium mine. It is crucial to understand the original microbial community characteristics before the in-situ bioremediation. However, there are limited studies on the groundwater microbial characteristics in the decommissioned acid in-situ uranium mine. To this end, we collected groundwater samples, including the groundwater that originally residual in the borehole (RW) and the aquifer water (AW), from a decommissioned acid in-situ uranium mine in the southern margin of Ili Basin in Xinjiang, China. The occurrence characteristics of the groundwater microbial communities and their correlation with environmental factors were systematically studied based on the high throughput 16S rRNA gene sequencing data and geochemical data. Results found that the AW samples had higher alpha- and beta- diversity than the RW samples. The relative abundance of Sporosarcina, Sulfobacillus, Pedobacter and Pseudomonas were significantly different in the AW and RW samples, which had significant correlation with pH, metals, and sulfate, etc. A series of reducing microorganisms were discovered, such as sulfate reduction (e.g., Desulfosporosinus) and metal reduction (e.g., Arthrobacter, Bacillus, Clostridium, Pseudomonas, and Rhodanobacter), which have the potential to attenuate sulfate and uranium in groundwater. In addition, we found that pH and redox potential (Eh) were the dominant environmental factors affecting the microbial composition. This study extends our knowledge of microbial community structure changes in the decommissioned acid in-situ uranium mine and has positive implications for assessing the potential of natural attenuation and bioremediation strategies.

Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches

Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.

Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage

Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.

Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.

Multi-Omics-Based Functional Characterization of Hybrid Fermented Broussonetia papyrifera: A Preliminary Study on Gut Health of Laying Hens

More attention has been paid in recent times to the application of Broussonetia papyrifera (BP) silage in ruminants, owing to its nutritional value. This study aimed to characterize the functionality of fermented BP and preliminarily explore its dietary effects on the gut health of laying hens. In this study, we characterized the antioxidant and antibacterial activities, bioactive compound profile, and bacterial community in Lactobacillus plantarum-fermented BP (FBP), as well as its dietary effects on intestinal morphology, microbiota and gene expression of laying hens. Improved contents of protein, total polyphenol and flavonoids as well as antioxidant and antibacterial activities were found after fermentation of BP. Untargeted metabolomics displayed more abundant apigenin, luteolin, diosmetin, and quercetin within the FBP, which may contribute to its functionality. Microbiome demonstrated increased abundance of Firmicutes at the expense of Cyanobacteria phylum, accompanied with raised levels of Lactobacillus genus. The results of a feeding trial showed dietary FBP supplementation increased the serum superoxide dismutase, but down-regulated gene expression of aryl hydrocarbon receptor (AhR), mucin2, and ZO-2, without obviously affecting the intestinal morphology and colonic microbiota. These findings suggest that FBP warrants further investigation as it may serve as a functional dietary supplement in laying hen feed.

Effects of different cutting methods and additives on the fermentation quality and microbial community of Saccharum arundinaceum silage

To develop a new high-yielding and polysaccharide-containing forage resource for livestock, the effects of different cutting methods and additives on Saccharum arundinaceum silage were evaluated. The wilted S. arundinaceum were chopped and knead-wired. The silages from each cutting method were treated with Lactobacillus plantarum (LP), cellulase (CE) and the combination of LP and CE (LP + CE) for 3, 7, 15, 30, and 60 days. Compared with the CK treatment, CE treatment exhibited better effects in the degradation of neutral detergent fiber (NDF), LP exhibited a better performance in preserving the content of dry matter (DM), and adding LP + CE significantly enhanced (P &lt; 0.05) the contents of lactic acid (LA), crude protein (CP) and DM and significantly reduced (P &lt; 0.05) the pH and NDF content during ensiling. In addition, both additives exerted a remarkable effect on the silage bacterial community (P &lt; 0.05), with a dramatic increase in the Lactobacillus abundance and a decrease in the abundance of Enterobacter. Lactic acid bacteria (LAB) became the most dominant bacteria that affected the fermentation quality of LP and LP + CE silages. Meanwhile, chopped silages showed better fermentation quality and nutrient preservation and a higher abundance of LAB. Our research indicated that the chopped S. arundinaceum ensiling with LP + CE could exert a positive effect on LA fermentation and preservation of nutrient substances by shifting the bacterial community. In conclusion, S. arundinaceum can serve as a new silage resource for feed utilization by the ensiling method of LP + CE-chopped.

Changes in the fermentation products, taxonomic and functional profiles of microbiota during high-moisture sweet sorghum silage fermentation

The purpose of this study was to evaluate the fermentation quality, microbial community, and functional shifts of sweet sorghum during ensiling. The high-moisture sweet sorghum (SS) was naturally ensiled for 1, 3, 7, 15, 30, and 60 days. After 60 days of ensiling, sweet sorghum silage (SSS) showed homolactic fermentation with absent butyric acid, low pH value, acceptable concentrations of propionic acid, ethanol, and ammonia nitrogen and high lactic acid concentration. Acinetobacter, Sphingomonas, and Pseudomonas were the advantage genera in SS. While, Lactococcus, Weissella, and Pediococcus were dominant in 3-day SSS and subsequently replaced by Lactobacillus in 60-day SSS. Spearman’s correlation heatmap showed that Pediococcus and Leuconostoc were negatively related to the pH value of SSS. There were great differences in the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional profiles of SS and SSS. Ensiling process downregulated the metabolism of amino acid, energy, cofactors, and vitamins, but upregulated the metabolism of nucleotides and carbohydrates. Overall, next-generation sequencing in conjunction with KEGG functional prediction revealed the distinct differences in the initial and late phases of ensiling in terms of both community succession and functional shifts. The knowledge regarding bacterial community dynamics and functional shifts of SS during ensiling is important for understanding the fermentation mechanism and may contribute to the production of high-quality sweet sorghum silage.

Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.

Complex Trophic Interactions in an Acidophilic Microbial Community

Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.

Effects of urea supplementation on the nutritional quality and microbial community of alfalfa (Medicago sativa L.) silage

The objectives of this study were to evaluate the contribution of urea on the nutritional quality and microbial community of ensiled alfalfa (Medicago sativa L.). Alfalfa silage was control group without urea (AL), supplementation with 0.5% urea (AU1), or supplementation with 1% urea (AU2). The silage tanks were opened and sampled after silage at 0, 15, 30, and 60 d. Results showed that AU2 had higher pH, ratio of (ammonia-N)/(total nitrogen) (NH₃-N/TN) and crude protein (CP) content than those in AL and AU1, while AU1 had higher acid detergent fiber (ADF) than that in AL and AU2 after 15 d silage. Richness and diversity indices of microbial communities in silage were no significant differences among AL, AU1 and AU2 group. Proteobacteria (58.23%) and Firmicutes (40.95%) were the predominant phylum in three groups during the silage process. The percent of community abundances on genera level of Enterobacteriaceae (37.61%) and Klebsiella (41.78%) in AL were a little higher than those in AU1 (30.39%, 25.02%) and AU2 (33.48%, 26.92%). These results showed that silage with urea alone could not improve the quality of alfalfa.

Optimized Ensiling Conditions and Microbial Community in Mulberry Leaves Silage With Inoculants

Mulberry leaves (ML) are a promising alternative fodder source due to their high protein content and the abundance of active components. A test of three inoculants in various combinations revealed that high-quality ML silage was produced at an inoculum ratio of 1:1:0 (50% Saccharomyces cerevisiae, 50% Lactobacillus plantarum, and 0% Bacillus subtilis). Using dry matter (DM) loss, pH, ammonia-N and amino acid contents, total antioxidant activity, and total flavonoids content to evaluate silage quality, this inoculant mixture was shown to produce high-quality silage within a range of inoculum size (5–15%), moisture contents (50–67%), ensiling temperatures (27–30°C), and ensiling duration (14–30 days). A third trial comparing silages produced after 30 days at 28°C and 50% moisture content revealed that silage E, prepared using an L. plantarum inoculant alone, displayed the lowest DM loss and pH, and low bacterial diversity, and it was dominated by Lactobacillus (88.6%), with low abundance of Enterobacter (6.17%). In contrast, silage B5, prepared with equal ratios of L. plantarum and S. cerevisiae, was dominated by Enterococcus (67.16%) and Lactobacillus (26.94%), with less marked yeast persistence, and reducing the DM content from 50 to 40% altered these relative abundances to 5.47 and 60.61, respectively. Control silages produced without an inoculant had the highest pH and ammonia-N content (indicative of poor quality), had the lowest antioxidant activity, had higher bacterial diversity, and were dominated by Carnobacterium (74.28%) and Enterococcus (17.3%). In summary, ensiling of ML conditions with proper inoculants yielded high-quality silage with a favorable microbial community composition.

Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States

Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.

A Two-Stage Biogas Desulfurization Process Using Cellular Concrete Filtration and an Anoxic Biotrickling Filter

A two-stage desulfurization process including an abiotic filtration using cellular concrete waste (first stage) and an anoxic biotrickling filter filling with an inoculated expanded schist material (second stage) was investigated to remove H2S in mimic biogas with limited O2 amount (ranged from 0.5 to 0.8%). The two-stage process was able to satisfactorily remove H2S for all experimental conditions (RE > 97%; H2S concentration = 1500 mg m−3; total Empty Bed Residence Time (EBRT) = 200 s; removal capacity (RC) = 26 g m−3 h−1). Moreover, at a total EBRT = 360 s (i.e., 180 s for each stage), the H2S loading rate (LR) was almost treated by the bed of cellular concrete alone, indicating that abiotic filtration could be applied to satisfactorily remove H2S contained in the gas. According to the H2S concentration entering the biotrickling filter, the majority end-product was either elemental sulfur (S0) or sulfate (SO42−). Thus, the ability of the abiotic filter to remove a significant part of H2S would avoid the clogging of the biotrickling filter due to the deposit of S0. Consequently, this two-stage desulfurization process is a promising technology for efficient and economical biogas cleaning adapted to biogas containing limited O2 amounts, such as landfill biogas.

Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation

Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33–68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30–65°C, retaining 20–61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.

Aquatic Ecological Risk of Heavy-Metal Pollution Associated with Degraded Mining Landscapes of the Southern Africa River Basins: A Review

Africa accounts for nearly 30% of the discovered world’s mineral reserves, with half of the world’s platinum group metals deposits, 36% of gold, and 20% of cobalt being in Southern Africa (SA). The intensification of heavy-metal production in the SA region has exacerbated negative human and environmental health impacts. In recent years, mining waste generated from industrial and artisanal mining has significantly affected the ecological integrity of SA aquatic ecosystems due to the accelerated introduction and deposition of heavy metals. However, the extent to which heavy-metal pollution associated with mining has impacted the aquatic ecosystems has not been adequately documented, particularly during bioassessments. This review explores the current aquatic ecological impacts on the heavily mined river basins of SA. It also discusses the approaches to assessing the ecological risks, inherent challenges, and potential for developing an integrated ecological risk assessment protocol for aquatic systems in the region. Progress has been made in developing rapid bioassessment schemes (RBS) for SA aquatic ecosystems. Nevertheless, method integration, which also involves heavy-metal pollution monitoring and molecular technology, is necessary to overcome the current challenges of the standardisation of RBS protocols. Citizenry science will also encourage community and stakeholder involvement in sustainable environmental management in SA.

Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System

Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.

Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge

BACKGROUND

Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field.

RESULTS

In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields.

CONCLUSIONS

This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.

The Novel Strain Acidomyces acidophilum Isolated from Acidophilic Biofilms (Snottites) Located in the Sheki-Heh Cave (North Caucasus)

A novel acidophilic fungal strain isolated from snottites in the active sulfuric acid speleogenesis (SAS) Sheki-Heh Cave (North Caucasus, Chechen Republic) was identified and characterized. The Sheki-Heh Cave is one of three cavities of the joint SAS speleosystem; to date, it remains the only of such cave explored in Russia. Highly acidic biofilms termed snottites are found sporadically on the cave roof in sulfurous water degassing zones. Only dark-colored micromycete colonies were isolated from these microbial biofilms using direct inoculation onto Czapek agar. The dominant fungal isolate was selected for further characterization. This work aimed to identify the micromycete strain isolated from cave snottites and explore its growth characteristics. Based on the phylogenetic analysis of the rDNA ITS region (540 bp), the novel fungal strain was identified as Acidomyces acidophilum with a similarity level of 99.26%. The physiological properties of the strain were examined; the optimal pH and temperature for its growth were pH 3 and 20-28 °C, respectively. Strain IB-G85 is able to grow under NaCl concentrations up to 3%. Although IB-G85 was isolated from an oligotrophic environment and was growing under nutrient deficiency, it could utilize some sugars and proteins as well as recalcitrant substrates, such as chitin and tannin. Compared to base Czapek-Dox Agar, lactic acid and colloidal chitin as the sole carbon sources enhanced fungal growth by 100 and 59%, respectively. The occurrence of A. acidophilum and closely related fungal species within acidophilic microbial communities inhabiting sulfur-containing ecosystems is discussed in view of their contribution to snottite structure formation in SAS caves.

Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem

Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.

Effects of applying cellulase and starch on the fermentation characteristics and microbial communities of Napier grass (Pennisetum purpureum Schum.) silage

This study investigated the effects of applying cellulase and starch on the fermentation characteristics and microbial communities of Napier grass silage after ensiling for 30 d. Three groups were studied: No additives (control); added cellulase (Group 1); and added cellulase and starch (Group 2). The results showed that the addition of cellulase and starch decreased the crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF) and pH significantly (p < 0.05) and increased water-soluble carbohydrate (WSC) content (p < 0.05). The addition of additives in two treated groups exerted a positive effect on the lactic acid (LA) content, lactic acid bacteria (LAB) population, and lactic acid / acetic acid (LA/AA) ratio, even the changes were not significant (p > 0.05). Calculation of Flieg’s scores indicated that cellulase application increased silage quality to some extent, while the application of cellulase and starch together significantly improved fermentation (p < 0.05). Compared with the control, both additive groups showed increased microbial diversity after ensiling with an abundance of favorable bacteria including Firmicutes and Weissella, and the bacteria including Proteobacteria, Bacteroidetes, Acinetobacter increased as well. For alpha diversity analysis, the combined application of cellulase and starch in Group 2 gave significant increases in all indices (p < 0.05). The study demonstrated that the application of cellulase and starch can increase the quality of Napier grass preserved as silage.

Prokaryotic communities in the historic silver mine Reiche Zeche

The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history of silver production in the Ore Mountains. The mine was set up at the end of the fourteenth century and became part of the “Bergakademie Freiberg” in 1919. Galena, pyrite, sphalerite, arsenopyrite, and chalcopyrite are the most common minerals found in the mine. As acid mine drainage is generated from the dissolution of sulfidic ores, the microbial habitats within the adits and galleries are characterized by low pH and high concentrations of metal(loid)s. The community composition was investigated at locations characterized by biofilm formation and iron-rich bottom pools. Amplicon libraries were sequenced on a MiSeq instrument. The taxonomic survey yielded an unexpected diversity of 25 bacterial phyla including ten genera of iron-oxidizing taxa. The community composition in the snottites and biofilms only slightly differed from the communities found in acidic bottom pools regarding the diversity of iron oxidizers, the key players in most investigated habitats. Sequences of the Candidate Phyla Radiation as, e.g., Dojkabacteria and Eremiobacterota were found in almost all samples. Archaea of the classes Thermoplasmata and Nitrososphaeria were detected in some biofilm communities.

Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO₂ into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO₂ emissions.

Effect of Lactic Acid Bacteria on the Fermentation Quality and Mycotoxins Concentrations of Corn Silage Infested with Mycotoxigenic Fungi

This study was conducted to evaluate the effect of lactic acid bacteria (LAB) on fermentation quality, mycotoxin concentrations, and microbial communities of whole-crop corn silages infested with mycotoxigenic fungi. Cultured spores (10⁶ cfu/mL) of mycotoxigenic Aspergillus flavus and Fusarium graminearum were sprayed (5 mL) on corn forage on 27 July and 10 August 2018. On 21 August 2018, sprayed (FI; 3 plots) and unsprayed (NFI; 3 plots) corn forage were harvested at the 1/2 kernel milk line stage, followed by chopping and ensiling without inoculants (CON), or with Lactobacillus buchneri (LB, 1 × 10⁶ cfu/g FW), Lactobacillus plantarum (LT, 1 × 10⁶ cfu/g FW), or L. buchneri + L. plantarum (BT: both L. buchneri and L. plantarum applied at 0.5 × 10⁶ cfu/g FW). After 90 d of ensiling, FI silages had a higher (p < 0.05) pH value and higher acetic acid (ACA), ethanol, and ammonia nitrogen (ammonia N) concentrations, but lower (p < 0.05) lactic acid (LA) concentrations than NFI silage. The inoculants decreased pH and increased LA concentration and LA/ACA compared with CON. The aflatoxin B₁ (AFB₁) was only detected in FI fresh corn and silages; ensiling decreased (p < 0.05) AFB₁ concentration compared with fresh corn, and LB and BT decreased AFB₁ concentration compared with CON. The zearalenone (ZEN), deoxynivalenol (DON), and fumonisin B₁ (FB₁) concentrations were similar (p < 0.05) for NFI silages, while ZEN concentration in BT was the lowest (p < 0.05) among all FI silages; DON and FB₁ concentrations in LB, LT, and BT silages were significantly lower (p < 0.05) than those of CON in FI silages. The fungal infestation increased the bacterial and fungal diversity of silages compared with NFI silages. The FI silages had a higher relative abundance (RA) of Lactobacillus, Weissella, Wickerhamomyces, Pichia, and Epicoccum than the corresponding NFI silages. The RA of Aspergillus and Fusarium markedly decreased after 90 d of ensiling, and the inoculation expanded this trend irrespective of fungal infestation. The Penicillium in FI silages survived after 90 d of ensiling, while the inoculants decreased the RA of Penicillium. Inoculants mitigate the adverse effects of fungal infestation on corn silage quality by changing the bacterial and fungal communities.

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.

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals

Drains from coal mines remain a worrisome point-source of toxic metal/metalloid pollutions to the surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through microbiome and geochemical data can provide valuable information on the problem. Furthermore, the autochthonous microorganisms offer a potential means to remediate such contamination. The drains from Onyeama coal mine in Nigeria contained characteristic sulphates (313.0 ± 15.9 mg l⁻¹), carbonate (253.0 ± 22.4 mg l⁻¹), and nitrate (86.6 ± 41.0 mg l⁻¹), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (Degree of contamination: 3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. The microbiome of the drains revealed the dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among the bacterial community, whereas Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial taxa exhibited excellent urease activities (≥ 253 µmol urea min⁻¹) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg ml⁻¹). The drain is a point source for metals/metalloid pollution, and its bioremediation is achievable with the bacteria consortium.

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria.

IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO₂ fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace ¹³CO₂ incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6-85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. ¹³CO₂ incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0-5.3% relative ¹³C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO₂ fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains

Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO₆₀₀) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO₆₀₀) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.

Characterization of copper stress response in Fusarium tricinctum M6: A metal-resistant microorganism isolated from an acid mine drainage-affected environment

Acid mine drainage-affected environments are interesting microbial niches for the isolation of metal-resistant microorganisms. In this sense, the aim of the present work is to isolate and characterize metal-resistant microorganisms from sediments of an abandoned gold mine located in San Luis (Argentina). For these purposes, the metal removal capacity and the microelemental composition of the biomass exposed to metals were evaluated. Likewise, proteomic techniques were applied to understand the removal and resistance mechanisms. Fusarium tricinctum M6 was isolated and identified as tolerant to Cu(II), Fe(II) and Cr(VI). When faced with 40 µg mL-1 Cu(II), the growth was affected by 60% and the removal capacity was 30-35%. Copper was found uniformly distributed in the biomass (5.23% w/w) and variations in the proportion of other biomass constituent elements were detected. When exposed to Cu(II), F. tricinctum M6 showed differential expression of intra and extracellular proteins involved in different metabolic processes. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The results obtained in the present work indicated bioadsorption of the metal on the cell surface and an important readjustment of the protein expression to counteract the stress produced by Cu(II).

Performance of microbial community dominated by Bacillus spp. in acid mine drainage remediation systems: A focus on the high removal efficiency of SO4 2-, Al3+, Cd2+, Cu2+, Mn2+, Pb2+, and Sr2

A consortium of microbial community was used for the treatment of acid mine drainage wastewater laden with sulphate and heavy metals. The wastewater was treated in an anaerobic continuously stirred tank bioreactor. The microbial community activity increased the pH from 5.6 to 6.5, and improved sulphate removal up to 85% from an initial sulphate concentration of 8080 mg SO42−/L in a continuous mode, following enrichment for 21 d. The maximum heavy metal removal percentage was observed for Cd (98%), Al (97%), Mn (95%), Pb (94%), Sr (94%) and Cu (91%). The microbial community showed synergy between strictly anaerobic and facultative Firmicutes sp., which were responsible for the bioreactor performance. The biochemical reaction indicated the microbial community has a wider range of substrates dominated by metallo-aminopeptidases.