Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey

A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota

Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.

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

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

Microbial Communities in Volcanic Glacier Ecosystems

Glaciers constitute a polyextremophilic environment characterized by low temperatures, high solar radiation, a lack of nutrients, and low water availability. However, glaciers located in volcanic regions have special characteristics, since the volcanic foci provide them with heat and nutrients that allow the growth of microbial communities highly adapted to this environment. Most of the studies on these glacial ecosystems have been carried out in volcanic environments in the northern hemisphere, including Iceland and the Pacific Northwest. To better know, the microbial diversity of the underexplored glacial ecosystems and to check what their specific characteristics were, we studied the structure of bacterial communities living in volcanic glaciers in Deception Island, Antarctica, and in the Kamchatka peninsula. In addition to geographic coordinates, many other glacier environmental factors (like volcanic activity, altitude, temperature, pH, or ice chemical composition) that can influence the diversity and distribution of microbial communities were considered in this study. Finally, using their taxonomic assignments, an attempt was made to compare how different or similar are the biogeochemical cycles in which these microbiomes are involved.

Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling

Extremophilic bacteria have numerous uncovered biotechnological potentials. Acidophilic bacteria are important iron oxidizers that are valuable in bioleaching and in studying extreme environments on earth and in space. Despite their obvious potential, little is known about the genetic traits that underpin their metabolic functions, which are equally poorly understood from a mechanistic perspective. Novel bioinformatics and computational biology pipelines can be used to analyze whole genomes to obtain insights into the phenotypic potential of organisms as well as develop a mathematical model representation of metabolism. Whole-genome sequence analysis and a genome-scale metabolic network model was curated for an iron-oxidizing bacterium initially isolated from an acid mine drainage in Turkey, previously identified as Alicyclobacillus tolerans. The genome contained a high proportion of genes for energy generation from carbohydrates, amino acids synthesis and conversion, nucleic acid metabolism and repair which contribute to robust adaption to their extreme environments. Several candidate genes for pyrite metabolism, iron uptake, regulation and storage, as well as genes for resistance to important heavy metals were annotated. A curated genome-scale metabolic network analysis accurately predicted facultative anaerobic growth, heterotrophic characteristics, and growth on a wide variety of carbon sources. This is the first in-depth in silico analysis of A. tolerans to the best of our knowledge which is expected to lay the groundwork for future research and drive innovations in environmental microbiology and biotechnological applications. The genomic data and mechanistic framework will have applications in biomining, synthetic geomicrobiology on earth, as well as for space exploration and settlement.

Exploring the microbial community inhabiting the phosphogypsum stacks of Huelva (SW SPAIN) by a high throughput 16S/18S rDNA sequencing approach

Around 100 Mt of phosphogypsum (PG) have been deposited in large stacks on the salt marshes of the Tinto River estuary in Huelva (SW Spain), covering about 1000 ha. These stacks contain extremely acidic water (pH < 2) with high concentrations of pollutants which can cause emissions into their surroundings, generating important environmental concerns. Despite many chemical, geological or hydrological studies have been conducted to characterize the PG stacks of Huelva, the microbial community inhabiting this extreme environment remains unexplored. Using a 16S/18S-rRNA-high throughput sequencing approach, we have uncovered the main taxonomic groups able to live in the acidic metal-contaminated water, which is in direct contact with the PG, demonstrating for the first time the existence of a huge diversity of microbial species in these extreme conditions. In addition, the physicochemical characteristics of the water sampled have been analyzed. These studies have revealed that the most abundant bacteria found in two different leachate samples of the PG stacks belong to the genera Acidiphilium, Pseudomonas, Leptosprillum, Acidithrix, or Acidithiobacillus, typically found in acid mine drainage (AMD) environments, which in total represent around 50% of the total bacterial community. Biodiversity of eukaryotes in PG water is lower than that of prokaryotes, especially in the water collected from the perimeter channel that surrounds the PG stacks, where the pH reaches a value of 1.5 and the activity concentrations exceed 300 Bq L^-1 for ²³⁸U or 20 Bq L^-1 for ²¹⁰Po, values which are from four to five orders of magnitude higher than those usually found in unperturbed surface waters. Even so, an unexpected diversity of algae, fungi, and ciliates have been found in the PG stacks of Huelva, where chlorophyte microalgae and basidiomycetes fungi are the most abundant eukaryotes. Additional bioinformatics tools have been used to perform a functional analysis and predict the most common metabolic pathways in the PG microbiota. The obtained data indicate that the extreme conditions of these PG stacks hide an unexpected microbial diversity, which can play an important role in the dynamics of the contaminating compounds of the PG and provide new strains with unique biotechnological applications.

Simulated acid mine drainage treatment in iron oxidizing ceramic membrane bioreactor with subsequent co-precipitation of iron and arsenic

Acid mine drainage (AMD), generated in the active and abandoned mine sites, is characterized by low pH and high metal concentrations. One AMD treatment possibility is biologically oxidizing Fe²⁺ followed by precipitation through pH control. As compared to autotrophic iron oxidizing microbial community, a microbial community enriched in the presence of organic nutrients was hypothesized to yield higher biomass during commissioning the bioreactor. In this study, the treatment of Fe, Cu, Co, Mn, Zn, Ni, and As containing simulated AMD was studied using an iron-oxidizing ceramic membrane bioreactor (CMBR) at varying hydraulic retention times (HRTs) (6-24 h) and two different feed Fe²⁺ concentrations (250 and 750 mg/L). The impact of tryptone soya broth (TSB) on the CMBR performance was also investigated. Almost complete Fe²⁺ oxidation and sustainable flux at around 5.0 L/(m².h) were obtained in the CMBR with the Alicyclobacillus tolerans and Acidiphilium cryptum dominated enrichment culture. The Fe²⁺ oxidation rate, as assessed in batch operation cycles of CMBR, increased significantly with increasing Fe²⁺ loading to the bioreactor. The iron oxidation rate decreased by the elimination of organic matter from the feed. The increase of the CMBR permeate pH to 3.5-4.0 resulted in selective co-precipitation of As and Fe (over 99%) with the generation of biogenic schwertmannite.

Redox stress response and UV tolerance in the acidophilic iron-oxidizing bacteria Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans

The oxidative stress response represents a sum of antioxidative mechanisms that are essential for determining the adaptation and abundance of microorganisms in the environment. Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans are chemolithotrophic bacteria that obtain their energy from the oxidation of ferrous ion. Both microorganisms are important for bioleaching of sulfidic ores and both are tolerant to high levels of heavy metals and other factors that can induce oxidative stress. In this work, we compared the tolerance and response of L. ferriphilum and At. ferrooxidans to Fe³⁺, H₂O₂, K₂CrO₄, and UV-C radiation. We evaluated growth, generation of reactive oxygen species (ROS), oxidative damage to lipid membranes and DNA, and the activity of antioxidative proteins in cells exposed to these stressors. L. ferriphilum had higher cell density, lower ROS content and less lipid and DNA damage than At. ferrooxidans. Consistent with this, the activity levels of thioredoxin and superoxide dismutase in L. ferriphilum were upregulated and higher than in At. ferrooxidans. This indicated that L. ferriphilum has a higher capacity to respond to oxidative stress and to manage redox homeostasis. This capacity could largely contribute to the high abundance of this species in natural and anthropogenic sites.

Development of silica protective layer on pyrite surface: a column study

An appealing technique to prevent and/or minimize pyrite oxidation and subsequent acid generation in mine waste sites is the formation of a protective coating on the surface of sulfide grains. To investigate the conditions for the formation of an efficient coating on pyritic tailings, column tests were performed. These tests involved the treatment with a coating solution, which was continuously recycled through the packed bed of tailings. The coating solution was consisted of SiO₄^-4 oxyanions, an oxidant (H₂O₂), and adjusted to pH 6. The effect of the volume of coating solution per mass of material (L/S ratio), Si concentration and treatment duration on coating formation was studied. Based on the results, a protective coating can be developed on the pyrite particles following treatment with a solution of 0.1 mM Si concentration, which resulted in the reduction of sulfate release by 84% compared to non-treated pyrite samples.

Generation of acid mine drainage around the Karaerik copper mine (Espiye, Giresun, NE Turkey): implications from the bacterial population in the Acısu effluent

The Karaerik Cu mine is a worked-out deposit with large volumes of tailings and slags which were left around the mine site without any protection. Natural feeding of these material and run-off water from the mineralised zones into the Acısu effluent causes a serious environmental degradation and creation of acid mine drainage (AMD) along its entire length. This research aims at modelling the formation of AMD with a specific attempt on the characterisation of the bacterial population in association with AMD and their role on its occurrence. Based on 16SrRNA analyses of the clones obtained from a composite water sample, the bacterial community was determined to consist of Acidithiobacillus ferrivorans, Ferrovum myxofaciens, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans as iron-oxidising bacteria, Acidocella facilis, Acidocella aluminiidurans, Acidiphilium cryptum and Acidiphilium multivorum as iron-reducing bacteria, and Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Acidiphilium cryptum as sulphur-oxidising bacteria. This association of bacteria with varying roles was interpreted as evidence of a concomitant occurrence of sulphur and iron cycles during the generation of AMD along the Acısu effluent draining the Karaerik mine.