Acidophilic Microbial Communities Research Articles

Investigating the acidophilic microbial community's adaptation for enhancement indium bioleaching from high pulp density shredded discarded LCD panels

As part of electronic waste (e-waste), the fastest growing solid waste stream in the world, discarded liquid crystal displays (LCDs) contain substantial amounts of both valuable and potentially harmful metal, offering valuable opportunities for resource extraction but posing environmental threats. The present comprehensive study is an investigation into the bioleaching of indium from discarded LCD panels, with a particular focus on high pulp density shredded (Sh-LCDs) and powdered (P-LCDs) materials. This study involved an acidophilic consortium, with two pathways, namely the mixed sulfur-iron pathways and sulfur pathways, being explored to understand the bioleaching mechanisms. Indium bioleaching efficiencies through the mixed sulfur-iron pathway were approximately 60% and 100% for Sh-LCDs and P-LCDs, respectively. Three mechanisms were involved in the extraction of indium from LCD samples: acidolysis, complexolysis, and redoxolysis. The microbial community adapted to a pulp density of 32.5 g/L was streak-plated and it was revealed that sulfur-oxizing bacteria dominated, resulting in the minimum indium extraction of 10% and 55% for both Sh-LCDs and P-LCDs samples, respectively. It was generally accepted that ferric ions as oxidants were effective for indium bioleaching from both the Sh-LCDs and P-LCDs. This implies that the cooperation or interaction within the microbial community used in the bioleaching process had a beneficial impact, enhancing the overall effectiveness of extracting indium from LCD panels. The adapted consortium utilizes a combination of microbial transformation, efflux systems, and chelation through extracellular substances to detoxify heavy metals. The adapted microbial community demonstrated better indium leaching efficiency (50%) compared to the non-adapted microbial community which achieved a maximum of 29% and 5% respectively from Sh-LCDs and P-LCDs at a pulp density of 32.5 g/L. The advantages of an adapted microbial community for indium leaching efficiency, attributing this advantage to factors such as high metabolic activity and improved tolerance to heavy metals. Additionally, the protective role of the biofilm formed by the adapted microbial community is particularly noteworthy, as it contributes to the community's resilience in the presence of inhibitory substances. This information is valuable for understanding and optimizing bioleaching processes for indium recovery, and by extension to possibly other metals.

New Features of Acidophilic Bacteria of the Genus Sulfobacillus: Polysaccharide Biosynthesis and Degradation Pathways

Bacteria of the genus Sulfobacillus are predominant members of acidophilic microbial communities involved in the bioprocessing of sulfide raw materials. Genomic analysis of different Sulfobacillus species revealed a starch/glycogen GlgE-dependent biosynthesis pathway of α-glucans from trehalose in S. thermotolerans and S. thermosulfidooxidans. The key enzyme of this pathway, a fused maltose-trehalose/α-amylase protein, was not encoded in the genomes of other Sulfobacillus bacteria. At the same time, the presence of all genes encoding enzymes for α-glucan decomposition allowed the prediction of polysaccharide degradation pathways in these two species. Despite the optimum mixotrophic type of metabolism, a gradual adaptation of Sulfobacillus bacteria to polysaccharides resulted in their active organotrophic growth. Moreover, the enzyme assay determined the activities of the extracellular enzymes involved in glycogen and starch degradation. In acidophilic communities of natural and industrial habitats, an essential function of polysaccharides in the composition of extracellular polymeric substances of slime matrices is to promote the attachment of the microbial cells to solid surfaces, such as mineral particles. Polysaccharides can also be storage compounds used for energy and carbon metabolism under specific environmental conditions. Understanding the metabolic capabilities of Sulfobacillus bacteria in consuming and synthesizing α-glucans, which are provided in this study, is of fundamental importance in understanding acidophilic microbial communities and their application in practice.

Bulk flotation followed by selective leaching with biogenic ferric iron is a promising solution for eco-friendly processing of complex sulfidic ores.

The development of cost-effective environmentally friendly technologies is of current importance for the intensification of metal recovery. Here, we propose a new direction in the use of a two-step process for the treatment of complex sulfidic ores. In the first step, ore flotation allows the obtainment of a bulk copper-zinc concentrate and low-toxicity waste. In the second step, zinc is selectively extracted by chemical leaching with a biogenic ferric iron solution, while copper is accumulated in the leach residue. Importantly, the efficiency of this step depends on the chemical and mineralogical composition of polymetallic concentrates. Four samples of the copper-zinc sulfide concentrate with various contents of copper and zinc have been leached in multiple cycles at 80°C, 10% of pulp density, and pH 1.3-1.5. The leaching of the concentrate that contained 14.7% of copper and 5.0% of zinc for three leaching cycles (total duration, 5.75h) allowed the obtainment of a leach residue containing 15.3 and 0.14% of copper and zinc, respectively. At the same time, the leaching of another concentrate that contained 19.2% of copper and 2.64% of zinc after one leaching cycle (total duration, 0.67h) led to copper and zinc contents of 19.1 and 0.72%, respectively, in the leach residue. Therefore, the treatment of only two concentrates allowed the obtainment of high-grade copper concentrates containing low amounts of zinc. Ferric iron, the oxidant of sulfide minerals, was fully regenerated in leachate within 30-35h at 40°C using an acidophilic microbial community dominated by Leptospirillum ferriphilum, Sulfobacillus spp., and Ferroplasma acidiphilum. The loss of copper and zinc in solid waste of the bioregeneration did not exceed 1.0% and 1.8%, respectively. The proposed flowsheet of bulk concentrate processing has several important advantages over conventional technologies, including short duration of leaching, formation of low-toxicity solid waste, and pyrometallurgical processing of only high-grade copper concentrates. This approach can be a promising solution for the efficient processing of polymetallic bulk concentrates.

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.

Comparison of Bio- and Ferric Leaching for Beneficiation of Bulk Copper-Nickel Sulfidic Concentrate

Processing of sulfidic raw materials, including bulk concentrates of nonferrous metals, is a problem of current importance in metallurgy and waste recycling. In this study, leaching with a chemical ferric iron reagent was compared to two bio-approaches to process a bulk copper-nickel concentrate: (1) ferric leaching with a solution obtained by microbial oxidation and (2) stirred-tank bioleaching using an active acidophilic microbial community. The results of both the chemical and bio-processes indicated nickel dissolution, while copper was accumulated in leach residues. After short-term high-temperature leaching with the chemical or bio- solution (Fe3+, 10 g/L), the nickel content in solids decreased by 0.7 and 2.6%, respectively, while the copper content slightly increased (by 1.5–3.2%). Bioleaching at 40°C was characterized by a considerably higher efficacy of the process: nickel leaching reached 86.7%, and the copper content increased by ~5% in the bioleach residue. Based on these results, ferric leaching can be considered an inefficient method for selective nickel removal, while bioleaching may be a promising cost-effective approach characterized by relatively low environmental hazards to obtain a high-grade copper product. Moreover, ferric leaching with the bio-solution can improve the grade of monometallic sulfidic concentrates due to additional selective nickel extraction.

A Case of Predominance of Alicyclobacillus tolerans in Microbial Community during Bioleaching of Pentlandite-Chalcopyrite Concentrate

Bacterial isolates assigned to the species Alicyclobacillus tolerans, which occupies an intermediate position between an organotrophic genus Alicyclobacillus and mixotrophic genus Sulfobacillus, were revealed as members of the acidophilic chemolithotrophic community during stirred-tank bioleaching of violarite–pentlandite–chalcopyrite concentrate at 40 °C. Surprisingly, this species succeeded more common iron-oxidizing community members after a series of bioleaching processes in bioreactors. The possibility of mixotrophic and organoheterotrophic growth of Al. tolerans, tolerance to low pH values (1.0–1.15), as well as preservation of cells via sporulation under unfavorable conditions, may explain its key role in the bioleaching of the copper–nickel bulk concentrate. Isolation of two other sulfur-oxidizing pure cultures dominating the microbial community, together with their phylogenetic characterization, allowed the assignment of these isolates to the species Acidithiobacillus caldus. This and other studies of acidophilic microbial communities are important for the development and intensification of the bioleaching processes, including a biobeneficiation approach previously proposed by us.

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 (540bp), 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.

Biobeneficiation of bulk copper-zinc and copper-nickel concentrates at different temperatures

One of the problems associated with polymetallic ore concentration is the separation of bulk concentrates, which is difficult due to the textural and structural characteristics of mineral particles. In this paper, we proposed selective bioleaching of zinc and nickel from bulk copper-zinc and copper-nickel sulfide concentrates, respectively, to extract these metals into solution and to produce high-grade copper concentrates. In the copper-zinc concentrate, zinc occurred in sphalerite (ZnS). In the copper-nickel concentrate, nickel occurred in pentlandite ((Ni,Fe)9S8) and violarite (FeNi2S4). In both concentrates, which also contained pyrite (FeS2) and pyrrhotite (Fe1-xS), copper occurred in chalcopyrite (CuFeS2). Bioleaching of the concentrates by acidophilic microbial communities at 30 and 40 °C was compared. Bioleaching at increased temperature was characterized by the higher intensity of the process. Complete removal of zinc from the copper-zinc concentrate occurred within 15 days at 30 °C and 4 days at 40 °C, while the copper content in the bioleach residue increased by 7.5 and 5.9%, respectively. Nickel leaching was less efficient: 67.6% at 30 °C and 86.7% at 40 °C after 22 days of the process. At the same time, the copper content in the bioleach residue increased by 2.7 and 5.7%. Dissolution of violarite proceeded more rapidly than that of pentlandite. More efficient zinc and nickel leaching from the concentrates at 40 °C could be associated with a higher microbial diversity in the communities formed at this temperature. An increase in the proportion of bacteria of the genera Sulfobacillus and Ferrimicrobium, as well as archaea of the families Ferroplasmaceae and Cuniculiplasmataceae, was shown. At both temperatures, Acidithiobacillus and Leptospirillum bacteria prevailed during the biooxidation of both, the copper-zinc and copper-nickel concentrates.

Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans.

Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Physiological properties of Acidithiobacillus ferrooxidans strains isolated from sulfide ore deposits in Kazakhstan

Acidithiobacillus ferroxidans strains were isolated from acidophilic microbial communities of Kazakhstan sulfide ore deposits. Their biotechnologically important properties (optimal and maximal growth temperatures and resistance to NaCl) were determined. While temperature optima of the strains were the same (30-32 degrees C), temperature ranges were different. Thus, strain TFBK oxidized iron very poorly at 37 degrees C, while for strain TFV, the iron oxidation rate at this temperature was insignificantly lower than at lesser temperatures. NaCl inhibited the oxidative activity of both strains. Iron oxidation by strain TFV was inhibited at 5 g/L NaCl and was suppressed almost completely at 20 g/L. Iron oxidation by strain TFBK was inhibited by NaCl to a lesser degree, so that iron oxidation rate was relatively high at 10 g/L, while at 20 g/L NaCl the process was not suppressed completely, although the oxidation rate was low. Sulfur oxidation by these strains was less affected by NaCl than oxidation of ferrous iron. Sulfur oxidation by strain TFV was considerably inhibited only at 20 g/L NaCl, but was not suppressed completely. Sulfur oxidation by strain TFBK was more affected by NaCl. At 10 g/L NaCl the oxidation rate was much lower than at lower NaCl concentrations (sulfate concentrations after 6 days of oxidation at 5 and 10 g/L NaCl were -130 and -100 mM, respectively). While sulfur oxidation by strain TFBK was considerably inhibited at 10 and 20 g/L NaCl, similar to strain TFV it was not suppressed completely. Our results indicate the adaptation of the species A. ferrooxidans to a broad range of growth conditions.

Effect of the aeration mode and yeast extract on the oxidation of high-pyrrhotite sulfide ore flotation concentrate and on the composition of the acidophilic chemolithotrophic microbial community

Optimal aeration conditions were determined and the effect of yeast extract on biooxidation of high-pyrrhotite sulfide ore flotation concentrate in the course of continuous cultivation of an acidophilic chemolithotrophic microbial community was studied in a line of four sequential laboratory reactors; the aeration rate was 3 L/(L min), yeast extract concentration was 0.02%. The gold recovery level was 96.45% at 2.23% elemental sulfur content in the solid residue. The dominant strains identified in the community responsible for biooxidation were Acidithiobacillus caldus OL13-1, At. caldus OL13-3 = At. caldus OL12-3, and an ‘Acidiferrobacter’ strain. Strains Sulfobacillus thermosulfidooxidans OL13-2 = S. thermosulfidooxidans OL12-1 and Ferroplasma acidiphilum OL13-4 = F. acidiphilum OL12-4 were isolated in pure culture and identified.

Thermoacidophilic microbial community oxidizing the gold-bearing flotation concentrate of a pyrite-arsenopyrite ore

An aboriginal community of thermophilic acidophilic chemolithotrophic microorganisms (ACM) was isolated from a sample of pyrite gold-bearing flotation concentrateat 45-47 degrees C and pH 1.8-2.0. Compared to an experimental thermoacidophilic microbial consortium formed in the course of cultivation in parallel bioreactors, it had lower rates of iron leaching and oxidation, while its rate of sulfur oxidation was higher. A new thermophilic acidophilic microbial community was obtained by mutual enrichment with the micioorganisms from thie experimental and aboriginal communities during oxidation of sulfide ore flotation concentrate at 47 degrees C. The dominant bacteria of this new ACM community were Acidithiobacillus caldus strains (the most active sulfur oxidizers) and Sulfobacillus thermotolerans strains (active oxidizers of both iron and sulfur), while iron-oxidizing archaea of the family Ferroplasmaceae and heterotrophic bacteria Alicyclobacillus tolerans were the minor components. The new ACM community showed promise for leaching/oxidation of sulfides from flotation concentrates at high pulp density (S:L = 1:4).

Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces

To investigate the acidophilic bacterial communities involved in microbially induced concrete corrosion (MICC). Our study sites located downstream from a forced main provided a unique opportunity to study the microbial communities involved in MICC under different environmental conditions (gradients of atmospheric H(2)S, sulphate concentration and pH) and under pipe modifications (coated vs uncoated). Bacterial cell density estimated by both cultivation- and DNA-based methods was low in the corroded sewer samples. Pyrosequencing and cloning showed that Mycobacterium and Acidithiobacillus dominated the acidophilic microbial communities. Methylacidiphilum was also dominant in samples where methane was detected. Correlation analysis indicated that Mycobacterium and Acidithiobacillus were significantly affected by pH and that Mycobacterium could better withstand highly acidic conditions compared to Acidithiobacillus. Communities dominated by Mycobacterium favoured conditions in the lined sewer pipes, while communities with a higher relative abundance of Acidithiobacillus favoured the unlined sewer pipes. Identifying the key micro-organisms involved in MICC and knowing how they interact with their environment are essential aspects for identifying steps towards concrete corrosion management.

Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

The fractionation of hydrogen stable isotopes during lipid biosynthesis is larger in autotrophic than in heterotrophic microorganisms, possibly due to selective incorporation of hydrogen from water into NAD(P)H, resulting in D-depleted lipids. An analogous fractionation should occur during amino acid biosynthesis. Whereas these effects are traditionally measured using gas-phase isotope ratio on 1H-1H and 1H-2H, using an electrospray mass spectrometry-based technique on the original biomolecular structure and fitting of isotopic patterns we measured the hydrogen isotope compositions of proteins from an acidophilic microbial community with organism specificity and compared values with those for lipids. We showed that lipids were isotopically light by -260 ‰ relative to water in the growth solution; alternatively protein isotopic composition averaged -370 ‰. This difference suggests that steps in addition to NAD(P)H formation contribute to D/H fractionation. Further, autotrophic bacteria sharing 94% 16S rRNA gene sequence identity displayed statistically significant differences in protein hydrogen isotope fractionation, suggesting different metabolic traits consistent with distinct ecological niches or incorrectly annotated gene function. In addition, it was found that heterotrophic, archaeal members of the community had isotopically light protein (-323 ‰) relative to growth water and were significantly different from coexisting bacteria. This could be attributed to metabolite transfer from autotrophs and unknown aspects of fractionation associated with iron reduction. Differential fractionation of hydrogen stable isotopes into metabolites and proteins may reveal trophic levels of members of microbial communities. The approach developed here provided insights into the metabolic characteristics of organisms in natural communities and may be applied to analyze other systems.

New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and "Leptospirillum rubarum" (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species "Leptospirillum group IV UBA BS." These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.

Lipid signatures of acidophilic microbial communities in an extreme acidic environment – Río Tinto, Spain

The Río Tinto in Spain is a naturally occurring example of an extreme environment, characterized by a low mean pH of ca. 2.2 and high heavy metal concentration, consequences of pyrite oxidation of the source rock and strong buffering capacity of the abundant iron. To describe the microbial community, we combined the analysis of intact polar lipids (IPLs) and total fatty acids (FAs) with a carbon isotope labeling experiment to trace autotrophic processes. IPL analysis revealed clear differences between the four different sampling sites, while also indicating the presence of abundant eukaryotic algal and fungal biomass. Lipid-based estimates of the prokaryotic contribution were between 10% and 32%. We investigated the lipid composition of the predominant bacteria to determine their lipid footprints in the environmental samples. The relatively 13C-enriched carbon isotopic composition of the iso- and anteiso-C15 and C17 FAs suggests that the chemolithoautotrophic community members in sediments underlying phototrophic mats were limited by CO2 availability. The isotopic composition of cycC19:0/C19:1 was in the range for major heterotrophs, indicating an origin in acidophilic chemolithoheterotrophs. Labeling experiments with 13C labeled HCO3- indicated that photoautotrophic eukaryotes are most important for carbon fixation in Río Tinto.

Geomicrobiology of extremely acidic subsurface environments

Extreme acidophiles (microorganisms with pH optima of <3) can colonize and exploit subterranean environments, such as abandoned metal sulfide mines, that have the potential for developing widespread or isolated pockets of acidity. Although acidophiles can utilize a wide range of electron donors, inorganic materials (reduced sulfur, ferrous iron, and possibly hydrogen) are often the most abundant sources of energy for acidophiles in the subsurface. The diversity and interactions of acidophilic microbial communities in two abandoned sulfide mineral mines (in Iron Mountain, California, and the Harz mountains in Germany) and a sulfidic cave (Frasissi, Italy) are reviewed. In addition, the contrasting geomicrobiology of two abandoned sulfide mineral mines in north Wales is described. Both are extremely acidic (pH~2) and low-temperature (8-9°C) sites, but one (Cae Coch) is essentially a dry mine with isolated pockets of water, while the other (Mynydd Parys) contains a vast underground lake that was partially drained several years ago. The microbial communities in these two mines exhibit different relative abundances and often different species of archaea and bacteria. Wooden pit props, submerged in the underground lake, act as a slow-release source of organic carbon in the subterranean Mynydd Parys lake, supporting a microbial community that is more enriched with heterotrophic microorganisms.

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the approximately 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.