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Simple Summary: The application of extremophilic, acidophilic microbial populations for the bio-oxidation of gold-bearing sulfide concentrates in industry is a source of great interest in the research of these populations. Understanding the effects of different factors on the activity of such acidophilic populations may allow for the performance of the bio-oxidation of sulfide concentrates to be regulated. In the present work, we studied the effects of different temperatures as well as carbon sources (carbon dioxide and molasses) on the rate of the bio-oxidation of a gold-bearing pyrite–arsenopyrite concentrate as well as on the composition of the microbial population performing this process. It was shown that an increase in the temperature from 40 to 50 °C led to a decrease in the intensity of bio-oxidation, while the application of additional carbon dioxide as a carbon source made it possible to prevent the inhibition of bio-oxidation due to a temperature increase. An analysis of the populations formed under different experimental conditions revealed that both temperature and carbon dioxide affected the composition of the microbial population which, in turn, may explain the effect on the bio-oxidation performance. Thus, the use of additional carbon dioxide may be proposed as the method to increase the efficiency of bio-oxidation and to prevent the negative effect of a temperature increase on the activity of bio-oxidation. In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate at temperatures of 40–50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov. [ABSTRACT FROM AUTHOR]

The Parys Mountain copper mine (Wales, UK) contains a wide range of discrete environmental microniches with various physicochemical conditions that shape microbial community composition. Our aim was to assess the microbial community in the sediments and overlying water column in an acidic mine drainage (AMD) site containing abundant filamentous biogenic growth via application of a combination of chemical analysis and taxonomic profiling using 16S rRNA gene amplicon sequencing. Our results were then compared to previously studied sites at Parys Mt. Overall, the sediment microbiome showed a dominance of bacteria over archaea, particularly those belonging to Proteobacteria (genera Acidiphilium and Acidisphaera), Acidobacteriota (subgroup 1), Chloroflexota (AD3 cluster), Nitrospirota (Leptospirillum) and the uncultured Planctomycetota/CPIa-3 termite group. Archaea were only present in the sediment in small quantities, being represented by the Terrestrial Miscellaneous Euryarchaeota Group (TMEG), Thermoplasmatales and Ca. Micrarchaeota (Ca. Micracaldota). Bacteria, mostly of the genera Acidiphilium and Leptospirillum, also dominated within the filamentous streamers while archaea were largely absent. This study found pH and dissolved solutes to be the most important parameters correlating with relative proportions of bacteria to archaea in an AMD environment and revealed the abundance patterns of native acidophilic prokaryotes inhabiting Parys Mt sites and their niche specificities. [ABSTRACT FROM AUTHOR]

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

"Candidatus Micrarchaeota" are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high-throughput amplicon sequencing of V3-V4 region of 16S rRNA genes), we surveyed the occurrence of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage stream (Wales, UK). We detected "Ca. Micrarchaeota" in thermophilic heterotrophic enrichment cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely "Ca. Mancarchaeum acidiphilum"-, and ARMAN-2-related, alongside their potential hosts, Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These clusters of "Ca. Micrarchaeota" together with three other groups were also present in mesophilic acid mine drainage community. Present work expands our knowledge on the diversity of "Ca. Micrarchaeota" in thermophilic and mesophilic acidic environments, suggests cultivability patterns of acidophilic archaea and establishes potential links between low-abundance species of thermophilic "Ca. Micrarchaeota" and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ. [ABSTRACT FROM AUTHOR]