Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature

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 <i>Thermoplasmataceae</i> (<i>Acidiplasma</i>, <i>Ferroplasma</i>, <i>Cuniculiplasma</i>, and A-plasma group) and bacteria of the genera <i>Leptospirillum</i>, with <i>Sulfobacillus</i> and <i>Acidithiobacillus</i> 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 <i>Acidiplasma</i> and <i>Sulfobacillus</i> and decreases in the relative abundances of <i>Ferroplasma</i>, <i>Leptospirillum</i>, and <i>Acidithiobacillus</i>, while <i>Cuniculiplasma</i> 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 <i>Thermoplasmatales</i> 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 “<i>Candidatus</i> Carboxiplasma ferriphilum” gen. nov., spec. nov.