An Autochthonous Acidithiobacillus ferrooxidans Metapopulation Exploited for Two-Step Pyrite Biooxidation Improves Au/Ag Particle Release from Mining Waste

Pyrite bio-oxidation by chemolithotrophic acidophile bacteria has been applied in the mining industry to bioleach metals or to remove pyritic sulfur from coal. In this process, it is desirable to use autochthonous and already adapted bacteria isolated directly from the mining sites where biomining will be applied. Bacteria present in the remnant solution from a mining company were identified through cloning techniques. For that purpose, we extracted total RNA and performed reverse transcription using a novel pair of primers designed from a small region of the 16S gene (V1–V3) that contains the greatest intraspecies diversity. After cloning, a high proportion of individuals of the strains ATCC-23270 (NR_074193.1 and NR_041888.1) and DQ321746.1 of the well-known species Acidithiobacillus ferrooxidans were found, as well as two new wild strains of A. ferrooxidans. This result showed that the acidic remnant solution comprises a metapopulation. We assayed these strains to produce bioferric flocculant to enhance the subsequent pyrite bio-oxidation, applying two-stage chemical–bacterial oxidation. It was shown that the strains were already adapted to a high concentration of endogenous Fe2+ (up to 20 g·L−1), increasing the volumetric productivity of the bioferric flocculant. Thus, no preadaptation of the community was required. We detected Au and Ag particles originally occluded in the old pyritic flotation tailings assayed, but the extraction of Au and Ag by cyanidation resulted in ca. 30.5% Au and 57.9% Ag.

Blocking bacterial naphthohydroquinone oxidation and ADP-ribosylation improves activity of rifamycins against Mycobacterium abscessus

Rifampicin is an effective drug for treating tuberculosis (TB) but is not used to treat M. abscessus infections due to poor in vitro activity. While rifabutin, another rifamycin, has better anti- M. abscessus activity, its activity is far from the nanomolar potencies of rifamycins against M. tuberculosis . Here, we asked i) why is rifabutin more active against M. abscessus than rifampicin, and ii) why is rifabutin’s anti- M. abscessus activity poorer than its anti-TB activity. Comparative analysis of naphthoquinone versus naphthohydroquinone-containing rifamycins suggested that the improved activity of rifabutin over rifampicin is linked to its less readily oxidizable naphthoquinone core. Although rifabutin is resistant to bacterial oxidation, metabolite and genetic analyses showed that this rifamycin is metabolized by the ADP-ribosyltransferase Arr Mab like rifampicin, preventing it from achieving the nanomolar activity it displays against M. tuberculosis . Based on the identified dual mechanism of intrinsic rifamycin resistance, we hypothesized that rifamycins more potent than rifabutin should contain the molecule’s naphthoquinone core plus a modification that blocks ADP-ribosylation at its C23. To test these predictions, we performed a blinded screen of a diverse collection of 189 rifamycins and identified two molecules more potent than rifabutin. As predicted, these compounds contained both a more oxidatively-resistant naphthoquinone core and C25 modifications that blocked ADP-ribosylation. Together, this work revealed dual bacterial metabolism as the mechanism of intrinsic resistance of M. abscessus to rifamycins and provides proof of concept for the repositioning of rifamycins for M. abscessus disease by developing derivatives that resist both bacterial oxidation and ADP-ribosylation.

Authentication of Three Source Spices of Arnebiae Radix Using DNA Barcoding and HPLC

Arnebia decumbens (Vent.) Coss. et Kralik, A. euchroma (Royle) Johnst and A. guttata Bunge, three commonly used traditional Chinese medicinal plants have been widely used for the clinical treatment of inflammatory diseases caused by fungal, bacterial, oxidation, and other related pathogens. However, precise identification at the similar species level is usually challenging due to the influence of the source of medicinal materials, traditional ethnic medicine and medicinal habits. Here we developed a comprehensive and efficient identification system for three source spices of Arnebiae Radix based on DNA barcoding and HPLC fingerprinting. A total of 599 samples from thirty-five wild populations were collected and identified by using DNA barcodes of ITS2 regions, and the chemotypes of seven naphthoquinoneswere revealed by HPLC quantitative analysis including principal component analysis and hierarchical clustering analysis. Our results showed that the ITS2 sequences can distinguish three source spices of Arnebiae Radix from adulterants. However, it was difficult to identify them by HPLC-specific chromatograms combined with chemometric analysis. These results indicated that DNA barcoding was a more powerful method than HPLC fingerprinting for the identification of related species that were genetically similar. DNA barcoding analysis could be a promising and reliable tool to accurately confirm the identities of medicinal materials, especially for those whose sources are multiple and difficult to be identified by conventional chromatography.

Prerequisites for Processing a Foam Product in the Process of Bacterial Oxidation of Gold-Bearing Concentrates in a Separate Cycle

The recovery of gold from refractory ores and concentrates is a significant problem in the modern gold processing industry. The use of bacterial oxidation technology at the Navoi Mining and Metallurgical Combine (Uzbekistan) made it possible to increase the share of recoverable gold during the processing of refractory ores from the Kokpatas and Daugyztau deposits. However, during the operation of the biological installation, a problem arose of abundant foaming in bacterial oxidation reactors. This article is devoted to the issue of foaming during biooxidation and its negative impact on the oxidation process. Methods of combating foaming and the choice of the optimal solution, providing for the processing of bio-oxidation foam in a separate cycle, have been analyzed.

Bacterial oxidation of methane within seeps in the northern Laptev Sea

<p>Increase of methane concentration in atmosphere due to emission from Arctic shelf subsea deposits can play considerable role in climate change [1-2]. Methane seeps in East-Siberian and Laptev Seas were investigated in frames of complex research cruise АМК-78 onboard R/V «Akademik Mstislav Keldysh», (September 17 - October 22, 2019).</p><p>In the seep areas gas was collected to study its molecular and stable isotopes composition and reveal the genesis of discharging methane. Sediments were collected using box-corer for detailed lithological investigations and characterization of mineral inclusions. At the sampling station within methane seep in the Northern Laptev Sea, dark grey to black clays with hydrotroilite were collected.  They contained rounded inclusions of light grey carbonates with size up to 3x4cm.</p><p>Methane that migrates to the seafloor surface is characterized by wide range of stable isotopes composition values with predominance of <sup>13</sup>C depleted biogenic component [3-4].</p><p>Stable carbon and oxygen isotopes composition of carbonate inclusions was measured. The carbonates are strongly depleted in <sup>13</sup>C up to -32,4 ‰VPDB. δ<sup>18</sup>О varies in wide range between -3 and +4,4 ‰VPDB. Depletion of the carbonates in <sup>13</sup>C indicates its formation as a result of bacterial oxidation of methane in anaerobic conditions. Anaerobic oxidation of methane is an important biogeochemical process in the areas of methane emissions. The size and isotopes data of the authigenic methane-derived carbonates provide information on the intensity and time of methane discharge, geochemical characteristics of the fluids, including water. Enrichment of the carbonate inclusions in <sup>18</sup>O can be explained by the migration of isotopically heavy water from dissociating gas hydrates [5].</p><p>Obtained results of the complex study of discharging fluids and authigenic minerals allow to characterize the biochemogenic processes in seep sediments, local variations in the environmental conditions and methane flux and isotopic effects during bacterial oxidation of methane.</p><p> </p><p>Literature:</p><ol><li>Shakhova N., Semiletov I., Chuvilin E. Understanding the permafrost-hydrate system and associated methane releases in the East Siberian Arctic Shelf<strong> // </strong>Geosciences, 2019, 9, 251.</li> <li>Shakhova N.E., Sergienko V.I., Semiletov I.P. Contribution of East-Siberian shelf to the modern methane cycle // RAS bulletin, 2009, vol. 79, №6, pp. 507-518.</li> <li>Whiticar, M.J. Correlation of natural gases with their sources. In: Magoon, L., Dow, W. Eds., The Petroleum System — From Source to Trap. AAPG Memoir 60, 1994, pp. 261–284.</li> <li>Sapart, C. J., Shakhova, N., Semiletov, I., Jansen, J., Szidat, S., Kosmach, D., Dudarev, O., van der Veen, C., Egger, M., Sergienko, V.,; Salyuk, A., Tumskoy, V., Tison, J.L., Rockmann, T. The origin of methane in the East Siberian Arctic Shelf unraveled with triple isotope analysis // Biogeosciences, 14, 9, 2283-2292, 2017.</li> <li>Bohrman G., Suess E., Greinert J., Teichert B., Naehr T. Has hydrate carbonates from Hydrate ridge, Cascadia convergent margin: indicators of near-seafloor clathrate deposits // Fourth Int. Conf. Gas Hydrates: Yokohama, Japan, 19023:102-107. 2002.</li> </ol>

Intramolecular isotopic evidence for bacterial oxidation of propane in subsurface natural gas reservoirs

Microbial anaerobic oxidation of hydrocarbons is a key process potentially involved in a myriad of geological and biochemical environments yet has remained notoriously difficult to identify and quantify in natural environments. We performed position-specific carbon isotope analysis of propane from cracking and incubation experiments. Anaerobic bacterial oxidation of propane leads to a pronounced and previously unidentified13C enrichment in the central position of propane, which contrasts with the isotope signature associated with the thermogenic process. This distinctive signature allows the detection and quantification of anaerobic oxidation of hydrocarbons in diverse natural gas reservoirs and suggests that this process may be more widespread than previously thought. Position-specific isotope analysis can elucidate the fate of natural gas hydrocarbons and provide insight into a major but previously cryptic process controlling the biogeochemical cycling of globally significant greenhouse gases.