Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

Dziewit L, Pyzik A, Szuplewska M, et al. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Frontiers in Microbiology. 2015;6: 152.The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface

Uranium mobility in organic matter-rich sediments: A review of geological and geochemical processes

Uranium (U) is of enormous global importance because of its use in energy generation, albeit with potential environmental legacies. While naturally occurring U is widespread in the Earth's crust at concentrations of ~1 to 3 ppm, higher concentrations can be found, includingwithin organicmatter (OM)-rich sediments, leading to economic extraction opportunities. The primary determinants of U behaviour in ore systems are pH, Eh, U oxidation state (U(IV), U(VI)) and the abundance of CO3 2– ions. The concentration/availability and interrelationships among such determinants vary, and the solubility and mobility of ions (e.g. OH-, CO3 2–, PO4 3-, SiO4 4-, SO4 2-) that compete for U (primarily as U(VI)) will also influence the mobility of U. In addition, the presence of OM can influence U mobility and fate by the degree of OMsorption to mineral surfaces (e.g. Fe- and Si- oxides and hydroxides). Within solid-phase OM, microbes can influence U oxidation state and U stability through direct enzymatic reduction, biosorption, biomineralisation and bioaccumulation. The biogenic UO2 product is, however, reported to be readily susceptible to reoxidation and therefore more likely remobilised over longer time periods. Thus several areas of uncertainty remain with respect to factors contributing to U accumulation, stability and/or (re)mobilisation. To address these uncertainties, this paper reviews U dynamics at both geological and molecular scales. Here we identify U-OMbond values that are in agreement, relatively strong, independent from ionic strength and which may facilitate either U mobilisation or immobilisation, depending on environmental conditions. We also examine knowledge gaps in the literature, with U-OM solubility data generally lacking in comparison to data for U sorption and dissolution, and little information available on multi-component relationships, such as UOM-V (V as vanadate). Furthermore, the capability ofOMto influence the oxidation state of U at near surface conditions remains unclear, as it can be postulated that electron shuttling by OM may contribute to changes in U redox state otherwise mediated by bacteria. Geochemical modelling of the environmental mobility of U will require incorporation of data from multi-corporation studies, as well as from studies of U-OM microbial interactions, all of which are considered in this review

Sedimentary Cobalt Protoporphyrin as a Potential Precursor of Prosthetic Heme Group for Bacteria Inhabiting Fossil Organic Matter-Rich Shale Rock

This study hypothesizes that bacteria inhabiting shale rock affect the content of the sedimentary cobalt protoporphyrin present in it and can use it as a precursor for heme synthesis. To verify this hypothesis, we conducted qualitative and quantitative comparative analyses of cobalt protoporphyrin as well as heme, and heme iron in shale rock that were (i) inhabited by bacteria in the field, (ii) treated with bacteria in the laboratory, and with (iii) bacterial culture on synthetic cobalt protoporphyrin. Additionally, we examined the above-mentioned samples for the presence of enzymes involved in the heme biosynthesis and uptake as well as hemoproteins. We found depletion of cobalt protoporphyrin and a much higher heme concentration in the shale rock inhabited by bacteria in the field as well as the shale rock treated with bacteria in the laboratory. Similarly, we observed the accumulation of protoporphyrin in bacterial cells grown on synthetic cobalt protoporphyrin. We detected numerous hemoproteins in metaproteome of bacteria inhabited shale rock in the field and in proteomes of bacteria inhabited shale rock and synthetic cobalt protoporhyrin in the laboratory, but none of them had all the enzymes involved in the heme biosynthesis. However, proteins responsible for heme uptake, ferrochelatase and sirohydrochlorin cobaltochelatase/sirohydrochlorin cobalt-lyase were detected in all studied samples

The method of contact angle measurements and estimation of work of adhesion in bioleaching of metals

<p>In this paper, we present our method for the measurement of contact angles on the surface of minerals during the bioleaching process because the standard deviation obtained in our measurements achieved unexpectedly low error. Construction of a goniometer connected with a specially prepared computer program allowed us to repeat measurements several times over a short time course, yielding excellent results.</p> <p>After defining points on the outline of the image of a drop and its baseline as well of the first approximation of the outline of the drop, an iterative process is initiated that is aimed at fitting the model of the drop and baseline. In turn, after defining the medium for which measurements were made, the work of adhesion is determined according to Young-Dupré equation. Calculations were made with the use of two methods named the L-M and L-Q methods

Postdiagenetic Changes in Kerogen Properties and Type by Bacterial Oxidation and Dehydrogenation

A significant part of organic carbon found on the earth is deposited as fossil organic matter in the lithosphere. The most important reservoir of carbon is shale rocks enriched with organic matter in the form of kerogen created during diagenesis. The purpose of this study was to analyze whether the bacterial communities currently inhabiting the shale rocks have had any impact on the properties and type of kerogen. We used the shale rock located on the Fore-Sudetic Monocline, which is characterized by oil-prone kerogen type II. We were able to show that shale rock inhabited by bacterial communities are characterized by oxidized and dehydrated kerogen type III (gas-prone) and type IV (nonproductive, residual, and hydrogen-free). Bacterial communities inhabiting shale rock were dominated by heterotrophs of the Proteobacteria, Firmicutes, and Actinobacteria phyla. Additionally, we detected a number of protein sequences in the metaproteomes of bacterial communities matched with enzymes involved in the oxidative metabolism of aliphatic and aromatic hydrocarbons, which may potentially contribute to the postdiagenetic oxidation and dehydrogenation of kerogen. The kerogen transformation contributes to the mobilization of fossil carbon in the form of extractable bitumen dominated by oxidized organic compounds

Extracellular elements-mobilizing compounds produced by consortium of indigenous bacteria isolated from kupferschiefer black shale – implication for metals biorecovery from neutral and alkaline polymetallic ores

Extracellular compounds produced by a consortium of indigenous bacteria interact with the polymetallic Kupferschiefer black shale and implicate for elements mobilization and/or complexation. The extracellular compounds were identified by GC-MS as carboxylic acids, but also aromatic acids and alcohols. Due to their action in batch experiment 16 elements were mobilized from black shale. Among mobilized elements precious metals (Cu, Ni, Co, V) as well as toxic heavy metals (As) were determined. Extracellular metabolites produced by studied consortium may be utilized in non-contact biorecovery of precious metals from neutral or slightly alkaline ores, and in the bioremediation of heavy metalcontaminated sites

The method of contact angle measurements and estimation of work of adhesion in bioleaching of metals

In this paper, we present our method for the measurement of contact angles on the surface of minerals during the bioleaching process because the standard deviation obtained in our measurements achieved unexpectedly low error. Construction of a goniometer connected with a specially prepared computer program allowed us to repeat measurements several times over a short time course, yielding excellent results. After defining points on the outline of the image of a drop and its baseline as well of the first approximation of the outline of the drop, an iterative process is initiated that is aimed at fitting the model of the drop and baseline. In turn, after defining the medium for which measurements were made, the work of adhesion is determined according to Young-Dupré equation. Calculations were made with the use of two methods named the L-M and L-Q methods

Microbial transformations of fossil organic matter of kupferschiefer black shale – elements mobilization from metalloorganic compounds and metalloporphyrins by a community of indigenous microorganisms

The presented article describes the role of community of indigenous microorganisms occurring in the Kupferschiefer black shale in elements mobilization from fossil organic matter of the deposit. The short description of metalloorganic compounds and metalloporphyrins extracted from black shale was presented as well as the characterization of indigenous microorganisms. The processes of fossil organic matter colonization, biofilm development and elements mobilization accompanying bacterial growth was summarized