Bacterial weathering of fossil organic matter and organic carbon mobilization from subterrestrial Kupferschiefer black shale: long-term laboratory studies

A large part of the organic carbon present in the lithosphere is trapped in fossil organic matter deposited in sedimentary rocks. Only specialized microorganisms are able to degrade it contributing to the return of the carbon to the global cycle. The role of bacteria in this process is not yet completely understood. In the present laboratory studies, subterrestrial organic-rich ∼256-million-year-old Kupferschiefer black shale was exposed to the activity of an indigenous consortium of lithobiontic bacteria for 365 days under aerobic conditions. An interdisciplinary research approach was applied, consisting of a detailed comparison of the chemical composition of extractable bitumens as well as resistant to extraction kerogen of the unweathered black shale to that of the bioweathered and chemically weathered, identification of mobilized organic compounds and spectrometry-based determination of proteomic composition of the bacterial biofilm. The oxidative bioweathering of bitumens and kerogen was confirmed. The mobilization of organic carbon in the form of oxidized organic compounds, such as monohydroxy and dihydroxy alcohols, aldehydes, monocarboxylic and dicarboxylic acids and esters due to the microbial activity, was documented. The enzymes crucial for the aerobic metabolism of aliphatic and aromatic hydrocarbons such as monooxygenases and dehydrogenases were identified in the epilithic biofilm inhabiting the black shale.

Solubilization of Pb-bearing apatite Pb5(PO4)3Cl by bacteria isolated from polluted environment

The main purpose of this study was to test if microorganisms isolated from heavily polluted environments can enhance dissolution of Pb-apatite (pyromorphite) resulting in remobilization of lead. Three bacterial strains belonging to the genus Pseudomonas isolated from underground mines in SW Poland were used in batch experiments of pyromorphite solubilization carried out in phosphate reach and phosphate poor media. Bacteria growth and evolution of Pb and phosphate concentrations as well as pH were determined. Additionally the concentration of bacterial siderophores in leaching solution was assayed. All bacterial strains were able to grow in both media in the presence of pyromorphite. The number of bacterial cells was from one to two orders of magnitude higher in the phosphate rich media. In the phosphate poor media the only source of P was the dissolving lead apatite. Bacteria enhanced the solubility of pyromorphite resulting in elevated Pb concentrations, up to 853 μg L^-1 in phosphate-rich medium and 6112 μg L^-1 in phosphate-poor medium, compared to less than 100 μg L^-1 in an abiotic control sample. Production of siderophores was characteristic for each culture and was much lower (10-1000 fold) in the phosphate-poor medium. This study demonstrates for the first time that indigenous bacteria can directly and indirectly promote the mobilization of lead from pyromorphite. This phenomenon should be considered in long term risk assessment of Pb contaminated soils after reclamation processes because bacteria can play a significant role in the efficiency of clean-up efforts and overall geochemical cycling of Pb.

Arsenic Mobilization from Historically Contaminated Mining Soils in a Continuously Operated Bioreactor: Implications for Risk Assessment

Concentrations of soil arsenic (As) in the vicinity of the former Złoty Stok gold mine (Lower Silesia, southwest Poland) exceed 1000 μg g(-1) in the area, posing an inherent threat to neighboring bodies of water. This study investigated continuous As mobilization under reducing conditions for more than 3 months. In particular, the capacity of autochthonic microflora that live on natural organic matter as the sole carbon/electron source for mobilizing As was assessed. A biphasic mobilization of As was observed. In the first two months, As mobilization was mainly conferred by Mn dissolution despite the prevalence of Fe (0.1 wt % vs 5.4 for Mn and Fe, respectively) as indicated by multiple regression analysis. Thereafter, the sudden increase in aqueous As[III] (up to 2400 μg L(-1)) was attributed to an almost quintupling of the autochthonic dissimilatory As-reducing community (quantitative polymerase chain reaction). The aqueous speciation influenced by microbial activity led to a reduction of solid phase As species (X-ray absorption fine structure spectroscopy) and a change in the elemental composition of As hotspots (micro X-ray fluorescence mapping). The depletion of most natural dissolved organic matter and the fact that an extensive mobilization of As[III] occurred after two months raises concerns about the long-term stability of historically As-contaminated sites.

Determination of factors responsible for the bioweathering of copper minerals from organic-rich copper-bearing Kupferschiefer black shale

The aim of this study was to investigate the bioweathering of copper minerals present in the alkaline, copper-bearing and organic-rich Kupferschiefer black shale through the action of a consortium of indigenous lithobiontic, heterotrophic, neutrophilic bacteria isolated from this sedimentary rock. The involvement of microorganisms in the direct/enzymatic bioweathering of fossil organic matter of the rock was confirmed. As a result of bacterial activity, a spectrum of various organic compounds such as urea and phosphoric acid tributyl ester were released from the rock. These compounds indirectly act on the copper minerals occurring in the rock and cause them to weather. This process was reflected in the mobilization of copper, iron and sulfur and in changes in the appearance of copper minerals observed under reflected light. The potential role of identified enzymes in biodegradation of fossil organic matter and role of organic compounds released from black shale as a result of this process in copper minerals weathering was discussed. The presented results provide a new insight into the role of chemical compounds released by bacteria during fossil organic matter bioweathering potentially important in the cycling of copper and iron deposited in the sedimentary rock. The originality of the described phenomenon lies in the fact that the bioweathering of fossil organic matter and, consequently, of copper minerals occur simultaneously in the same environment, without any additional sources of energy, electrons and carbon.

Extracellular compounds produced by bacterial consortium promoting elements mobilization from polymetallic Kupferschiefer black shale (Fore-Sudetic Monocline, Poland)

Culture experiments employing Fe-deficient medium showed that a consortium of indigenous microorganisms isolated from Kupferschiefer black shale produced a mixture of extracellular compounds containing siderophores which could form complexes with a wide range of elements and were able to mediate element mobilization from polymetallic black shale. The mobilization of a diverse array of elements including a number of essential trace elements (Co, Cu, Mn, Mo, Zn) and toxic species (As) was shown. Since the bacteria used in this study were originally obtained from a subsurface copper deposit, these results highlight the potential importance of extracellular compounds in biogeochemical cycles of elements in underground environment and their ecological significance in promoting the uptake of essential trace metals and resistance to toxic elements.

Biotransformation of copper from Kupferschiefer black shale (Fore-Sudetic Monocline, Poland) by yeast Rhodotorula mucilaginosa LM9

This study describes the yeast Rhodotorula mucilaginosa strain LM9 isolated from copper-bearing, organic-rich Kupferschiefer black shale and its role in copper biotransformation. Strain LM9 exhibited great ability to simultaneously mobilize and immobilize copper from this sedimentary rock. In addition, it showed considerable resistance to copper and high uptake of this metal. Moreover, malic and oxalic acid as well as siderophore (rhodotorulic acid) produced by this strain enhanced its resistance by promoting the mobilization and complexation of copper from black shale. These processes, characterized here under laboratory conditions, are assumed to play a role in copper cycling in black shale as well as in the adaptation of strain LM9 to the conditions prevailing in its natural mine habitat. The findings of this study indicate that yeast strain LM9 might be used for the recovery of copper particularly from alkaline or slightly neutral ores in a non-chemical environmentally-friendly procedure.

SNF1-related protein kinases type 2 are involved in plant responses to cadmium stress

Cadmium ions are notorious environmental pollutants. To adapt to cadmium-induced deleterious effects plants have developed sophisticated defense mechanisms. However, the signaling pathways underlying the plant response to cadmium are still elusive. Our data demonstrate that SnRK2s (for SNF1-related protein kinase2) are transiently activated during cadmium exposure and are involved in the regulation of plant response to this stress. Analysis of tobacco (Nicotiana tabacum) Osmotic Stress-Activated Protein Kinase activity in tobacco Bright Yellow 2 cells indicates that reactive oxygen species (ROS) and nitric oxide, produced mainly via an l-arginine-dependent process, contribute to the kinase activation in response to cadmium. SnRK2.4 is the closest homolog of tobacco Osmotic Stress-Activated Protein Kinase in Arabidopsis (Arabidopsis thaliana). Comparative analysis of seedling growth of snrk2.4 knockout mutants versus wild-type Arabidopsis suggests that SnRK2.4 is involved in the inhibition of root growth triggered by cadmium; the mutants were more tolerant to the stress. Measurements of the level of three major species of phytochelatins (PCs) in roots of plants exposed to Cd(2+) showed a similar (PC2, PC4) or lower (PC3) concentration in snrk2.4 mutants in comparison to wild-type plants. These results indicate that the enhanced tolerance of the mutants does not result from a difference in the PCs level. Additionally, we have analyzed ROS accumulation in roots subjected to Cd(2+) treatment. Our data show significantly lower Cd(2+)-induced ROS accumulation in the mutants' roots. Concluding, the obtained results indicate that SnRK2s play a role in the regulation of plant tolerance to cadmium, most probably by controlling ROS accumulation triggered by cadmium ions.

Bioweathering of Kupferschiefer black shale (Fore-Sudetic Monocline, SW Poland) by indigenous bacteria: implication for dissolution and precipitation of minerals in deep underground mine

The Upper Permian polymetallic, organic-rich Kupferschiefer black shale in the Fore-Sudetic Monocline is acknowledged to be one of the largest Cu-Ag deposits in the world. Here we report the results of the first study of bioweathering of this sedimentary rock by indigenous heterotrophic bacteria. Experiments were performed under laboratory conditions, employing both petrological and microbiological methods, which permitted the monitoring and visualization of geomicrobiological processes. The results demonstrate that bacteria play a prominent role in the weathering of black shale and in the biogeochemical cycles of elements occurring in this rock. It was shown that bacteria directly interact with black shale organic matter to produce a widespread biofilm on the Kupferschiefer shale surface. As a result of bacterial activity, the formation of pits, bioweathering of ore and rock-forming minerals, the mobilization of elements and secondary mineral precipitation were observed. The chemistry of the secondary minerals unequivocally demonstrates the mobilization of elements from minerals comprising Kupferschiefer. The redistribution of P, Al, Si, Ca, Mg, K, Fe, S, Cu and Pb was confirmed. The presence of bacterial outer membrane vesicles on the surface of black shale was observed for the first time. Biomineralization reactions occurred in both the membrane vesicles and the bacterial cells.

Arsenic response of AtPCS1- and CePCS-expressing plants - effects of external As(V) concentration on As-accumulation pattern and NPT metabolism

Phytochelatins (PCs) are small, cysteine-rich peptides, known to play a major role in detoxification of both cadmium and arsenic. The aim of this study was to determine whether overexpression of either of two PC synthase (PCS) genes, AtPCS1 and CePCS in Nicotiana tabacum (previously shown to cause decrease and increase, respectively, of cadmium tolerance of tobacco - Wojas et al., 2008) also contributes to such contrasting phenotypes with respect to arsenic (As) tolerance and accumulation, and how observed responses relate to non-protein thiol (NPT) metabolism. The expression of both genes resulted in an increase of As-tolerance, with CePCS plants most tolerant. We showed for the first time that the response of PCS overexpressing plants to As qualitatively depends on the external As(V) concentration. At the less toxic 50muM As(V), AtPCS1 and CePCS transformants accumulated more As in roots and leaves than WT. An increase in PC production and the level of PC2 species was detected in leaves of AtPCS1 and CePCS plants, which might explain their enhanced As-accumulation and tolerance. In contrast, at the highly toxic 200muM As(V), several disturbances in thiol metabolism of PCS overexpressing plants were found, surprisingly, including decrease of PC levels both in roots and leaves of transgenic plants relative to WT. The increase in As-tolerance and accumulation due to AtPCS1 and CePCS overexpression, observed at the As(V) concentrations similar to those found in As-contaminated soils, makes these genes promising candidates for plant engineering for phytoremediation.

Search for a plant for phytoremediation--what can we learn from field and hydroponic studies?

The main aim of the study was to evaluate the strategies for coping with arsenic toxicity developed by the mine species (Calamagrostis arundinacea, Fragaria vesca, Stachys sylvatica, and Epilobium parviflorum), and to compare results obtained from plants exposed to arsenic present in contaminated soil (2000-3500 mg/kg dw) and in hydroponic solution (2 microM and 12 microM arsenate). Here we report basic differences in plant responses to arsenic depending on growth conditions (hydroponic/soil) with respect to uptake, root-to-shoot translocation, distribution, and detoxification/speciation. Calamagrostis has the highest level of As-tolerance among the tested species. When grown in soil, it accumulated the highest amount of As in roots and shoots relative to other species, however, when exposed to arsenic in hydroponics, it had lower As concentrations. The efficiency of arsenic root-to-shoot translocation was also different, being less effective in soil-grown Calamagrostis compared with hydroponics. Furthermore, in Calamagrostis exposed to arsenate in liquid medium, As(III) was the predominant arsenic form, in contrast to plants grown in As-contaminated soil, in which As(V) predominated. In addition, comparison of the level of phytochelatins showed that only PC2 was detected in plants from hydroponics, whereas in those from soil, additionally PC3 and PC4 were found. The results show that the basic components of a plant's response to arsenic, including uptake, accumulation as well as detoxification, change depending on the experimental conditions (arsenic in liquid medium or contaminated soil).

Ectopic expression of Arabidopsis ABC transporter MRP7 modifies cadmium root-to-shoot transport and accumulation

Arabidopsis MRPs/ABCCs have been shown to remove various organic and inorganic substrates from the cytosol to other subcellular compartments. Here we first demonstrate that heterologous expression of AtMRP7 in tobacco (Nicotiana tabacum var. Xanthi) modifies cadmium accumulation, distribution and tolerance. Arabidopsis MRP7 was localized both in the tonoplast and in the plasma membrane when expressed in tobacco. Its overexpression increased tobacco Cd-tolerance and resulted in enhanced cadmium concentration in leaf vacuoles, indicating more efficient detoxification by means of vacuolar storage. Heterologous AtMRP7 expression also led to more efficient retention of Cd in roots, suggesting a contribution to the control of cadmium root-to-shoot translocation. The results underscore the use of AtMRP7 in plant genetic engineering to modify the heavy-metal accumulation pattern for a broad range of applications.

Overexpression of phytochelatin synthase in tobacco: distinctive effects of AtPCS1 and CePCS genes on plant response to cadmium

Phytochelatins, heavy-metal-binding polypeptides, are synthesized by phytochelatin synthase (PCS) (EC 2.3.2.15). Previous studies on plants overexpressing PCS genes yielded contrasting phenotypes, ranging from enhanced cadmium tolerance and accumulation to cadmium hypersensitivity. This paper compares the effects of overexpression of AtPCS1 and CePCS in tobacco (Nicotiana tabacum var. Xanthi), and demonstrates how the introduction of single homologous genes affects to a different extent cellular metabolic pathways leading to the opposite of the desired effect. In contrast to WT and CePCS transformants, plants overexpressing AtPCS1 were Cd-hypersensitive although there was no substantial difference in cadmium accumulation between studied lines. Plants exposed to cadmium (5 and 25 muM CdCl2) differed, however, in the concentration of non-protein thiols (NPT). In addition, PCS activity in AtPCS1 transformants was around 5-fold higher than in CePCS and WT plants. AtPCS1 expressing plants displayed a dramatic accumulation of gamma-glutamylcysteine and concomitant strong depletion of glutathione. By contrast, in CePCS transformants, a smaller reduction of the level of glutathione was noticed, and a less pronounced change in gamma-glutamylcysteine concentration. There was only a moderate and temporary increase in phytochelatin levels due to AtPCS1 and CePCS expression. Marked changes in NPT composition due to AtPCS1 expression led to moderately decreased Cd-detoxification capacity reflected by lower SH:Cd ratios, and to higher oxidative stress (assessed by DAB staining), which possibly explains the increase in Cd-sensitivity. The results indicate that contrasting responses to cadmium of plants overexpressing PCS genes might result from species-dependent differences in the activity of phytochelatin synthase produced by the transgenes.

The growth, ferrous iron oxidation and ultrastructure of Acidithiobacillus ferrooxidans in the presence of dibutyl phthalate

The iron-oxidizing bacteria Acidithiobacillus ferrooxidans is an example of strictly chemolitotrophic extremophile occurring in acidic environments. The prime niche of these microorganisms is an environment with low pH and high concentrations of iron, sulfide minerals or sulfur. Besides these environments, A. ferrooxidans is also isolated from heavy metal contaminated environments such as soil and sewage sludge and is known to be useful in bioremediation processes of these environments. In the current study, the influence of dibutyl phthalate on the growth, activity and ultrastructure of A. ferrooxidans ATCC19859 was shown. The presence of dibutyl phthalate in 9K medium did not influence A. ferrooxidans growth or ability to oxidize ferrous iron although changes in growth medium were accompanied by changes in the protein expression profiles of periplasmic fractions and remarkable changes in ultrastructure of the cell.

Influence of DnaK and DnaJ chaperones on Escherichia coli membrane lipid composition

The content of fatty acids extracted from the membranes of E. coli MC 1061 harboring the wild-type dnaKdnaJ alleles and its delta dnaJ and delta dnaKdnaJ derivatives was compared. It was demonstrated that dodecanoic acid was missing in NPLs fraction extracted from both mutants grown at 42 degrees C. Phospholipids extracted from mutant strains were deprived of hexadecanoic acid methyl ester and octadecanol, the latter being correlated with the presence of octadecanoic acid. The amount of LPS extracted from delta dnaKdanJ mutant was significantly lower when compared with wild-type strain and delta dnaJ mutant.

The role of microorganisms in dispersion of thallium compounds in the environment

Thallium is a highly toxic element and very rarely studied in the context of environmental hazards connected with zinc and non-ferrous metal industry. Microorganisms naturally existing in post-flotation and smelt wastes can participate in thallium release from waste deposits and can contribute to its dispersion in the environment. Twenty-one isolates were obtained from wastes of a non-ferrous smelter in Southern Poland characterised by high heavy metal contamination. Ten isolates showed high activity in thallium leaching from wastes (post-flotation and smelt wastes) as well as from pure thallous sulphide. Additionally, cadmium and lead were bioleached from wastes. The isolated bacteria indicated thallium resistance at a concentration up to 100 mg/l and some of them were able to survive in good condition at a concentration of up to 4 g/l. The same bacteria were isolated from rivers and wastewater in this region. A preliminary characterisation of isolates was performed. It was shown that some petroleum products i.e. asphalt-base crude occasionally used for waste immobilisation at the edge of pond or flotation surfactants partially stopped the activity of sulphide oxidising bacteria.

Polythionates and adenosine-5-phosphosulfate formation during thiosulfate oxidation by Thiobacillus neapolitanus

The intermediates formed during thiosulfate oxidation by Thiobacillus neapolitanus were examined. Tetrathionate occurred as an intermediate compound and trithionate as one of the by-products. Adenosine-5-phosphosulfate was formed from the inner sulfur of the thiosulfate molecule, without reductive cleavage of Na2S2O3. A pathway for thiosulfate oxidation by T. neapolitanus is proposed.