Microbiological Sulfide Removal-From Microorganism Isolation to Treatment of Industrial Effluent

Management of excessive aqueous sulfide is one of the most significant challenges of treating effluent after biological sulfate reduction for metal recovery from hydrometallurgical leachate. The main objective of this study was to characterize and verify the effectiveness of a sulfide-oxidizing bacterial (SOB) consortium isolated from post-mining wastes for sulfide removal from industrial leachate through elemental sulfur production. The isolated SOB has a complete sulfur-oxidizing metabolic system encoded by sox genes and is dominated by the Arcobacter genus. XRD analysis confirmed the presence of elemental sulfur in the collected sediment during cultivation of the SOB in synthetic medium under controlled physicochemical conditions. The growth yield after three days of cultivation reached ~2.34 g_protein/mol_sulfid, while approximately 84% of sulfide was transformed into elemental sulfur after 5 days of incubation. Verification of isolated SOB on the industrial effluent confirmed that it can be used for effective sulfide concentration reduction (~100% reduced from the initial 75.3 mg/L), but for complete leachate treatment (acceptable for discharged limits), bioaugmentation with other bacteria is required to ensure adequate reduction of chemical oxygen demand (COD).

Granulated Bog Iron Ores as Sorbents in Passive (Bio)Remediation Systems for Arsenic Removal

The main element of PbRS (passive (bio)remediation systems) are sorbents, which act as natural filters retaining heavy metals and carriers of microorganisms involved in water treatment. Thus, the effectiveness of PbRS is determined by the quality of the (ad)sorbents, which should be stable under various environmental conditions, have a wide range of applications and be non-toxic to (micro)organisms used in these systems. Our previous studies showed that bog iron ores (BIOs) meet these requirements. However, further investigation of the physical and chemical parameters of BIOs under environmental conditions is required before their large-scale application in PbRS. The aim of this study was (i) to investigate the ability of granulated BIOs (gBIOs) to remove arsenic from various types of contaminated waters, and (ii) to estimate the application potential of gBIOs in technologies dedicated to water treatment. These studies were conducted on synthetic solutions of arsenic and environmental samples of arsenic contaminated water using a set of adsorption columns filled with gBIOs. The experiments performed in a static system revealed that gBIOs are appropriate arsenic and zinc adsorbent. Dynamic adsorption studies confirmed these results and showed, that the actual sorption efficiency of gBIOs depends on the adsorbate concentration and is directly proportional to them. Desorption analysis showed that As-loaded gBIOs are characterized by high chemical stability and they may be reused for the (ad)sorption of other elements, i.e., zinc. It was also shown that gBIOs may be used for remediation of both highly oxygenated waters and groundwater or settling ponds, where the oxygen level is low, as both forms of inorganic arsenic (arsenate and arsenite) were effectively removed. Arsenic concentration after treatment was <100 μg/L, which is below the limit for industrial water.

Raoultella sp. SM1, a novel iron-reducing and uranium-precipitating strain

The main aim of this study was the characterisation of novel Raoutella isolate, an iron-reducing and uranium-precipitating strain, originating from microbial mats occurring in the sediments of a closed down uranium mine in Kowary (SW Poland). Characterisation was done in the context of its potential role in the functioning of these mats and the possibility to use them in uranium removal/recovery processes. In our experiment, we observed the biological precipitation of iron and uranium's secondary minerals containing oxygen, potassium, sodium and phosphor, which were identified as ningyoite-like minerals. The isolated strain, Raoultella sp. SM1, was also able to dissimilatory reduce iron (III) and uranium (VI) in the presence of citrate as an electron donor. Our studies allowed us to characterise a new strain which may be used as a model microorganism in the study of Fe and U respiratory processes and which may be useful in the bioremediation of uranium-contaminated waters and sediments. During this process, uranium may be immobilised in ningyoite-like minerals and can then be recovered in nano/micro-particle form, which may be easily transformed to uraninite.

The influence of thermal treatment on bioweathering and arsenic sorption capacity of a natural iron (oxyhydr)oxide-based adsorbent

Adsorption plays a significant role in remediation of waters contaminated with arsenic, but the efficiency of the process varies depending on the sorbent properties. Bog iron ores (BIOs), characterized by high sorption capacity and widespread availability, seem to be an optimal sorbent of arsenic. However, the use of BIOs for arsenic removal from waters may be limited by the high amount of organic matter, which may stimulate microbial activity, and thus decomposition of the sorbent. The aim of this study was to determine the effect of organic matter removal by thermal transformation (roasting) on the bioavailability of BIOs and their arsenic sorption capacity. For this purpose, the influence of bacterial growth and activity on untreated and treated BIOs, unloaded and loaded with arsenic, was studied. Moreover, the chemical and physical properties (including FTIR and desorption of arsenic) of BIOs were investigated as well. The results show that the removal of organic matter increases the stability of BIOs, and thus reduces the bioavailability of the immobilized arsenic.

The role of dissimilatory arsenate reducing bacteria in the biogeochemical cycle of arsenic based on the physiological and functional analysis of Aeromonas sp. O23A

Dissimilatory arsenate reducing bacteria (DARB) are known to contribute to the mobilization of arsenic and other elements from minerals. Despite this, metabolic capabilities of only a few DARB strains have been thoroughly investigated so far, and the influence of these bacteria on the bioavailability of arsenic in the environment is still a topic for discussion. In this study, Aeromonas sp. O23A, one of the dominant DARB strains found in the Zloty Stok mine (SW Poland), was subjected to a detailed physiological and functional analysis aimed to identify the actual environmental impact of this strain. Physiological analyses revealed that O23A is a facultative anaerobe, capable of utilizing arsenate as a respiratory substrate and acetate, citrate and lactate as electron donors. Arsenate reduction was observed within the first 24h of culturing. The strain shows high resistance to arsenic and several other heavy metals (i.a. Cu, Fe, Ni and Zn) as well tolerance to a broad range of physico-chemical conditions. Metabolic preferences of O23A were thoroughly investigated using Biolog™ MicroArray assay. The strain was found to produce hydroxamate siderophores, potentially involved in the mobilization of iron and co-occurring heavy metals from minerals. On the other hand, O23A showed high adherence abilities, and its involvement in biofilm formation may lead to the entrapment of dissolved arsenic species and other toxic ions. The results shed light on the importance of arsenic respiration and resistance in the overall metabolism of Aeromonas sp. O23A and confirmed its key role in the biogeochemical cycle of arsenic, also in the context of self-purification of heavy-metal-contaminated waters.

Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD) consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin) on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i) an agricultural biogas plant (ABP) which utilizes maize silage as a main substrate, (ii) cattle slurry (CS), which contain elevated levels of lignocelluloses materials, and (iii) raw sewage sludge (RSS) with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS) and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS) prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic Methanosarcinaceae was observed by the end of the experiment. As a result, three independent, functional communities that syntrophically produced methane from acetate (primarily) and H₂/CO₂, methanol and methylamines were adapted. This study provides new insights into the specific process by which different inocula sampled from typical methanogenic environments that are commonly used to initiate industrial installations gradually adapted to allow biogas production from maize silage.

Physiological and Metagenomic Analyses of Microbial Mats Involved in Self-Purification of Mine Waters Contaminated with Heavy Metals

Two microbial mats found inside two old (gold and uranium) mines in Zloty Stok and Kowary located in SW Poland seem to form a natural barrier that traps heavy metals leaking from dewatering systems. We performed complex physiological and metagenomic analyses to determine which microorganisms are the main driving agents responsible for self-purification of the mine waters and identify metabolic processes responsible for the observed features. SEM and energy dispersive X-ray microanalysis showed accumulation of heavy metals on the mat surface, whereas, sorption experiments showed that neither microbial mats were completely saturated with heavy metals present in the mine waters, indicating that they have a large potential to absorb significant quantities of metal. The metagenomic analysis revealed that Methylococcaceae and Methylophilaceae families were the most abundant in both communities, moreover, it strongly suggest that backbones of both mats were formed by filamentous bacteria, such as Leptothrix, Thiothrix, and Beggiatoa. The Kowary bacterial community was enriched with the Helicobacteraceae family, whereas the Zloty Stok community consist mainly of Sphingomonadaceae, Rhodobacteraceae, and Caulobacteraceae families. Functional (culture-based) and metagenome (sequence-based) analyses showed that bacteria involved in immobilization of heavy metals, rather than those engaged in mobilization, were the main driving force within the analyzed communities. In turn, a comparison of functional genes revealed that the biofilm formation and heavy metal resistance (HMR) functions are more desirable in microorganisms engaged in water purification than the ability to utilize heavy metals in the respiratory process (oxidation-reduction). These findings provide insight on the activity of bacteria leading, from biofilm formation to self-purification, of mine waters contaminated with heavy metals.

Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production

The use of lignocellulosic biomass as a substrate in agricultural biogas plants is very popular and yields good results. However, the efficiency of anaerobic digestion, and thus biogas production, is not always satisfactory due to the slow or incomplete degradation (hydrolysis) of plant matter. To enhance the solubilization of the lignocellulosic biomass various physical, chemical and biological pretreatment methods are used. The aim of this study was to select and characterize cellulose-degrading bacteria, and to construct a microbial consortium, dedicated for degradation of maize silage and enhancing biogas production from this substrate. Over 100 strains of cellulose-degrading bacteria were isolated from: sewage sludge, hydrolyzer from an agricultural biogas plant, cattle slurry and manure. After physiological characterization of the isolates, 16 strains (representatives of Bacillus, Providencia, and Ochrobactrum genera) were chosen for the construction of a Microbial Consortium with High Cellulolytic Activity, called MCHCA. The selected strains had a high endoglucanase activity (exceeding 0.21 IU/mL CMCase activity) and a wide range of tolerance to various physical and chemical conditions. Lab-scale simulation of biogas production using the selected strains for degradation of maize silage was carried out in a two-bioreactor system, similar to those used in agricultural biogas plants. The obtained results showed that the constructed MCHCA consortium is capable of efficient hydrolysis of maize silage, and increases biogas production by even 38%, depending on the inoculum used for methane fermentation. The results in this work indicate that the mesophilic MCHCA has a great potential for application on industrial scale in agricultural biogas plants.

Construction of the recombinant broad-host-range plasmids providing their bacterial hosts arsenic resistance and arsenite oxidation ability

The plasmid pSinA of Sinorhizobium sp. M14 was used as a source of functional phenotypic modules, encoding proteins involved in arsenite oxidation and arsenic resistance, to obtain recombinant broad-host-range plasmids providing their bacterial hosts arsenic resistance and arsenite oxidative ability. An arsenite oxidation module was cloned into pBBR1MCS-2 vector yielding plasmid vector pAIO1, while an arsenic resistance module was cloned into pCM62 vector yielding plasmid pARS1. Both plasmid constructs were introduced (separately and together) into the cells of phylogenetically distant (representing Alpha-, Beta-, and Gammaproteobacteria) and physiologically diversified (unable to oxidize arsenite and susceptible/resistant to arsenite and arsenate) bacteria. Functional analysis of the modified strains showed that: (i) the plasmid pARS1 can be used for the construction of strains with an increased resistance to arsenite [up to 20mM of As(III), (ii) the presence of the plasmid pAIO1 in bacteria previously unable to oxidize As(III) to As(V), contributes to the acquisition of arsenite oxidation abilities by these cells, (iii) the highest arsenite utilization rate are observed in the culture of strains harbouring both the plasmids pAIO1 and pARS1, (iv) the strains harbouring the plasmid pAIO1 were able to grow on arsenic-contaminated mine waters (∼ 3.0 mg As L(-1)) without any supplementation.

Arsenic-transforming microbes and their role in biomining processes

It is well known that microorganisms can dissolve different minerals and use them as sources of nutrients and energy. The majority of rock minerals are rich in vital elements (e.g., P, Fe, S, Mg and Mo), but some may also contain toxic metals or metalloids, like arsenic. The toxicity of arsenic is disclosed after the dissolution of the mineral, which raises two important questions: (1) why do microorganisms dissolve arsenic-bearing minerals and release this metal into the environment in a toxic (also for themselves) form, and (2) How do these microorganisms cope with this toxic element? In this review, we summarize current knowledge about arsenic-transforming microbes and their role in biomining processes. Special consideration is given to studies that have increased our understanding of how microbial activities are linked to the biogeochemistry of arsenic, by examining (1) where and in which forms arsenic occurs in the mining environment, (2) microbial activity in the context of arsenic mineral dissolution and the mechanisms of arsenic resistance, (3) the minerals used and technologies applied in the biomining of arsenic, and (4) how microbes can be used to clean up post-mining environments.

Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine

In this paper we characterize the biofilm community from an ancient Złoty Stok gold and arsenic mine. Bacterial diversity was examined using a culture-independent technique based on 16S rRNA gene amplification, cloning and sequencing. We show that unexpectedly the microbial diversity of this community was extremely high (more than 190 OTUs detected), with the most numerous members from Rhizobiales (α-Proteobacteria). Although the level of rock biofilm diversity was similar to the microbial mat community we have previously characterized in the same adit, its taxonomic composition was completely different. Detailed analysis of functional arrA and aioA genes, chemical properties of siderophores found in pore water as well as the biofilm chemical composition suggest that the biofilm community contributes to arsenic pollution of surrounding water in a biogeochemical cycle similar to the one observed in bacterial mats. To interpret our results concerning the biological arsenic cycle, we applied the theory of ecological pyramids of Charles Elton.

Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance

Plasmid pSinA of Sinorhizobium sp. M14 (Alphaproteobacteria) is the first described, natural, self-transferable plasmid harboring a complete set of genes for oxidation of arsenite. Removal of this plasmid from cells of the host strain caused the loss of resistance to arsenic and heavy metals (Cd, Co, Zn and Hg) and abolished the ability to grow on minimal salt medium supplemented with sodium arsenite as the sole energy source. Plasmid pSinA was introduced into other representatives of Alphaproteobacteria which resulted in acquisition of new abilities concerning arsenic resistance and oxidation, as well as heavy metals resistance. Microcosm experiments revealed that plasmid pSinA can also be transferred via conjugation into other indigenous bacteria from microbial community of As-contaminated soils, including representatives of Alpha- and Gammaproteobacteria. Analysis of "natural" transconjugants showed that pSinA is functional (expresses arsenite oxidase) and is stably maintained in their cells after approximately 60 generations of growth under nonselective conditions. This work clearly demonstrates that pSinA is a self-transferable, broad-host-range plasmid, which plays an important role in horizontal transfer of arsenic metabolism genes.

The contribution of microbial mats to the arsenic geochemistry of an ancient gold mine

The ancient Zloty Stok (SW Poland) gold mine is such an environment, where different microbial communities, able to utilize inorganic arsenic species As(III) and As(V), are found. The purpose of the present study was to (i) estimate prokaryotic diversity in the microbial mats in bottom sediments of this gold mine, (ii) identify microorganisms that can metabolize arsenic, and (iii) estimate their potential role in the arsenic geochemistry of the mine and in the environment. The oxidation/reduction experiments showed that the microbial mat community may significantly contribute to arsenic contamination in groundwater. The presence of both arsenite oxidizing and dissimilatory arsenate reducing bacteria in the mat was confirmed by the detection of arsenite oxidase and dissimilatory arsenate reductase genes, respectively. This work also demonstrated that microorganisms utilizing other compounds that naturally co-occur with arsenic are present within the microbial mat community and may contribute to the arsenic geochemistry in the environment.

Biodegradation of Kupferschiefer black shale organic matter (Fore-Sudetic Monocline, Poland) by indigenous microorganisms

This study provides the first evidence for the direct biodegradation of persistent organic matter extracted from the organic-rich polymetallic black shale ore Kupferschiefer, one of the most important sources of metals in the world. It was demonstrated that an enriched community of indigenous heterotrophic microorganisms isolated from black shale grown under aerobic conditions could utilize shale organic matter as the sole carbon and energy source. Colonization of shale organic matter was observed. The main biodegradation intermediates and products such as phosphonic acid dioctadecyl ester and isoindole-1,3 were detected in the aqueous phase of cultures. The bacterial community showed the ability to PAH biodegradation, assimilation of organic acids and esters as well as lipase activity. The intracellular accumulation of phosphorus by bacteria during growth on organic matter was confirmed. Strains within the genus Pseudomonas were found to dominate the bacterial population at the end of the experiment. The results of this study confirm that indigenous bacteria are likely to play a role in the biotransformation of black shale and can influence the geochemical cycles of ancient organic carbon in the deep terrestrial subsurface. This process may also occur in tailings ponds containing black shale, and cause the mobilization of potentially toxic compounds to the soil and groundwater.

Biotransformation of organic-rich copper-bearing black shale by indigenous microorganisms isolated from lubin copper mine (Poland)

The role of indigenous microorganisms in the biotransformation of refractory organic-rich copper-bearing black shale ore (Kupferschiefer) was confirmed in laboratory experiments. The persistent shale's organic matter was utilized by a mixture of bacterial strains as the sole carbon and energy source, and bacterial growth was accompanied by chemical and structural changes of black shale. The release of metallic elements and organic compounds into the aqueous phase was shown. Chemical analysis revealed the presence of long-chain aliphatic hydrocarbons and further biodegradation of these compounds by bacterial action. In this study, the release of metals from metalloorganic compounds present in organic-rich copper-bearing black shale was shown for the first time. The results have also confirmed the biotransformation of metalloporphyrins naturally occurring in black shale by indigenous microorganisms. Moreover, changes in the surface area and quantitative mineral composition of black shale were detected following bacterial treatment. This biotransformation activity is of potential use in biotechnological procedures for the recovery of copper and other valuable metals from tailings that contain up to 16% black shale. On the other hand, the release of organic carbon and heavy metals from black shale by biodegradation may significantly add to anthropogenic pollution.

The culturable bacteria isolated from organic-rich black shale potentially useful in biometallurgical procedures

AIMS

The aim of this study was the isolation and characterization of micro-organisms from Lubin copper mine potentially useful in biotechnology of metal recovery from copper bearing black shale.

METHODS AND RESULTS

Eight bacterial strains were isolated from black shale ore. Phylogenetic analysis based on 16S rRNA gene homology showed that five strains belonged to the gamma-Proteobacteria, one to the Firmicutes and two to the Actinobacteria. The ability of the isolates to transform bituminous shale and use them as carbon and energy sources, as well as high resistance to metals and metalloids, esterase and lipase activities, assimilation of organic acids, degradation of phenanthrene and siderophores production were shown.

CONCLUSIONS

The indigenous bacteria exhibited a broad range of physiological properties related to geochemical parameters of the examined environment and potentially useful in biometallurgical procedures.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results have yielded new insights into the microbiology of black shale. It can be suggested that isolated micro-organisms might play a role in the geochemical cycle of carbon and metals occurring in the organic fraction of black shale ore and might be of potential use in biotechnological procedures for the copper recovery and other valuable metals from tailings containing black shale as well as organic rich ore.

Bacteria, hypertolerant to arsenic in the rocks of an ancient gold mine, and their potential role in dissemination of arsenic pollution

The aim of the present study was to find out if bacteria present in ancient gold mine could transform immobilized arsenic into its mobile form and increase its dissemination in the environment. Twenty-two arsenic-hypertolerant cultivable bacterial strains were isolated. No chemolithoautotrophs, which could use arsenite as an electron donor as well as arsenate as an electron acceptor, were identified. Five isolates exhibited hypertolerance to arsenic: up to 500mM of arsenate. A correlation between the presence of siderophores and high resistance to arsenic was found. The results of this study show that detoxification processes based on arsenate reductase activity might be significant in dissemination of arsenic pollution. It was concluded that the activity of the described heterotrophic bacteria contributes to the mobilization of arsenic in the more toxic As(III) form and a new mechanism of arsenic mobilization from a scorodite was proposed.

Adaptive responses of chemolithoautotrophic acidophilic Acidithiobacillus ferrooxidans to sewage sludge

AIM

The aim of the present study was to investigate the phenotypic and genotypic variability of two strains of Acidithiobacillus ferrooxidans genus during growth in sewage sludge.

METHODS AND RESULTS

Compared with A. ferrooxidans cells grown in mineral medium, those grown in sewage sludge demonstrated remarkable changes in ultrastructure (transmission electron microscopy) and significantly elongated lag phases. These latter cells also lacked carboxysomes and rusticyanin, showed lower level of cytochromes and exhibited modifications to their outer membrane proteins (SDS-PAGE). Restriction fragment length polymorphism analysis using pulsed-field gel electrophoresis showed that most restriction fragments were highly conserved and shared by strains grown under different conditions. However, in relation to cells grown in mineral medium, sludge-grown A. ferrooxidans lacked a number of restriction fragments, clearly indicating structural changes to the chromosomal DNA of the organism.

CONCLUSIONS

In combination, the results of this study provide evidence of adaptive responses by chemolithoautotrophic acidophilic A. ferrooxidans to facilitate growth in sewage sludge.

SIGNIFICANCE AND IMPACT OF THE STUDY

The obtained results are important from scientific as well as industrial application point of view, because they confirmed that A. ferrooxidans highly sensitive to organic compounds bacteria is useful in biotechnologies of heavy metal removal from shale ore, polluted soils and sewage sludge containing organic hazardous compounds.

Adaptive changes of chemolithoautotrophic acidophilic sulfur-oxidizing bacteria during growth in sewage sludge

A chemolithoauthotrophic, acidophilic, sulfur-oxidizing strain was isolated from sewage sludge and identified as Acidithiobacillus thiooxidans. The morphology and physiology of the isolate grown in mineral medium or sterilized sewage sludge were investigated. Morphological and ultrastructural differences between cells grown in mineral medium and sewage sludge were clearly visible. Sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed some changes in the protein expression profiles in the periplasmic fraction as well as a lower level of cytochromes. Adaptation of A. thiooxidans to sewage sludge was not only a physiological process but also included genetic changes. Restriction fragment length polymorphism analysis using pulsed field gel electrophoresis showed structural changes in chromosomal DNA of such bacteria. Most of the restriction fragments were highly conserved and shared by strains grown under different conditions. Cultivation in mineral medium did, however, lead to the appearance of an additional restriction fragment. In combination, the obtained results provide evidence of adaptive responses by A. thioxidans during growth in sewage sludge and confirm that this bacteria can be useful in biotechnologies of heavy metal bioleaching from different environments polluted with hazardous compounds.