Studies on the growth of Thiobacillus ferrooxidans

Siderite and vivianite as energy sources for the extreme acidophilic bacterium Acidithiobacillus ferrooxidans in the context of mars habitability

Past and present habitability of Mars have been intensely studied in the context of the search for signals of life. Despite the harsh conditions observed today on the planet, some ancient Mars environments could have harbored specific characteristics able to mitigate several challenges for the development of microbial life. In such environments, Fe2+ minerals like siderite (already identified on Mars), and vivianite (proposed, but not confirmed) could sustain a chemolithoautotrophic community. In this study, we investigate the ability of the acidophilic iron-oxidizing chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans to use these minerals as its sole energy source. A. ferrooxidans was grown in media containing siderite or vivianite under different conditions and compared to abiotic controls. Our experiments demonstrated that this microorganism was able to grow, obtaining its energy from the oxidation of Fe2+ that came from the solubilization of these minerals under low pH. Additionally, in sealed flasks without CO2, A. ferrooxidans was able to fix carbon directly from the carbonate ion released from siderite for biomass production, indicating that it could be able to colonize subsurface environments with little or no contact with an atmosphere. These previously unexplored abilities broaden our knowledge on the variety of minerals able to sustain life. In the context of astrobiology, this expands the list of geomicrobiological processes that should be taken into account when considering the habitability of environments beyond Earth, and opens for investigation the possible biological traces left on these substrates as biosignatures.

Sticky bacteria: Combined effect of galactose and high ferric iron concentration on extracellular polymeric substances production and the attachment of Acidithiobacillus ferrooxidans on a polymetallic sulfide ore surface

Adaptation and microbial attachment mechanisms for the degradation of sulfide ores are mediated by the production of extracellular polymeric substances (EPS) and their role in biofilm formation. EPS production responds to induction mechanisms associated with environmental conditions. In this study, the double induction of EPS with galactose and high ferric iron concentrations in planktonic cells of Acidithiobacillus ferrooxidans, and their attachment on the surface of a polymetallic sulfide ore from Bella Rica-Azuay in Ecuador were evaluated. A. ferrooxidans cells were previously adapted to different concentrations of galactose [0, 0.15, and 0.25% (w/v)], using two ferrous iron concentrations as an energy source (9 and 18 g L^–1) in a 9K culture medium. EPS production and its effect on mineral attachment were determined at the time point of maximal growth. The results obtained show a maximum cell attachment of 94.1% within 2 h at 0.15% of galactose and 18 g^⋅L^–1 of ferric iron concentration, compared to 71.4% without galactose and 9 g^⋅L^–1 of ferric iron. The maximum concentration of EPS was obtained with a 0.25% galactose concentration; however, it did not result in greater attachment compared to 0.15% galactose concentration. Through the combined induction of low galactose concentration and high ferric iron concentration, the percentage of bacterial attachment can be increased and, therefore, a possible increase in the rate of biooxidation and bioleaching could be obtained.

Physical, Chemical, and Microbiological Characterization of Kettara Mine Tailings, Morocco

The mining industry is of major importance to Morocco’s economy. However, the abandoned pyritic mines are a source of potentially toxic elements that can cause the disruption of the surrounding ecosystems, constituting a huge threat to wellbeing and human health. The present study aimed to analyze the physical and chemical characteristics of different types of tailings and to investigate the microbial populations of acidophilic bacteria involved in the oxidation of pyrite. Coarse and fine tailings collected from different zones of the mine (dike and pond) at two different depths (oxidized and non-oxidized residues) were analyzed for their pH, electrical conductivity, total organic carbon, total nitrogen, available P, major elements, and pseudo-total metal concentrations. The abundance of acidophilic bacteria was determined, and some acidophilic bacterial strains were isolated and tested for their metal tolerance. Tailings showed a pH ≈ 2, very low nutritional content, and high concentrations of Cu, As, Zn, and Pb, which were higher in the non-oxidized samples. The microbial counts of iron- and sulfur-oxidizing bacteria were higher than heterotrophic bacteria, with the highest numbers detected in the oxidized fine tailings. The five acidophilic bacteria isolated from the tailings were affiliated to genera Alicyclobacillus and Sulfobacillus, commonly found in this kind of environment.

OUP accepted manuscript

Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: ‘Candidatus Nitrosocosmicus franklandus C13’, Nitrososphaera viennensis EN76 and ‘Candidatus Nitrosotalea sinensis Nd2’. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both ‘Ca. N. franklandus C13’ and N. viennensis EN76 tolerated Phytagel™ while the acidophilic ‘Ca. N. sinensis Nd2’ was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel™ and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from ‘Ca. N. franklandus C13’ and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.

Prokaryotic communities in the historic silver mine Reiche Zeche

The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history of silver production in the Ore Mountains. The mine was set up at the end of the fourteenth century and became part of the “Bergakademie Freiberg” in 1919. Galena, pyrite, sphalerite, arsenopyrite, and chalcopyrite are the most common minerals found in the mine. As acid mine drainage is generated from the dissolution of sulfidic ores, the microbial habitats within the adits and galleries are characterized by low pH and high concentrations of metal(loid)s. The community composition was investigated at locations characterized by biofilm formation and iron-rich bottom pools. Amplicon libraries were sequenced on a MiSeq instrument. The taxonomic survey yielded an unexpected diversity of 25 bacterial phyla including ten genera of iron-oxidizing taxa. The community composition in the snottites and biofilms only slightly differed from the communities found in acidic bottom pools regarding the diversity of iron oxidizers, the key players in most investigated habitats. Sequences of the Candidate Phyla Radiation as, e.g., Dojkabacteria and Eremiobacterota were found in almost all samples. Archaea of the classes Thermoplasmata and Nitrososphaeria were detected in some biofilm communities.

Enhancing the plants growth and arsenic uptake from soil using arsenite-oxidizing bacteria

Plants, that naturally inhabit arsenic-contaminated areas may be used for effective arsenic-uptake from soil. The efficiency of this process may be increased by the reducing arsenic phytotoxicity and stimulating the activity of indigenous soil microbiota. As we showed, it can be achieved by the bioaugmenting of soil with arsenite-oxidizing bacteria (AOB). This study aimed to investigate the influence of soil bioaugmentation with AOB on the structure, quantity, and activity of the indigenous soil microbiota as well as to estimate the effect of such changes on the morphology, growth rate, and arsenic-uptake efficiency of plants. Plants-microbes interactions were investigated using the effective arsenites oxidizer Ensifer sp. M14 and the native plant alfalfa. The experiments were performed both in potted garden soil enriched with arsenic and in highly arsenic polluted, natural soil. The presence of M14 strain in soil contributed to the increase both in plants growth intensity and arsenic-uptake efficiency with regard to the soil without M14. After 40 days of plants culture, their average biomass increased by about 60% compared to non-bioaugmented soil, while the arsenic accumulation increased more than two times. The soil bioaugmentation contributed also to the increase in the quantity and activity of soil microorganisms without disturbing the natural microbial community structure. In the bioaugmented soil, the noticable increase in the quantity of heterotrophic, denitrifying, nitrifying and cellulolytic bacteria as well as in the activity of dehydrogenases and cellulases were observed. Soil bioaugmentation with M14 enables the application of native and commonly occurring plant species for enhancing the treatment of arsenic-contaminated soil. This in situ strategy may constitute a valuable alternative both to the chemical and physical methods of arsenic removal from soil and to the biological ways based on the arsenic hyperaccumulating plants and/or the arsenic mobilizing bacteria.

Biooxidation of Iron by Acidithiobacillus ferrooxidans in the Presence of D-Galactose: Understanding Its Influence on the Production of EPS and Cell Tolerance to High Concentrations of Iron

Acidithiobacillus ferrooxidans, together with other microorganisms, has an important role on biohydrometallurgical processes. Such bacterium gets its energy from the oxidation of ferrous ion and reduced sulfur; in the first case, the accumulation of ferric ion as a product can cause its inhibition. It is known that the extracellular polymeric substances (EPS) may have an important role in the adaptation and tolerance to diverse inhibiting conditions. In the present study, it was tested how D-galactose can influence the production of extracellular polymeric substances (EPS) on At. ferrooxidans by evaluating at the same time its biooxidant activity and capacity to tolerate high concentrations of ferric ion. The visualization and quantification of EPS was done through a confocal laser scanning microscope (CLSM). The results show that at low cellular concentrations, the D-galactose inhibits the microbial growth and the biooxidation of ferrous ion; however, when the quantity of microorganisms is high enough, the inhibition is not present. By means of chemostat tests, several concentrations of D-galactose (0; 0.15; 0.25; and 0.35%) were evaluated, thus reaching the highest production of EPS when using 0.35% of this sugar. In cultures with such concentration of D-galactose, the tolerance of the bacterium was tested at high concentrations of ferric ion and it was compared with cultures in which sugar was not added. The results show that cultures with D-galactose reached a higher tolerance to ferric ion (48.15 ± 1.9 g L^-1) compare to cultures without adding D-galactose (38.7 ± 0.47 g L^-1 ferric ion). Also it was observed a higher amount of EPS on cells growing in the presence of D-galactose suggesting its influence on the greater tolerance of At. ferrooxidans to ferric ion. Therefore, according to the results, the bases of a strategy are considered to overproduce EPS by means of At. ferrooxidans in planktonic state, so that, it can be used as a pre-treatment to increase its resistance and tolerance to high concentrations of ferric ion and improve the efficiency of At. ferrooxidans when acting in biohydrometallurgical processes.

Immobilized Microbial Catalytic Oxidation Preparation and Application of Biopolymeric Ferric Sulfate

A novel inorganic polymer flocculant, biopolymeric ferric sulfate (BPFS), was prepared by immobilization technology of microorganisms and by oxidation of ferrous sulfate using domestic Thiobacillus ferrooxidans (T. f) under acidic condition. T. f was isolated on the agarose single-plate medium, which exhibited an unusual trait on the utilization of low concentration of the nitrogen source and phosphorus as the nutrient substance. Under the optimal conditions, the microorganism could grow and reproduce normally and maintain the strong catalytic oxidation activity to Fe2+. The immobilization of T. f on the polyurethane as the support matrix was investigated. Cycling batch operation was applied to the preparation of 40 kg/m3, 60 kg/m3, and 80 kg/m3 BPFS when the optimal conditions are pH value of 1.8, circulation flow rate of 0.28–0.30 L/h, and reaction temperature of 28 ± 1°C. When the prepared BPFS and SPFS (solid biopolymeric ferric sulfate) were used to dispose Songhua River water, the removal rate of turbidity and CODMn of BPFS was slightly better than that of SPFS. The removal efficiencies of turbidity and CODMn by BPFS could reach 93.9% and 79.7%, respectively. The result suggests that the BPFS has good flocculating activity.

Genomic Analysis of Shewanella sp. O23S-The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction

Shewanella sp. O23S is a dissimilatory arsenate reducing bacterial strain involved in arsenic transformations within the abandoned gold mine in Zloty Stok (SW Poland). Previous physiological studies revealed that O23S may not only release arsenic from minerals, but also facilitate its immobilization through co-precipitation with reduced sulfur species. Given these uncommon, complementary characteristics and the application potential of the strain in arsenic-removal technologies, its genome (~5.3 Mbp), consisting of a single chromosome, two large plasmids (pSheA and pSheB) and three small plasmid-like phages (pSheC-E) was sequenced and annotated. Genes encoding putative proteins involved in heavy metal transformations, antibiotic resistance and other phenotypic traits were identified. An in-depth comparative analysis of arsenic respiration (arr) and resistance (ars) genes and their genetic context was also performed, revealing that pSheB carries the only copy of the arr genes, and a complete ars operon. The plasmid pSheB is therefore a unique natural vector of these genes, providing the host cells arsenic respiration and resistance abilities. The functionality of the identified genes was determined based on the results of the previous and additional physiological studies, including: the assessment of heavy metal and antibiotic resistance under various conditions, adhesion-biofilm formation assay and Biolog^TM metabolic preferences test. This combined genetic and physiological approach shed a new light on the capabilities of O23S and their molecular basis, and helped to confirm the biosafety of the strain in relation to its application in bioremediation technologies.

Bioleaching for Copper Extraction of Marginal Ores from the Brazilian Amazon Region

The use of biotechnology to explore low-grade ore deposits and mining tailings is one of the most promising alternatives to reduce environmental impacts and costs of copper extraction. However, such technology still depends on improvements to be fully applied in Brazil under industrial scale. In this way, the bioleaching, by Acidithiobacillus ferrooxidans, in columns and stirred reactors were evaluated regarding to copper extraction of a mineral sulfide and a weathered ore from the Brazilian Amazon region. Samples (granulometry of 2.0/4.75 mm) were characterized by X-ray diffraction (XRD), energy dispersive X-ray fluorescence (EDXRF) spectrometry and scanning electrons microscopy (SEM). The pH and Oxidation-reduction potential (Eh) were daily monitored and leachate samples were collected for copper extraction determination by EDXRF. After 47 days, the columns bioleaching efficiency was 1% (1298 mg Cu·L−1) and 0.95% (985 mg Cu·L−1) for 2.00/4.75 mm sulfide ore, respectively, whereas the stirred reactors bioleaching resulted in 4% (348 mg Cu·L−1) for the mineral sulfide and 47% (295.5 mg Cu·L−1) for the weathered ore.

Microbial and geochemical controls on waste rock weathering and drainage quality

Bacteria can adversely affect the quality of drainage released from mine waste by catalyzing the oxidation of sulfide minerals and thereby accelerating the release of acidity and metals. However, the microbiological and geochemical controls on drainage quality from unsaturated and geochemically heterogeneous waste rock remain poorly understood. Here, we identified coexisting neutrophilic and acidophilic bacteria in different types of waste rock, indicating that robust endemic consortia are sustained within pore-scale microenvironments. Subsequently, natural weathering was simulated in laboratory column experiments with waste rock that contained either in-situ microbial consortia or suppressed populations with up to 1000 times smaller abundance and reduced phenotypic diversity after heating and drying. Drainage from waste rock with in-situ populations was up to two pH units lower and contained up to 16 times more sulfate and heavy metals compared to drainage from waste rock bearing treated populations, indicating significantly higher sulfide-oxidation rates. The drainage chemistry was further affected by sorption and formation of secondary-mineral phases (e.g., gypsum and hydroxy-carbonates). This study provides direct evidence for the existence of diverse microbial communities in waste rock and their important catalytic role on weathering rates, and illustrates the mutual controls of microbiology and geochemistry on waste-rock drainage quality.

The minimum inhibitory concentration (MIC) assay with Escherichia coli: An early tier in the environmental hazard assessment of nanomaterials?

There are now over a thousand nano-containing products on the market and the antibacterial properties of some nanomaterials has created interest in their use as cleaning agents, biocides and disinfectants. Engineered nanomaterials (ENMs) are being released into the environment and this raises concerns about their effects on microbes in the receiving ecosystems. This study evaluated the bacterial toxicity of a wide range of nanomaterials with different surface coatings on Escherichia coli K-12 MG1655. The minimum inhibitory concentration (MIC) assay, which quantifies the threshold for growth inhibition in suspensions of bacteria, was used to rank the toxicity of silver (Ag), cupric oxide (CuO), cadmium telluride (CdTe) quantum dots, titanium dioxide (TiO₂), nanodiamonds and multi-walled carbon nanotubes (MWCNTs). Bacteria were exposed for 12 h at 37 °C to a dilution series of the test suspensions in 96-well plates. The precision and accuracy of the method was good with coefficients of variation < 10%. In terms of the measured MIC values, the toxicity order of the ENMs was as follows: CdTe quantum dots ammonium-coated, 6 mg L^-1 > Ag nanoparticles, 12 mg L^-1 > CdTe quantum dots carboxylate-coated, 25 mg L^-1 > CdTe quantum dots polyethylene glycol-coated, 100 mg L^-1. The MIC values were above the highest test concentration used (100 mg L^-1) for CuO, TiO₂, nanodiamonds and MWCNTs, indicating low toxicity. The MIC assay can be a useful tool for the initial steps of ENMs hazard assessment.

Application of capillary electrophoresis combined with conductometric and UV detection to monitor meteorite simulant bioleaching by Acidithiobacillus ferrooxidans

The importance of microorganisms and biotechnology in space exploration and future planets colonization has been discussed in the literature. Meteorites are interesting samples to study microbe-mineral interaction focused on space exploration. The chemolithotropic bacterium Acidithiobacillus ferrooxidans has been used as model to understand the iron and sulfur oxidation. In this work, capillary electrophoresis with capacitively coupled contactless conductivity detection and UV detection was used to monitor bacterial growth in a meteorite simulant by measuring the conversion of Fe²⁺ into Fe⁺³ . The effect of Co²⁺ and Ni²⁺ (metals also found in meteorites) on the bacterial growth was also evaluated. The presented method allowed the analyses of all metals in a single run (less than 8 min). The background electrolyte was composted of 10 mmol/L α-hydroxyisobutyric acid/Histidine. For comparison purpose, the samples were also analyzed by UV-Vis spectrophotometry. The Fe²⁺ conversion into Fe³⁺ by A. ferrooxidans was observed up to 36 h with the growth rate constant of 0.19/h and 0.21/h in Tuovinen and Kelly (T&K) and in meteorite simulant media, respectively. The developed method presents favorable prospect to monitor the growth of other chemolithotropic microorganisms for biotechnology applications.

An electrochemical sensing approach for scouting microbial chemolithotrophic metabolisms

The present study was aimed to test an electrochemical sensing approach for the detection of an active chemolithotrophic metabolism (and therefore the presence of chemolithotrophic microorganisms) by using the corrosion of pyrite by Acidithiobacillus ferrooxidans as a model. Different electrochemical techniques were combined with adhesion studies and scanning electron microscopy (SEM). The experiments were performed in presence or absence of A. ferrooxidans and without or with ferrous iron in the culture medium (0 and 0.5 g L^-1, respectively). Electrochemical parameters were in agreement with voltammetric studies and SEM showing that it is possible to distinguish between an abiotically-induced corrosion process (AIC) and a microbiologically-induced corrosion process (MIC). The results show that our approach not only allows the detection of chemolithotrophic activity of A. ferrooxidans but also can characterize the corrosion process. This may have different kind of applications, from those related to biomining to life searching missions in other planetary bodies.

Response of soil microbial communities and microbial interactions to long-term heavy metal contamination

Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions.

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.

Missing Iron-Oxidizing Acidophiles Highly Sensitive to Organic Compounds

The genus Acidithiobacillus includes iron-oxidizing lithoautotrophs that thrive in acidic mine environments. Acidithiobacillus ferrooxidans is a representative species and has been extensively studied for its application to the bioleaching of precious metals. In our attempts to cultivate the type strain of A. ferrooxidans (ATCC 23270^T), repeated transfers to fresh inorganic media resulted in the emergence of cultures with improved growth traits. Strains were isolated from the resultant culture by forming colonies on inorganic silica-gel plates. A representative isolate (strain NU-1) was unable to form colonies on agarose plates and was more sensitive to organics, such as glucose, than the type strain of A. ferrooxidans. Strain NU-1 exhibited superior growth traits in inorganic iron media to those of other iron-oxidizing acidithiobacilli, suggesting its potential for industrial applications. A draft genome of NU-1 uncovered unique features in catabolic enzymes, indicating that this strain is not a mutant of the A. ferrooxidans type strain. Our results indicate that the use of inorganic silica-gel plates facilitates the isolation of as-yet-unexamined iron-oxidizing acidithiobacilli from environmental samples and enrichment cultures.

Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments?

Bioleaching is a consolidated biotechnology in the mining industry and in bio-hydrometallurgy, where microorganisms mediate the solubilisation of metals and semi-metals from mineral ores and concentrates. Bioleaching also has the potential for ex-situ/on-site remediation of aquatic sediments that are contaminated with metals, which represent a key environmental issue of global concern. By eliminating or reducing (semi-)metal contamination of aquatic sediments, bioleaching may represent an environmentally friendly and low-cost strategy for management of contaminated dredged sediments. Nevertheless, the efficiency of bioleaching in this context is greatly influenced by several abiotic and biotic factors. These factors need to be carefully taken into account before selecting bioleaching as a suitable remediation strategy. Here we review the application of bioleaching for sediment bioremediation, and provide a critical view of the main factors that affect its performance. We also discuss future research needs to improve bioleaching strategies for contaminated aquatic sediments, in view of large-scale applications.

Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing

Emissions of biogenic volatile organic compounds (bVOCs), are an important element in the global carbon cycle, accounting for a significant proportion of fixed carbon. They contribute directly and indirectly to global warming and climate change and have a major effect on atmospheric chemistry. Plants emit isoprene to the atmosphere in similar quantities to emissions of methane from all sources and each accounts for approximately one third of total VOCs. Although methanotrophs, capable of growth on methane, have been intensively studied, we know little of isoprene biodegradation. Here, we report the isolation of two isoprene-degrading strains from the terrestrial environment and describe the design and testing of polymerase chain reaction (PCR) primers targeting isoA, the gene encoding the active-site component of the conserved isoprene monooxygenase, which are capable of retrieving isoA sequences from isoprene-enriched environmental samples. Stable isotope probing experiments, using biosynthesized (13) C-labelled isoprene, identified the active isoprene-degrading bacteria in soil. This study identifies novel isoprene-degrading strains using both culture-dependent and, for the first time, culture-independent methods and provides the tools and foundations for continued investigation of the biogeography and molecular ecology of isoprene-degrading bacteria.

Efecto de la cisteína en un proceso de biodepiritización de carbones en lecho empacado

<p>Se llevaron a cabo procesos de biodesulfurización de dos carbones colombianos ricos en azufre (“Mina Vieja” y “Vampiro”), en reactores de lecho empacado a nivel de erlenmeyer, utilizando un consorcio de Acidithiobacillus ferrooxidans (ATCC 23270) y Acidithiobacillus thiooxidans (ATCC 15494), evaluando la adición de cisteína a la solución lixiviante. Los ensayos fueron monitoreados por medidas de hierro en solución, pH y potencial redox. Adicionalmente, se hicieron análisis mineralógicos por difracción de rayos X (DRX) antes y después de los experimentos. Los ensayos sin adición de cisteína alcanzaron una oxidación de pirita de 45.3% y 57.9% para “Mina Vieja” y “Vampiro” respectivamente. Cuando se adicionó cisteína, la oxidación aumentó en 14.9% para “Mina Vieja” y 6.4% para “Vampiro”. Por otra parte, todos los ensayos evidenciaron remoción de caolinita, debido a su interacción con el ácido sulfúrico del medio. Con base en los resultados obtenidos, los componentes del carbón influenciaron tanto crecimiento bacteriano como la eficiencia de la cisteína sobre el grado de pirita oxidada.</p>

Permanent draft genome sequence of Acidiphilium sp. JA12-A1

The tenacious association between strains of the heterotrophic alphaproteobacterial genus Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron oxidizing mixed culture derived from a pilot plant for bioremediation of acid mine drainage, was determined with the aim to reveal metabolic properties that are fundamental for the syntrophic interaction between Acidiphilium sp. JA12-A1 and the co-occurring chemolithoautotrophic iron oxidizer. The genome sequence consists of 4.18 Mbp on 297 contigs and harbors 4015 protein-coding genes and 50 RNA genes. Additionally, the molecular and functional organization of the Acidiphilium sp. JA12-A1 draft genome was compared to those of the close relatives Acidiphilium cryptum JF-5, Acidiphilium multivorum AIU301 and Acidiphilium sp. PM DSM 24941. The comparative genome analysis underlines the close relationship between these strains and the highly similar metabolic potential supports the idea that other Acidiphilium strains play a similar role in various acid mine drainage communities. Nevertheless, in contrast to other closely related strains Acidiphilium sp. JA12-A1 may be able to take up phosphonates as an additional source of phosphor.

Comparative analyses of extrachromosomal bacterial replicons, identification of chromids, and experimental evaluation of their indispensability

Bacterial genomic information can be divided between various replicons, including chromosomes, plasmids, and chromids (essential plasmid-like replicons with properties of both chromosomes and plasmids). Comparative analyses of bacterial plasmids, including homology searches, phylogenetic and phylogenomic analyses, as well as network construction for the characterization of their relationships, are good starting points for the identification of chromids. Chromids possess several chromosome-like genetic features (e.g., codon usage, GC content), but most significantly, they carry housekeeping genes, which make them indispensable for cell viability. However, it is important to confirm in silico predictions experimentally. The essential nature of a predicted chromid is usually verified by the application of a target-oriented replicon curing technique, based on the incompatibility phenomenon. Further tests examining growth in various media are used to distinguish secondary chromids from plasmids, and mutational analysis (e.g., using the yeast FLP/FRT recombination system) is employed to identify essential genes carried by particular chromids.

Methylophaga lonarensis sp. nov., a moderately haloalkaliphilic methylotroph isolated from the soda lake sediments of a meteorite impact crater

A moderately haloalkaliphilic methylotrophic bacterium possessing the ribulose monophosphate pathway for carbon assimilation, designated MPLT, was isolated from Lonar Lake sediment microcosms that were oxidizing methane for two weeks. The isolate utilized methanol and was an aerobic, Gram-negative, asporogenous, motile, short rod that multiplied by binary fission. The isolate required NaHCO3 or NaCl for growth and, although not auxotrophic for vitamin B12, had enhanced growth with vitamin B12. Optimal growth occurred with 0.5–2 % (w/v) NaCl, at 28–30 °C and at pH 9.0–10.0. The cellular fatty acid profile consisted primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1ω7c and C18 : 1ω7c. The major ubiquinone was Q-8. The dominant phospholipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Cells accumulated ectoine as the main compatible solute. The DNA G+C content was 50.0 mol%. The isolate exhibited 94.0–95.4 % 16S rRNA gene sequence similarity with the type strains of methylotrophs belonging to the genus Methylophaga and 31 % DNA–DNA relatedness with the reference strain, Methylophaga alcalica VKM B-2251T. It is proposed that strain MPLT represents a novel species, Methylophaga lonarensis sp. nov. (type strain MPLT = VKM B-2684T = MCC 1002T).

Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR

Acidithiobacillus ferrooxidans is one of the most widely used microorganisms in bioleaching operations to recover copper from low-grade copper sulfide ores. This work aimed to investigate the relative expression of genes related to the iron uptake system when A. ferrooxidans LR was maintained in contact with chalcopyrite or bornite as the sole energy source. Real-time quantitative PCR analysis revealed that the presence of bornite had no effect on the expression of seven genes related to the siderophore-mediated Fe(III) uptake system, while in the presence of chalcopyrite the expression of the genes was up-regulated. Bioinformatic analysis of the genomic region where these genes were found revealed the existence of three new putative DNA-binding sequences for the ferric iron uptake transcriptional regulator (Fur). Electrophoretic mobility shift assays demonstrated that a purified A. ferrooxidans His-tagged Fur protein was able to bind in vitro to each of these putative Fur boxes, suggesting that Fur regulated the expression of these genes. The expression of fur and two known Fur-regulated genes, mntH and dsrK, was also investigated in the presence of chalcopyrite. While the expression of fur and mntH was up-regulated, the expression of dsrK was down-regulated. The low amount of ferrous iron in the medium was probably responsible for the up-regulation of fur and the genes related to the siderophore-mediated Fe(III) uptake system when A. ferrooxidans LR was kept in the presence of chalcopyrite. A homology model of the A. ferrooxidans Fur was constructed and revealed that the putative DNA-binding surface presents conserved positively charged residues, supporting a previously suggested mode of interaction with DNA. The up-regulation of fur and the siderophore-mediated Fe(III) uptake genes, and the down-regulation of dsrK suggest that in the presence of chalcopyrite Fur acts as a transcription inducer and repressor.

Interfacial activity and leaching patterns of Leptospirillum ferrooxidans on pyrite

The leaching ability of Leptospirillum ferrooxidans goes beyond the mere oxidation of Fe(2+) to Fe(3+). Addition of these bacteria to pyrite triggers interfacial phenomena that lead to bacterial attachment and local forms of corrosion (surface pitting). As the leaching process proceeds, bacterial cells undergo changes, characterized by the release of extracellular polymeric substances (EPS) and the uptake and storage of electro-dense nanoparticles. The latter are embedded in an exopolymeric capsule, which coats the bacterial surface leading to distinctive biomineralized assemblages. High-resolution scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses, quantitative energy-dispersive X-ray measurements and electron diffraction established that the embedded electron-dense nanoparticles comprise pyrite with a well-defined stoichiometry. Addition of Fe(3+) alone did not induce any form of local corrosion on pyrite, which indicates that the reactions taking place between the attached bacteria and the underlying pyrite surface are responsible for the leaching patterns observed in this study. The observed corrosion process resembles that of 'electrochemical machining', because it uses a corrosion promoter, namely the locally concentrated Fe(3+) in the biofilm environment, formed by the attached cells.

Role of respiration and glutathione in cadmium-induced oxidative stress in Escherichia coli K-12

Cadmium is a widespread pollutant that has been associated with oxidative stress, but the mechanism behind this effect in prokaryotes is still unclear. In this work, we exposed two glutathione deficient mutants (DeltagshA and DeltagshB) and one respiration deficient mutant (DeltaubiE) to a sublethal concentration of cadmium. The glutathione mutants show a similar increase in reactive oxygen species as the wild type. Experiments performed using the DeltaubiE strain showed that this mutant is more resistant to cadmium ions and that Cd-induced reactive oxygen species levels were not altered. In the light of these facts, we conclude that the interference of cadmium with the respiratory chain is the cause of the oxidative stress induced by this metal and that, contrary to previously proposed models, the reactive oxygen species increase is not due to glutathione depletion, although this peptide is crucial for cadmium detoxification.

Quorum sensing detected by atomic force microscopy imaging of corrals surrounding multicellular arrangement of bacteria

Connectivity of the glycocalyx covering of small communities of Acidithiobacillus ferrooxidans bacteria deposited on hydrophilic mica plates was imaged by atomic force microscopy. When part of the coverage was removed by water rinsing, an insoluble structure formed by corrals surrounding each individual bacterium was observed. A collective ring structure with clustered bacteria (>or=3) was observed, which indicates that the bacteria perceived the neighborhood in order to grow a protective structure that results in smaller production of exopolysaccharides material. The most surprising aspect of these collective corral structures was that they occur at a low bacterial cell density. The deposited layers were also analyzed by confocal Raman microscopy and shown to contain polysaccharides, protein, and glucoronic acid.

Identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of Methylosulfonomonas methylovora

Recently identified genes located downstream (3') of the msmEF (transport encoding) gene cluster, msmGH, and located 5' of the structural genes for methanesulfonate monooxygenase (MSAMO) are described from Methylosulfonomonas methylovora. Sequence analysis of the derived polypeptide sequences encoded by these genes revealed a high degree of identity to ABC-type transporters. MsmE showed similarity to a putative periplasmic substrate binding protein, MsmF resembled an integral membrane-associated protein, and MsmG was a putative ATP-binding enzyme. MsmH was thought to be the cognate permease component of the sulfonate transport system. The close association of these putative transport genes to the MSAMO structural genes msmABCD suggested a role for these genes in transport of methanesulfonic acid (MSA) into M. methylovora. msmEFGH and msmABCD constituted two operons for the coordinated expression of MSAMO and the MSA transporter systems. Reverse-transcription-PCR analysis of msmABCD and msmEFGH revealed differential expression of these genes during growth on MSA and methanol. The msmEFGH operon was constitutively expressed, whereas MSA induced expression of msmABCD. A mutant defective in msmE had considerably slower growth rates than the wild type, thus supporting the proposed role of MsmE in the transport of MSA into M. methylovora.

Volume of extracellular polymeric substance coverage of individual Acidithiobacillus ferrooxidans bacterium measured by atomic force microscopy

The Acidithiobacillus ferrooxidans response to stress associated with the drying process is known to be the production of extracellular polymeric substance (EPS) coverage. Here, samples of A. ferrooxidans suspensions grown in 1.8 pH and 3.0 pH and dried on mica and silicon are shown to form a structure of isolated bacteria. Individual bacteria coverage patterns were imaged by atomic force microscopy (AFM) on hydrophobic (silicon) and hydrophilic (mica) substrates. A comparison of images of covered and uncovered bacteria establish the volume of individual EPS coverage. The EPS production for bacteria on hydrophobic substrates shows a substantial decrease (a factor of 30) in the EPS volume per bacterium when compared with the one on hydrophilic substrates. Shape and volume determination of EPS structures on bacteria as a function of hydrophobicity or hydrophilicity of the substrate may help to determine the functions of EPS on bacterial aggregates.

The passivation of pyrrhotite by surface coating

The potential of triethylenetetramine (TETA) to inhibit the oxidation of three pyrrhotites, Garson, McCreedy and Po-97 has been studied systematically and confirmed by comparing the release of Fe and SO4(2-) from samples with and without coating treatment. Each sample, original or coated by TETA, was exposed to oxygen, 1 x 10(-3) M FeCl3, and Acidithiobacillus ferrooxidans, respectively, for specific oxidation periods. Both abiotic and biotic oxidation of samples treated by this passivating agent has been reduced significantly in this study. Under the aerobic condition, lower concentrations of ferric, total Fe or SO4(2-) were obtained from the coated samples than those from the uncoated samples. In the presence of 1 x 10(-3) M FeCl3 at 30 degrees C, TETA was able to reduce oxidation rates of Garson, McCreedy and Po-97 by 83%, 79%, and 81% (based on Fe release), respectively. A higher pH, lower Eh, and lower concentrations of total Fe and SO4(2-) were also observed in the biotic oxidation of coated Garson by Acidithiobacillus ferrooxidans. The protection of pyrrhotite surface from oxidant attack by TETA barrier and the alkaline property of this coating agent can be used to interpret the inhibition of oxidation.

A simple procedure for elimination of fungal contamination for enumeration of iron-oxidizing bacteria from bioleaching matrix of sewage sludge

Enumeration of iron-oxidizing bacteria from the bioleaching matrix of sewage sludge is always confronted by fungal contamination. The objective of the present study was to find a reliable and simple method to remove fungal growth and to shorten the incubation time for facilitating enumeration of the iron-oxidizers from complex sludge samples. The results demonstrated that filtering the sludge sample through sterile No. 5 Whatman filter paper before serial dilution was effective in eliminating the fungal growth on agarose media. Both the counts and the incubation time required for enumeration were highly dependent on the medium pH, with maximum counts at pH 2.5–2.75. Medium prepared at pH values outside of this range led to lower counts and a longer lag time for colony formation. However, the introduction of heterotrophic microorganisms into the solid medium did not show further improvement in enumeration efficiency and shortening of the incubation period. By incorporating the optimal conditions obtained, the incubation time could be reduced to 7 and 10 d for pure cultures and sludge samples, respectively.Key words: Acidithiobacillus ferrooxidans, iron-based bioleaching process, growth media, sewage sludge.

Bioleaching of metals from anaerobic sewage sludge: effects of total solids, leaching microorganisms, and energy source

The effects of municipal sewage sludge solids concentration, leaching microorganisms (Thiobacillus thiooxidans or Thiobacillus ferrooxidans) and the addition of energy source (S0 or Fe(II)) on the bioleaching of metals from sewage sludge has been investigated under laboratory conditions using shake flasks. The results show that metal solubilization was better accomplished if additional energy source is supplemented to the microorganisms and that T. thiooxidans furnishes, in general, more adequate conditions for the bioleaching than T. ferrooxidans. At a total solids concentration of 70 g L-1 (originally present in the sludge) pH drop and ORP increase are attenuated, so metal solubilization is negatively affected. It was also demonstrated that if lead (Pb) solubilization is to be achieved, than a special combination of microorganism/energy source must be applied.

Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms

The vertical distribution of sulfate-reducing bacteria (SRB) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. To correlate the vertical distribution of SRB populations with their activity, the microprofiles of O(2), H(2)S, NO(2)(-), NO(3)(-), NH(4)(+), and pH were measured with microelectrodes. In addition, a cross-evaluation of the FISH and microelectrode analyses was performed by comparing them with culture-based approaches and biogeochemical measurements. In situ hybridization revealed that a relatively high abundance of the probe SRB385-stained cells (approximately 10(9) to 10(10) cells per cm(3) of biofilm) were evenly distributed throughout the biofilm, even in the oxic surface. The probe SRB660-stained Desulfobulbus spp. were found to be numerically important members of SRB populations (approximately 10(8) to 10(9) cells per cm(3)). The result of microelectrode measurements showed that a high sulfate-reducing activity was found in a narrow anaerobic zone located about 150 to 300 microm below the biofilm surface and above which an intensive sulfide oxidation zone was found. The biogeochemical measurements showed that elemental sulfur (S(0)) was an important intermediate of the sulfide reoxidation in such thin wastewater biofilms (approximately 1,500 microm), which accounted for about 75% of the total S pool in the biofilm. The contribution of an internal Fe-sulfur cycle to the overall sulfur cycle in aerobic wastewater biofilms was insignificant (less than 1%) due to the relatively high sulfate reduction rate.

A Tn7-like transposon is present in the glmUS region of the obligately chemoautolithotrophic bacterium Thiobacillus ferrooxidans

The region downstream of the Thiobacillus ferrooxidans ATCC 33020 atp operon was examined, and the genes encoding N-acetylglucosamine-1-uridyltransferase (glmU) and glucosamine synthetase (glmS) were found. This atpEFHAGDC-glmUS gene order is identical to that of Escherichia coli. The T. ferrooxidans glmS gene was shown to complement E. coli glmS mutants for growth on minimal medium lacking glucosamine. A Tn7-like transposon, Tn5468, was found inserted into the region immediately downstream of the glmS gene in a manner similar to the site-specific insertion of transposon Tn7 within the termination region of the E. coli glmS gene. Tn5468 was sequenced, and Tn7-like terminal repeat sequences as well as several open reading frames which are related to the Tn7 transposition genes tnsA, tnsB, tnsC, and tnsD were found. Tn5468 is the closest relative of Tn7 to have been characterized to date. Southern blot hybridization indicated that a similar or identical transposon was present in three T. ferrooxidans strains isolated from different parts of the world but not in two Thiobacillus thiooxidans strains or a Leptospirillum ferrooxidans strain. Since T. ferrooxidans is an obligately acidophilic autotroph and E. coli is a heterotroph, ancestors of the Tn7-like transposons must have been active in a variety of physiologically different bacteria so that their descendants are now found in bacteria that occupy very different ecological niches.

Essential interactions between Thiobacillus ferrooxidans and heterotrophic microorganisms during a wastewater sludge bioleaching process

The stimulating effect of heterotrophic microorganisms was investigated on the growth and on the ferrous iron oxidation of Thiobacillus ferrooxidans in synthetic media and in wastewater sludge. The addition of a sediment. Rhodotorula rubra isolate or a strain of T. acidophilus on two-layer agarose-gelled medium doubled the plating efficiency of T. ferrooxidans. In liquid cultures, R. rubra had a slight but significant effect on the growth rate of T. ferrooxidans. Moreover, the yeast allowed a faster initiation of the ferrous iron oxidation and acidification by T. ferrooxidans. In the bioleaching process, the co-culture of T. ferrooxidans with R. rubra or with the indigenous microbial assemblage from sludge was shown to be essential since the pure culture of T. ferrooxidans failed to oxidize ferrous iron and to acidify wastewater sludge. These results emphasize the importance of active heterotrophic microorganisms in the metal bioleaching activity of T. ferrooxidans in sludge.