Evolutionary relationships among sulfur- and iron-oxidizing eubacteria

The Exploitation of a Hempseed Byproduct to Produce Flavorings and Healthy Food Ingredients by a Fermentation Process

Following the One Health principles in food science, the challenge to valorize byproducts from the industrial sector is open. Hemp (Cannabis sativa subsp. sativa) is considered an important icon of sustainability and as an alternative food source. Hemp seed bran, in particular, is a byproduct of industrial hemp seed processing, which is not yet valorized. The success, and a wider market diffusion of hemp seed for food applications, is hindered by its unpleasant taste, which is produced by certain compounds that generally overwhelm the pleasant bouquet of the fresh product. This research concerns the exploration of hemp seed bran through fermentation using beneficial lactobacilli, focusing on the sensorial and bioactive traits of the products when they are subjected to bacterial transformation. By studying of the aromatic profile formation during the fermentation process the aim was to modulate it in order to reduce off-odors without affecting the presence of healthy volatile organic compounds (VOCs). Applying multivariate analyses, it was possible to target the contribution of processing parameters to the generation of flavoring and bioactive compounds. To conclude, the fermentation process proposed was able to reduce unpleasant VOCs, whilst at the same time keeping the healthy ones, and it also improved nutritional quality, depending on time and bacterial starters. The fermentation proposed was a sustainable biotechnological approach that fitted perfectly with the valorization of hemp byproducts from the perspective of a green-oriented industrial process that avoids synthetic masking agents.

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo₃ ubiquinol oxidases.

Colonic In Vitro Model Assessment of the Prebiotic Potential of Bread Fortified with Polyphenols Rich Olive Fiber

The use of olive pomace could represent an innovative and low-cost strategy to formulate healthier and value-added foods, and bakery products are good candidates for enrichment. In this work, we explored the prebiotic potential of bread enriched with Polyphenol Rich Fiber (PRF), a defatted olive pomace byproduct previously studied in the European Project H2020 EcoProlive. To this aim, after in vitro digestion, the PRF-enriched bread, its standard control, and fructo-oligosaccharides (FOS) underwent distal colonic fermentation using the in vitro colon model MICODE (multi-unit colon gut model). Sampling was done prior, over and after 24 h of fermentation, then metabolomic analysis by Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (SPME GCMS), 16S-rDNA genomic sequencing of colonic microbiota by MiSeq, and absolute quantification of main bacterial species by qPCR were performed. The results indicated that PRF-enriched bread generated positive effects on the host gut model: (i) surge in eubiosis; (ii) increased abundance of beneficial bacterial groups, such as Bifidobacteriaceae and Lactobacillales; (iii) production of certain bioactive metabolites, such as low organic fatty acids; (iv) reduction in detrimental compounds, such as skatole. Our study not only evidenced the prebiotic role of PRF-enriched bread, thereby paving the road for further use of olive by-products, but also highlighted the potential of the in vitro gut model MICODE in the critical evaluation of functionality of food prototypes as modulators of the gut microbiota.

Lack of Microbial Diversity in an Extreme Mars Analog Setting: Poás Volcano, Costa Rica

The Poás volcano in Costa Rica has been studied as a Mars geochemical analog environment, since both the style of hydrothermal alteration present and the alteration mineralogy are consistent with Mars' relict hydrothermal systems. The site hosts an active volcano, with high-temperature fumaroles (up to 980°C) and an ultra-acidic lake. This lake, Laguna Caliente, is one of the most dynamic environments on Earth, with frequent phreatic eruptions, temperatures ranging from near-ambient to almost boiling, a pH range of -1 to 1.5, and a wide range of chemistries and redox potential. Martian acid-sulfate hydrothermal systems were likely similarly dynamic and equally challenging to life. The microbiology existing within Laguna Caliente was characterized for the first time, with sampling taking place in November, 2013. The diversity of the microbial community was surveyed via extraction of environmental DNA from fluid and sediment samples followed by Illumina sequencing of the 16S rRNA gene. The microbial diversity was limited to a single species of the bacterial genus Acidiphilium. This organism likely gets its energy from oxidation of reduced sulfur in the lake, including elemental sulfur. Given Mars' propensity for sulfur and acid-sulfate environments, this type of organism is of significant interest to the search for past or present life on the Red Planet. Key Words: Mars astrobiology-Acid-sulfate hydrothermal systems-Extremophiles-Acidic-High temperature-Acidiphilium bacteria. Astrobiology 18, 923-933.

Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model.

First report of Wautersiella falsenii genomovar 2 isolated from the respiratory tract of an immunosuppressed man

Wautersiella falsenii is a Gram-negative, non-motile rod, which grows aerobically on common isolation media and is the only acknowledged species among the genus Wautersiella. Two genomovars, namely 1 and 2, phenotypically indistinguishable but genotypically different, are described. To date, few case reports detailing the clinical disease associated with W. falsenii have been reported, all describing localized infection. To our knowledge, this study reports the first isolation of W. falsenii genomovar 2 from a respiratory sample of an immunosuppressed man. Our hypothesis is that the patient was harboring W. falsenii genomovar 2 and both the immunosuppression and the antimicrobial treatments provided a chance for this organism to emerge. The clinical significance of this result is yet to be evaluated. Although infection with W. falsenii remains rare, this bacterium should not be underestimated mainly because of its natural resistance to many available antimicrobials.

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

Biofilm formation, communication and interactions of leaching bacteria during colonization of pyrite and sulfur surfaces

Bioleaching of metal sulfides is an interfacial process where biofilm formation is considered to be important in the initial steps of this process. Among the factors regulating biofilm formation, molecular cell-to-cell communication such as quorum sensing is involved. A functional LuxIR-type I quorum sensing system is present in Acidithiobacillus ferrooxidans. However, cell-to-cell communication among different species of acidophilic mineral-oxidizing bacteria has not been studied in detail. These aspects were the scope of this study with emphasis on the effects exerted by the external addition of mixtures of synthetic N-acyl-homoserine-lactones on pure and binary cultures. Results revealed that some mixtures had inhibitory effects on pyrite leaching. Some of them correlated with changes in biofilm formation patterns on pyrite coupons. We also provide evidence that A. thiooxidans and Acidiferrobacter spp. produce N-acyl-homoserine-lactones. In addition, the observation that A. thiooxidans cells attached more readily to pyrite pre-colonized by living iron-oxidizing acidophiles than to heat-inactivated or biofilm-free pyrite grains suggests that other interactions also occur. Our experiments show that pre-cultivation conditions influence A. ferrooxidans attachment to pre-colonized pyrite surfaces. The understanding of cell-to-cell communication may consequently be used to develop attempts to influence biomining/bioremediation processes.

Proposal for a new class within the phylum Proteobacteria , Acidithiobacillia classis nov., with the type order Acidithiobacillales , and emended description of the class Gammaproteobacteria

The order Acidithiobacillales was previously assigned to the class Gammaproteobacteria . Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes Betaproteobacteria and Gammaproteobacteria . We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order Acidithiobacillales and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia, with the type order Acidithiobacillales , comprising the families Acidithiobacillaceae and Thermithiobacillaceae with the type genus Acidithiobacillus .

Acidocella aromatica sp. nov.: an acidophilic heterotrophic alphaproteobacterium with unusual phenotypic traits

Three obligately heterotrophic bacterial isolates were identified as strains of a proposed novel species of extremely acidophilic, mesophilic Alphaproteobacteria, Acidocella aromatica. They utilized a restricted range of organic substrates, which included fructose (but none of the other monosaccharides tested), acetate and several aromatic compounds (benzoate, benzyl alcohol and phenol). No growth was obtained on complex organic substrates, such as yeast extract and tryptone. Tolerance of the proposed type strain of the species (PFBC) to acetic acid was much greater than that typically reported for acidophiles. The bacteria grew aerobically, and catalyzed the dissimilatory reductive dissolution of the ferric iron mineral schwertmannite under both micro-aerobic and anaerobic conditions. Strain PFBC did not grow anaerobically via ferric iron respiration, though it has been reported to grow in co-culture with acid-tolerant sulfidogenic bacteria under strictly anoxic conditions. Tolerance of strains of Acidocella aromatica to nickel were about two orders of magnitude greater than those of other Acidocella spp., though similar levels of tolerance to other metals tested was observed. The use of this novel acidophile in solid media designed to promote the isolation and growth of other (aerobic and anaerobic) acidophilic heterotrophs is discussed.

Phylogenetic and morphologic complexity of giant sulphur bacteria

The large sulphur bacteria, first discovered in the early nineteenth century, include some of the largest bacteria identified to date. Individual cells are often visible to the unaided eye and can reach 750 μm in diameter. The cells usually feature light-refracting inclusions of elemental sulphur and a large internal aqueous vacuole, which restricts the cytoplasm to the outermost periphery. In some taxa, it has been demonstrated that the vacuole can also serve for the storage of high millimolar concentrations of nitrate. Over the course of the past two centuries, a wide range of morphological variation within the family Beggiatoaceae has been found. However, representatives of this clade are frequently recalcitrant to current standard microbiological techniques, including 16S rRNA gene sequencing and culturing, and a reliable classification of these bacteria is often complicated. Here we present a summary of the efforts made and achievements accomplished in the past years, and give perspectives for investigating the heterogeneity and possible evolutionary developments in this extraordinary group of bacteria.

Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from the Galapagos Rift Hydrothermal Vent

Pseudomonas stutzeri strain NF13 was isolated from a water sample taken at a hydrothermal vent in the Galapagos rift. It was selected for its ability to metabolize sulfur compounds and to grow diazotrophically. Here, we report the first draft genome of a member of genomovar 19 of the species.

Microbial communities associated with wet flue gas desulfurization systems

Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.

What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH

Leptothrix ochracea is a common inhabitant of freshwater iron seeps and iron-rich wetlands. Its defining characteristic is copious production of extracellular sheaths encrusted with iron oxyhydroxides. Surprisingly, over 90% of these sheaths are empty, hence, what appears to be an abundant population of iron-oxidizing bacteria, consists of relatively few cells. Because L. ochracea has proven difficult to cultivate, its identification is based solely on habitat preference and morphology. We utilized cultivation-independent techniques to resolve this long-standing enigma. By selecting the actively growing edge of a Leptothrix-containing iron mat, a conventional SSU rRNA gene clone library was obtained that had 29 clones (42% of the total library) related to the Leptothrix/Sphaerotilus group (≤96% identical to cultured representatives). A pyrotagged library of the V4 hypervariable region constructed from the bulk mat showed that 7.2% of the total sequences also belonged to the Leptothrix/Sphaerotilus group. Sorting of individual L. ochracea sheaths, followed by whole genome amplification (WGA) and PCR identified a SSU rRNA sequence that clustered closely with the putative Leptothrix clones and pyrotags. Using these data, a fluorescence in-situ hybridization (FISH) probe, Lepto175, was designed that bound to ensheathed cells. Quantitative use of this probe demonstrated that up to 35% of microbial cells in an actively accreting iron mat were L. ochracea. The SSU rRNA gene of L. ochracea shares 96% homology with its closet cultivated relative, L. cholodnii, This establishes that L. ochracea is indeed related to this group of morphologically similar, filamentous, sheathed microorganisms.

Iron-oxidizing bacteria: an environmental and genomic perspective

In the 1830s, iron bacteria were among the first groups of microbes to be recognized for carrying out a fundamental geological process, namely the oxidation of iron. Due to lingering questions about their metabolism, coupled with difficulties in culturing important community members, studies of Fe-oxidizing bacteria (FeOB) have lagged behind those of other important microbial lithotrophic metabolisms. Recently, research on lithotrophic, oxygen-dependent FeOB that grow at circumneutral pH has accelerated. This work is driven by several factors including the recognition by both microbiologists and geoscientists of the role FeOB play in the biogeochemistry of iron and other elements. The isolation of new strains of obligate FeOB allowed a better understanding of their physiology and phylogeny and the realization that FeOB are abundant at certain deep-sea hydrothermal vents. These ancient microorganisms offer new opportunities to learn about fundamental biological processes that can be of practical importance.

Bacterial community in copper sulfide ores inoculated and leached with solution from a commercial-scale copper leaching plant

Most copper bioleaching plants operate with a high concentration of sulfate salts caused by the continuous addition of sulfuric acid and the recycling of the leaching solution. Since the bacteria involved in bioleaching have been generally isolated at low sulfate concentrations, the bacterial population in ores leached with the high-sulfate solution (1.25 M) employed in a copper production plant was investigated. The complexity of the original population was assessed by the length pattern of the spacer regions between the 16S and 23S rRNA genes, observed after PCR amplification of the DNA extracted from the leached ore. Six main spacers were distinguished by electrophoretic migration, but they could be further resolved into eight spacers by nucleotide sequence homology. The degree of homology was inferred from the electrophoretic migration of the heteroduplexes formed after hybridization. One of the spacers was indistinguishable from that found in Thiobacillus thiooxidans, four could be related to Thiobacillus ferrooxidans, and three could be related to Leptospirillum ferrooxidans. Only five of the spacers in the original sample could be recovered after culturing in media containing different inorganic energy source. Altogether, the results indicate that the bacteria in the leached ore formed a community composed of at least three species: a fairly homogeneous population of T. thiooxidans strains and two heterogeneous populations of T. ferrooxidans and L. ferrooxidans strains.

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments

The distribution of Thioploca populations was investigated in Danish fjords, brackish lakes and coastal waters. Thioploca was found in three geographically distinct populations, where biomasses reached 33.8+/-14.3 g wet weight m(-2) (mean+/-SD). Mats or lawns were not formed at the sediment surfaces and Thioploca biomasses peaked 4-7 cm into the sediment and extended down to 18 cm depth. Morphology and 16S rRNA gene sequences classified all populations as Thioploca ingrica. A sequence divergence of 1.7-2.2% indicated that T. ingrica comprise at least two genotypes. Physiological analysis showed that T. ingrica accumulate nitrate in concentrations of approximately 3 mM and that bicarbonate and acetate are used as a carbon source. The presence of oxygen promoted carbon incorporation, but T. ingrica could survive up to 3 months without an external supply of nitrate or oxygen. Thioploca ingrica populations were exclusively found close to river outlets in a bioturbated sediment with separate sulphidic spots and worm burrow walls containing nitrate and oxygen. It is hypothesized that the subsurface T. ingrica have a special advantage in this heterogeneous environment using their sheath surrounding the bacterial trichomes when navigating between electron donor and acceptor.

16S rDNA and 16S-23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Acidithiobacillus phylogeny

In order to contribute to our understanding of Acidithiobacillus taxonomy, we determined 16S rDNA sequences and the 16S-23S internally transcribed spacer (ITS) sequence of 35 Chinese Acidithiobacillus isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and Acidithiobacillus strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polymorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter- and intraspecific genealogical relationships of the genus Acidithiobacillus. Similarity values of the ITSs varied from 60.5 % to 84.7 % between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13 %. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three Acidithiobacillus ferrooxidans phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese Acidithiobacillus-like isolates represent one or two new species of the genus Acidithiobacillus. The ITS may be a potential target for the development of fluorescent in situ hybridization probes for more accurately detecting distinct ecotypes of Acidithiobacillus strains and other closely related sulfur-oxidizing bacteria.

Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalmine-derived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O(2). Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.

Variability in Halothiobacillus neapolitanus type strain cultures

Numerous microbial species are reported to utilize oxidation and/or reduction of sulfur containing compounds in the energy producing portions of their metabolism Halothiobacillus neapolitanus cultures obtained from different commercial sources appear to display considerable variability in terms of growth rate, carbonate consumption and activity of individual enzymes.

Microbial populations in acid mineral bioleaching systems of Tong Shankou Copper Mine, China

AIMS

To understand the composition and structure of microbial communities in different acid mineral bioleaching systems, and to present a more complete picture of microbially mediated acid mine drainage production.

METHODS AND RESULTS

In Tong Shankou Copper Mine, China, two samples (named K1 and K2) from two different sites with bioleaching were studied. A bacterial 16S rDNA library and an archaeal 16S rDNA library of the sample from each site were constructed by 16S rDNA polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing. A total of 18 bacterial representative sequences and 12 archaeal representative sequences were obtained. Phylogenetic analysis indicated that 77.09% of the total bacterial clones were affiliated with Proteobacteria, and 21.22% of the total bacterial clones were closely related to Nitrospira. The rest of the bacterial clones were related to Firmicutes (1.68%). Sequences affiliated with the archaea of the Thermoplasma and Ferroplasma lineages were detected abundantly in the two samples. Unexpectedly, sequences affiliated with Sulfolobales and Methanothermus genera were also detected.

CONCLUSIONS

The molecular studies appear to be consistent with the environmental conditions existing at the sites, which coincides with previous studies. High concentrations of some elements (such as copper, iron and sulfur) seemed to be the key factors resulting in the diverse distribution of typical iron-oxidizing bacteria such as Leptospirillum species and Acidithiobacillus ferrooxidans.

SIGNIFICANCE AND IMPACT OF THE STUDY

Research on micro-organisms present in bioleaching systems especially archaea is not abundant. The acidophiles in the two bioleaching sites obtained from Tong Shankou Copper Mine, China, have not been reported until now. These results may expand our knowledge of the microbial diversity in the acid mineral bioleaching systems.

Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in China

The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity.

Identification of novel n-4 series polyunsaturated fatty acids in a deep-sea clam, Calyptogena phaseoliformis

Novel fatty acids originated from the cold-seep clam Calyptogena phaseoliformis, collected from hydrothermal vents in the Japan Trench at a depth of 6354-6367 m, were determined by using gas chromatography-mass spectrometry analysis of the 4,4-dimethyloxazoline derivatives. The major fatty acids present in the C. phaseoliformis lipids belong to the n-4 family non-methylene interrupted polyunsaturated fatty acids (NMI-PUFA): 20:3n-4,7,15, 20:4n-1,4,7,15, and 21:3n-4,7,16, with significant levels of 20:2n-7,15 and 21:2n-7,16 as non-methylene interrupted n-7 dienes. Compared with the lipids of shallow-water clam Mactra chinensis, which contains photosynthetic n-3 PUFA, such as docosahexaenoic acid and icosapentaenoic acid, C. phaseoliformis might have an intrinsic mechanism in vivo so as to maintain the fluidity of the high-melting fatty acids in the membrane lipids by exogenous n-4 family PUFA adaptation as substitutes. Such special kinds of fatty acids are assimilated by the symbiotic chemosynthetic bacteria, which use geothermal energy and minerals from the cold-seep vents. Its unique fatty acid composition corresponding to the novel n-4 family NMI-PUFA markedly differs from those of the reported lipid compositions of other marine animals, which depend on the marine grazing food chain originating from phytoplankton. Thus, the present findings confirm a perfect and closed novel food chain in the cold-seep bivalve and in its symbionts, which is independent from the photosynthetic food chain.

Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation

Disulfide reductases of host-colonising bacteria are involved in the expression of virulence factors, resistance to drugs, and elimination of toxic compounds. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes. Specific bioinformatic analyses served to identify putative disulfide reductases in the Campylobacterales Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri which colonise the gastrointestinal tract of higher animals. Three filters applied to the genomes of these species yielded 35, 25, 28 and 34 genes, respectively, encoding proteins with the characteristics of disulfide reductases. Ten proteins were common to the four species, including four belonging to the thioredoxin system. The presence of thioredoxin reductase activities was detected in the four bacterial species by observing dithiobis-2-nitrobenzoic acid reduction with beta-nicotinamide adenine dinucleotide phosphate as cofactor. Phylogenetic analyses of the thioredoxin reductases TrxB(1) and TrxB(2) of the four Campylobacterales were performed. Their TrxB(1) proteins were more closely related to those of Firmicutes than to the corresponding proteins of other Proteobacteria. The Campylobacterales TrxB(2) proteins were closer to glutathione reductases of other organisms than to their respective TrxB(1) proteins. The phylogenetic features of the Campylobacterales thioredoxin reductases suggested a special role for these enzymes in the physiology of these bacteria.

Inter- and intraspecific genomic variability of the 16S–23S intergenic spacer regions (ISR) in representatives ofAcidithiobacillus thiooxidansandAcidithiobacillus ferrooxidans

The complete sequences of 32 intergenic spacer regions (ISR) from Acidithiobacillus strains, including 29 field strains isolated from coal, copper, molybdenum mine wastes or sediment of different geoclimatic regions in China, reference strain ATCC19859 and the type strains of the two species were determined. These data, together with other sequences available in the GenBank database, were used to carry out the first detailed assessment of the inter- and intraspecific genomic variability of the ISR sequences and to infer phylogenetic relationships within the genus. The total length of the 16S-23S rRNA intergenic spacer regions of the Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans strains ranged from 451 to 490 bp, and from 434 to 456 bp, respectively. The degree of intrageneric ISR sequence similarity was higher than the degree of intergeneric similarity, and the overall similarity values of the ISRs varied from 60.49% to 84.71% between representatives of different species of the genus Acidithiobacillus. Sequences from the spacer of the A. thiooxidans and A. ferrooxidans strains ranged from 86.71% to 99.56% and 92.36% to 100% similarity, respectively. All Acidithiobacillus strains were separated into three phylogenetic major clusters and seven phylogenetic groups. ISR may be a potential target for the development of in situ hybridization probe aimed at accurately detecting acidithiobacilli in the various acidic environments.

The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin

Proteorhodopsin (PR) is a protein that is abundant in marine bacterioplankton. PR is hypothesized to be a light-dependent proton pump, thus creating a proton gradient that can be used for energy production without electron transport. Currently, the only culture that has been reported to possesses PR is the highly abundant alphaproteobacterium "Candidatus Pelagibacter ubique" (SAR11 clade), but surprisingly, its growth in batch culture was not enhanced by light. Here, we present the first cultured gammaproteobacterium that possesses a PR gene. Genome sequencing and analysis of HTCC2207 showed that the PR gene is present as a lone transcriptional unit directly followed by an operon containing genes that are presumably involved in the synthesis of retinal, the chromophore of PR. Half-time decay times of different PR intermediates in native HTCC2207 cells ranged between 2 and 15 ms, and the absorbance maximum of PR was determined to be 528 nm. Proteorhodopsin was identified in three additional strains, using a specific PCR assay on other cultured members of the SAR92 clade. Phylogenetic analyses of the PR genes determined that they form a deeply rooting cluster not closely related to any PR genes recovered so far. Fluorescence in situ hybridization and RNA blots showed that the SAR92 clade reaches up to 10% of the total bacterial population in surface waters close to the Oregon coast and decreases over depth and distance from the shore. Although the growth of HTCC2207 is limited by the amount of available carbon that is present in the medium applied, these cultures do not grow at higher rates nor do they have higher growth yields when incubated under light.

Evidence for the involvement of betaproteobacterial Thiobacilli in the nitrate-dependent oxidation of iron sulfide minerals

The Thiobacilli are an important group of autotrophic bacteria occurring in nature linking the biogeochemical cycles of sulfur and nitrogen. Betaproteobacterial Thiobacilli are very likely candidates for mediating the process of nitrate-dependent anoxic iron sulfide mineral oxidation in freshwater wetlands. A Thiobacillus denitrificans-like bacterium was present in an enrichment on thiosulfate and nitrate, derived from an iron-sulfide- and nitrate-rich freshwater environment. Preliminary FISH analysis showed that the 16S rRNA gene-based bacterial probe mix showed great variation in intensity under different culture conditions. Furthermore, the widely applied 23S rRNA gene-based probe set BET42a/GAM42a incorrectly identified the T. denitrificans-like bacterium as a member of the Gammaproteobacteria. To circumvent these problems, the 23S rRNA genes of two T. denitrificans strains were partially sequenced and a new 23S rRNA gene-based probe (Betthio 1001) specific for betaproteobacterial Thiobacilli was designed. Use of this new probe Betthio 1001, combined with field measurements, indicates the involvement of Thiobacilli in the process of nitrate-dependent iron sulfide mineral oxidation.

Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus

The transfer of Thiobacillus delicatus to the genus Thiomonas as a distinct species, Thiomonas delicata (type strain NBRC 14566T), is confirmed by its morphological and physiological properties, DNA–DNA hybridization and the grouping of its 16S rRNA gene sequence with those of other species of the genus. An emended formal description of Thiomonas delicata is given. The status of Thiomonas cuprina DSM 5495T as a member of the genus is reconsidered.

Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria

Within the last 10 years, numerous SSU rRNA sequences have been collected from natural populations of conspicuous, vacuolate, colorless sulfur bacteria, which form a phylogenetically cohesive cluster (large-vacuolate sulfur bacteria clade) in the gamma-Proteobacteria. Currently, this clade is composed of four named or de facto genera: all known Thioploca and Thiomargarita strains, all vacuolate Beggiatoa strains, and several strains of vacuolate, attached filaments, which bear a superficial similarity to Thiothrix. Some of these vacuolate bacteria accumulate nitrate for respiratory purposes. This clade encompasses the largest known prokaryotic cells (Thiomargarita namibiensis) and several strains that are important in the global marine sulfur cycle. Here, we report additional sequences from five pure culture strains of Beggiatoa spp., including the only two cultured marine strains (nonvacuolate), which firmly establish the root of this vacuolate clade. Each of several diverse metabolic motifs, including obligate and facultative chemolithoautotrophy, probable mixotrophy, and seemingly strict organoheterotrophy, is represented in at least one of the nonvacuolate strains that root the vacuolate clade. Because the genus designation Beggiatoa is interspersed throughout the vacuolate clade along with other recognized or de facto genera, the need for taxonomic revision is clear.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

A 16S rRNA gene database ( http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

"Candidatus Thiobios zoothamnicoli," an ectosymbiotic bacterium covering the giant marine ciliate Zoothamnium niveum

Zoothamnium niveum is a giant, colonial marine ciliate from sulfide-rich habitats obligatorily covered with chemoautotrophic, sulfide-oxidizing bacteria which appear as coccoid rods and rods with a series of intermediate shapes. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the ectosymbiont of Z. niveum belongs to only one pleomorphic phylotype. The Z. niveum ectosymbiont is only moderately related to previously identified groups of thiotrophic symbionts within the Gammaproteobacteria, and shows highest 16S rRNA sequence similarity with the free-living sulfur-oxidizing bacterial strain ODIII6 from shallow-water hydrothermal vents of the Mediterranean Sea (94.5%) and an endosymbiont from a deep-sea hydrothermal vent gastropod of the Indian Ocean Ridge (93.1%). A replacement of this specific ectosymbiont by a variety of other bacteria was observed only for senescent basal parts of the host colonies. The taxonomic status "Candidatus Thiobios zoothamnicoli" is proposed for the ectosymbiont of Z. niveum based on its ultrastructure, its 16S rRNA gene, the intergenic spacer region, and its partial 23S rRNA gene sequence.

H2S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter

In this study, 16S rRNA- and rDNA-based denaturing gradient gel electrophoresis (DGGE) were used to study the temporal and spatial evolution of the microbial communities in a compost biofilter removing H(2)S and in a control biofilter without H(2)S loading. During the first 81 days of the experiment, the H(2)S removal efficiencies always exceeded 93% at loading rates between 4.1 and 30 g m(-3) h(-1). Afterwards, the H(2)S removal efficiency decreased to values between 44 and 71%. RNA-based DGGE analysis showed that H(2)S loading to the biofilter increased the stability of the active microbial community but decreased the activity-based diversity and evenness. The most intense band in both the RNA- and DNA-based DGGE patterns of the H(2)S-degrading biofilter represented the sulfur oxidizing bacterium Thiobacillus thioparus. This suggested that T. thioparus constituted a major part of the bacterial community and was an important primary degrader in the H(2)S-degrading biofilter. The decreasing H(2)S removal efficiencies near the end of the experiment were not accompanied by a substantial change of the DGGE patterns. Therefore, the decreased H(2)S removal was probably not caused by a failing microbiology but rather by a decrease of the mass transfer of substrates after agglutination of the compost particles.

The use of RAPD genomic fingerprinting to study relatedness in strains of Acidithiobacillus ferrooxidans

Twelve strains of Acidithiobacillus ferrooxidans were recovered from acid mine drainage (AMD) sites from three different geographical locations: Copper Cliff, Ontario, Canada; Mineral City, OH, USA; and Cornwall, England. The spread-plate technique and various culture media were used to isolate and purify all strains. DNA was extracted from each purified culture and amplified using PCR and twenty, 10-mer primers. Amplification products were separated by gel electrophoresis and photographed under UV light. The RAPD (Randomly Amplified Polymorphic DNA) profiles were compared on the basis of the presence or absence of each DNA band and a data matrix was constructed. Strain diversity was calculated using the Jaccard's coefficient and UPGMA (Unweighted Pair-Group Arithmetic Average Clustering) cluster analysis. The variations in the banding patterns indicated genomic variability among the twelve A. ferrooxidans strains tested. The primers used in this study grouped the twelve strains into five major groups. Similarities between the strains ranged from 5.49% to 85.14%. These results show that the strains have a high degree of genomic diversity and that the RAPD procedure is a powerful technique to assess strain variability in this bacterium.

Differentiation and identification of iron-oxidizing acidophilic bacteria using cultivation techniques and amplified ribosomal DNA restriction enzyme analysis

Acidophilic iron-oxidizing microorganisms are important both environmentally and in biotechnological applications. Although, as a group, they are readily detected by their ability to generate ferric iron (resulting in a distinctive color change in liquid media), these microbes highly diverse phylogenetically. Various other characteristics, such as optimum growth temperature, response to organic carbon sources, and cellular morphologies, facilitate, in some cases, identification of isolates to a genus or species level, although this approach has limitations and may give erroneous results. In this study, a combined approach of using physiological traits together with amplified ribosomal DNA restriction enzyme analysis (ARDREA) has been successful in identifying all known acidophilic iron-oxidizing bacteria to the species level. Computer-generated maps were used to identify restriction enzymes that allow the differentiation of the acidophiles, and these were confirmed experimentally using authentic bacterial strains. To test further the validity of this approach, six acidophilic moderately thermophilic iron-oxidizing bacteria isolated from Montserrat (West Indies) were analysed using the ARDREA protocol. Three of the isolates were identified as Sulfobacillus acidophilus-like, and one as Sulfobacillus thermosulfidooxidans-like bacteria. The fifth isolate gave DNA digest patterns that were distinct from all known strains of iron-oxidizing acidophiles. Subsequent sequencing of the 16S rRNA genes of these isolates confirmed the identity of the four Sulfobacillus isolates, and also that the fifth isolate was a novel species. Schematic diagrams showing how ARDREA may be used to rapidly identify all known acidophilic iron-oxidizing bacteria are presented.

Nitrogen fixation in acidophile iron-oxidizing bacteria: The nif regulon of Leptospirillum ferrooxidans

The Gram-negative iron-oxidizing bacterium Leptospirillum ferrooxidans contains all genes necessary for nitrogen fixation, from genes encoding the Mo-Fe nitrogenase, the specific regulator (nifA), global regulators like glnB and ntrC like genes, to other sensors and transport systems somehow related to nitrogen assimilation. We review current knowledge about the nif regulon and its connection with other metabolic functions in L. ferrooxidans.

Molecular basis of bacterial outer membrane permeability revisited

Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.

Natural attenuation of trichloroethylene in fractured shale bedrock

This paper describes one of the first well-documented field examples of natural attenuation of trichloroethylene (TCE) in groundwater in a fractured shale bedrock. The study was carried out adjacent to a former waste burial site in Waste Area Grouping 5 (WAG5) on the Oak Ridge Reservation, Oak Ridge, TN. A contaminant plume containing TCE and its daughter products were detected downgradient from the buried waste pits, with most of the contamination occurring in the upper 6 m of the bedrock. The monitoring well array consists of a 35-m-long transect of multilevel sampling wells, situated along a line between the waste pits and a seep which discharges into a small stream. Concentrations of volatile organic carbons (VOCs) were highest in the waste trenches and decreased with distance downgradient towards the seep. Sampling wells indicated the presence of overlapping plumes of TCE, cis-dichloroethylene (cDCE), vinyl chloride (VC), ethylene, ethane, and methane, with the daughter products extending further downgradient than the parent (TCE). This type of distribution suggests anaerobic biodegradation. Measurements of redox potential at the site indicated that iron-reduction, sulfate reduction, and potentially methanogensis were occurring and are conducive to dechlorination of TCE. Bacteria enrichment of groundwater samples revealed the presence of methanotrophs, methanogens, iron-reducing bacteria and sulfate-reducing bacteria, all of which have previously been implicated in anaerobic biodegradation of TCE. 16S rDNA sequence from DNA extracted from two wells were similar to sequences of organisms previously implicated in the anaerobic biodegradation of chlorinated solvents. The combined data strongly suggest that anaerobic biodegradation of the highly chlorinated compounds is occurring. Aerobic biodegradation may also be occurring in oxygenated zones, including near a seep where groundwater exits the site, or in the upper bedrock during seasonal fluctuations in water table elevation and oxygen levels.

Characterization and identification of an iron-oxidizing, Leptospirillum-like bacterium, present in the high sulfate leaching solution of a commercial bioleaching plant

Most copper bioleaching plants operate with a high concentration of sulfate salts, caused by the continuous addition of sulfuric acid and the recycling of the leaching solution. Since the bacteria involved in bioleaching have been generally isolated at low sulfate concentrations, the bacterial population present in the high-sulfate (150 gl(-1)) leaching solution, employed in a copper production plant, was investigated. The iron-oxidizing bacteria able to grow in the leaching solution were enriched by several batch cultivations and, after serial dilution, an abundant bacterial strain was isolated. This strain, called LA, exhibited a relatively constant rate of iron-oxidation in media containing sulfate ions at concentrations ranging from 10 to 150 gl(-1). Culture collection strains of Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans showed limited abilities to grow at sulfate ion concentrations higher than 70 gl(-1). In spite of its tolerance to high sulfate concentrations, strain LA was as sensitive to NaCl as A. ferrooxidans. Comparative sequence analysis of the 16S rRNA gene of strain LA indicated that it is phylogenetically related to strains described as Leptospirillum ferrooxidans. Bacterial community DNA restriction patterns of 16S rRNA genes suggested that strain LA was a minor component of the bacterial population present in leaching solution, but is abundant in ore leached with this solution.

Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and gamma-proteobacteria from the deep sea

We report the isolation and physiological characterization of novel, psychrophilic, iron-oxidizing bacteria (FeOB) from low-temperature weathering habitats in the vicinity of the Juan de Fuca deep-sea hydrothermal area. The FeOB were cultured from the surfaces of weathered rock and metalliferous sediments. They are capable of growth on a variety of natural and synthetic solid rock and mineral substrates, such as pyrite (FeS(2)), basalt glass ( approximately 10 wt% FeO), and siderite (FeCO(3)), as their sole energy source, as well as numerous aqueous Fe substrates. Growth temperature characteristics correspond to the in situ environmental conditions of sample origin; the FeOB grow optimally at 3 to 10 degrees C and at generation times ranging from 57 to 74 h. They are obligate chemolithoautotrophs and grow optimally under microaerobic conditions in the presence of an oxygen gradient or anaerobically in the presence of nitrate. None of the strains are capable of using any organic or alternate inorganic substrates tested. The bacteria are phylogenetically diverse and have no close Fe-oxidizing or autotrophic relatives represented in pure culture. One group of isolates are gamma-Proteobacteria most closely related to the heterotrophic bacterium Marinobacter aquaeolei (87 to 94% sequence similarity). A second group of isolates are alpha-Proteobacteria most closely related to the deep-sea heterotrophic bacterium Hyphomonas jannaschiana (81 to 89% sequence similarity). This study provides further evidence for the evolutionarily widespread capacity for Fe oxidation among bacteria and suggests that FeOB may play an unrecognized geomicrobiological role in rock weathering in the deep sea.

Heavy metal mining using microbes

The use of acidiphilic, chemolithotrophic iron- and sulfur-oxidizing microbes in processes to recover metals from certain types of copper, uranium, and gold-bearing minerals or mineral concentrates is now well established. During these processes insoluble metal sulfides are oxidized to soluble metal sulfates. Mineral decomposition is believed to be mostly due to chemical attack by ferric iron, with the main role of the microorganisms being to reoxidize the resultant ferrous iron back to ferric iron. Currently operating industrial biomining processes have used bacteria that grow optimally from ambient to 50 degrees C, but thermophilic microbes have been isolated that have the potential to enable mineral biooxidation to be carried out at temperatures of 80 degrees C or higher. The development of higher-temperature processes will extend the variety of minerals that can be commercially processed.

Genetic and immunochemical characterization of thiocyanate-degrading bacteria in lake water

Natural aquatic and soil samples were screened for the presence of thiocyanate-degrading bacteria. Using thiocyanate supplementation, we established an enrichment culture containing such bacteria from lake water. The dominant bacteria had the scnC-LS5 gene encoding thiocyanate hydrolase, which was closely related to the enzyme found previously in Thiobacillus thioparus THI115 isolated from activated sludge.