Heterotrophic bacteria from cultures of autotrophic Thiobacillus ferrooxidans: relationships as studied by means of deoxyribonucleic acid homology

Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates

Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.

Feasibility of bioleaching of heavy metals from sediment with indigenous bacteria using agricultural sulfur soil conditioners

Sediment bioleaching using a sulfur substrate is a promising approach to the removal of heavy metals. Compared with commercial sulfur powder used as the sulfur substrate, agricultural sulfur soil conditioners may reduce secondary pollution and facilitate the reuse of sediment. This study explored the bioleaching effect of three agricultural sulfur soil conditioners, including sulfur-coated urea, bentonite sulfur, and bio-sulfur, and the bioleaching potential of the indigenous sediment bacteria. The results showed that the sulfur-coated urea had a comparable bioleaching effect with sulfur powder (Ni 35.35%, Cu 74.27%, Zn 69.92%) and the highest maximum bioleaching rate because of the additional nitrogen. The bentonite sulfur leached the least but increased the proportion of the residual state due to its adsorption of heavy metal. Similar changes to the microbial flora structure and bioleaching mechanism were found with the use of sulfur powder, sulfur-coated urea, and bentonite sulfur as the bioleaching substrate. There was no significant difference between the indigenous bacteria and the sludge-enriched bacteria in the bioleaching effect except for bio-sulfur, which only performed well with the sludge-enriched bacteria. In the absence of inoculum, the bio-sulfur hindered the bioleaching process due to high levels of organic matter. This study provides insights into the practical application of bioleaching heavy metal removal technology from the perspective of sulfur substrate selection.

Active fluid with Acidithiobacillus ferrooxidans: correlations between swimming and the oxidation route

To explore engineering platforms towards 'active bacterial baths', we grow and characterize native and commercial strains of Acidithiobacillus ferrooxidans to promote swimming locomotion. Three different energy sources were used, namely elemental sulfur, ferrous sulfate, and pyrite. The characteristics of the culture, such as pH, Eh, and the concentration of cells and ions, are monitored to seek correlations between the oxidation route and the transport mechanism. We found that only elemental sulfur induces swimming mobility in the commercial DSMZ - 24,419 strain, while ferrous sulfate and the sulfide mineral, pyrite, did not activate swimming on any strain. The bacterial mean squared displacement and the mean velocity are measured to provide a quantitative description of the bacterial mobility. We found that, even if the A. ferrooxidans strain is grown in a sulfur-rich environment, it preferentially oxidizes iron when an iron-based material is included in the media. Similar to other species, once the culture pH decreases below 1.2, the active locomotion is inhibited. The engineering control and activation of swimming in bacterial cultures offer fertile grounds towards applications of active suspensions such as energy-efficient bioleaching, mixing, drug delivery, and bio-sensing.

Testing culture purity in prokaryotes: criteria and challenges

Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer's personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by 'culturomics' will overcome this obstacle.

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.

Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum"

Background

Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce.

Objective

In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12.

Phylogeny and Lifestyle

The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively.

Unique Metabolic Features

The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in “Ferrovum” strain JA12. Therefore, the results of the present study extend our understanding of the genus “Ferrovum” and provide a comprehensive framework for future comparative genome and metagenome studies.

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.

The hydroxyectoine gene cluster of the non-halophilic acidophile Acidiphilium cryptum

Acidiphilium cryptum is an acidophilic, heterotrophic α-Proteobacterium which thrives in acidic, metal-rich environments (e.g. acid mine drainage). Recently, an ectABCDask gene cluster for biosynthesis of the compatible solutes ectoine and hydroxyectoine was detected in the genome sequence of A. cryptum JF-5. We were able to demonstrate that the type strain A. cryptum DSM 2389(T) is capable of synthesizing the compatible solute hydroxyectoine in response to moderate osmotic stress caused by sodium chloride and aluminium sulphate, respectively. Furthermore, we used the A. cryptum JF-5 sequence to amplify the ectABCDask gene cluster from strain DSM 2389(T) and achieved heterologous expression of the gene cluster in Escherichia coli. Hence, we could for the first time prove metabolic functionality of the genes responsible for hydroxyectoine biosynthesis in the acidophile A. cryptum. In addition, we present information on specific enzyme activity of A. cryptum DSM 2389(T) ectoine synthase (EctC) in vitro. In contrast to EctCs from halophilic microorganisms, the A. cryptum enzyme exhibits a higher isoelectric point, thus a lower acidity, and has maximum specific activity in the absence of sodium chloride.

New cultivation medium for "Ferrovum" and Gallionella-related strains

Since the first isolation of the well-known iron oxidizer Acidithiobacillus ferrooxidans various media and techniques have been developed to isolate new species of acidophilic iron-oxidizing bacteria. A successful strategy in many cases was the use of iFeo medium in double-layer plates with a heterotrophic strain in the underlayer. However, even with samples which had been shown by molecular techniques to be dominated by "Ferrovum myxofaciens" and Gallionella-related bacteria, these bacteria were isolated considerably less frequently than Acidithiobacillus spp. on iFeo. Therefore, a new medium was designed which corresponded largely to the chemical composition of the mine water in a treatment plant dominated by the bacterial groups mentioned and was called artificial pilot-plant water (APPW). The analyses of approximately 500 colonies obtained from mine waters of two different sampling sites by PCR with primers specific for Acidithiobacillus spp., "Ferrovum" spp., Gallionella relatives, and Acidiphilium spp. revealed higher abundances of "Ferrovum" spp. and Gallionella relatives on the newly designed APPW medium than on iFeo which favored Acidithiobacillus spp. Molecular analysis of the colonies obtained indicated the occurrence of at least two species of iron-oxidizing bacteria and/or the heterotrophic Acidiphilium spp. in most of the colonies. Furthermore, the influence on the isolation of the concentrations of iron, phosphate, and ammonium of APPW, in levels of the iFeo medium previously described was studied.

Development of a markerless gene replacement system for Acidithiobacillus ferrooxidans and construction of a pfkB mutant

The extremely acidophilic, chemolithoautotrophic Acidithiobacillus ferrooxidans is an important bioleaching bacterium of great value in the metallurgical industry and environmental protection. In this report, a mutagenesis system based on the homing endonuclease I-SceI was developed to produce targeted, unmarked gene deletions in the strain A. ferrooxidans ATCC 23270. A targeted phosphofructokinase (PFK) gene (pfkB) mutant of A. ferrooxidans ATCC 23270 was constructed by homologous recombination and identified by PCR with specific primers as well as Southern blot analysis. This potential pfkB gene (AFE_1807) was also characterized by expression in PFK-deficient Escherichia coli cells, and heteroexpression of the PFKB protein demonstrated that it had functional PFK activity, though it was significantly lower (about 800-fold) than that of phosphofructokinase-2 (PFK-B) expressed by the pfkB gene from E. coli K-12. The function of the potential PFKB protein in A. ferrooxidans was demonstrated by comparing the properties of the pfkB mutant with those of the wild type. The pfkB mutant strain displayed a relatively reduced growth capacity in S(0) medium (0.5% [wt/vol] elemental sulfur in 9K basal salts solution adjusted to pH 3.0 with H(2)SO(4)), but the mutation did not completely prevent A. ferrooxidans from assimilating exogenous glucose. The transcriptional analysis of some related genes in central carbohydrate metabolism in the wild-type and mutant strains with or without supplementation of glucose was carried out by quantitative reverse transcription-PCR. This report suggests that the markerless mutagenesis strategy could serve as a model for functional studies of other genes of interest from A. ferrooxidans and multiple mutations could be made in a single A. ferrooxidans strain.

Examination of Lipopolysaccharide (O-Antigen) Populations of Thiobacillus ferrooxidans from Two Mine Tailings

Net acid-generating capacities of 39.74 kg of H(2)SO(4) per ton (ca. 0.05 kg/kg) (pH 2.68) for the Lemoine copper mine tailings (closed ca. 8 years ago; located 40 km west of Chibougamau, Quebec, Canada) and 16.07 kg of H(2)SO(4) per ton (ca. 0.02 kg/kg) (pH 3.01) for the Copper Rand tailings (in current use and 50 km distant [east] from those of Lemoine) demonstrate that these sulfide tailings can support populations of acidophilic thiobacilli. Oxidized regions in both tailings environments were readily visible, were extremely acidic (Lemoine, pH 2.36; Copper Rand, pH 3.07), and provided natural isolates for our study. A 10% (wt/vol) oxalic acid treatment, which solubilizes both ferric sulfate and ferric hydroxide precipitates (B. Ramsay, J. Ramsay, M. deTremblay, and C. Chavarie, Geomicrobiol. J. 6:171-177, 1988), enabled the recovery of intact bacterial cells from the tailings material and from liquid synthetic medium for lipopolysaccharide analysis. No viable cells could be cultured after this oxalic acid treatment. Sodium dodecyl sulfate-polyacrylamide gel electro-phoretic profiles of lipopolysaccharides extracted from the Lemoine tailings were complex, indicating a heterogeneous population of Thiobacillus ferrooxidans. Six T. ferrooxidans subspecies as identified by lipopolysaccharide analysis (i.e., lipopolysaccharide chemotypes) were eventually isolated from a total of 112 cultures from the Lemoine tailings. Using the same isolate and lipopolysaccharide typing techniques, we identified only a single lipopolysaccharide chemotype from 20 cultures of T. ferrooxidans isolated from the Copper Rand tailings. This homogeneity of lipopolysaccharide chemotype was much different from what was found for the older Lemoine tailings and may reflect a progressive lipopolysaccharide heterogeneity of Thiobacillus isolates as tailings leach and age.

The role ofAcidithiobacillus ferrooxidansin alleviating the inhibitory effect of thiosulfate on the growth of acidophilicAcidiphiliumspecies isolated from acid mine drainage samples from Garubathan, India

Several acidophilic chemolithoautotrophic and heterotrophic strains were isolated from acid mine drainage samples from Garubathan, West Bengal, India. The strains, chemolithoautotrophic DK6.1 and heterotrophic DKAP1.1, used in this study were assigned to the species Acidithiobacillus ferrooxidans and Acidiphilium cryptum , respectively. Unamended filtered and subsequently autoclaved elemental sulfur spent medium of A. ferrooxidans was used as the medium to study heterotrophic growth of A. cryptum DKAP1.1. While characterizing the heterotrophic strain, an inhibitory effect of thiosulfate on A. cryptum DKAP1.1 was identified. The lethality of thiosulfate broth was directly related to the concentration of thiosulfate in the medium. Nonviability of A. cryptum DKAP1.1 in the presence of thiosulfate was alleviated by A. ferrooxidans DK6.1 in co-culture. Microbiological data on a positive growth effect for A. ferrooxidans DK6.1 caused by co-culturing in solid media in the presence of A. cryptum DKAP1.1 is also presented.

Adaptive responses of chemolithoautotrophic acidophilic Acidithiobacillus ferrooxidans to sewage sludge

AIM

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

METHODS AND RESULTS

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

CONCLUSIONS

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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

Influence of heterotrophic microbial growth on biological oxidation of pyrite

The rate and extent of pyrite oxidation by the iron-oxidizing bacteria Acidithiobacillus ferrooxidans was limited by the growth of the heterotrophic microbe Acidiphilium acidophilum. In batch systems containing a mixture of both organisms, the maximum zero-order rate of ferric iron accumulation was about 1.4 mg of Fe3+ L(-1) d(-1) as compared to 9.4 mg of Fe3+ L(-1) d(-1) for pure cultures of A. ferrooxidans under the same conditions. Pyrite oxidation was limited in cases where both cultures of organisms were initially present as well as situations where the heterotrophic organisms were added to established, pyrite-oxidizing systems containing A. ferrooxidans. Results also indicated that organic carbon remaining in solution following heterotrophic bacterial growth reduced the rate of abiotic pyrite oxidation by the ferric ion. Furthermore, a cell-free solution of the residual organic carbon resulted in a lag of A. ferrooxidans growth in soluble ferrous medium. The residual organic carbon solution that accumulated during the growth of Aph. acidophilum had a diverse molecular weight distribution, indicating that different compounds could be responsible for the inhibition of chemical pyrite oxidation and the A. ferrooxidans growth lag observed. Titration of dissolved copper ions with residual dissolved organic carbon originating from Aph. acidophilum cultures indicated that a metal complexation mechanism could be responsible for the lower rates of pyrite oxidation observed. These data suggest that encouraging the growth of heterotrophic microorganisms under acid mine drainage conditions may be a feasible strategy for decreasing both the rate and the extent of sulfide mineral oxidation.

Aerobic anoxygenic photosynthetic bacteria with zinc-bacteriochlorophyll

Naturally occurring chlorophyllous pigments, which function as the cofactor in the early photochemical reaction of photosynthesis, have been proven beyond question to be magnesium-complexed porphyrin derivatives. Phototrophic organisms that use (bacterio)chlorophylls ([B]Chls) containing metals other than Mg were unknown for a long time. This common knowledge of natural photosynthesis has recently been modified by the striking finding that a novel purple pigment, zinc-chelated-BChl (Zn-BChl) a, is present as the major and functional pigment in species of the genus Acidiphilium. Acidiphilium species are obligately acidophilic chemoorganotrophic bacteria that grow and produce photopigments only under aerobic conditions. Although the mechanism of photosynthesis with Zn-BChl a in Acidiphilium species is similar to that seen in common purple bacteria, some characteristic photosynthetic features of the acidophilic bacteria are also found. The discovery of natural photosynthesis with Zn-BChl has not only provided a new insight into our understanding of bacterial photosynthesis but also raised some interesting questions to be clarified. The major questions are why the acidophilic bacteria have selected Zn-BChl for their photosynthesis and how they synthesize Zn-BChl and express photosynthetic activity with it in their natural habitats. In this article we review the current knowledge of the biology of Acidiphilium as aerobic photosynthetic bacteria with Zn-BChl a and discuss the interesting topics noted above.

Physiology and taxonomy of thiobacillus strain TJ330, which oxidizes carbon disulphide (CS2)

A bacterium (strain TJ330) capable of using carbon disulphide (CS2) as its sole energy source in an acidic environment was isolated from a peat biofilter used in experiments to remove CS2 and hydrogen sulphide (H2S) from air. Its physiology and taxonomy are described here. The strain oxidized CS2, H2S and elemental sulphur to sulphate chemolithotrophically. The rate of sulphate production was highest at pH 2. The maximum growth rate constant (micromax) using CS2 as a substrate was 3.9 x 10(-2) h(-1) (generation time 18 h) and the Monod constant (Ks) was 0.97-2.6 micromol l(-1) CS2 (74-198 microg l(-1)), corresponding to an equilibrium with 15-40 ppm CS2 in the headspace. The optimum growth temperature using elemental sulphur as a substrate was 28 degrees C. The strain bears morphological and physiological similarities to Thiobacillus thiooxidans, but the latter is incapable of oxidizing CS2. The strain TJ330 (DSM 8985) showed only 44.2 + 11.8% DNA homology with the type strain T. thiooxidans ATCC 19377, while its homology with T. ferrooxidans ATCC 23270 was 17.1 + 3.4%. The strain TJ 330 represents a high-affinity bacterium which can effectively remove low CS2 concentrations in an acid environment. These properties can be utilized in biotechnological purification applications.

Evaluation of a fluorescent lectin-based staining technique for some acidophilic mining bacteria

A fluorescence-labeled wheat germ agglutinin staining technique (R. K. Sizemore et al., Appl. Environ. Microbiol. 56:2245-2247, 1990) was modified and found to be effective for staining gram-positive, acidophilic mining bacteria. Bacteria identified by others as being gram positive through 16S rRNA sequence analyses, yet clustering near the divergence of that group, stained weakly. Gram-negative bacteria did not stain. Background staining of environmental samples was negligible, and pyrite and soil particles in the samples did not interfere with the staining procedure.

Transformation of Escherichia coli with a large plasmid of Acidiphilium multivorum AIU 301 encoding arsenic resistance

Acidiphilium multivorum AIU 301 isolated from acid mineral water had strong arsenic resistance. This bacterium harbored a number of plasmids with different molecular sizes. A plasmid of 56 kbp, named pKW301, was isolated from A. multivorum AIU 301. When pKW301 was transferred into Escherichia coli JM109 by electroporation, an E. coli transformant carrying pKW301 exhibited resistance to sodium arsenite, sodium arsenate, and mercuric (II) chloride.

Direct 5S rRNA Assay for Monitoring Mixed-Culture Bioprocesses

This study demonstrates the efficacy of a direct 5S rRNA assay for the characterization of mixed microbial populations by using as an example the bacteria associated with acidic mining environments. The direct 5S rRNA assay described herein represents a nonselective, direct molecular method for monitoring and characterizing the predominant, metabolically active members of a microbial population. The foundation of the assay is high-resolution denaturing gradient gel electrophoresis (DGGE), which is used to separate 5S rRNA species extracted from collected biomass. Separation is based on the unique migration behavior of each 5S rRNA species during electrophoresis in denaturing gradient gels. With mixtures of RNA extracted from laboratory cultures, the upper practical limit for detection in the current experimental system has been estimated to be greater than 15 different species. With this method, the resolution was demonstrated to be effective at least to the species level. The strength of this approach was demonstrated by the ability to discriminate between Thiobacillus ferrooxidans ATCC 19859 and Thiobacillus thiooxidans ATCC 8085, two very closely related species. Migration patterns for the 5S rRNA from members of the genus Thiobacillus were readily distinguishable from those of the genera Acidiphilium and Leptospirillum. In conclusion, the 5S rRNA assay represents a powerful method by which the structure of a microbial population within acidic environments can be assessed.

Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments

A range of autotrophic and heterotrophic enrichment cultures were established to determine the cultural bacterial diversity present in samples obtained from the acidic runoff of a chalcocite overburden heap and from laboratory-scale (1- to 4-liter) batch and continuous bioreactors which were being used for the commercial assessment of the bioleachability of zinc sulfide ore concentrates. Strains identified as Thiobacillus ferrooxidans, Thiobacillus thiooxidans, "Leptospirillum ferrooxidans," and Acidiphilium cryptum were isolated from both the natural site and the batch bioreactor, but only "L. ferrooxidans," a moderately thermophilic strain of T. thiooxidans, and a moderately thermophilic iron-oxidizing bacterium could be recovered from the continuous bioreactor running under steady-state conditions. Sequence analysis of the 16S rRNA genes of 33 representative strains revealed that all of the strains were closely related to strains which have been sequenced previously and also confirmed the phylogenetic diversity of bacteria present in bioleaching environments.

Glucose Catabolism in Strains of Acidophilic, Heterotrophic Bacteria

Pathways of glucose catabolism, potentially operational in six strains of obligately aerobic, acidophilic bacteria, including Acidiphilium cryptum strain Lhet2, were investigated by short-term radiorespirometry and enzyme assays. Short-term radiorespirometry was conducted at pH 3.0 with specifically labeled [ 14 C]glucose. The high rate and yield of C-1 oxidized to CO 2 indicated that the Entner-Doudoroff, pentose phosphate, or both pathways were operational in all strains. Apparent nonequivalent yields of CO 2 from C-1 and estimated CO 2 from C-4 (C-1 > C-4) were suggestive of simultaneous glucose catabolism by both pathways in all strains tested. Variation in the relative contribution of the two pathways of glucose catabolism appears to account for observed strain differences. Calculation of the actual percent pathway participation was not feasible. Enzyme assays were completed with crude extracts of glucose-grown cells to substantiate the results obtained by radiorespirometry. The key enzymes of the pentose phosphate pathway (6-phosphogluconate dehydrogenase) and the Entner-Doudoroff pathway (2-keto-3-deoxy-6-phosphogluconate aldolase and 6-phosphogluconate dehydrase) were present in all strains examined (PW2, Lhet2, KLB, OP, and QBP). However, none of the strains exhibited detectable levels of the key enzyme of the Embden-Meyerhof-Parnas pathway, 6-phosphofructokinase. All strains contained glucose-6-phosphate dehydrogenase and fructose bisphosphate aldolase. The results of the enzyme study supported the contention that the pentose phosphate and Entner-Doudoroff pathways are operational for glucose catabolism in the acidophilic heterotrophs, and that the Embden-Meyerhof-Parnas pathway is apparently absent.

Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences

5S rRNA nucleotide sequences from Thiobacillus neapolitanus, Thiobacillus ferrooxidans, Thiobacillus thiooxidans, Thiobacillus intermedius, Thiobacillus perometabolis, Thiobacillus thioparus, Thiobacillus versutus, Thiobacillus novellus, Thiobacillus acidophilus, Thiomicrospira pelophila, Thiomicrospira sp. strain L-12, and Acidiphilium cryptum were determined. A phylogenetic tree, based upon comparison of these and other related 5S rRNA sequences, is presented. The results place the thiobacilli, Thiomicrospira spp., and Acidiphilium spp. in the "purple photosynthetic" bacterial grouping which also includes the enteric, vibrio, pseudomonad, and other familiar eubacterial groups in addition to the purple photosynthetic bacteria. The genus Thiobacillus is not an evolutionarily coherent grouping but rather spans the full breadth of the purple photosynthetic bacteria.

Mixotrophic Growth of a Thiobacillus ferrooxidans Strain

Mixotrophic growth of a Thiobacillus ferrooxidans strain is described. DNA moles percent guanine plus cytosine and homology determinations confirmed that the mixotrophically grown T. ferrooxidans cultures were not contaminated with heterotrophic Acidiphilium strains.

Microbiology of thiobacilli and other sulphur-oxidizing autotrophs, mixotrophs and heterotrophs

Recent studies on the ecophysiology of the obligate chemolithotroph Thiobacillus neapolitanus have given better insight into its specialization for an autotrophic mode of life. This appears not only from its high constitutive levels of autotrophic enzymes, but also from its possession of carboxysomes, which seem to be specialized organelles for CO2 fixation and concentrating reducing power. At the same time, these organisms are metabolically versatile with respect to nitrogen assimilation pathways, and during starvation are able to utilize endogenous resources such as polyglucose for carbon and energy. Studies on the facultative chemolithotrophs such as Thiobacillus novellus and Thiobacillus A2 have shown that they can grow mixotrophically on mixtures of inorganic and organic substrates, i.e. they can utilize these compounds simultaneously provided that they are growth limiting. Thiobacillus A2 displays a remarkable flexibility not only with respect to the organic substrates that it can utilize but, for example, also in the choice of various pathways for glucose metabolism. Competition experiments carried out between specialized and versatile thiobacilli strongly indicate that the ecological advantage of the versatile thiobacilli may lie not so much in their short-term flexibility, but rather in their ability to grow mixotrophically. Studies on most heterotrophic chemolithotrophs are still in their infancy. Promising progress has been made in the study of the physiology of Beggiatoa species. Renewed interest in the sulphur-oxidizing bacteria stems from recent findings about their role in food chains, and their possible application in industry.

Glucose transport system in a facultative iron-oxidizing bacterium, Thiobacillus ferrooxidans

Properties of a heat-labile glucose transport system in Thiobacillus ferrooxidans strain AP-44 were investigated with iron-grown cells. [14C]glucose was incorporated into cell fractions, and the cells metabolized [14C]glucose to 14CO2. Amytal, rotenone, cyanide, azide, 2,4-dinitrophenol, and dicyclohexylcarbodiimide strongly inhibited [14C]glucose uptake activity, suggesting the presence of an energy-dependent glucose transport system in T. ferrooxidans. Heavy metals, such as mercury, silver, uranium, and molybdate, markedly inhibited the transport activity at 1 mM. When grown on mixotrophic medium, the bacteria preferentially utilized ferrous iron as an energy source. When iron was exhausted, the cells used glucose if the concentration of ferrous sulfate in the medium was higher than 3% (wt/vol). However, when ferrous sulfate was lower than 1%, both of the energy sources were consumed simultaneously.

Acidophilic, Heterotrophic Bacteria of Acidic Mine Waters

Obligately acidophilic, heterotrophic bacteria were isolated both from enrichment cultures developed with acidic mine water and from natural mine drainage. The bacteria were grouped by the ability to utilize a number of organic acids as sole carbon sources. None of the strains were capable of chemolithotrophic growth on inorganic reduced iron and sulfur compounds. All bacteria were rod shaped, gram negative, nonencapsulated, motile, capable of growth at pH 2.6 but not at pH 6.0, catalase and oxidase positive, strictly aerobic, and capable of growth on citric acid. The bacteria were cultivatable on solid nutrient media only if agarose was employed as the hardening agent. Bacterial densities in natural mine waters ranged from approximately 20 to 250 cells per ml, depending upon source and culture medium. Ferric hydrates and stream vegetation contained from 1,500 to over 7 × 10 6 cells per g.