Molecular characterization of Acidithiobacillus ferrooxidans and A. thiooxidans strains isolated from mine wastes in Brazil

Biolixiviation of Metals from Computer Printed Circuit Boards by Acidithiobacillus ferrooxidans and Bioremoval of Metals by Mixed Culture Subjected to a Magnetic Field

Crushed and ground printed circuit board (PCB) samples were characterized to evaluate copper, lead, and aluminum using X-ray fluorescence spectroscopy (XRF) and the morphology was done by scanning electron microscopy (SEM). The XRF characterizations showed 0.12% lead, 3.72% copper, and 12.73% aluminum in the PCBs. The metal solubilization experiments using Acidithiobacillus ferrooxidans indicated higher values of total metal solubilization when the initial pH of the inoculum was adjusted. However, these experiments did not show higher metal solubilization by bioleaching. The sequential bioremoval experiments using mixed culture after bioleaching assays with A. ferrooxidans with initial adjustment of inoculum pH and without applying a magnetic field removed 100% of Al, 27.34% of Cu, and 96.43% of Pb from the lixiviate medium; with magnetic field application, 100% of Al, 83.82% of Cu, and 98.27% of Pb were removed. A similar bioleaching experiment without inoculum pH adjustment and without field application achieved 99.74% removal for Cu and 91.92% for Pb. When the magnetic field was applied, 100% of Cu and 95.76% of Pb were removed. Bioreactors with a magnetic field do not show significantly better removal of any of the metals analyzed.

Acidithiobacillus thiooxidans and its potential application

Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.

Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile

10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate moderate chloride concentrations (up to 15 g L-1 Cl-), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199 strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of 10.1601/nm.2199 populations.

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.

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

To study the phylogenetic relationships and genetic heterogeneity of 21 Acidithiobacillus strains isolated from different environments, we amplified and sequenced the 16S-23S rRNA gene intergenic spacers (ITS) of all these strains. These sequence data, combined with related sequences available from GenBank, were divided into six phylogenetic groups by 16S rRNA gene and by 16S-23S rRNA gene sequence analysis. The results of phylogenetic analysis were consistent with those obtained by repetitive element PCR and arbitrarily primed PCR. In this research, the Acidithiobacillus ferrooxidans (A. ferrooxidans) strains were always separated into two groups in phylogenetic and cluster analyses. Genotypic analyses of the genes rusA, rusB, hip and iro suggest that these two groups may have different biochemical mechanisms for oxidizing ferrous iron. Strains in one A. ferrooxidans group were detected with rusA gene that encodes rusticyanin A which plays a very important role in the iron respiratory chain. The second A. ferrooxidans group was found to contain rusB gene which encode a homologous protein (RusB). The data suggested that ITS-based phylogeny is an effective tool to elucidate the relationships of Acidithiobacillus and that a different iron oxidation pathway may exist in different A. ferrooxidans groups.

Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation

Phenotypic, metabolic and genetic properties of several Acidithiobacillus caldus strains indicate the existence of as yet undefined levels of variation within the species. Inspite of this, intraspecies genetic diversity has not yet been explored in detail. In this study, the design and implementation of a Multi Locus Sequence Typing (MLST) scheme for At. caldus is described. This represents the first MLST-based study applied to industrial isolates of the species. Seven informative and discriminant MLST markers were selected using a sequence-driven approach and a custom-designed bioinformatic pipeline. The allelic profiles of thirteen At. caldus strains from diverse geographical origins and industrial settings were derived using this scheme. MLST-based population structure analysis indicated only moderate amounts of genetic diversity within the set of strains, further supporting their current assignment to a single species. Also, no clear evidence for geographical isolation could be derived from this study. However, the prevalence of sequence type 1 in heap leaching industrial settings support the view that bioprocess conditions and dynamics may have a strong influence on At. caldus (microbial) microdiversity patterns. The MLST scheme presented herein is a valuable tool for the identification and classification of strains of At. caldus for either ecological or evolutionary studies and possibly also for industrial monitoring purposes.

A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment

Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.

Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

Autotrophic acidophilic iron- and sulfur-oxidizing bacteria of the genus Acidithiobacillus constitute a heterogeneous taxon encompassing a high degree of diversity at the phylogenetic and genetic levels, though currently only two species are recognized (Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans). One of the major functional disparities concerns the biochemical mechanisms of iron and sulfur oxidation, with discrepancies reported in the literature concerning the genes and proteins involved in these processes. These include two types of high-potential iron–sulfur proteins (HiPIPs): (i) Iro, which has been described as the iron oxidase; and (ii) Hip, which has been proposed to be involved in the electron transfer between sulfur compounds and oxygen. In addition, two rusticyanins have been described: (i) rusticyanin A, encoded by the rusA gene and belonging to the well-characterized rus operon, which plays a central role in the iron respiratory chain; and (ii) rusticyanin B, a protein to which no function has yet been ascribed. Data from a multilocus sequence analysis of 21 strains of Fe(II)-oxidizing acidithiobacilli obtained from public and private collections using five phylogenetic markers showed that these strains could be divided into four monophyletic groups. These divisions correlated not only with levels of genomic DNA hybridization and phenotypic differences among the strains, but also with the types of rusticyanin and HiPIPs that they harbour. Taken together, the data indicate that Fe(II)-oxidizing acidithiobacilli comprise at least four distinct taxa, all of which are able to oxidize both ferrous iron and sulfur, and suggest that different iron oxidation pathways have evolved in these closely related bacteria.

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.

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.

Structure Analysis of 16S rDNA Sequences from Strains of Acidithiobacillus ferrooxidans

Four strains of Acidithiobacillus ferrooxidans with different iron oxidation capacity were isolated from different mine drainage stations. The 16S rRNA gene of these strains were cloned and sequenced. Based on our sequences analysis on the four strain and the data on the other strains deposited in Genbank, all A. ferrooxidans may be classified into three phylogenetic groups. The analysis data showed that nucleotide variables (signature sites) were detected in 21 positions, and most of them were found in the first 800 bp from 5' terminal except position 970 and 1375. Interestingly, the first 13 signature sites were located in two main regions: the first region (position 175-234) located in V2 while the second region (position 390-439) were detected in constant region between V2 and V3. Furthermore, the secondary structure and minimal free energy were determined in two regions among strains of three groups. These results may be useful in characterizing the microevolutionary mechanisms of species formation and monitoring in biohydrometallurgical application.

Diversity of 16S ribosomal DNA-defined bacterial population in acid rock drainage from Japanese pyrite mine

Four acidophilic bacteria (YARDs1-4) were isolated from an acid rock drainage (ARD) from Yanahara mine, Okayama prefecture, Japan. The physiological and 16S rDNA sequence analyses revealed that YARD1 was closely affiliated with Acidithiobacillus ferrooxidans, YARD2 was an Acidiphilium-like bacterium, and YARD3 and YARD4 were sulfur-oxidizing bacteria with a relatively close relationship to A. ferrooxidans in the phylogenetic analysis. A molecular approach based on the construction of a 16S rDNA clone library was used to investigate the microbial population of the ARD. Small-subunit rRNA genes were PCR amplified, subsequently cloned and screened for variation by a restriction fragment length polymorphism (RFLP) analysis. A total of 284 clones were grouped into 133 operational taxonomic units (OTUs) by the RFLP analysis. Among them, an OTU showing the same RFLP pattern as those of the isolates from the ARD was not detected. The phylogenetic analysis based on the 16S rDNA sequences from 10 major OTUs and their close relatives revealed that 4 OTUs containing 32.1% of the total clones were loosely affiliated with Verrucomicrobia, 2 OTUs containing 6.6% of the total clones were loosely affiliated with Chloribi, and other OTUs were affiliated with Actinobacteria, Nitrospirae, and beta-Proteobacteria.

Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S–23S rDNA spacer polymorphism analysis

Restriction fragment length polymorphism (RFLP) and sequence analyses of the PCR-amplified 16S-23S rDNA intergenic spacer (ITS) were used for differentiating Acidithiobacillus thiooxidans strains from other related acidithiobacilli, including A. ferrooxidans and A. caldus. RFLP fingerprints obtained with AluI, DdeI, HaeIII, HinfI and MspI enabled the differentiation of all Acidithiobacillus reference strains into species groups. The A. thiooxidans strains investigated (metal mine isolates) yielded identical RFLP patterns to the A. thiooxidans type strain (ATCC 19377(T)), except for strain DAMS, which had a distinct pattern for all enzymes tested. Fourteen A. ferrooxidans mine strains were assigned to 3 RFLP groups, the majority of which were grouped with A. ferrooxidans ATCC 23270(T). The spacer region of one representative strain from each of the RFLP groups obtained was subjected to sequence analysis, in addition to eleven additional A. thiooxidans strains isolated from sediment and water samples, and A. caldus DSM 8584(T). The tRNA(IIe) and tRNA(Ala) genes, present in all strains analyzed, showed high sequence similarity. Phylogenetic analysis of the ITS sequences differentiated all three Acidithiobacillus species. Inter- and infraspecific genetic variations detected were mainly due to the size and sequence polymorphism of the ITS3 region. Mantel tests showed no significant correlation between ITS sequence similarity and the geographical origin of strains. The results showed that the 16S-23S rDNA spacer region is a useful target for the development of molecular-based methods aimed at the detection, rapid differentiation and identification of acidithiobacilli.