Introduction

Acidithiobacillus thiooxidans, originally named Thiobacillus thiooxidans, was first isolated by Waksman and Joffe in 1921 from compost soil (Waksman and Joffe 1921; Waksman and Joffe 1922). It is an aerobic mesophilic, extremely acidophilic, chemolithoautotrophic, gram-negative, γ-proteobacterium, non-sporulating, rod-shaped microorganism (Jorge et al. 2011; Kelly and Wood 2000; Zhang et al. 2016a). A. thiooxidans is affiliated to the genus Acidithiobacillus, its phylogenetic relationship to other species among genus Acidithiobacillus can be mirrored by a phylogenetic tree based on 16S rRNA gene sequence (Fig. 1). It has been found that this bacterium plays a major role in sulfur oxidation, acid production, and bioleaching (Marín et al. 2017). This bacterium obtains energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs) to support its autotrophic growth (Kelly and Wood 2015). The RISCs can act as an electron donor and reducing power during the oxidation process, including elemental sulfur (S0), polysulfides (Sn2−) and sulfide minerals, such as pyrite (FeS2), chalcopyrite (CuFeS2), or sphalerite (ZnS) (Garcia-Meza et al. 2018). It was probably one of the pioneer microorganisms on our planet and can fix carbon from the CO2 of the atmosphere, get nitrogen from ammonium sulfate, and obtain mineral element from inorganic salts (Waksman and Joffe 1922; Wen et al. 2014). This bacteria has been considered as a vital sulfur cycle microorganism (Konishi et al. 1995).

Fig. 1
figure 1

Maximum-likelihood (ML) phylogenetic relationships of Acidithiobacillus spp based on 16S rRNA gene sequences. Seven species affiliated in this genus, including A. albertensis, A. caldus, A. cuprithermicus, A. ferridurans, A. ferriphilus, A. ferrivorans, A. ferrooxidans, and A. thiooxidans

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A. thiooxidans can inhabit many extreme environments including sulfidic caves, mineral leaching heaps, mine dumps, and other natural-acidic and man-made sulfur-rich environments because of its high acid resistance and high tolerance to metal ions such as copper and zinc (Chang et al. 2008; Pathak et al. 2009; Quatrini et al. 2017). A. thiooxidans grows in the optimum pH range of 2.0–3.5, and the optimum temperature is 28–30 °C (Suzuki et al. 1999). Until now, eleven draft genome sequence of A. thiooxidans strains have been sequenced and were recorded in NCBI (https://www.ncbi.nlm.nih.gov/). The genomic sequence of A. thiooxidans contains a number of pseudogenes, the genome size ranges from 3.02 to 3.97 Mb, and the G + C content is in the range of 48.8–53.2%. It has been reported that a linear plasmid named pTTY16 with a length of 1665 bp was identified in A. thiooxidans (Baldini et al. 1999). As one of the sulfur-oxidizing bacteria, its sulfur oxidation process is much complicated, and the relative research progress is plodding. During the sulfur oxidation process, elemental sulfur and RISCs were entirely oxidized by a series of enzymes or enzyme complexes and electron transport chain reactions to form sulfates finally (Dopson and Johnson 2012).

A. thiooxidans is often used in the metal extraction from tannery sludge, spent petroleum refinery catalyst, metal-containing sludge treatment field, and sulfide ore systems (Peng 2009). In addition, A. thiooxidans can be used to effectively remove sulfur from coal, waste rubber, and gases based on its ability to oxidize RISCs (Lee et al. 2006). Traditional methods for extracting metals from these fields by pyrometallurgy and hydrometallurgy can generate many pollutants, such as furans, dioxins, and highly acidic wastewater which would lead to secondary pollution (Zhao and Wang 2019). The characteristic of bioleaching is low cost, low energy consumption, and being environmentally friendly. Thus, the study of this bacterium has mainly focused on bioleaching, soil remediation, and bioremoval sulfur to improve the application for industry, environmental protection, and agriculture (Bosecker 1997).

Although A. thiooxidans was the first isolated acidophile, its investigation lags behind other members of the genus, especially A. ferrooxidans, for which extensive knowledge on its basic ecophysiology and biotechnological use has been gathered. Here, we elaborate the general biological features of A. thiooxidans including morphology, genetic diversity, and genomics. And the sulfur oxidation pathway of this bacterium was described. Then we present the potential application of A. thiooxidans in metal recycling from metal-bearing wastes, soil remediation, and biological desulfurization from solids and gases. Finally, some perspectives and possible directions of A. thiooxidans genomics, sulfur metabolism pathways, and their applications are briefly presented.

General biological features

Ecological distribution and morphology

A. thiooxidans widely distributes in natural-acidic and man-made environments with elemental sulfur or soluble RISCs including hot spring (Urbieta et al. 2012), crater lake (Urbieta et al. 2012), seawater (Kamimura et al. 2003), and acid mine drainage (Natarajan 2008), sulfidic caves (Jones et al. 2012), sulfidic shales (Khan et al. 2012), sewer pipes, mineral leaching heaps, uranium mine, coal mine, and copper mine (Quatrini et al. 2017). This bacterium has short rods, single, paired, or in short chains, and the average size of cells is about 0.5 × 1.0–2.0 μm (Waksman and Joffe 1922). It moves through the polar flagella (Doetsch et al. 1967; Kelly and Wood 2000). The media reported for laboratory studies of A. thiooxidans mainly include Waksman medium (Waksman and Joffe 1922) and Starky medium (Starkey 1925). The microcolonies (0.5–1.0 mm) grown on thiosulfate solid medium showed transparent or whitish-yellow and bright color in prolonged culture with full margins. The colony in a solid medium usually have a characteristic smell of elemental sulfur (Khan et al. 2012). The cultivation of A. thiooxidans using solid media is relatively challenging because of its slow growth rate, autotrophic chemical metabolism, and sulfuric acid production during growth (Bergamo et al. 2004).

Physico-biochemical traits

A. thiooxidans generally grow in the pH range of 0.5–6.0 with an optimum 2.0–3.5, but unlikely survive at pH above 6.0 or below 0.5 (Lors et al. 2009; Suzuki et al. 1999; Waksman and Joffe 1922). It lives within a certain temperature range (2–40 °C) in nature where RISCs are relatively abundant, the optimum temperature is 28–30 °C, and the temperature of 55–60 °C is sufficient to kill the organism (Banerjee et al. 2017). The ability of the bacterium to oxidize elemental sulfur was better than that to oxidize other RISCs. A. thiooxidans uses atmospheric oxygen as an electron acceptor and get energy from inorganic sulfur, which produces sulfuric acid (H2SO4) (Khan et al. 2012). It derives CO2 in the atmosphere as the only carbon source (Khan et al. 2012; Waksman and Joffe 1922), and the CO2 can be fixed by Calvin–Benson–Bassham (CBB) cycle (Valdés et al. 2008). However, the CBB of A. thiooxidans cycle is incomplete, which lacks the gene coding for α-ketoglutarate dehydrogenase (Valdés et al. 2008). Therefore, this bacterium cannot completely obtain energy from the tricarboxylic acid (TCA) cycle; it must get energy from RISC. The high redox potential of RISC and the small energy supply lead to long generation time and a low cell yield (Smith et al. 1967). Studies have reported that A. thiooxidans lack the genes for N2 fixation (nifHDK), so it cannot fix atmospheric nitrogen (Valdés et al. 2008; Zhang et al. 2016c). However, A. thiooxidans can assimilate nitrate, nitrite, and ammonium to satisfy nitrogen requirement. The genome analysis of the A. thiooxidans indicated that the presence of conserved genes involved in nitrate and nitrite assimilation, such as narB and nirBD (Levicán et al. 2008; Zhang et al. 2016a).

Previous studies have found that some metals can inhibit the growth of A. thiooxidans. It has been documented that nickel can bind to the plasma membrane of A. thiooxidans and inhibit the activation of sulfur dioxygenase and sulfite oxidase, which lead to the growth inhibition of bacterial cell (Nogami et al. 1997). Low concentrations of sodium tungstate (50 mM) have also been found to completely inhibit the growth and sulfur-oxidation enzyme system of A. thiooxidans (Negishi et al. 2005). It has also been reported that many A. thiooxidans strains are inhibited by moderate NaCl concentrations except A. thiooxidans strain SH (NBRC 101132) (Quatrini et al. 2017). Therefore, nickel, tungsten and moderate NaCl concentrations can be used as a bacteriostatic agent to prevent concrete corrosion caused by A. thiooxidans. Additionally, this microorganism cannot grow in an environment containing organic matter, some organic substances such as glucose, starch, formic acid, and acetic acid could inhibit the sulfur oxidation ability of A. thiooxidans (Tian et al. 2003; Waksman and Joffe 1922).

Genetic diversity and genome

Some A. thiooxidans strains share a large number of shared genes, but there are also many unique genes. Therefore, A. thiooxidans can be divided into different genomovars, and the increase in the number of genomic phenotypic features leads to the emergence of phylogenetically heterogeneous species and separate strains. Six A. thiooxidans strains isolated from different geographical environments (soil, river water, acidic sulfate soil, sulfur-producing lake, copper and zinc mine water, uranium mine water) were divided into two DNA homologous groups with the G + C contents diverse much from 52 to 62% (Harrison 1982). It also has been reported that six A. thiooxidans strains isolated from coal, copper, gold, and uranium mines in Brazil showed a high degree of genetic variability by using a combination of systematic molecular methods, namely ribotyping, BOX- and ERIC-PCR, and DNA–DNA hybridization assays (Paulino et al. 2001).

Moreover, A. thiooxidans strains derived from different environments in China were assigned to three systematic groups, and the strains Licanantay (DSM 17318) (first strain isolated from copper ore) with much more strain-specific genes had the advantage to adapt the environmental conditions (Zhang et al. 2016a). The researchers found A. thiooxidans Licanantay and two other A. thiooxidans strains (ATCC 19377 and A01) shared a large core genome consisted of 2109 coding sequences by comparative genomic analysis, and their average nucleotide identity was over 98%. However, the presence of the 841 strain-specific genes (just present in the A. thiooxidans Licanantay) implied that Licanantay adapts specifically to its particular biomining environment (Travisany et al. 2014). It has been demonstrated that the sizeable flexible gene pool could confer an advantage for dealing with local environmental conditions. The genetic diversity of A. thiooxidans was not only potentially related to the geographic distribution and geochemical conditions of their habitats (Zhang et al. 2016a), but also aroused by the use of different culture treatments under laboratory conditions (Harrison 1982).

In recent years, more and more A. thiooxidans have been isolated, but only eleven A. thiooxidans strains have been sequenced by whole-genome analysis so far. The whole-genome shotgun strategy was used to determine the complete draft sequence of representative strain ATCC 19377. It has a total length of 3,019,868 base pairs and 3235 predicted proteins with a G + C of 53.1% (Jorge et al. 2011). In addition, The strain Licanantay presence of 841 strain-specific genes (absent in other A. thiooxidans strains) suggests its significant difference with other strains (Travisany et al. 2014). In short, the genome of A. thiooxidans is in the range of 3.02–3.97 Mb and with a G + C content of 48.8–53.2%, and contains a number of pseudogenes (Table 1). However, the strain DSM 612 with 62 mol% G + C (Table 1) isolated by Hans Hippe (Gottingen) from acidic soil in the Netherlands showed negligible DNA homology with other strains (Harrison Jr 1984).

Table 1 Comparison of genomic characteristics of eleven A. thiooxidans strains
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The genomics research of A. thiooxidans mainly focused on carbon metabolism, nitrogen metabolism, and sulfur metabolism. The crucial enzyme in the CBB cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO), which has been detected in A. thiooxidans (Zhang et al. 2016c). All A. thiooxidans strains were predicted to harbor a carboxysome-associated gene cluster, which potentially encodes type I Rubisco large and small subunits, carboxysome shell carbonic anhydrase, several copies of carboxysome shell proteins, and carbon dioxide-concentrating proteins. Additionally, a three-gene cluster (coxLMS) encoding putative carbon-monoxide dehydrogenase (EC: 1.2.7.4) were identified in A. thiooxidans genomes (Zhang et al. 2018b). Genomic analysis revealed that several genes associated with nitrate and nitrite assimilation exist in A. thiooxidans (except for ATCC 19377), including genes coding for nitrate and/or nitrite transporters, such as nitrate reductase A (narGHJI), nitrate reductase (narB), and nitrite reductase (nirBD) (Zhang et al. 2016b; Zhang et al. 2016c). It has been reported that a number of genes in A. thiooxidans were predicted to be involved in electron transport during sulfur oxidation through pan-genome analysis, including cydAB, cyoABCD, and nuoABCDEFGHIJKLMN (Zhang et al. 2018b). In addition, some genes related to environmental adaptation have been reported, including genes for bacterial adhesion and biofilm formation, heavy metal resistance, and temperature homeostasis. The luxA-galE-galK-pgm-galM gene cluster was identified in A. thiooxidans and involved in its adhesion and biofilm formation. The cueO gene was also detected in the draft genome of A. thiooxidans ATCC 19377 and found to be closely related to copper tolerance by using the gene knockout technique. It has been reported that the arsCRB gene cluster was involved in resistance to antimonium, arsenite, and arsenate. The merRAPT operon was identified in A. thiooxidans and related to mercury resistance through genome analysis (Wen et al. 2014).

Chemotactic movement and quorum sensing

Chemotaxis is the behavior of bacteria in response to a concentration gradient of multiple chemical substances. Just like A. ferrooxidans, A. thiooxidans approaches its beneficial substances through positive chemotaxis and avoids harmful substances through negative chemotaxis (Zhang et al. 2018a). It was reported that a variety of chemotaxis-related che genes are distributed in the genome of A. thiooxidans (Valdés et al. 2007; Zhang et al. 2016c). The chemotactic transduction system regulates the motility of A. thiooxidans by controlling the direction of flagellum rotation (Jerez 2001). This chemotactic motility can allow bacteria to move more favorable environments. It has been reported that the genes for flagella movement exist in A. thiooxidans. It has been demonstrated that a full suite of fla or fla-related genes were found in A. thiooxidans including flaB2, flhF, flhG, fliH, fliK, fliR, fliS2, fleS, and fleQ1 and might confer a competitive advantage under aquatic circumstances (Castro et al. 2017; Valdés et al. 2008; Zhang et al. 2016c). Meanwhile, the flagellar proteins were detected in this bacterium through pan-genome analysis, such as MotAB, FlgABCDEFGHIJKLMN, FliACDEFGHIJKLMNOPQRS, and flagellar motion-related proteins, flagellar biosynthesis protein FlhABFG, and flagellar regulatory protein FlrABC (Zhang et al. 2016c). It has been shown that the genes for Che two-component signaling transduction system also exist in A. thiooxidans (Valdés et al. 2008).

Quorum sensing (QS) refers to a density-dependent behavior in which bacteria regulate the expression of genes according to the number of cells during growth, and QS system plays an essential role in coordinating gene expression and functional regulation of bacterial population (Montgomery et al. 2013). QS system has been detected in A. thiooxidans, and it can produce acylated homoserine lactones (AHLs) signaling molecules, and it might be involved in the regulation of cell adhesion on minerals (Montgomery et al. 2013). It has been reported that A. thiooxidans produce three kinds of AHL signaling molecules including 3-O-C8-AHL, C10-AHL, and C12-AHL (Bellenberg et al. 2014). This system has also been found to be related to the control of biofilm formation (Zhang et al. 2018a). Because of the close phylogeny and functional relationship between A. thiooxidans and A. ferrooxidans, the QS system of A. thiooxidans may be similar to that of A. ferrooxidans. It has been suggested that A. ferrooxidans have AI-1 QS system and Lux-like QS system, and these two QS systems may relate to bacteria–mineral interactions during bioleaching (Zhang et al. 2018a). Therefore, the chemotaxis and quorum sensing of A. thiooxidans might be play important roles in environmental adaption and growth of cells.

Sulfur-oxidizing system

A. thiooxidans, an autotrophic bacterium, uses inorganic sulfur compounds (S0, S2−, S2O32−, SO32−, S4O62−) to satisfy its energy demand (Zhang et al. 2018b). Elemental sulfur must be adsorbed by bacterial cells and transported to periplasmic space mediated by outer membrane proteins (OMP) (Zhan et al. 2019). It is eventually oxidized to sulfate ions and released outside the cell after a series of bio-oxidation. Until now, the research progress of the sulfur oxidation system is slow, and the study is not complete due to its complexity (Zhang et al. 2018a). In the sulfur oxidation pathway, elemental sulfur exists mainly in the form of sulfides, elemental sulfur, sulfites, thiosulfates, and tetrathionates, which are completely oxidized by a series of enzymes or enzyme complexes and electron transport chain reactions to form sulfates (Dopson and Johnson 2012).

The pathway of sulfur oxidation consists of four essential steps. (1) The elemental sulfur (S8) is transported to the periplasmic space after activation of the outer membrane to form thiol-bound sulfane sulfur atoms (R-S-SnH); (2) After that, in the periplasm, the R-S-S-H is further oxidized by SDO, TetH, and Sox systems perform their respective functions to oxidize R-S-S-H further; (3) The SQR and TQO on the cytoplasmic membrane direct the catalytic reaction and transfer electrons to the coenzyme Q; (4) Finally, In the cytoplasm, a series of catalytic reactions occur in the sulfur-containing intermediate metabolites, eventually producing sulfate (Fig. 2) (Zhang et al. 2016b; Zhang et al. 2015).

Fig. 2
figure 2

Model of sulfur oxidation electron transport pathway of A. thiooxidans. Abbreviations: SOD, sulfur dioxygenase; TQO, thiosuirate quinine oxidoreductase; TetH, tetrathionate hydrolase; SQR, sulfide quinone reductase; SOR, sulfur oxygenase reductase; TST, thiosulfate sulfurtransferase; HDR, heterodisulfidereductase; APS, Adenosine phosphate sulfate; PAPS, phosphoadenosine phosphosulfate; A, phosphoadenosine phosphosulfate reductase; B, adenylylsulfate kinase

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Sulfur oxidation pathway of A. thiooxidans

In nature, elemental sulfur exists in the form of a stable octahedral sulfane ring (S8), which belongs to the orthorhombic crystal and is extremely hydrophobic. The elemental sulfur needs to be activated before it enters the body, and the most critical stage in the activation process is to open the ring under the action of the thiol group of cysteine, resulting in an intermediate product R-S-Sn-H (Zhang et al. 2007a). Researches on the sulfur oxidation process of A. thiooxidans showed that the extracellular polysulfur (S8) is probably mobilized by thiol groups of special outer-membrane proteins and transported into the periplasmic space as persulfide sulfur (-S2H), and is oxidized by periplasmic sulfur dioxygenase (SDO) into SO32− accompanied with release few of H2S (Rohwerder and Sand 2003). After that, SO32− and H2S eventually produce sulfate via two different hypothesis pathways.

Oxidation of elemental sulfur in the cytoplasm

One of the putative pathways is that H2S can be converted to sulfur atom by sulfide quinone reductase (SQR) located in the cytoplasmic membrane of the cell. Sulfur accumulates in the periplasmic space to form polymeric sulfur (Sn), which then enters the cytoplasm through an unknown mechanism (Chen et al. 2012; Zhang et al. 2015). After that, the sulfur is catalyzed by sulfur oxygenase reductase (SOR) to produce products, such as sulfide, thiosulfate, and sulfite. Sulfide is catalyzed by SQR to form H2S and then transported to the periplasmic space, while thiosulfate is catalyzed by rhodanese or thiosulfate-sulfur transferase (TST) to form sulfite and sulfur atoms. Subsequently, cytoplasmic mercaptan protein (RSH), which acts as a sulfur atom receptor, obtains sulfur atoms to form sulfate (RSSH), and which was then catalyzed by heterodisulfide reductase complex (HDR) to regenerate RSH. Thus, a TST and HDR-dependent cycle is proposed. RSH obtains a sulfur atom from the catalytic reaction of thiosulfate mediated by TST, to produce RSSH, and then RSSH is utilized as a substrate of HDR for the regeneration of RSH. (Chen et al. 2012). A hypothesized pathway based on phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase has also been proposed: Sulfite is catalyzed by PAPS reductase and APS kinase, which in turn produces PAPS and APS, and the latter can produce SO42− as a final product via an unknown mechanism (Zhang et al. 2018b).

Oxidation of sulfites in the periplasm

Another supposed pathway of sulfur oxidation is that the periplasmic SO32− and S0 spontaneously react to form S2O32−, which is further catalyzed by thiosulfate, quinone oxidoreductase (TQO) located in the cytomembrane to produce S4O62−. The oxidation of thiosulfate catalyzed by TQO on cytomembrane was previously described in Acidianus ambivalens (A. ambivalens). The DoxD catalyzes the conversion of S2O32− to S4O62− and simultaneously produces two electrons, which then transfer to the quinone (Müller et al. 2004). After that, the S4O62− is in turn hydrolyzed by tetrathionate hydrolase (TetH), which in turn produces S2O32− and SO42− (Tano et al. 1996). Then S2O32− can be directly catalyzed by the Sox complex to generate SO42− (Bobadilla Fazzini et al. 2013; Dopson and Johnson 2012). There have been many reports on sox system pathways, which usually consists of four proteins including SoxYZ, SoxAX, SoxB, and Sox (CD)2 (Chen et al. 2012; Ghosh and Dam 2009; Ghosh et al. 2009; Meyer et al. 2007). However, according to the inference in the research, the Sox (CD)2 is absent in the Sox system of A. thiooxidans. The action mechanism of the putative sox system is as follows. Firstly, under the act of the SoxXA complex, the sulfane sulfur of thiosulfate combines with the SoxY-cysteine-sulfhydryl group of the SoxYZ complex to form SoxYZ-S-S-SO3−. And subsequently, under the action of SoxB, SoxYZ-S-S-SO3− is catalyzed to form SoxYZ-S-S− and the terminal -SO3−group released in the form of SO42−; the sulfur atom of SoxYZ-S-S− is detached by itself or oxidized by SDO to form SoxYZ-S-SO3− due to the lack of Sox (CD)2 complex. Finally, the sulfonate moiety of SoxYZ-S-SO3− is re-hydrolyzed by SoxB to produce SoxYZ. In addition, other forms of sulfur can be involved in the Sox pathway as appropriate intermediate metabolites by binding to soxY in an enzyme form (such as HS−) or a non-enzyme form (such as S8) (Ghosh and Dam 2009).

Related enzymes and genes in sulfur oxidation

The sulfur oxidation pathway metioned above indicated that many enzymes are related to sulfur oxidation, including sulfur dioxygenase (SDO) and thiosuirate quinine oxidoreductase (TQO); tetrathionate hydrolase (TetH), sulfide quinone reductase (SQR), sulfur oxygenase reductase (SOR), thiosulfate sulfurtransferase (TST), and heterodisulfidereductase (HDR); adenylylsulfate (APS) kinase; and phosphoadenosine phosphosulfate (PAPS) reductase (Holmes and Bonnefoy 2007; Suzuki 1965; Yin et al. 2014). With more and more A. thiooxidans genomic sequences were obtained, more genes involved in sulfur oxidation were identified. Up till now, the genes related to the sulfur oxidation pathway mainly include sdo, sqr, doxDA, tetH, soxABXYZ, hdrA, hdrB, and hdrC, cydAB, and cyoABCD, nuoABCDEFGHIJKLMN, and sor (Jorge et al. 2011; Travisany et al. 2014; Yin et al. 2014; Zhang et al. 2018b).

Electron transfer of A. thiooxidans

Up to now, there are few studies about the electron transfer chains in A. thiooxidans, but it has already been interpreted in A. ferrooxidans. The electrons produced by the sulfur oxidation pathway are directly transferred to the terminal enzyme complex bd or bo3 by QH2, or indirectly transferred to aa3 to generate protons via a bc1 complex and a cytochrome c (CycA2) or a high potential iron-sulfur protein (HiPIP) and then delivered to the NADH complex I to generate reducing power (Quatrini et al. 2009). However, A. thiooxidans only has two types of terminal oxidases including bo3 and bd identified in the genome of A. thiooxidans A01 (Yin et al. 2014). Thus, electrons from SQR, TQO, Sox compounds, and HDR are transferred to terminal oxidases (bd and bo3) via QH2 to generate proton gradients or to NADH complex I to produce reducing power (Yin et al. 2014; Zhang et al. 2016b)

Potential application of A. thiooxidans

Bioleaching of metals from metal-bearing wastes

Bioleaching is the biological transformation of an insoluble metal compound into a water-soluble form; the microorganisms involved in this process are iron-oxidizing bacteria and sulfur-oxidizing bacteria. A. thiooxidans is one of the most critical sulfur-oxidizing microbes species associated with the bioleaching process due to its autotrophy and high tolerance to heavy metals (Fazzini et al. 2011). The possible mechanisms including contact, non-contact, and cooperative mechanisms have been postulated to explain the bioleaching of metals from sulfide ores by A. thiooxidans (Couillard and Mercier 1990; Liu et al. 2003; Rulkens et al. 1995; Seidel et al. 2001). In the contact mechanism, the bacteria can directly attach on the surface of metal sulfide (MeS) through the extracellular polymeric substances (EPS) secreted by the bacteria, and directly oxidize metal sulfide through intracellular specific oxidase system to form soluble sulfate (Fowler and Crundwell 1999; Konishi et al. 1995; Takauwa et al. 1977). In the non-contact mechanism, elemental sulfur, or reduced sulfur compounds are oxidized to sulfuric acid by A. thiooxidans, which reduces the pH of the reaction system and finally dissolves the metal sulfide (Liu et al. 2008; Pathak et al. 2009). In actual bioleaching, contact and non-contact leaching mechanisms usually coexist, and their combination is called cooperative leaching (Suzuki 2001) (Fig. 3). In general, the mechanism of different sulfide mineral leaching is mainly based on the mineral itself and is closely related to the leaching strains, the leaching solution, and the operating conditions such as temperature, oxygen and carbon dioxide concentration, initial pH, and the types and concentration of substrates (Zhou et al. 2002). Compared with physical and chemical leaching, biological leaching mediated by bacteria has the characteristics of green environmental protection, cost-saving, and high recovery efficiency.

Fig. 3
figure 3

Models for the proposed contact, non-contact mechanism catalyzed by A. thiooxidans

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A. thiooxidans has been used in leaching metals such as chromium, nickel, vanadium, molybdenum, and aluminum from petroleum spent catalyst (Fig. 4) (Table 2). Metal leaching rate was significantly related to the affinity of A. thiooxidans cells and minerals and the leaching conditions (Gholami et al. 2011). A. thiooxidans can extract 2.4% Al, 83% Co, 95% Mo, and 16% Ni in the presence of sulfur from a spent Mo–Co–Ni refinery catalyst (Gholami et al. 2011). It has been reported that 89% of nickel can be leached from spent petroleum catalyst by A. thiooxidans (Sharma et al. 2015). The two-step bioleaching process (pre-culturing and leaching steps) which can provide better maintenance of medium pH and microbial population were found to significantly improve the leaching efficiency of metals from spent petroleum refinery catalyst, about 93% Ni, 44% Al, 34% Mo, and 94% V were leached (Srichandan et al. 2014). The extracted rate of nickel obtained by A. thiooxidans reach to 93%, which is much higher than that achieved by A. ferrooxidans (Srichandan et al. 2014). It has been reported that A. thiooxidans can extract 87% ± 5.5% Mo, 37% ± 2.6% Ni, and 15% ± 1.3% Al from spent catalyst after only 7 days of batch processing by using slurry bubble column bioreactor in pulp density of 0.9% (w/v), particle size of 60.7 μm, and aeration rate of 209 ml/min (Shahrabi-Farahani et al. 2014).

Fig. 4.
figure 4

Potential application of A. thiooxidans

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Table 2 Examples of metal-bearing wastes treated with A. thiooxidans
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Additionally, chromium, lead, cadmium, nickel, copper, and zinc can be efficiently leached from tannery sludge, sewage sludge, copper metallurgical slags, and sediment by using A. thiooxidans (Fig. 4) (Table 2). It has been reported that A. thiooxidans can efficiently leach copper and zinc from sewage sludge, and the leaching efficiency can reach 96% and 96.5%, respectively (Wen et al. 2012; Zhou and Wang 2001). Moreover, A. thiooxidans can leach more than 99% of chromium from tannery sludge (Wang et al. 2007). It has been found that A. thiooxidans is able to leach heavy metals from sewage sludge with 2% (w/v) solid concentration, 5.0 g/L sulfur concentration, and 10% (v/v) inoculum volume, and the recovery efficiencies were found to be 43.6%, 96.2%, 41.6%, and 96.5% for Cr, Cu, Pb, and Zn, respectively (Wen et al. 2012; Wen et al. 2010). A. thiooxidans can extract amounts of metals from different slag samples, and the extract rates ranged from 88–100% for Co, 40–70% for Mo, 70–99% for rare earth (REE), and 55–93% for V (Mikoda et al. 2019). A. thiooxidans can leach some metals from brooklet sediment including Cd, Cr, Ni, Cu, and Zn, and the leaching rates were 45%, 34%, 50%, 65%, and 55%, respectively (Zhang and Jia 2008). Similarly, A. thiooxidans also can successfully extract 80% of Zn and Cd from polluted sediment with the supply of sulfuric acid (600 mmol/Kg) and sulfur (20 g/Kg) (Löser et al. 2005).

A. thiooxidans have potential application in bioleaching printed circuit boards (PCBs) (Fig. 4). It was reported that leaching efficiency of Cu, Ni, Zn, and Pb leached by pure culture A. thiooxidans were found to be 78, 73, 75, and 71%, respectively. And their leaching rates were respectively found to be 94, 89, 90, and 86% by using the mixed culture of A. thiooxidans and A. ferrooxidans. It also has been reported that mixed culture A. thiooxidans and A. ferrooxidans can extract 92.6% copper from PCBs after 240 h cultivation with initial inoculums ratio (A. thiooxidans: A. ferrooxidans) 1:2, pH 1.56, FeSO4·7H2O 16.88 g/L, and S0 5.44 g/L, and PCBs 28.8 g/L (Liang et al. 2013). This indicated that the mixed culture of A. thiooxidans and A. ferrooxidans could improve the leaching rate (Liang et al. 2010).

A. thiooxidans can be successfully applied in extracting metals from low­grade sulfide ores and contaminated mine tailings (Fig. 4). It was reported that the copper recovery from low-grade copper sulfide ores could reach nearly 45% by using A. thiooxidans in column flotation experiments (Wang et al. 2014). Additionally, A. thiooxidans can leach 48.41% of phosphate from the low-grade phosphate ore, and surface-active agent Tween 80 can increase the leaching rate (Gong et al. 2007). The contaminated mine tailings containing a high amount of As (ca. 34,000 mg/Kg) can be extracted 50.5% As by A. thiooxidans (Lee et al. 2015). It has been reported that the addition of ferrous sulfate to the bioleaching system inoculated with A. thiooxidans can significantly enhance the recovery of Cu from sulfide ore (Donati and Edgardo 2000).

Soil remediation

Heavy metal pollution in the soil is one of the leading environmental impacts of urbanization and industrialization. Heavy metals are known to cause significant ecological damage and human health problems due to their mobility and solubility (Mulligan et al. 2001). The remediation methods for heavy metal contamination of soils primarily include physical and chemical methods and bioremediation technologies. The physicochemical process is subject to some limitations, mainly including operating costs, process efficiencies, and high energy requirements. The previous study has shown that A. thiooxidans can effectively leach copper, zinc, chromium, manganese, lead, and other heavy metals from soil to achieve the purpose of soil remediation (Fig. 4) (Kumar and Nagendran 2007; Kumar and Nagendran 2009). It has been founded that the solubilization rate of Cr, Zn, Cu, Pb, and Cd in contaminated soil is between 11 and 99% with ≥ 0.7 sulfur/soil ratio by using A. thiooxidans (Nareshkumar et al. 2008). It has been reported that A. thiooxidans can effectively promote the dissolution of radionuclide plutonium in contaminated soil by continuous acid production (Yuan 2009). It also has been documented that 89% of nickel can be leached from spent petroleum catalyst by A. thiooxidans (Sharma et al. 2015).

Based on the characteristic of sulfuric acid production, A. thiooxidans not only use in removing heavy metals from the contaminated soil, but also take the neutralization reaction to OH- in saline-alkali land (Fig. 4), which is not conducive to agricultural production and vegetation growth (Bao et al. 2016). Acidification of the soil facilitates the dissolution of some insoluble phosphorus or potassium compounds, which can significantly enhance the available content of phosphorus and available potassium, and ultimately increase the effective nutrients in the soil (Li-shu et al. 2013). The improvement of saline-alkali land by biological treatment using this bacterium is regarded as a new economical, efficient, and feasible method. It has been demonstrated that A. thiooxidans can reduce the pH value of soil from 7.5 to 7.2. Moreover, it can improve the solubility of soil minerals and provide more nutrients to crops (Zhang et al. 2009). Shuochao Bao has suggested that A. thiooxidans can effectively reduce the pH of the saline-alkali soil located in Jilin, China, with initial pH between 7.5 and 8, and 50 ml content of A. thiooxidans were found to be optimal (Bao et al. 2016). It was reported that the simultaneous addition of A. thiooxidans and sulfur could significantly improve alkaline soils and increase agricultural production (Li-shu et al. 2013). However, A. thiooxidans cannot survive on the saline-alkali soil with pH over 9.0 due to the growth restriction. From a long-term point of view, A. thiooxidans has great application potential in the improvement of saline-alkali soils.

Bioremoval of sulfur from solids and gases

Various inorganic sulfur compounds such as sulfur dioxide, hydrogen sulfide, and sulfate are mainly found in fossil fuels, biogas, and some wastewater, which are the main toxic substances causing environmental sulfur pollution. A. thiooxidans is one of the most critical microbial species in biodesulfurization (Fig. 4). Compared with traditional physical and chemical methods, biodesurization technology has the advantages of low temperature, low energy consumption, high specificity, and small secondary pollution. Several techniques have been successfully utilized in desulfurization of coal using A. thiooxidans, including batch, fed-batch, fluidized-bed, packedbed, airlift reactor, and heap leaching (Zhang et al. 2018a). Biodesurization using A. thiooxidans has been applied in removing sulfur from solids such as coal and waste rubber. It has been reported that 85–95% reduction of pyritic sulfur, and 31–51% of total sulfur can be removed by using A. thiooxidans and A. ferrooxidans from coals (Cardona and Márquez 2009). It has been showed that the mixed culture of A. ferrooxidans, A. thiooxidans, and Leptospirillum ferrooxidans (L. ferrooxidans) can remove 28.66% total sulfur from coal (Yang et al. 2012). It has been documented that A. thiooxidans can desulfurize waste rubber powder (Raghavan et al. 1990).

The removal technologies for H2S from gas using A. thiooxidans including batch, fed-batch, packed-bed, and stirred-tank reactor. The desulfurization efficiency was found to be in the range of 91.0–99.0%, which were the same as or higher than the desulfurization efficiency used by A. ferrooxidans (Aroca et al. 2007; Lee et al. 2006; Oprime et al. 2001; Zhang et al. 2007b). The bench-scale biofilter inoculated with A. thiooxidans can effectively remove SO2 from biogas with an average efficiency of 75 ± 13% and a maximum efficiency of 97% (Aita et al. 2016). The H2S removal efficiency can almost reach to 100% when H2S is alone supplied to the ceramic biofilter inoculated with A. thiooxidans TAS (KCTT8930P) (Lee et al. 2005). It has been reported that 99.4–99.6% H2S can be removed when inlet H2S concentration was below 500 ppm (Cho et al. 2000). A. thiooxidans can remove 98.7% of H2S from biogas under the optimum conditions of pH 2.5, operation time 180 min, gas flow 40 mL min−1, initial H2S concentration 8 g/m3, and bacterial biomass dosage (OD600) 0.40 (Lei et al. 2014). It has also been reported that A. thiooxidans was used in a sewage treatment plant to remove H2S in the foul gas, and the effective rate was found to be 99.9% (Shinabe et al. 2000). These surveys all indicated that A. thiooxidans have high removal efficiency for H2S and SO2 from gases.

This bacterium can not only oxidize sulfur compounds to sulfuric acid but also promote the adhesion of cells to the surface of sulfide particles, so it can be used as an effective biosorbent. Previous research showed that A. thiooxidans can remove 87.5% and 91.4% of the dye and color from sulfur dyeing wastewater (Nguyen et al. 2016). Additionally, A. thiooxidans has been used as microbial sensors to determine free HSO3−, SO32−, SO2− in wine (Nakamura et al. 1989). It has been reported that acid phosphatase (APase) in whole cells of A. thiooxidans also have been used for measuring sulfate in waters according to the activity of the APase which was determined sulfate content in waters (Nakamura et al. 1997). Additionally, A. thiooxidans can remove organic pollutant from wool scouring effluent, and about 92% chemical oxygen demand (COD) of the organic pollutant can be removed (He and Zhou 2010).

Industrial application of A. thiooxidans

Although A. thiooxidans has various potential application in the areas as mentioned above, its commercial use has been slow to develop. The practical application of A. thiooxidans are mostly concentrating on the recovery of Cu, Ni, Zn, Co, and Au from ores since the adoption of biohydrometallurgy for copper bioleaching at Kennecott's Bingham mine in the late 1950s (Brierley and Brierley 2013). It was reported that the mixed acidophiles contained A. thiooxidans has been successfully applied in extracting Cu from low-grade (ca. 0.5% Cu) ores by heap leaching at Escondida mine, northern Chile (Galleguillos et al. 2009). The mixed culture of A. thiooxidans and iron-oxidizing bacteria have been commercially used to recover Cu, Ni, Zn, and Co from stockpiled pyrite concentrate in stirred-tank reactors located in Kasese District, Western Uganda (Morin 2007). The bioleaching was commissioned in 2000, and each tank with a 1380 m3 volume is operated at 42 °C (Brierley and Brierley 2013). In 2005, a plant with a 50,000 tons heap leaching was established at Talvivaara mine, Finland (Riekkola-Vanhanen 2010). The bioleaching was inoculated with mixed indigenous acidophiles contained A. thiooxidans and the recoveries for Ni, Zn, Cu, and Co were respectively 94%, 83%, 3%, and 14% by the end of 2006 (Brierley and Brierley 2013). The Jinchuan deposit located in northwest China with 0.5 billion tons of ore reserves is the third-largest magmatic Ni sulfide deposit (ca. 1.2% Ni, 0.03% Co) (Keays et al. 2004). The 84.6% of Ni and 75.0% Co can be extracted after heap leaching for 350 days inoculating with a mixture of A. thiooxidans, A. ferrooxidans, and L. ferrooxidans (Qin et al. 2009).

A. thiooxidans has also been practiced in the processing of gold-bearing ores or concentrates. The BIOX® technology which was pioneered and developed by Gencor has been industrially applied to enhance the recovery of gold, and A. thiooxidans was one of the inoculums in the practical BIOX® reactor (Brierley and Brierley 2013). This technology has been adopted commercially in the plants located in several locations including Fairview of South Africa, Sao Bento of Brazil, Wiluna of Australia, and Ashanti of Ghana (Brierley and Brierley 2001). These plants operate at 40 °C to about 45 °C using a mixed inoculum included A. thiooxidans. The actual tonnages for Fairview, Sao Bento, Wiluna, and Ashanti BIOX® plants were found to be 40, 150, 155, and 960 tons/day, respectively (Dew et al. 1997). It has been reported that the largest plant in the word with a capacity of 1069 tons/day based on BIOX® process has been built and industrialized in Uzbekistan (Van Aswegen et al. 2007). Additionally, a BIOX® plant with a tonnage of 2000 tons/day has been developed in Dachang gold deposit, Qinghai, China (Free 2014).

Perspectives and directions for future research

Due to the slow growth of A. thiooxidans, its study and application are not as extensive as A. ferrooxidans. Therefore, there are many theoretical and practical issues that remain to be solved and clarified. Significant breakthroughs can be expected in the following areas.

  1. (1)

    The diversity of A. thiooxidans remains to be discovered. The genomic data is not comprehensive and complete, and it is necessary to supplement much more complete genomic sequences to promote the development and to deepen of pan-genomics and micro-evolutionary biology.

  2. (2)

    The sulfur metabolic pathway of A. thiooxidans is dreadfully complex, and its clarifying is a long and arduous task. Although some genes and proteins involved in sulfur oxidation have been characterized, there is still a lack of information related to genes and proteins and sulfur metabolism as well as their metabolically coupled metabolism. Defining the role of sulfur oxidation mechanism of A. thiooxidans in the natural sulfur cycle is still an important and challenging job.

  3. (3)

    More study should be performed to discover the relationship between the distribution of A. thiooxidans and environmental adaptation. In addition, the synergistic mechanisms of A. thiooxidans with other microorganisms should be conducted with increased efforts.

  4. (4)

    Aiming at the shortcomings of A. thiooxidans, such as long growth cycle and slow bioleaching rate, we can consider through physical, chemical, or biological genetics methods to improve the growth characteristics of A. thiooxidans and bioleaching efficiency. Optimizing the operating conditions, choosing a more reasonable or effective process, and considering the coculture with other microorganisms would be the beneficial strategies used in practical application.