Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China

Chen, Peng; Yan, Lei; Wu, Zhengrong; Xu, Ruixiang; Li, Suyue; Wang, Ning Bo; Liang, Ning; Li, Hongyu

doi:10.1016/j.gdata.2015.10.018

Cited by 13 publications

(7 citation statements)

References 8 publications

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“…The pH value is one of the determining parameters of the metabolic activity of A. ferrooxidans cells. However, the optimal pH for growth and cellular oxidation, as well as the pH cut-off at which the bacterium is able to perform basic biological functions, varies in many sources [4,[15][16][17][18]. In previous studies, the dependence of pH value and extraction efficiency was investigated, but, for other bacterial species [19], for non-stationary systems [20][21][22], or the research focused only on iron [23].…”

Section: Introductionmentioning

confidence: 99%

Bioleaching of Iron, Copper, Lead, and Zinc from the Sludge Mining Sediment at Different Particle Sizes, pH, and Pulp Density Using Acidithiobacillus ferrooxidans

Rouchalova

Janáková

et al. 2020

Minerals

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Globally, the amounts of metal ore deposits have been declining, so the research directions investigating the extraction of metals from materials that are classified as waste are gaining more importance every year. High concentrations of Cu, Pb, Zn, and Fe were analyzed in the sludge sediment (Zlaté Hory, Czech Republic), which is a waste product of the mining industry. In the bioleaching process, bacterial cells have been established as being able to convert metals from solid to liquid phase. However, the most important parameters of bioleaching are particle size, pH, and pulp density, thus our research focused on their optimization. The acidophilic and mesophilic bacteria Acidithiobacillus ferrooxidans were applied due to the high Fe content in the sample. The recovery of metals in the leachate was determined by F-AAS and the residual metal concentrations in the waste fraction were analyzed by XRF. The grain size fractions <40 µm –200 µm were investigated. The atomic absorption spectrometry (AAS) results show that the highest Fe (76.48%), Cu (82.01%), and Pb (88.90%) recoveries were obtained at particle size of 71–100 μm. Zn was dissolved for all fractions above 90%. Experiments with different pH values were performed at a pH of 1.6–2.0. The highest dissolution rates of Zn, Fe, and Cu were achieved with a suspension pH of 1.8, where 98.73% of Zn, 85.42% of Fe, and 96.44% of Cu were recovered. Due to the high percentage dissolution of metals, experiments were performed under pilot conditions in a bioreactor at a pulp density of 2.5% and 4.2% (w/v). From an economic point of view, the leaching time of 28 days was evaluated as sufficient.

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Section: Introductionmentioning

confidence: 99%

Bioleaching of Iron, Copper, Lead, and Zinc from the Sludge Mining Sediment at Different Particle Sizes, pH, and Pulp Density Using Acidithiobacillus ferrooxidans

Rouchalova

Janáková

et al. 2020

Minerals

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“…A. ferrooxidans YNTRS-40, ATCC 23270, ATCC 53993 YQH-1 [9] CCM 4253, DSM 16786 [10], Hel18, PQ506 [10], PQ505 [10], CF3 [10], F221, BY0502, RVS1, DLC-5 [11], COP1 [10], S10 [10], BY-3 [12], ATCC 8085 [10], ZBY, DMC [12], A02 [12], Licanantay [13], JYC-17 [12], ATCC 15494 [10], BY-02 [12], A01 [14] A. caldus MTH-04, ATCC 51756 [15], SM-1 [16] KU [10], CV18-1 [10], 6 [10], MELC5 [10], BC13 [10], VAN18-3 [10], DX [17], ZBY [17], ZJ [17], MNG [10], C-SH12 [10], F [10], S1 [17] L. ferrooxidans C2-3 [18] L. ferriphilum ML-04 [19], YSK [20] UBA6657 [21], UBA5695 [21], UBA6673 [21], UBA6674 [21], UBA7872 [21], UBA7391 [21], UBA7384 [21], UBA7870 [21], UBA7392 [21], UBA6677 [21] DSM 14647 [22], pb_238, DX…”

Section: Complete Genome Scaffold Contigmentioning

confidence: 99%

Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Wen

2021

Microb Cell Fact

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Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.

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“…sulfuriphilus (ex Acidithiobacillus sulfuriphilus ) ( Falagán et al, 2019 ); (ii) Igneacidithiobacillus including species I. copahuensis ( Moya-Beltrán et al, 2021 ), Candidatus I. taiwanensis ( Moya-Beltrán et al, 2021 ), and Candidatus I. yellowstonensis ( Moya-Beltrán et al, 2021 ); (iii) Fervidacidithiobacillus with F. caldus (ex- Acidithiobacillus caldus ) ( Hallberg and Lindström, 1994 ; Valdes et al, 2009 ; You et al, 2011 ; Zhang et al, 2016b ); and (iv) the Acidithiobacillus genus formed by A. thiooxidans ( Waksman and Joffe, 1922 ; Valdes et al, 2011 ; Travisany et al, 2014 ; Yin et al, 2014 ; Zhang et al, 2016a , 2018 ; Quatrini et al, 2017 ; Camacho et al, 2020 ), A. albertensis ( Bryant et al, 1983 ; Castro et al, 2017 ), Acidithiobacillus sp. SH ( Kamimura et al, 2018 ) plus the iron/sulfur oxidizers A. ferrooxidans ( Temple and Colmer, 1951 ; Valdés et al, 2008 ; Chen P. et al, 2015 ; Yan et al, 2015 ; Kucera et al, 2016 ; Ulloa et al, 2019 ), A. ferridurans ( Hedrich and Johnson, 2013 ; Miyauchi et al, 2018 ), A. ferrivorans ( Hallberg et al, 2010 ; Liljeqvist et al, 2011 ; Talla et al, 2014 ; Tran et al, 2017 ), and A. ferriphilus ( Falagán and Johnson, 2016 ) represented by A. ferrooxidans BY0502 for which phylogenetic and nucleotide identity analysis is suggested to be reclassified as an A. ferriphilus -like species ( González et al, 2016 ; Fariq et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…Genome sequences are available for many of the acidophilic species ( Neira et al, 2020 ) including A. ferrooxidans ( Valdés et al, 2008 ; Chen P. et al, 2015 ; Yan et al, 2015 ; Kucera et al, 2016 ; Ulloa et al, 2019 ), A. ferrivorans ( Liljeqvist et al, 2011 ; Talla et al, 2014 ; Tran et al, 2017 ), A. ferridurans ( Hedrich and Johnson, 2013 ; Miyauchi et al, 2018 ), A. ferrianus ( Norris et al, 2020 ), A. thiooxidans ( Valdes et al, 2011 ; Travisany et al, 2014 ; Yin et al, 2014 ; Zhang et al, 2016a , 2018 ; Quatrini et al, 2017 ; Camacho et al, 2020 ), F. caldus ( Valdes et al, 2009 ; You et al, 2011 ; Zhang et al, 2016b ), and Am. sulfuriphilus ( Falagán et al, 2019 ) along with the neutrophile Thermithiobacillus tepidarius ( Boden et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle

et al. 2022

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Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as “first line of defense” were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for “second line of defense” systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to “hedge bet” in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.

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Draft genome sequence of extremely acidophilic bacterium Acidithiobacillus ferrooxidans DLC-5 isolated from acid mine drainage in Northeast China

Cited by 13 publications

References 8 publications

Bioleaching of Iron, Copper, Lead, and Zinc from the Sludge Mining Sediment at Different Particle Sizes, pH, and Pulp Density Using Acidithiobacillus ferrooxidans

Bioleaching of Iron, Copper, Lead, and Zinc from the Sludge Mining Sediment at Different Particle Sizes, pH, and Pulp Density Using Acidithiobacillus ferrooxidans

Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle

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