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Lalropuia L, Kucera J, Rassy WY, Pakostova E, Schild D, Mandl M, Kremser K, Guebitz GM. Metal recovery from spent lithium-ion batteries via two-step bioleaching using adapted chemolithotrophs from an acidic mine pit lake. Front Microbiol 2024; 15:1347072. [PMID: 38348186 PMCID: PMC10861312 DOI: 10.3389/fmicb.2024.1347072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
The demand for lithium-ion batteries (LIBs) has dramatically increased in recent years due to their application in various electronic devices and electric vehicles (EVs). Great amount of LIB waste is generated, most of which ends up in landfills. LIB wastes contain substantial amounts of critical metals (such as Li, Co, Ni, Mn, and Cu) and can therefore serve as valuable secondary sources of these metals. Metal recovery from the black mass (shredded spent LIBs) can be achieved via bioleaching, a microbiology-based technology that is considered to be environmentally friendly, due to its lower costs and energy consumption compared to conventional pyrometallurgy or hydrometallurgy. However, the growth and metabolism of bioleaching microorganisms can be inhibited by dissolved metals. In this study, the indigenous acidophilic chemolithotrophs in a sediment from a highly acidic and metal-contaminated mine pit lake were enriched in a selective medium containing iron, sulfur, or both electron donors. The enriched culture with the highest growth and oxidation rate and the lowest microbial diversity (dominated by Acidithiobacillus and Alicyclobacillus spp. utilizing both electron donors) was then gradually adapted to increasing concentrations of Li+, Co2+, Ni2+, Mn2+, and Cu2+. Finally, up to 100% recovery rates of Li, Co, Ni, Mn, and Al were achieved via two-step bioleaching using the adapted culture, resulting in more effective metal extraction compared to bioleaching with a non-adapted culture and abiotic control.
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Affiliation(s)
| | - Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Wadih Y. Rassy
- Department of Science and Technology, Institute of Biotechnology, IMC University of Applied Sciences, Krems, Austria
- Faculty of Technical Chemistry, TU Wien, Vienna, Austria
| | - Eva Pakostova
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON, Canada
| | - Dominik Schild
- Department of Science and Technology, Institute of Biotechnology, IMC University of Applied Sciences, Krems, Austria
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Klemens Kremser
- Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna BOKU, Tulln an der Donau, Austria
| | - Georg M. Guebitz
- Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna BOKU, Tulln an der Donau, Austria
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Huynh D, Haferburg G, Bunk B, Kaschabek SR, Sand W, Schlömann M. Alicyclobacillus sp. SO9, a novel halophilic acidophilic iron-oxidizing bacterium isolated from a tailings-contaminated beach, and its effect on copper extraction from chalcopyrite in the presence of high chloride concentration. Res Microbiol 2024; 175:104150. [PMID: 37926348 DOI: 10.1016/j.resmic.2023.104150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Many acidophilic iron-oxidizing bacteria used in the mining industry for the bioleaching of sulfidic minerals are intolerant to high chloride concentrations, resulting in problems where chloride occurs in the deposit at high concentrations or only seawater is available. In search for strains tolerating such conditions a tetrathionate- and iron-oxidizing bacterium was isolated from a tailings-contaminated beach sample at Portman Bay, Cartagena-La Union mining district, Spain, in the presence of 20 g l-1 (0.34 M) sodium chloride. The isolate was able to form spores, did not grow in the absence of NaCl, and oxidized ferrous iron in the presence of up to 1.5 M (∼87 g l-1) NaCl. Genome sequencing based on a combination of Illumina and PacBio reads revealed two contigs, a circular bacterial chromosome of 5.2 Mbp and a plasmid of 90 kbp, respectively. The chromosome comprised seven different 16S rRNA genes. Submission of the chromosome to the Type (Strain) Genome Server (TYGS) without preselection of similar sequences revealed exclusively type strains of the genus Alicyclobacillus. In the TYGS analyses the respective most similar species were dependent on whether the final tree was derived from just 16S rRNA, from the genomes, or from the proteomes. Thus, TYGS analysis clearly showed that isolate SO9 represents a novel species of the genus Alicyclobacillus. In the presence of artificial seawater with almost 0.6 M chloride, the addition of Alicyclobacillus sp. SO9 improved copper dissolution from chalcopyrite (CuFeS2) compared to abiotic leaching without bacteria. The new isolate SO9, therefore, has potential for bioleaching at elevated chloride concentrations.
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Affiliation(s)
- Dieu Huynh
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Götz Haferburg
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH Dept. Bioinformatics, IT and Databases, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Stefan R Kaschabek
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Wolfgang Sand
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Michael Schlömann
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
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3
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Deng W, Zhao Z, Li Y, Cao R, Chen M, Tang K, Wang D, Fan W, Hu A, Chen G, Chen CTA, Zhang Y. Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem. MICROBIOME 2023; 11:270. [PMID: 38049915 PMCID: PMC10696704 DOI: 10.1186/s40168-023-01712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms. RESULTS We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions. CONCLUSIONS Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.
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Affiliation(s)
- Wenchao Deng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yufang Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Rongguang Cao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Guangcheng Chen
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Chen-Tung Arthur Chen
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
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Ma L, Yang W, Huang S, Liu R, Li H, Huang X, Xiong J, Liu X. Integrative Assessments on Molecular Taxonomy of Acidiferrobacter thiooxydans ZJ and Its Environmental Adaptation Based on Mobile Genetic Elements. Front Microbiol 2022; 13:826829. [PMID: 35250944 PMCID: PMC8889020 DOI: 10.3389/fmicb.2022.826829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Acidiferrobacter spp. are facultatively anaerobic acidophiles that belong to a distinctive Acidiferrobacteraceae family, which are similar to Ectothiorhodospiraceae phylogenetically, and are closely related to Acidithiobacillia class/subdivision physiologically. The limited genome information has kept them from being studied on molecular taxonomy and environmental adaptation in depth. Herein, Af. thiooxydans ZJ was isolated from acid mine drainage (AMD), and the complete genome sequence was reported to scan its genetic constitution for taxonomic and adaptative feature exploration. The genome has a single chromosome of 3,302,271 base pairs (bp), with a GC content of 63.61%. The phylogenetic tree based on OrthoANI highlighted the unique position of Af. thiooxydans ZJ, which harbored more unique genes among the strains from Ectothiorhodospiraceae and Acidithiobacillaceae by pan-genome analysis. The diverse mobile genetic elements (MGEs), such as insertion sequence (IS), clustered regularly interspaced short palindromic repeat (CRISPR), prophage, and genomic island (GI), have been identified and characterized in Af. thiooxydans ZJ. The results showed that Af. thiooxydans ZJ may effectively resist the infection of foreign viruses and gain functional gene fragments or clusters to shape its own genome advantageously. This study will offer more evidence of the genomic plasticity and improve our understanding of evolutionary adaptation mechanisms to extreme AMD environment, which could expand the potential utilization of Af. thiooxydans ZJ as an iron and sulfur oxidizer in industrial bioleaching.
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Affiliation(s)
- Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Weiyi Yang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Shanshan Huang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Huiying Li
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Junming Xiong
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Examining the Osmotic Response of Acidihalobacter aeolianus after Exposure to Salt Stress. Microorganisms 2021; 10:microorganisms10010022. [PMID: 35056469 PMCID: PMC8781986 DOI: 10.3390/microorganisms10010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
Acidihalobacter aeolianus is an acidophilic, halo-tolerant organism isolated from a marine environment near a hydrothermal vent, an ecosystem whereby levels of salinity and total dissolved salts are constantly fluctuating creating ongoing cellular stresses. In order to survive these continuing changes, the synthesis of compatible solutes—also known as organic osmolytes—is suspected to occur, aiding in minimising the overall impact of environmental instability. Previous studies on A. aeolianus identified genes necessary for the accumulation of proline, betaine and ectoine, which are known to act as compatible solutes in other halophilic species. In this study, the impact of increasing the osmotic stress as well as the toxic ion effect was investigated by subjecting A. aeolianus to concentrations of NaCl and MgSO4 up to 1.27 M. Exposure to high concentrations of Cl− resulted in the increase of ectC expression in log-phase cells with a corresponding accumulation of ectoine at stationary phase. Osmotic stress via MgSO4 exposure did not trigger the same up-regulation of ectC or accumulation of ectoine, indicating the transcriptionally regulated response against osmotic stress was induced by chloride toxicity. These findings have highlighted how the adaptive properties of halo-tolerant organisms in acidic environments are likely to differ and are dependent on the initial stressor.
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Khaleque HN, González C, Johnson DB, Kaksonen AH, Holmes DS, Watkin ELJ. Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov. Int J Syst Evol Microbiol 2020; 70:6226-6234. [PMID: 33112221 PMCID: PMC8049490 DOI: 10.1099/ijsem.0.004519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022] Open
Abstract
The genus Acidihalobacter has three validated species, Acidihalobacter ferrooxydans, Acidihalobacter prosperus and Acidihalobacter aeolinanus, all of which were isolated from Vulcano island, Italy. They are obligately chemolithotrophic, aerobic, acidophilic and halophilic in nature and use either ferrous iron or reduced sulphur as electron donors. Recently, a novel strain was isolated from an acidic, saline drain in the Yilgarn region of Western Australia. Strain F5T has an absolute requirement for sodium chloride (>5 mM) and is osmophilic, growing in elevated concentrations (>1 M) of magnesium sulphate. A defining feature of its physiology is its ability to catalyse the oxidative dissolution of the most abundant copper mineral, chalcopyrite, suggesting a potential role in biomining. Originally categorized as a strain of A. prosperus, 16S rRNA gene phylogeny and multiprotein phylogenies derived from clusters of orthologous proteins (COGS) of ribosomal protein families and universal protein families unambiguously demonstrate that strain F5T forms a well-supported separate branch as a sister clade to A. prosperus and is clearly distinguishable from A. ferrooxydans DSM 14175T and A. aeolinanus DSM14174T. Results of comparisons between strain F5T and the other Acidihalobacter species, using genome-based average nucleotide identity, average amino acid identity, correlation indices of tetra-nucleotide signatures (Tetra) and genome-to-genome distance (digital DNA-DNA hybridization), support the contention that strain F5T represents a novel species of the genus Acidihalobacter. It is proposed that strain F5T should be formally reclassified as Acidihalobacter yilgarnenesis F5T (=DSM 105917T=JCM 32255T).
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Affiliation(s)
- Himel Nahreen Khaleque
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
- CSIRO Land and Water, Floreat, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - D. Barrie Johnson
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
- Faculty of Health and Life Sciences, Coventry University, Coventry, CV1 5RW, UK
| | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Universidad San Sebastian, Santiago, Chile
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Kanao T, Sharmin S, Tokuhisa M, Otsuki M, Kamimura K. Identification of a gene encoding a novel thiosulfate:quinone oxidoreductase in marine Acidithiobacillus sp. strain SH. Res Microbiol 2020; 171:281-286. [PMID: 33031917 DOI: 10.1016/j.resmic.2020.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 11/30/2022]
Abstract
Sulfur-oxidizing bacteria that are halophilic and acidophilic have gained interest because of their potential use in bioleaching operations in salt-containing environments. Acidithiobacillus sp. strain SH, which was previously identified as Acidithiobacillus thiooxidans based on its 16S rRNA gene sequence, is a chemolithoautotrophic marine bacterium exhibiting sodium chloride-stimulated thiosulfate-oxidizing activities. A novel thiosulfate:quinone oxidoreductase from strain SH (SH-TQO) has been purified from its solubilized membrane fraction. The gene for SH-TQO was determined from the draft genome sequence of the strain SH. Amino acid sequences of peptides generated by the in-gel trypsin digestion of SH-TQO were found in a protein encoded by locus tag B1757_09800 of the genome of the strain SH. The gene encoded 444 amino acids with a signal peptide of 29 amino acids and was annotated to encode a porin. The gene was located in a unique genomic region, not found in A. thiooxidans strains, suggesting that the strain SH acquired this region through a horizontal gene transfer. A protein-protein basic local alignment search revealed that sulfur-oxidizing bacteria, such as Acidithiobacillus species have proteins homologous to SH-TQO, though the degree of homologies was relatively low. The protein, DoxXA, which is homologous to TQO from Acidianus amvibalens, was also found in the genomic region.
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Affiliation(s)
- Tadayoshi Kanao
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Sultana Sharmin
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Mirai Tokuhisa
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Maho Otsuki
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
| | - Kazuo Kamimura
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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Norris PR, Davis-Belmar CS, Calvo-Bado LA, Ogden TJ. Salt-tolerant Acidihalobacter and Acidithiobacillus species from Vulcano (Italy) and Milos (Greece). Extremophiles 2020; 24:593-602. [PMID: 32451688 DOI: 10.1007/s00792-020-01178-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/12/2020] [Indexed: 12/25/2022]
Abstract
Ferrous iron- and sulfur-oxidizing Acidihalobacter species and similar so far unclassified bacteria have been isolated from the islands of Vulcano (Italy) and Milos (Greece), specifically from where seawater was acidified at sulfide-rich geothermal sites. Acidithiobacillus species which tolerated concentrations of chloride that inhibit most Acidithiobacillus spp. were also isolated from sites on both islands: these were At. thiooxidans strains and an unclassified species, Acidithiobacillus sp. strain V1. The potential of salt-tolerant acidophiles for industrial application in promoting copper extraction from mineral sulfides where chloride is naturally present at concentrations which would inhibit most acidophiles, or where seawater rather than fresh water is available, appears to be limited by the sensitivity of ferrous-iron oxidizing Acidihalobacter spp. to copper. However, tolerance of copper and chloride shown by At. thiooxidans strain A7 suggests it could oxidize sulfur and benefit acid leaching if ferric iron or copper was provided as the primary oxidant of sulfide ores.
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Affiliation(s)
- Paul R Norris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- College of Engineering, Maths and Physical Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Carol S Davis-Belmar
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- BHP Billiton Chile, Base Metals, Av. Américo Vespucio Sur 100, Las Condes, PO Box 7580150, Santiago, Chile
| | - Leonides A Calvo-Bado
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Micropathology Ltd, University of Warwick Science Park, Venture Centre, Sir William Lyons Road, Coventry, CV4 7EZ, UK
| | - Thomas J Ogden
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
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9
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Hussain S, Min Z, Xiuxiu Z, Khan MH, Lifeng L, Hui C. Significance of Fe(II) and environmental factors on carbon-fixing bacterial community in two paddy soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109456. [PMID: 31398779 DOI: 10.1016/j.ecoenv.2019.109456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
The seasonal flooding and drainage process affect the paddy soils, the existence of the iron state either Fe(III) or Fe(II) is the main redox system of paddy soil. Its morphological transformation affects the redox nature of paddy soils, which also affects the distribution of bacterial community diversity. This study based on molecular biological methods (qPCR, Illumina MiSeq sequencing technique) to investigate the effect of Fe(II) and environmental factors on cbbM genes containing carbon fixing microbes. Both Eh5 and pH were reduced with Fe(II) concentrations. The Fe(II) addition significantly affects the cbbM gene copy number in both texture soils. In loamy soil, cbbM gene copy number increased with high addition of Fe(II), while both low and high concentrations significantly reduced the cbbM gene copy number in sandy soil. Chemotrophic bacterial abundance significantly increased by 79.7% and 54.8% with high and low Fe(II) addition in loamy soil while in sandy soil its abundance decreased by 53% and 54% with the low and high Fe(II) accumulation. The phototrophic microbial community increased by 37.8% with low Fe(II) concentration and decreased by 16.2% with a high concentration in loamy soil, while in sandy soil increased by 21% and 14.3% in sandy soil with low and high Fe(II) addition. Chemoheterotrophic carbon fixing bacterial abundance decreased with the Fe(II) accumulation in both soil textures in loamy soil its abundance decreased by 5.8% and 24.8%, while in sand soil 15.7% and 12.8% with low and high Fe(II) concentrations. The Fe(II) concentration and soil textures maybe two of the major factors to shape the bacterial community structure in paddy soils. These results provide a scientific basis for management of paddy soil fertility and it can be beneficial to take measures to ease the greenhouse gases effect.
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Affiliation(s)
- Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhang Min
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhu Xiuxiu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Lifeng
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cao Hui
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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10
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Khaleque HN, González C, Kaksonen AH, Boxall NJ, Holmes DS, Watkin ELJ. Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (=DSM 14174 =JCM 32253) and 'Acidihalobacter ferrooxidans' V8 (=DSM 14175 =JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively. Int J Syst Evol Microbiol 2019; 69:1557-1565. [DOI: 10.1099/ijsem.0.003313] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Himel N. Khaleque
- 1School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
- 2CSIRO Land and Water, Floreat, Australia
| | - Carolina González
- 3Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | - David S. Holmes
- 3Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Elizabeth L. J. Watkin
- 1School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
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11
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Khaleque HN, González C, Shafique R, Kaksonen AH, Holmes DS, Watkin ELJ. Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis. Front Microbiol 2019; 10:155. [PMID: 30853944 PMCID: PMC6396713 DOI: 10.3389/fmicb.2019.00155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and "A. ferrooxidans" DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and "A. ferrooxidans" DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.
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Affiliation(s)
- Himel N. Khaleque
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- CSIRO Land and Water, Floreat, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
| | | | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Elizabeth L. J. Watkin
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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Identification of Thiobacillus bacteria in agricultural soil in Iran using the 16S rRNA gene. Mol Biol Rep 2018; 45:1723-1731. [PMID: 30443822 DOI: 10.1007/s11033-018-4316-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/16/2018] [Indexed: 10/27/2022]
Abstract
Thiobacillus, as useful soil bacteria, plays an important role in sulfur cycling. The purpose of this study was to identify the species Thiobacillus thioparus, Thiobacillus novellas and Thiobacillus denitrificans in rainfed and irrigated lands soil in Ajabshir, Ilam, Qorveh, Rojintaak, Sonqor, Kermanshah and Research Farm of Razi University in Iran. Sampling was performed as randomized completely with three replications at depth of 0-30 cm. The Thiobacillus species were determined via 16S rRNA characteristics. The results of agarose gel electrophoresis indicated that T. thioparus was the highest amount in the irrigated land in Research Farm and its lowest amount was in the Rojintaak rainfed land. These species not found in four locations and conditions including the Ajabshir irrigated, Qorveh rainfed, Research Farm rainfed and Rojintaak irrigated lands. The results of the T. novellas indicated that this was found in Ilam irrigated, Qorveh rainfed, Research Farm irrigated, Rojintaak irrigated and Rojintaak rainfed lands. The highest and lowest amount of T. novellas was indicated in the Rojintaak and Ilam irrigated lands respectively. The T. denitrificans gene showed that this bacterium was observed only in both samples of Ajabshir. Our study showed that Thiobacillus was not detected in all of the soils. If sulfur fertilizer is given to the soil without this bacterium, it is necessary to use sulfur fertilizer with Thiobacillus bacteria inoculation for better sulfur oxidation.
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Bulaev AG, Chernyshov AN. Effect of Light Metal Ions and Chloride on Activity of Moderately Thermophilic Acidophilic Iron-Oxidizing Microorganisms. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sharma V, Siedenburg G, Birke J, Mobeen F, Jendrossek D, Prakash T. Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y. PLoS One 2018; 13:e0197448. [PMID: 29851965 PMCID: PMC5979037 DOI: 10.1371/journal.pone.0197448] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 05/02/2018] [Indexed: 11/19/2022] Open
Abstract
The pathway of rubber (poly [cis-1,4-isoprene]) catabolism is well documented for Gram-positive rubber degraders but only little information exists for Gram-negative species. The first documented potent rubber degrading Gram-negative strain is Xanthomonas sp. strain 35Y that uses extracellular rubber oxygenases for the initial cleavage of the polyisoprene molecule. However, neither the exact phylogenetic position of Xanthomonas sp. strain 35Y nor the catabolic pathway of the primary polyisoprene cleavage products have been investigated. In this contribution, we started to address both these issues by a comprehensive taxonomic characterization and by the analysis of the draft genome sequence of strain 35Y. Evaluation of the 16S rRNA gene sequence pointed to a borderline taxonomic position of strain 35Y as a novel species of the genus Steroidobacter. Further, substantial differences in the genotypic properties of strain 35Y and the members of the genus Steroidobacter, including average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), resolved the taxonomic position of strain 35Y and suggested its positioning as a novel species of the genus Steroidobacter. This was further confirmed by comparative analysis of physiological and biochemical features of strain 35Y with other members of the genus Steroidobacter. Thus, we conclude that strain 35Y represents a novel species of the genus Steroidobacter, for which we propose the designation Steroidobacter cummioxidans sp. nov., strain 35YT. A comprehensive analysis of the draft genome of S. cummioxidans strain 35Y revealed similarities but also substantial differences to rubber degrading Gram-positive counterparts. In particular, the putative transporters for the uptake of polyisoprene cleavage products differ from Gram-positive rubber degrading species. The draft genome sequence of S. cummioxidans strain 35Y will be useful for researchers to experimentally verify the predicted similarities and differences in the pathways of polyisoprene catabolism in Gram-positive and Gram-negative rubber degrading species.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, Mandi, India
| | | | - Jakob Birke
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, Mandi, India
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, Mandi, India
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Norris PR, Laigle L, Slade S. Cytochromes in anaerobic growth of Acidithiobacillus ferrooxidans. Microbiology (Reading) 2018; 164:383-394. [DOI: 10.1099/mic.0.000616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul R. Norris
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Ludovic Laigle
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: The Native Antigen Company, Langford Locks, Kidlington, Oxford, OX5 1LH, UK
| | - Susan Slade
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Present address: Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
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Dopson M, Holmes DS, Lazcano M, McCredden TJ, Bryan CG, Mulroney KT, Steuart R, Jackaman C, Watkin ELJ. Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions. Front Microbiol 2017; 7:2132. [PMID: 28111571 PMCID: PMC5216662 DOI: 10.3389/fmicb.2016.02132] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022] Open
Abstract
Extremely acidophilic microorganisms (pH optima for growth of ≤3) are utilized for the extraction of metals from sulfide minerals in the industrial biotechnology of “biomining.” A long term goal for biomining has been development of microbial consortia able to withstand increased chloride concentrations for use in regions where freshwater is scarce. However, when challenged by elevated salt, acidophiles experience both osmotic stress and an acidification of the cytoplasm due to a collapse of the inside positive membrane potential, leading to an influx of protons. In this study, we tested the ability of the halotolerant acidophile Acidihalobacter prosperus to grow and catalyze sulfide mineral dissolution in elevated concentrations of salt and identified chloride tolerance mechanisms in Ac. prosperus as well as the chloride susceptible species, Acidithiobacillus ferrooxidans. Ac. prosperus had optimum iron oxidation at 20 g L−1 NaCl while At. ferrooxidans iron oxidation was inhibited in the presence of 6 g L−1 NaCl. The tolerance to chloride in Ac. prosperus was consistent with electron microscopy, determination of cell viability, and bioleaching capability. The Ac. prosperus proteomic response to elevated chloride concentrations included the production of osmotic stress regulators that potentially induced production of the compatible solute, ectoine uptake protein, and increased iron oxidation resulting in heightened electron flow to drive proton export by the F0F1 ATPase. In contrast, At. ferrooxidans responded to low levels of Cl− with a generalized stress response, decreased iron oxidation, and an increase in central carbon metabolism. One potential adaptation to high chloride in the Ac. prosperus Rus protein involved in ferrous iron oxidation was an increase in the negativity of the surface potential of Rus Form I (and Form II) that could help explain how it can be active under elevated chloride concentrations. These data have been used to create a model of chloride tolerance in the salt tolerant and susceptible species Ac. prosperus and At. ferrooxidans, respectively.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University Kalmar, Sweden
| | - David S Holmes
- Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile; Center for Bioinformatics and Genome Biology, Fundacion Ciencia y VidaSantiago, Chile
| | - Marcelo Lazcano
- Facultad de Ciencias Biologicas, Universidad Andres BelloSantiago, Chile; Center for Bioinformatics and Genome Biology, Fundacion Ciencia y VidaSantiago, Chile
| | - Timothy J McCredden
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Christopher G Bryan
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Kieran T Mulroney
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Robert Steuart
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Connie Jackaman
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
| | - Elizabeth L J Watkin
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University Perth, WA, Australia
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Holanda R, Hedrich S, Ňancucheo I, Oliveira G, Grail BM, Johnson DB. Isolation and characterisation of mineral-oxidising “Acidibacillus” spp. from mine sites and geothermal environments in different global locations. Res Microbiol 2016; 167:613-23. [DOI: 10.1016/j.resmic.2016.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
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Zhang X, Niu J, Liang Y, Liu X, Yin H. Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap. BMC Genet 2016; 17:21. [PMID: 26781463 PMCID: PMC4717592 DOI: 10.1186/s12863-016-0330-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/13/2016] [Indexed: 01/18/2023] Open
Abstract
Background Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Results Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Conclusion Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0330-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
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