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Huang S, Li H, Ma L, Liu R, Li Y, Wang H, Lu X, Huang X, Wu X, Liu X. Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus. BMC Genomics 2023; 24:282. [PMID: 37231368 DOI: 10.1186/s12864-023-09372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. RESULTS In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. CONCLUSIONS This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.
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Affiliation(s)
- Shanshan Huang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Huiying Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Yiran Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Hongmei Wang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xiaolu Lu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
| | - Xinhong Wu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
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Danilevich VN, Mulyukin AL, Machulin AV, Sorokin VV, Kozlov SA. Structural variability of DNA-containing Mg-pyrophosphate microparticles: optimized conditions to produce particles with desired size and morphology. J Biomol Struct Dyn 2018; 37:918-930. [PMID: 29457757 DOI: 10.1080/07391102.2018.1442747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our previous studies demonstrated the formation of structurally diverse DNA-containing microparticles (DNA MPs) in PCR with Mg-pyrophosphate (MgPPi) as the structure-forming component. These DNA MPs were referred to major structural types: microdisks (2D MPs) with nanometer thickness and 3D MPs with sophisticated morphology and constructed from intersecting disks and their segments. Little is known about factors that influence both the morphology and size of DNA MPs, and the present study was aimed at fulfilling this gap. We showed that the addition of Mn2+ cations to PCR mixtures caused the profound changes in MPs morphology, depending on DNA polymerase used (KlenTaq or Taq). Asymmetric PCR with 20-fold decrease in the concentration of one of two primers facilitated the predominant formation of microdisks with unusual structure. The addition of 1 mM Na-pyrophosphate to PCR mixtures with synthesized DNA and subsequent thermal cycling (10-15 cycles) were optimal to produce microdisks or nanometer 3D particles. Using electron microscopy, we studied also the structure of inorganic micro- and nanoparticles from MgPPi, formed during multiple heating and cooling cycles of a mixture of Mg2+ and Na-pyrophosphate in various regimes. Also, we found the conditions to yield planar (Mg·Mn)PPi nanocrystals (diameter ~100 nm and thickness ~10 nm) which efficiently adsorbed exogenous DNA. These inorganic nanoparticles are promising for DNA delivery in transfection studies. Mechanisms to be involved in structural modifications of MPs and perspectives of their practical application are discussed.
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Affiliation(s)
- Vasily N Danilevich
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
| | - Andrey L Mulyukin
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences . 33, bld. 2 Leninsky Ave., Moscow 119071 , Russia
| | - Andrey V Machulin
- c Skryabin Institute of Biochemistry and Physiology of Microorganisms , Russian Academy of Sciences , Pr. Nauki 5, Pushchino 142290 , Russia
| | - Vladimir V Sorokin
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences . 33, bld. 2 Leninsky Ave., Moscow 119071 , Russia
| | - Sergey A Kozlov
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
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Danilevich VN, Machulin AV, Lipkin AV, Kulakovskaya TV, Smith SS, Mulyukin AL. New insight into formation of DNA-containing microparticles during PCR: the scaffolding role of magnesium pyrophosphate crystals. J Biomol Struct Dyn 2015; 34:625-39. [PMID: 25891071 DOI: 10.1080/07391102.2015.1040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This work aims to study molecular mechanisms involved in the formation of DNA-containing microparticles and nanoparticles during PCR. Both pyrophosphate and Mg(2+) ions proved to play an important role in the generation of DNA microparticles (MPs) with a unique and sophisticated structure in PCR with Taq polymerase. Thus, the addition of Tli thermostable pyrophosphatase to a PCR mixture inhibited this process and caused the destruction of synthesized DNA MPs. Thermal cycling of Na-pyrophosphate (Na-PPi)- and Mg(2+)-containing mixtures (without DNA polymerase and dNTPs) under the standard PCR regime yielded crystalline oval or lenticular microdisks and 3D MPs composed from magnesium pyrophosphate (Mg-PPi). As shown by scanning electron microscopy (SEM), the produced Mg-PPi microparticles consisted of intersecting disks or their segments. They were morphologically similar but simpler than DNA-containing MPs generated in PCR. The incorporation of dNTPs, primers, or dsDNA into Mg-pyrophosphate particles resulted in the structural diversification of 3D microparticles. Thus, the unusual and complex structure of DNA MPs generated in PCR is governed by the unique feature of Mg-pyrophosphate to form supramolecular particles during thermal cycling. We hypothesize the Mg-pyrophosphate particles that are produced during thermal cycling serve as scaffolds for amplicon DNA condensation.
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Affiliation(s)
- Vasily N Danilevich
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
| | - Andrey V Machulin
- b Skryabin Institute of Biochemistry and Physiology of Microorganisms , Russian Academy of Sciences , Pr. Nauki 5, 142290 Pushchino , Moscow Region, Russia
| | - Alexey V Lipkin
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
| | - Tatyana V Kulakovskaya
- b Skryabin Institute of Biochemistry and Physiology of Microorganisms , Russian Academy of Sciences , Pr. Nauki 5, 142290 Pushchino , Moscow Region, Russia
| | - Steven S Smith
- c Beckman Research Institute and Division of Urology and Urologic Oncology , City of Hope National Medical Center , 1500 E. Duarte Rd., Duarte , CA 91010 , USA
| | - Andrey L Mulyukin
- d Winogradsky Institute of Microbiology , Russian Academy of Science , Pr. 60-letiya Oktyabrya 7/2, Moscow 117312 , Russia
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Danilevich VN, Artemov VV, Smith SS, Gainutdinov RV, Mulyukin AL. The structural peculiarities of condensed DNA micro- and nanoparticles formed in PCR. J Biomol Struct Dyn 2013; 32:1979-92. [DOI: 10.1080/07391102.2013.848411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chen L, Lin J, Liu X, Pang X, Lin H, Lin J. Transposition of IS elements induced by electroporation of suicide plasmid in Acidithiobacillus caldus. Enzyme Microb Technol 2013; 53:165-9. [PMID: 23830457 DOI: 10.1016/j.enzmictec.2013.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
Abstract
Transposition insertional mutagenesis of the insertion sequences (IS elements) was discovered for the first time in Acidithiobacillus caldus (A. caldus), when A. caldus MTH-04 hsdM (type I restriction-modification system M-subunit) mutant was constructed by electroporation of a suicide plasmid. The IS element, specifically inserting into hsdM gene, was analyzed, identified, and named ISAtc2. The transposition frequency of ISAtc2 was ranged from 4% to 7%, and no reverse mutation occurred in the mutants after 50 generations of proliferation without selective pressure. These results revealed that transposition of IS elements on A. caldus chromosome could regulate the gene expression and metabolic pathways by gene inactivation, gene loss and gene acquisition. Therefore, the transposition of IS elements in A. caldus may be an important and unique regulation mechanism for adaptation to the living condition.
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Affiliation(s)
- Linxu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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Danilevich VN, Gainutdinov RV. Morphology and ultrastructure of condensed DNA microparticles formed during PCR. DOKL BIOCHEM BIOPHYS 2013; 450:134-9. [DOI: 10.1134/s160767291303006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 11/22/2022]
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Danilevich VN, Vasilenko EA, Pechnikova EV, Grishin EV. New morphotypes of condensed DNA microparticles formed in PCR with KlenTaq and Taq polymerases and plasmid DNA as a template. Microbiology (Reading) 2012. [DOI: 10.1134/s002626171106004x] [Citation(s) in RCA: 2] [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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Kondrat’eva TF, Pivovarova TA, Tsaplina IA, Fomchenko NV, Zhuravleva AE, Murav’ev MI, Melamud VS, Bulayev AG. Diversity of the communities of acidophilic chemolithotrophic microorganisms in natural and technogenic ecosystems. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712010080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Danilevich VN, Vasilenko EA, Pechnikova EV, Sokolova OS, Grishin EV. Micro- and nanoparticles of condensed DNA Formed in PCR with Taq polymerase and plasmid DNA as a template. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711030088] [Citation(s) in RCA: 3] [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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Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms. Appl Microbiol Biotechnol 2010; 88:605-20. [DOI: 10.1007/s00253-010-2795-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 07/22/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
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Danilevich VN, Kadykov VA, Grishin EV. Condensed DNA particles formed in a PCR with plasmid templates: An electron microscopy study. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:535-46. [DOI: 10.1134/s1068162010040084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gene expression modulation by chalcopyrite and bornite in Acidithiobacillus ferrooxidans. Arch Microbiol 2010; 192:531-40. [DOI: 10.1007/s00203-010-0584-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 04/28/2010] [Accepted: 04/30/2010] [Indexed: 11/27/2022]
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13
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Danilevich VN, Grishin EV. Characteristics of microspheres formed in PCR with bacterial genomic DNA or plasmid DNA as templates. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709030114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Tupikina OV, Samorukova VD, Kondrat’eva TF. Patterns of growth and oxidation of natural pyrites by the representatives of acidophilic chemolithotrophic microorganisms. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709020064] [Citation(s) in RCA: 3] [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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Kondrat’eva TF, Danilevich VN, Karavaiko GI. The primary structure and characteristics of ISAfe600, an insertion sequence from Acidithiobacillus ferrooxidans strains. Microbiology (Reading) 2008. [DOI: 10.1134/s0026261708040139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Presence of a family of plasmids (29 to 65 kilobases) with a 26-kilobase common region in different strains of the sulfur-oxidizing bacterium Acidithiobacillus caldus. Appl Environ Microbiol 2008; 74:4300-8. [PMID: 18515486 DOI: 10.1128/aem.00864-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three large cryptic plasmids from different isolates of Acidithiobacillus caldus were rescued by using an in vitro transposition system that delivers a kanamycin-selectable marker and an Escherichia coli plasmid origin of replication. The largest of the plasmids, the 65-kb plasmid pTcM1, was isolated from a South African A. caldus strain, MNG. This plasmid was sequenced and compared to that of pTcF1 (39 kb, from strain "f," South Africa) and pC-SH12 (29 kb, from strain C-SH12, Australia). With the exception of a 2.7-kb insertion sequence, pC-SH12 appears to represent the DNA common to all three plasmids and includes a number of accessory genes plus the plasmid "backbone" containing the replication region. The two larger plasmids carry, in addition, a number of insertion sequences of the ISL3 family and a composite transposon related to the Tn21 subfamily containing a highly mosaic region within the borders of the inverted repeats. Genes coding for arsenic resistance, plasmid mobilization, plasmid stability, and a putative restriction-modification system occur within these mosaic regions.
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Ni YQ, He KY, Bao JT, Yang Y, Wan DS, Li HY. Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in China. FEMS Microbiol Ecol 2008; 64:248-59. [PMID: 18373686 DOI: 10.1111/j.1574-6941.2008.00457.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity.
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Affiliation(s)
- Yong-Qing Ni
- Key Laboratory of Arid and Grassland Ecology of the Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
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Ni YQ, Yang Y, Bao JT, He KY, Li HY. Inter- and intraspecific genomic variability of the 16Sâ23S intergenic spacer regions (ISR) in representatives ofAcidithiobacillus thiooxidansandAcidithiobacillus ferrooxidans. FEMS Microbiol Lett 2007; 270:58-66. [PMID: 17302937 DOI: 10.1111/j.1574-6968.2007.00660.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The complete sequences of 32 intergenic spacer regions (ISR) from Acidithiobacillus strains, including 29 field strains isolated from coal, copper, molybdenum mine wastes or sediment of different geoclimatic regions in China, reference strain ATCC19859 and the type strains of the two species were determined. These data, together with other sequences available in the GenBank database, were used to carry out the first detailed assessment of the inter- and intraspecific genomic variability of the ISR sequences and to infer phylogenetic relationships within the genus. The total length of the 16S-23S rRNA intergenic spacer regions of the Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans strains ranged from 451 to 490 bp, and from 434 to 456 bp, respectively. The degree of intrageneric ISR sequence similarity was higher than the degree of intergeneric similarity, and the overall similarity values of the ISRs varied from 60.49% to 84.71% between representatives of different species of the genus Acidithiobacillus. Sequences from the spacer of the A. thiooxidans and A. ferrooxidans strains ranged from 86.71% to 99.56% and 92.36% to 100% similarity, respectively. All Acidithiobacillus strains were separated into three phylogenetic major clusters and seven phylogenetic groups. ISR may be a potential target for the development of in situ hybridization probe aimed at accurately detecting acidithiobacilli in the various acidic environments.
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Affiliation(s)
- Yong-Qing Ni
- College of Life Sciences, Lanzhou University, Lanzhou, China
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Karavaiko GI, Dubinina GA, Kondrat’eva TF. Lithotrophic microorganisms of the oxidative cycles of sulfur and iron. Microbiology (Reading) 2006. [DOI: 10.1134/s002626170605002x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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