Relationship among acidophilic bacteria from diverse environments as determined by randomly amplified polymorphic DNA analysis (RAPD)

Akbar, Tanveer; Akhtar, Kalsoom; Ghauri, Muhammad Afzal; Anwar, Munir A.; Rehman, Moazur; Rehman, Mehboob-ur; Zafar, Yusuf; Khalid, Ahmad Mukhtar

doi:10.1007/s11274-004-3568-3

Cited by 8 publications

(2 citation statements)

References 9 publications

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“…The Acidithiobacillus strains exhibit high heterogeneity by DNA G ? C content, level of chromosome DNA-DNA homology and the patterns of genomic DNA produced by a series of DNA fingerprinting methods (Akbar et al 2005;Goebel and Stackebrandt 1994;Harrison 1982;Karavaiko et al 2003;Leduc et al 1994). Many PCR-based molecular methods were used to study the genetic and phylogenetic characterization of Acidithiobacillus.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

Liu

Zhang

et al. 2014

World J Microbiol Biotechnol

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

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Section: Introductionmentioning

confidence: 99%

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

Liu

Zhang

et al. 2014

World J Microbiol Biotechnol

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“…При RAPD-ПЛР використовують короткі довільні праймери, які гібридизуються з ДНК-мішенню за низької температурии відпалу та за використання консенсусного праймера М13 [6,14,23]. Хоча RAPD піддавали критиці за недостатню відтворюваність і чутливість умов реакції, цей метод використовували у дослідженні геномного різноманіття серед штамів A. ferrooxidans, що дало змогу провести як міжвидову, так і внутрішньовидову дискримінацію штамів [7,13,19,[26][27][28].…”

Section: ключові слова: Acidithiobacillus Ferrooxidans плр Rapd-плрunclassified

Definition of genetic polymorphism of strains Acidithiobacillus ferrooxidans that were isolated from waste of coal and energy industry of Ukraine

Vasylieva¹,

Brodiazhenko²,

Vasylieva³

et al. 2020

VLUBS

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The results of Acidithiobacillus ferrooxidans strains genetic variability studies that were first isolated from waste by coal and energy industries of Ukraine are reported in this article. These strains, according to the results of previous studies, are fully consistent with the biological properties of A. ferrooxidans bacteria given in Bergey’s Manual of Determinative Bacteriology and other original works [8, 10, 12, 18] also strains studied, regardless of habitat, were resistant to temperature and pH, had a mixed type of food, similar energy sources used by strains, etc. [1, 10, 11]. Using PCR was confirmed the affiliation of isolated from different of origin dumps of acidophilic chemolithotrophic strains with A. ferrooxidans. Genetic polymorphism of the strains was studied by RAPD-PCR using universal primer M13. It was shown that strains of A. ferrooxidans that were isolated from various dumps have a wide genetic diversity. By PCR, their affiliation with the species A. ferrooxidans was confirmed. Comparison analysis of the obtained RAPD profiles showed the variability of the strains which coincides with their main phenotypic properties, as described earlier [11]. The most heterogeneous profiles were characteristic of A. ferrooxidans DTV 1, A. ferrooxidans Lad 5 and A. ferrooxidans Lad 27. The obtained RAPD profiles served as the basis for the generation of the dendrogram constructed using the Neighbor-Joining method and calculating the similarity matrix, based on the coefficient of similarity of Nei & Li. Based on the obtained dendrogram, the formation of two clusters that combine similar strains is shown. The obtained indicators of the probability of formation of nodes of the constructed dendrogram range from 65.0 to 76.0 %%, which confirms the high degree of similarity between strains grouped by clusters. It is also shown that the first of the cluster includes strains that were isolated from coal and waste from its enrichment, and the second cluster includes strains that were isolated from coal waste. The obtained data confirm that the genetic variability of the strains depends on the primary location of isolation of the strains, and the coefficients of similarity between them varies from 0.182 to 0.80.

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DNA Extraction Methods, RAPD Profiling, Landfarm Soil

Amorim

Dias

Rezende

2013

Encyclopedia of Metagenomics

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Relationship among acidophilic bacteria from diverse environments as determined by randomly amplified polymorphic DNA analysis (RAPD)

Cited by 8 publications

References 9 publications

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

Definition of genetic polymorphism of strains Acidithiobacillus ferrooxidans that were isolated from waste of coal and energy industry of Ukraine

DNA Extraction Methods, RAPD Profiling, Landfarm Soil

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