Amplified ribosomal DNA restriction analysis in the differentiation of related species of mycobacteria

Kurabachew, Mekonnen; Enger, Øivind; Sandaa, Ruth Anne; Lemma, Eshetu; Bjorvatn, Bjarne

doi:10.1016/s0167-7012(03)00119-2

Cited by 14 publications

(10 citation statements)

References 35 publications

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“…This method has been used for genetic analysis and diversity studies of many bacteria such as Streptococcus (Sasaki et al 2004), Lactobacillus (Moreira et al 2005), Mycobacterium (Baere et al 2002;Kurabachew et al 2003), and type A toxin-producing Clostridium (Pooeshafie et al 2005). Furthermore, Vaneechoutte et al (1995) revealed that ARDRA can avoid DNA contamination in pure culture.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis

Bahri¹,

Wahyudi²,

Mubarik³

2009

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Plant-growth promoting rhizobacteria (PGPR) are rhizosphere associated soil-borne bacteria that can enhance plant growth and inhibit the development of root pathogens. Many soil bacteria have been used as PGPR, and one of them is Bacillus sp. The implementation of PGPR is constrained by genotype fluctuation that makes it inactive on the rhizosphere. Our previous study had characterized and revealed that 11 Bacillus sp. isolated from the soybean plant rhizosphere were PGPR. To asses and compare the genetic diversity of these isolates, Amplified Ribosomal DNA Restriction Analysis (ARDRA) and DNA sequence analysis of 16S rRNA were conducted. The construction of Neighbor-joining trees and bootstrap analysis of 100 resamples of ARDRA and 16S rRNA gene sequences were performed using Treecon software for windows ver. 1.3b. ARDRA analysis was done by using four restriction enzymes (RsaI, HaeIII, CfrI and HinfI), resulting in four phylotypes, respectively phylotype I (Bacillus sp. Cr24, Cr33, Cr64 and Cr68), phylotype II (Bacillus sp. Cr 31 and Cr66), phylotype III (Bacillus sp. Cr44 and Cr71) and phylotype IV (Bacillus sp. Cr67, Cr28 and Cr69). Results of BLASTN from 16S rRNA gene sequences showed that these isolates are genetically diversed. The evolution relationship of Bacillus sp. could be shown by the 16S rRNA gene sequences analysis, while ARDRA based on the digestion sites showed their variability.Key words: Bacillus sp., plant-growth promoting rhizobacteria, 16S rDNA, ARDRA, genetic diversity * Corresponding author, Phone/Fax: +62-251-8622833, E-mail: aristri2003@yahoo.comThe slow growth of plant is a major handicap that can decrease food production and ecosystem stability. Synthetic fertilizers have been used to solve this problem. However, it can give negative effects on human and environment, such as pollution of the surrounding ecosystem and the death of non-target microbes. Therefore, efforts to find alternative solutions, among others by using plant-growth promoting rhizobacteria (PGPR), i.e. associated soil-borne bacteria on the rizosphere that can enhance plant growth and inhibit the growth of root pathogens, such as Bacillus sp.Bacillus is a motile, catalase-positive, Gram-positive rod, with 40-60% GC content. It forms endospore that is very resistant to extreme environmental conditions. Bacillus has been known for the production of phytohormone such as indole acetic acid (Glick 1995), siderophores (Compant et al. 2005) and antibiotics such as zwittermicin A (Silo-suh et al. 1994), bacilin, clorotetain and Iturin A (Phister et al. 2004). These compounds are natural and beneficial to promote plant growth. Hence, it is potential to utilize those mechanisms in agriculture. Its implementation, however, is constrained by the genotype fluctuation.The 16S rRNA gene has been routinely used as a reliable molecular marker for phylogeny identification. It contains conserved region, a unique array of sequences that are relative among species or different species (Woose 1987;Moyer et al. 1994). It is the basis of m...

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis

Bahri¹,

Wahyudi²,

Mubarik³

2009

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“…1998, 1999), the 23S rRNA‐encoding DNA (Minnick et al. 1995; Kurabachew et al. 2003), the recA (Torriani et al.…”

Section: Discussionmentioning

confidence: 99%

“…Given the increasing interest in using defined LAB cultures as starters in sourdough fermentation , it is evident that a need exists for reliable and rapid detection techniques for sourdough lactobacilli. Several methodologies to identify bacterial species have been used targeting the 16S rRNAencoding gene (Kaufmann et al 1997;Matsuki et al 1998Matsuki et al , 1999, the 23S rRNA-encoding DNA (Minnick et al 1995;Kurabachew et al 2003), the recA Krawczyk et al 2002;Chan et al 2003) and ldhD (Mora et al 1997) genes, the monoplex PCR (Chamberlain et al 1988), and the 16S-23S rRNA Rapid identification of sourdough Lactobacillus species using species-specific primers Figure 3 Alignment of L-ISR nucleotide sequences of 1, Lactobacillus plantarum (AF182722); 2, Lactobacillus pentosus (U97141); 3, Lactobacillus farciminis (AJ417499); 4, Lactobacillus nantensis (AY690836); 5, Lactobacillus alimentarius (AJ616015); 6, Lactobacillus paralimentarius (AY839296); 7, Lactobacillus panis (AY839296); 8, Lactobacillus pontis (AY839302); 9, Lactobacillus frumenti (AY839302); 10, Lactobacillus mindensis (AY839298); 11, Lactobacillus acidophilus (AF375937); 12, Lactobacillus helveticus (AM411112). The tRNAs are indicated by grey boxes.…”

Section: Discussionmentioning

confidence: 99%

A one-step reaction for the rapid identification of Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti using oligonucleotide primers designed from the 16S–23S rRNA intergenic sequences

et al. 2008

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Aims: Species‐specific primers targeting the 16S–23S ribosomal DNA (rDNA) intergenic spacer region (ISR) were designed to rapidly discriminate between Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti species recently isolated from French sourdough. Methods and Results: The 16S–23S ISRs were amplified using primers 16S/p2 and 23S/p7, which anneal to positions 1388–1406 of the 16S rRNA gene and to positions 207–189 of the 23S rRNA gene respectively, Escherichia coli numbering (GenBank accession number ). Clone libraries of the resulting amplicons were constructed using a pCR2·1 TA cloning kit and sequenced. Species‐specific primers were designed based on the sequences obtained and were used to amplify the 16S–23S ISR in the Lactobacillus species considered. For all of them, two PCR amplicons, designated as small ISR (S‐ISR) and large ISR (L‐ISR), were obtained. The L‐ISR is composed of the corresponding S‐ISR, interrupted by a sequence containing tRNAIle and tRNAAla genes. Based on these sequences, species‐specific primers were designed and proved to identify accurately the species considered among 30 reference Lactobacillus species tested. Conclusions: Designed species‐specific primers enable a rapid and accurate identification of L. mindensis, L. paralimentarius, L. panis, L. pontis and L. frumenti species among other lactobacilli. Significance and Impact of the Study: The proposed method provides a powerful and convenient means of rapidly identifying some sourdough lactobacilli, which could be of help in large starter culture surveys.

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“…This method has been used for genetic analysis and diversity studies of many bacteria such as Streptococcus [26], Lactobacillus [27], Mycobacterium [28], and type A toxin-producing Clostridium [29]. Furthermore, Vaneechoutte et al [30] revealed that ARDRA can avoid DNA contamination in pure culture.…”

Section: Ardramentioning

confidence: 99%

Genotypic and Phenotypic Profile of Alkalophile Proteolytic Bacillus sp. Associated with Rhizosphere of Apple Trees in Trans Himalayas

Guleria

Walia

Chauhan

et al. 2014

Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci.

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Rhizosphere of apple trees of Trans Himalayas is great niche of proteolytic bacteria which may have potential for use in industries. A total of 76 proteolytic bacteria were obtained from rhizosphere soil and root endosphere of apple trees from different sites of four locations viz., Chamba, Shimla, Kinnaur and Kullu of Himachal Pradesh, India, which were screened for plant growth promoting traits including production of indole acetic acid, phosphate solubilization, hydrogen cyanide production and production of antifungal metabolite. Among them, 17 isolates that exhibited maximum alkaline protease activity were selected. The diversity elucidation and differentiation of isolates was achieved through their biochemical characterization and amplified ribosomal DNA restriction analysis with three tetra-cutter restriction enzymes (HpaII, HinfI and TaqI), the representative cluster groups were identified by 16S rDNA sequencing. This brings to light the predominance of Bacillus sp. and presence of remarkable functional and genotypic intraspecific diversity in apple rhizosphere. Proteolytic activity among selected isolates ranged between 50 and 2,770 lg/ml/min at pH 8.0 and the maximum was observed for Bacillus amyloliquefaciens (2,770 lg/ml/min) followed by B. subtilis (1,300.97 lg/ml/min). Bacillus amyloliquifaciens in particular showed great potential of alkaline protease production which agrees its exploitation in detergent industry. To the best of authors' knowledge, this is first report for genetic and functional diversity of alkaline protease producing PGPR associated with apple rhizosphere in Trans-Himalayan region of Himachal Pradesh. Additionally the generated information may serve as a base line data for developing effective alkaline protease preparation for the industrial use.

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Amplified ribosomal DNA restriction analysis in the differentiation of related species of mycobacteria

Cited by 14 publications

References 35 publications

Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis

Genetic Diversity of Plant Growth Promoting Rhizobacteria of Bacillus sp. Based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis

A one-step reaction for the rapid identification of Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti using oligonucleotide primers designed from the 16S–23S rRNA intergenic sequences

Genotypic and Phenotypic Profile of Alkalophile Proteolytic Bacillus sp. Associated with Rhizosphere of Apple Trees in Trans Himalayas

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