Evaluation of the hypervariable region in the 16S rDNA sequence as an index for rapid species identification in the genus Paenibacillus.

Goto, Keiichi; Kato, Yuko; Asahara, Mika; Yokota, Akira

doi:10.2323/jgam.48.281

Cited by 21 publications

(6 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The isolates were discriminated based on the initial variable region of the 16S rRNA gene (HV region), which contains the V1‐V2 regions, considered the most variable and useful for the characterisation of Bacillus species (Goto et al , ). Similar analyses were also applied to classify Paenibacillus strains (Goto et al , ); 59 isolates were identified to this genus according to the GenBank and EzTaxon databases. The genera Bacillus and Paenibacillus represented 41.6% and 58.4% of all the isolates, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The V1‐V2 16S rRNA regions [also denominated the hypervariant (HV) region] of 101 isolates and 40 operational taxonomic units (OTU) of the closest type species of Bacillus and Paenibacillus were used to estimate the grouping of the bacilli strains by cluster analysis (Goto et al , ; Goto et al , ; Saxena, ). The accession numbers of type‐species sequences are shown next to their identification names in Fig.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential ofBacillus mycoidesB38V as biofertiliser

Ambrosini

Stefanski

Lisboa³

et al. 2015

Ann Appl Biol

View full text Add to dashboard Cite

The nitrogen fixation by strains belonging to the Bacillus genus remains poorly explored. In this work, the diversity of endospore-forming bacilli isolated from the rhizosphere of sunflower was evaluated. A total of 101 strains were identified based on the V1-V2 variable regions of the 16S rRNA gene. Strains belonging to the genera Bacillus and Paenibacillus represented 41.6% and 58.4%, respectively, of total isolates. The production of indolic compounds was a common trait among the isolates, and approximately 75% of them exhibited positive nitrogenase activity; but only 9.2% displayed activities higher than 1 nmol C 2 H 4 mg protein h −1 . Within the genus Bacillus, the isolates related to the B. cereus group displayed the highest nitrogenase activity and were the second most frequent group of Bacillus sp. isolated. Plants inoculated with the isolate B38V showed the highest N content, and their shoot dry weights were significantly increased compared with positive control. Our results indicated that B38V, which belongs to the B. mycoides species, has the potential to promote sunflower growth. The data obtained in this study provide additional information concerning the diversity of Gram-positive diazotrophic within the genera Bacillus and Paenibacillus and their potential for the biofertilisation of sunflower crops.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential ofBacillus mycoidesB38V as biofertiliser

Ambrosini

Stefanski

Lisboa³

et al. 2015

Ann Appl Biol

View full text Add to dashboard Cite

show abstract

“…Against this background, we have examined the use of the 5Ј end hyper-variable region (HV region) sequence of 16S rDNA (Goto et al, 2000(Goto et al, , 2002a(Goto et al, , b, 2004 as a tool for the rapid identification of Methylobacterium species. During these studies, inconsistencies were discovered regarding the phylogenetic classification of several Methylobacterium species.…”

mentioning

confidence: 99%

Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum

Kato¹,

Asahara²,

Arai³

et al. 2005

J. Gen. Appl. Microbiol.

Self Cite

View full text Add to dashboard Cite

Phylogenetic analysis based on 16S rDNA sequences was performed on all type strains of the 14 validly described Methylobacterium species to ascertain the genealogic relationships among these species. The results showed that type strains of Methylobacterium were divided into two monophyletic groups whose members were distinct species with sequence similarity values greater than 97.0% between any two of the members in the same group. Only M. organophilum

show abstract

“…Even with molecular analyses, such as amplified rDNA restriction analysis (ARDRA), identification of these species is not always simple (Logan et al, 2002). In our previous studies, we demonstrated that a hypervariable (HV) region that corresponds to the 59 end of 16S rDNA (nucleotide positions 70-344; Bacillus subtilis numbering) is a useful marker for rapid identification and grouping of Alicyclobacillus species (Goto et al, 2002a, b), Bacillus species (Goto et al, 2000) and Paenibacillus species (Goto et al, 2002c). In this study, to ascertain how well the region is conserved within Brevibacillus species, we investigated sequence similarities among 29 strains that were supplied as Brevibacillus brevis.…”

mentioning

confidence: 99%

Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.

Goto¹,

Fujita²,

Kato³

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

Self Cite

View full text Add to dashboard Cite

Reclassification ofBacillus brevis was first described by Migula (1900). Subsequently, many strains, including some that were not in accordance with the criteria of Bacillus brevis sensu stricto, were classified as Bacillus brevis, according mainly to phenotype; as a result, Bacillus brevis has become a heterogeneous species, similar to Bacillus circulans (Nakamura & Swezey, 1983a, b). In the 1990s, based on polyphasic taxonomic studies of Bacillus brevis and its relatives, many species or strains were reclassified as novel species of the genera Brevibacillus and Aneurinibacillus (Nakamura, 1991(Nakamura, , 1993Takagi et al., 1993; Shida et al., 1994a Shida et al., , b, 1995Shida et al., , 1996 MeierStauffer et al., 1996;Heyndrickx et al., 1997). Recently, Brevibacillus invocatus was proposed as a novel species, according to the polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens (Logan et al., 2002). Thus, at the time of writing, 11 species are recognized to belong to the genus Brevibacillus and three species are recognized to belong to the genus Aneurinibacillus. However, with the exception of the thermophilic species Brevibacillus thermoruber and Aneurinibacillus thermoaerophilus, distinguishing between these species is extremely difficult, as most strains are unreactive or weak in many biochemical tests and few have useful differential phenotypic characteristics (Heyndrickx Abbreviation: HV, hypervariable.

show abstract

Evaluation of the hypervariable region in the 16S rDNA sequence as an index for rapid species identification in the genus Paenibacillus.

Cited by 21 publications

References 18 publications

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential ofBacillus mycoidesB38V as biofertiliser

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential ofBacillus mycoidesB38V as biofertiliser

Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum

Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.

Contact Info

Product

Resources

About