rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains

Binde, Daisy Rickli; Menna, Pâmela; Bangel, Eliane Villamil; Barcellos, Fernando Gomes; Hungría, Mariangela

doi:10.1007/s00253-009-1927-6

Cited by 54 publications

(46 citation statements)

References 26 publications

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“…The average size of isolated 16S rDNAs of the 20 slow-growing STB strains around 1450 bp were in the same range previously reported 27,28 . However, sequences of only one gene, 16S rDNA, cannot be used to resolve differences amongst natural variants of the 7 B. elkanii and 6 B. japonicum STB strains observed in PCR-DNA fingerprints ( Fig.…”

Section: Discussionsupporting

confidence: 73%

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Maruekarajtinpleng¹,

Homhaul²,

Chansa-ngavej³

2012

ScienceAsia

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Soybean rhizobia are Gram negative bacteria that fix nitrogen in root nodules of soybeans. Selection of soybean rhizobia from present and previous soybean cultivation areas is one way to obtain efficient strains for inoculant production. At present, information on the diversity of soybean rhizobia in Thailand is scarce. The experiments aimed to isolate and characterize soybean rhizobium strains in soils from 16 subdistricts in Phitsanulok province, Thailand. Host trapping method was used to isolate bacteria from root nodules of 5 soybean cultivars grown in soils from the 16 subdistricts. Identical RAPD-PCR fingerprints revealed the 202 slow-growing isolates consisted of 121 strains. Authentication tests using 5 soybean cultivars showed all the 121 slow-growing strains had nodulated soybean roots. Four types of colony morphology on yeast extract mannitol containing congo red agar plates were obtained for all the isolated strains. Bromothymol blue (BTB) reactions on BTB agar plates revealed two types of slow-growing soybean rhizobia. Type 1 secreted alkali products after 5-day incubation, and acidic products upon prolonged incubation for another 5 days. Type 2 secreted only alkali products after 5-and 10-day incubation. Results from nucleotide sequences of 16S rDNA revealed 7, 6, and 2 strains of Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, respectively. The B. elkanii and B. japonicum strains were found to be natural variants with different RAPD-PCR fingerprints. This study is the first report on the findings of B. yuanmingense as well as natural variants of slow-growing soybean rhizobia in Thailand.

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Section: Discussionsupporting

confidence: 73%

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Maruekarajtinpleng¹,

Homhaul²,

Chansa-ngavej³

2012

ScienceAsia

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“…observed in our study. In contrast, other studies have found poor correlation between genotyping (rep-PCR) and DNA sequencing methods used to determine species/strain relationships of other bacterial genera (4,19). The 16S rRNA gene sequence of an environmental strain of Lactococcus garvieae served as an effective outgroup for the 16S rRNA gene dendrogram (Fig.…”

Section: Downloaded Frommentioning

confidence: 68%

Comparison of Genotypic and Phylogenetic Relationships of Environmental Enterococcus Isolates by BOX-PCR Typing and 16S rRNA Gene Sequencing

Badgley

Harwood

2011

Appl Environ Microbiol

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EnvironmentalEnterococcusspp. were compared by BOX-PCR genotyping and 16S rRNA gene sequencing to clarify the predictive relationship of BOX-PCR fingerprints to species designation. BOX-PCR and 16S rRNA gene relationships agreed for 77% of strains. BOX-PCR provided superior intraspecies discrimination but incorrectly identified some strains to the species level and divided some species into multiple groups.

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“…There was no evidence of codiversification (ParaFit; P ϭ 0.5129). Five species of Largidae from geographically distant areas (Argentina, Colombia, Costa Rica, Mexico, and the United States) harbored the same or very similar strains of Burkholderia, which closely matched the 16S rRNA sequences of PBE clade Burkholderia, including those of curated elite commercial inoculants used in agriculture for nodulation of legume crops in Brazil, housed in the SEMIA Rhizobium Culture Collection (e.g., 100% identical to Burkholderia SEMIA 6385 [GenBank accession number FJ025136.1] and SEMIA 6382 [GenBank accession number AY904775.1], iso-lated from Piptadenia gonoacantha and Mimosa caesalpiniifolia roots, respectively [54]). …”

Section: Resultsmentioning

confidence: 99%

Phylogenetic Evidence for Ancient and Persistent Environmental Symbiont Reacquisition in Largidae (Hemiptera: Heteroptera)

Gordon

McFrederick

Weirauch

2016

Appl Environ Microbiol

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The insect order Hemiptera, one of the best-studied insect lineages with respect to bacterial symbioses, still contains major branches that lack comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species] and Pyrrhocoridae [ϳ300 species]) is a clade of the hemipteran infraorder Pentatomomorpha. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes in these putative sister families. We surveyed the associated bacterial diversity of this group using paired-end Illumina sequencing and targeted Sanger sequencing of bacterial 16S rRNA amplicons of 30 pyrrhocoroid taxa, including 17 species of Largidae, in order to determine bacterial associates and the similarity of associated microbial communities among species. We also used molecular data (4,800 bp in 5 loci, for 57 ingroup and 12 outgroup taxa) to infer a phylogeny of the host superfamily, in order to trace the evolution of symbiotic complexes among Pentatomomorpha species. We undertook multiple lines of investigation (i.e., experimental rearing, fluorescence in situ hybridization microscopy, and phylogenetic and coevolutionary analyses) to elucidate potential transmission routes for largid symbionts. We found a prevalent and specific association of Largidae with Burkholderia strains of the plant-associated beneficial and environmental clade, housed in midgut tubules. As in other distantly related Heteroptera, symbiotic bacteria seem to be acquired from the environment every generation. We review the current understanding of symbiotic complexes within Pentatomomorpha and discuss means to further investigate the evolution and function of these symbioses. IMPORTANCEObligate symbioses with bacteria are common in insects, particularly Hemiptera, in which various forms of symbiosis occur. However, knowledge regarding symbionts remains incomplete for major hemipteran lineages. Thus, an accurate understanding of how these partnerships evolved and changed over millions of years is not yet achievable. We contribute to our understanding of the evolution of symbiotic complexes in Hemiptera by characterizing bacterial associates of Pyrrhocoroidea, focusing on the family Largidae. Members of Largidae are associated with specific symbiotic Burkholderia strains from a different clade than Burkholderia symbionts in other Burkholderia-associated Hemiptera. Evidence suggests that species of Largidae reacquire specific symbiotic bacteria from the environment every generation, which is a rare strategy for insects, with potentially volatile evolutionary ramifications, but one that must have persisted in Largidae and related lineages since their origin in the Cretaceous Period.

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rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains

Cited by 54 publications

References 26 publications

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Comparison of Genotypic and Phylogenetic Relationships of Environmental Enterococcus Isolates by BOX-PCR Typing and 16S rRNA Gene Sequencing

Phylogenetic Evidence for Ancient and Persistent Environmental Symbiont Reacquisition in Largidae (Hemiptera: Heteroptera)

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