Genetic diversity and phylogeny of rhizobia isolated from Caragana microphylla growing in desert soil in Ningxia, China

Dai, Jun; Liu, X; Wang, Y

doi:10.4238/2012.june.25.5

Cited by 19 publications

(6 citation statements)

References 35 publications

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“…Thus, other molecular finger printing tools that have a higher resolving power, such as third generation gene sequencing and phylogenetic analysis, should be adopted. Dai et al (2012) noted that the phylogenetic analyses of bacteria using 16S rDNA alone may not clearly show a distinctive relationship within and among the bacteria populations involved. In addition, horizontal gene transfer and genetic recombination could have possibly contributed to the limited genetic variation of rhizobia in Eastern Kenya.…”

Section: Discussionmentioning

confidence: 99%

Genetic Characterization and Diversity of Rhizobium Isolated From Root Nodules of Mid-Altitude Climbing Bean (Phaseolus vulgaris L.) Varieties

et al. 2018

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The increasing interest in the use of rhizobia as biofertilizers in smallholder agricultural farming systems of the Sub-Saharan Africa has prompted the identification of a large number of tropical rhizobia strains and led to studies on their diversity. Inoculants containing diverse strains of rhizobia have been developed for use as biofertilizers to promote soil fertility and symbiotic nitrogen fixation in legumes. In spite of this success, there is paucity of data on rhizobia diversity and genetic variation associated with the newly released and improved mid-altitude climbing (MAC) bean lines (Phaseolus vulgaris L.). In this study, 41 rhizobia isolates were obtained from the root nodules of MAC 13 and MAC 64 climbing beans grown in upper and lower midland agro-ecological zones of Eastern Kenya. Eastern Kenya was chosen because of its high production potential of diverse common bean cultivars. The rhizobia isolates were characterized phenotypically on the basis of colony morphology, growth and biochemical features. Rhizobia diversity from the different regions of Eastern Kenya was determined based on the amplified ribosomal DNA restriction analysis (ARDRA) of PCR amplified 16S rRNA genes using Msp I, EcoR I, and Hae III restriction enzymes. Notably, native rhizobia isolates were morphologically diverse and grouped into nine different morphotypes. Correspondingly, the analysis of molecular variance based on restriction digestion of 16S rRNA genes showed that the largest proportion of significant (p < 0.05) genetic variation was distributed within the rhizobia population (97.5%) than among rhizobia populations (1.5%) in the four agro-ecological zones. The high degree of morphological and genotypic diversity of rhizobia within Eastern Kenya shows that the region harbors novel rhizobia strains worth exploiting to obtain strains efficient in biological nitrogen fixation with P. vulgaris L. Genetic sequence analysis of the isolates and testing for their symbiotic properties should be carried out to ascertain their identity and functionality in diverse environments.

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Section: Discussionmentioning

confidence: 99%

Genetic Characterization and Diversity of Rhizobium Isolated From Root Nodules of Mid-Altitude Climbing Bean (Phaseolus vulgaris L.) Varieties

et al. 2018

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“…Also, the phylogenetic analysis of sequences of single locus may inadequately reflect the phylogenetic relationship among bacterial strains. Thus, the use of additional gene loci with great sequence divergence and sufficient conserved sequences for phylogenetic analysis has been recommended as an alternative to the analysis of only the 16S-rRNA gene [11].…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils

Puozaa

Jaiswal

Dakora

2019

Systematic and Applied Microbiology

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In the N 2 -fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S–23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S–23S rRNA region yielded single polymorphic bands of varying lengths (573–1298 bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard’s similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes ( glnII, gyrB, and atpD ) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae , Bradyrhizobium elkanii , Bradyrhizobium iriomotense , Bradyrhizobium pachyrhizi , and Bradyrhizobium yuanmingense ) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.

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“…Instead of sequencing an orthologous marker gene, such as the 16S rRNA (Lau, Ren, et al, 2007;Lau et al, 2013;Woo et al, 2014;Yuen et al, 2001), recA (Cesarini, Bevivino, Tabacchioni, Chiarini, & Dalmastri, 2009;Costechareyre et al, 2010;Dai, Liu, & Wang, 2012;McDowell, Perry, Lambert, & Patrick, 2008;Owusu-Kwarteng et al, 2012;Payne et al, 2005;Zhu et al, 2013) or groEL (Leclerque & Kleespies, 2008;Woo, Leung, Wong, Ho, & Yuen, 2001) and subsequently determining the phylogenetic position of the isolate in question to achieve identification, speciesspecific gene amplification represents a more intuitive approach that can be applied in the time-critical setting of a clinical laboratory or the rudimentary setting of field work. While the single-nucleotide resolution of gene sequencing methods enables precise phylogenetic placement and discrimination of closely related clones, species-specific gene amplification typing offers a yes or no, unambiguous answer to the identity of an organism .…”

Section: Identification By Species-specific Gene Amplificationmentioning

confidence: 99%

Gene Amplification and Sequencing for Bacterial Identification

Lau

Teng

et al. 2015

Methods in Microbiology

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Genetic diversity and phylogeny of rhizobia isolated from Caragana microphylla growing in desert soil in Ningxia, China

Cited by 19 publications

References 35 publications

Genetic Characterization and Diversity of Rhizobium Isolated From Root Nodules of Mid-Altitude Climbing Bean (Phaseolus vulgaris L.) Varieties

Genetic Characterization and Diversity of Rhizobium Isolated From Root Nodules of Mid-Altitude Climbing Bean (Phaseolus vulgaris L.) Varieties

Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils

Gene Amplification and Sequencing for Bacterial Identification

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