Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut ( Arachis hypogaea L.) in South Africa

Abstract

Groundnut is an economically important N​2-fixing legume that can contribute about 100–190 kg N ha−1 to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.

Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique

“…Multiple alleles in the rRNA operon of bacteria account for spacer variations between and among species and can be used for typing and identification of rhizobial species ( 38 ). The ITS ribosomal genes have been shown to be good markers for assessing rhizobial diversity ( 16 ). In this study, ITS-PCR analysis grouped the 99 rhizobial isolates into 17 distinct ITS types, which showed very high polymorphism (258 to 1,350 bp) within the ITS region of the rhizobial genomic DNA.…”

“…Such studies are important for generating a genetic resource base from which highly adapted and efficient rhizobial strains are selected for inoculant production ( 15 ). Therefore, well-tested, quick methods are required for differentiating rhizobial isolates ( 16 ). PCR of the BOX element (BOX-PCR) and PCR-restriction fragment length polymorphism (RFLP) analyses have become powerful tools for detecting diversity among rhizobial isolates at the genome level ( 16 , 17 ).…”

Can Bradyrhizobium strains inoculation reduce water deficit effects on peanuts?

“…Comparison of the almost complete sequence (1268 nt) of the 16S rRNA gene of strain ESA 123 showed that this isolate is classified within the B. japonicum clade with the most similarity to the strain type 14-3 T B. kavangense. This species has recently been described, isolated from peanut nodules in Namibia (Grönemeyer et al 2015) and bacteria with sequences of the 16S rRNA gene related to B. kavangense were later isolated in South Africa (Jaiswal et al 2017) and in Brazil (Santos et al 2017a). Although the 16S rRNA gene sequence shows high similarity (98.97%) to B. kavangense, the ESA 123 strain may represent a new species, since the taxonomy of Bradyrhizobium is complex and cannot be elucidated only with the 16S rRNA allele (Hungria et al 2015).…”

Técnicas aplicadas en la investigación agrícola para cuantificar la fijación de nitrógeno: una revisión sistemática

“…Los genes nifH se encuentran diversificados y su transcripción está controlada por la ARN polimerasa, que es una holoenzima alternativa, y también necesita una proteína activadora nifA (Satyanarayana, Krishna, Pavan, & Jeereddy, 2018). Otros genes identificados por PCR son 16S rRNA (Akemi et al, 2017;Jaiswal, Msimbira, & Dakora, 2017;Tahon & Willems, 2017), porque permite una clasificación filogenética más detallada a nivel de especie (Osei, Abaidoo, Ahiabor, & Boddey, 2018;Ribeiro et al, 2018), genes rec A, atpD, gln II y nod C con análisis de secuencia multilocus (MLSA) (Leite et al, 2017;Mwenda, Hara, De Meyer, Howieson, & Terpolilli, 2018;Rigonato et al, 2017). Con esta técnica, se ha logrado identificar el gen nifH en géneros Paenibacillus, Enterobacter, Klebsiella y Pantoea (Ndungu et al, 2018), que no son reconocidos por fijar nitrógeno, de modo que es posible que hayan obtenido la capacidad de fijación de nitrógeno a través de la transferencia lateral de genes; sin embargo, las fuerzas evolutivas de la transferencia lateral de genes no son bien conocidas (Khalifa & AlMalki, 2018).…”