Characterization and identification of some indigenous Rhizobia using 16S rDNA sequence analysis

Abstract

ENGLISH : The use of different characteristics (the polyphasic approach) to describe bacterial taxa is a prerequisite for a stable classification. The taxonomy of root- and stem-nodulating rhizobia is in a state of transition. As more legumes are studied, new species and genera of rhizobia are described. It is important to study the indigenous South African rhizobia, as without them a complete rhizobial taxonomy is not possible. Furthermore, strains with superior nitrogen fixation abilities may be discovered. Indigenous strains better adapted to the harsh South African environment are possible candidates for commercial inoculants for cropped legumes.Only two local studies have been done on the diversity of the indigenous rhizobia. These studies revealed the diversity of rhizobia existing in the South African context. As part of a polyphasic approach used to identify and determine the diversity of the indigenous rhizobia, 16S rDNA sequencing analysis was performed on some selected rhizobial and putative rhizobial isolates. The aim of the study was to characterise and identify the indigenous isolates by 16S rDNA sequencing analysis and compare our data with those available in the GenBank database. Results showed that most of the indigenous isolates were slow-growers belonging to the genus Bradyrhizobium. Two isolates from supposedly non-nodulating legume genera (Cassia and Senna) were found to belong to the genus Bradyrhizobium. Some of the isolates were shown to belong to the genera Mesorhizobium, Rhizobium and Sinorhizobium. The identity of five isolates was not clear and further studies need to be performed to unequivocally determine their taxonomic position. Partial sequence analysis of 16S rDNA proved a valuable tool to characterise and identify the indigenous isolates. However, the method was unable to clearly distinguish between closely related species and strains. AFRIKAANS : 'n Stabiele klassifikasiesisteem vir die beskrywing van bakteriese taksa is slegs moontlik deur verskillende eienskappe (die poli-fasiese benadering) te gebruik. Die taksonomie van die wortel- en stamnodulerende rhizobiums verander gedurig. 'n Volledige rhizobiumtaksonomie is slegs moontlik indien die inheemse Suid-Afrikaanse rhizobiums bestudeer word. Geharde inheemse rasse met voortreflike stikstofbindende vermoens kan ontdek word. Hierdie rasse is kandidate vir kommersiele inokulums vir verboude peulplante. Net twee plaaslike studies is gedoen om die diversiteit van die inheemse rhizobiums te bepaal. Die studies het bewys dat die inheemse rhizobiums baie divers is. As deel van die polifasiese benadering om die diversiteit van die inheemse rhizobiums te identifiseer en te bepaal, is 16S rDNS volgordebepaling gedoen op uitgesoekte rhizobia en sogenaamde rhizobia isolate. Die doel van die studie was die karakterisering en identifisering van die inheemse isolate deur 16S rDNS volgordebepaling en die vergelyking van die data met die beskikbaar in die GenBank databasis. Die resultate wys dat die meeste inheemse isolate stadige groeiers is en dus behoort aan die genus Bradyrhizobium. Twee isolate vanaf sogenaamde nie-nodulerende peulplantgenusse (Cassia en Senna) behoort ook tot die genus Bradyrhizobium. Sommige isolate behoort tot die genusse Mesorhizobium, Rhizobium en Sinorhizobium. Die identiteit van vyf isolate was nie duidelik nie en verdere studies is nodig om hul taksonomiese posisie ondubbelsinnig te bepaal. Die gedeeltelike volgordebepaling van die 16S rDNS was 'n waardevolle hulpmiddel om die inheemse isolate mee te karakteriseer en te identifiseer, alhoewel die metode nie tussen nabyverwante spesies en rasse kon onderskei nie. Copyright