Occurrence and genetic diversity of rhizobia nodulating Sesbania sesban in African soils

Abstract

The distribution, diversity and relative abundance of Sesbania sesban rhizobia in African soils were investigated by host-trapping and counting of rhizobia and characterization using restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA and the internally transcribed spacer (ITS) between the 16S and 23S rRNA genes. Isolates representative of the diverse 16S rRNA groups from the various soils were selected for sequence analysis of the first 750 bp of the 16S rRNA. Compatible rhizobia were detected in only 15 out of 55 soils, and were present generally in soils with more than 10% clay, and those from low-lying areas. Populations were small, generally much less than 50 cells g −1 soil. The rhizobia nodulating S. sesban were genetically diverse, with isolates bearing 16S rRNA sequences similar to those of rhizobia belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium and Allorhizobium. About 1% of the isolates recovered had sequences with close homology with Agrobacterium tumefaciens. Despite the wide phylogenetic distribution of the rhizobial isolates, the Mesorhizobium group was dominant in all soils examined, accounting for 90% of the isolates on average, with individual soil populations usually being comprised of two genera. There was a marked variability in the sequence and size of the ITS region among rhizobia nodulating Sesbania which indicates a broad diversity of ‘strain’ types both within and between soil populations, and within and between rhizobial genera.