Diversity and description of Bradyrhizobium species associated with invasive Acacia species in South Africa

Abstract

Chapter one of this dissertation provides a review of the literature pertaining to the bionts (i.e., rhizobia) and their role in both crop legumes and invasive Acacia. In the review, an emphasis was placed on Bradyrhizobium associating with invasive Acacia species in South Africa. The review also explored the current prospects for the taxonomy of rhizobia. The research presented in Chapter Two aimed to determine the taxonomic position of Bradyrhizobium species isolated from the root nodules of Acacia dealbata, Acacia decurrens and Acacia mearnsii in a previous study. This was achieved using various analyses typically used in studies focusing on bacterial systematics and delimiting species. These included delimited species based on the genealogical concordance of five housekeeping genes (i.e., 16S rRNA, dnaK, glnII, rpoB and recA), comparison with a multi-locus phylogenetic tree that was generated using the concatenated sequences of the individual genes, as well as calculating average nucleotide identities (ANIs) from whole genomes obtained in this study and those available from public databases. Conventional phenotypic tests were also done to associate phenotypic characteristics with the recognized species. In Chapter three, the research presented aimed to increase the knowledge of Bradyrhizobium diversity occurring in the root nodules of A. mearnsii, A. dealbata and A. decurrens growing in invasive settings. For this purpose, samples were obtained from sites in the KwaZulu Natal and Mpumalanga provinces of South Africa. Bacterial strains were isolated from the root nodules of the plants. The strains were identified through 16S rRNA sequencing analysis, and only strains identified as Bradyrhizobium using this approach were further used. The Bradyrhizobium strains were delineated into putative species using genealogical concordance analysis with sequences for the housekeeping genes gyrB, glnII, and rpoB. Multilocus sequence analysis was also conducted with the concatenated sequences for the rpoB and glnII genes to gain further support for the species identified. Lastly, phylogeographic inferences regarding the symbiotic properties were made based on phylogenetic analysis of sequences of the common nodulation gene nodA.