title: Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci.
abstract: The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic analysis of the genes responsible for their symbiotic abilities (i.e., those encoded on the nodulation [nod] and nitrogen-fixation [nif] loci) has facilitated the development of an extensive phylogeographic framework for the genus. This framework however contains only a few nodulating isolates from Africa. Here we focused on nodulating Bradyrhizobium isolates associated with native southern African legumes in the tribes Genisteae and Crotalarieae found along the Great Escarpment in the Mpumalanga Province of South Africa. The aims of this study were to: (1) obtain rhizobial isolates from legumes in the Genisteae and Crotalarieae; (2) verify their nodulation ability; (3) characterize them to species level based on phylogenetic analyses of several protein coding gene regions (atpD, dnaK, glnII, recA, rpoB and gyrB) and (4) determine their placement in the phylogeographic framework inferred from the sequences of the symbiotic loci nodA and nifD. Twenty of the 21 Bradyrhizobium isolates belonged to six novel species, while one was conspecific with the recently described B. arachidis. Among these isolates, the nodA phylogeny revealed several new clades, with 18 of our isolates found in Clades XIV and XV, and only three forming part of the cosmopolitan Clade III. These strains formed predominantly the same groups in the nifD phylogeny although with slight differences; indicating that both vertical and horizontal inheritance of the symbiotic loci occurred. These findings suggest that the largely unexplored diversity of indigenous African rhizobia are characterized by unique ancestries that might mirror the distribution of their hosts and the environmental factors driving their evolution.
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa. Electronic address: chrizelle.beukes@fabi.up.ac.za.
authors.forename: Chrizelle W
authors.initials: CW
authors.lastname: Beukes
authors.affiliation: Warsaw Agricultural University, ul. Nowoursynowska 166, 02-787 Warsaw, Poland. Electronic address: sttommic@yahoo.co.uk.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Stępkowski
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa. Electronic address: Fanus.venter@up.ac.za.
authors.forename: Stephanus N
authors.initials: SN
authors.lastname: Venter
authors.affiliation: Department of General and Environmental Microbiology, Poznań University of Life Sciences, ul. Szydłowska 50, 60-637 Poznań, Poland. Electronic address: tom.clapa@gmail.com.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Cłapa
authors.affiliation: Agricultural Research Council (ARC), Plant Protection Research Institute, Private Bag X134, Queenswood 0121, South Africa. Electronic address: PhalaneF@arc.agric.za.
authors.forename: Francina L
authors.initials: FL
authors.lastname: Phalane
authors.affiliation: South African National Biodiversity Institute (SANBI), Pretoria National Botanical Garden, Pretoria 0002, South Africa; Department of Botany and Plant Biotechnolog, University of Johannesburg, P.O. Box 524, South Africa. Electronic address: M.LeRoux@sanbi.org.za.
authors.forename: Marianne M
authors.initials: MM
authors.lastname: le Roux
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa. Electronic address: Emma.steenkamp@up.ac.za.
authors.forename: Emma T
authors.initials: ET
authors.lastname: Steenkamp
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D020369:Bradyrhizobium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D007887:Fabaceae / Q000235:genetics / Q000382:microbiology*; D058885:Multilocus Sequence Typing; D009586:Nitrogen Fixation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013019:South Africa; D013559:Symbiosis
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Bradyrhizobium; Crotalarieae; Genisteae; Phylogeography; nifD; nodA