title: Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa.
abstract: Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native regions, relatively few taxa have been formally described. For example, the Cape Floristic Region of South Africa is thought to represent one of the major centres of diversity for the rhizobial members of Burkholderia, yet only five species have been described from legumes occurring in this region and numerous are still awaiting taxonomic treatment. Here, we investigated the taxonomic status of 12 South African root-nodulating Burkholderia isolates from native papilionoid legumes (Hypocalyptus coluteoides, H. oxalidifolius, H. sophoroides and Virgilia oroboides). Analysis of four gene regions (16S rRNA, recA, atpD and rpoB) revealed that the isolates represent a genealogically unique and exclusive assemblage within the genus. Its distinctness was supported by all other aspects of the polyphasic approach utilized, including the genome-based criteria DNA-DNA hybridization (≥70.9%) and average nucleotide identities (≥96%). We accordingly propose the name B. kirstenboschensis sp. nov. for this taxon with isolate Kb15(T) (=LMG 28727(T); =SARC 695(T)) as its type strain. Our data showed that intraspecific genome size differences (≥0.81 Mb) and the occurrence of large DNA regions that are apparently unique to single individuals (16-23% of an isolate's genome) can significantly limit the value of data obtained from DNA-DNA hybridization experiments. Substitution of DNA-DNA hybridization with whole genome sequencing as a prerequisite for the description of Burkholderia species will undoubtedly speed up the pace at which their diversity are documented, especially in hyperdiverse regions such as the Cape Floristic Region.
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Emma.steenkamp@up.ac.za.
authors.forename: Emma T
authors.initials: ET
authors.lastname: Steenkamp
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Elritha.vanzyl@fabi.up.ac.za.
authors.forename: Elritha
authors.initials: E
authors.lastname: van Zyl
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Chrizelle.beukes@fabi.up.ac.za.
authors.forename: Chrizelle W
authors.initials: CW
authors.lastname: Beukes
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Juanita.avontuur@fabi.up.ac.za.
authors.forename: Juanita R
authors.initials: JR
authors.lastname: Avontuur
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Annie.chan@fabi.up.ac.za.
authors.forename: Wai Yin
authors.initials: WY
authors.lastname: Chan
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Marike.duplessis@fabi.up.ac.za.
authors.forename: Marike
authors.initials: M
authors.lastname: Palmer
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: MthombeniL@dwa.gov.za.
authors.forename: Lunghile S
authors.initials: LS
authors.lastname: Mthombeni
authors.affiliation: Agricultural Research Council (ARC), Plant Protection Research Institute, Pretoria, Gauteng, South Africa. Electronic address: PhalaneF@arc.agric.za.
authors.forename: Francina L
authors.initials: FL
authors.lastname: Phalane
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Theodorah.Sereme@ZA.nestle.com.
authors.forename: T Karabo
authors.initials: TK
authors.lastname: Sereme
authors.affiliation: Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa. Electronic address: Fanus.venter@up.ac.za.
authors.forename: Stephanus N
authors.initials: SN
authors.lastname: Venter
mesh_terms: D042521:Burkholderiaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D007887:Fabaceae / Q000382:microbiology*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D006180:Proton-Translocating ATPases / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011938:Rec A Recombinases / Q000235:genetics; D053204:Root Nodules, Plant / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013019:South Africa
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D011938:Rec A Recombinases; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D006180:Proton-Translocating ATPases
keywords: Average nucleotide identity (ANI); Beta-rhizobia; Burkholderia; DNA−DNA hybridization; Hypocalyptus; Virgilia