Taxonomic characterization of Paraburkholderia tuberum-like rhizobia from diverse legumes

Abstract

Paraburkholderia tuberum is an indigenous South African bacterial species and one of the first rhizobia to be described in the class Beta-proteobacteria. In the past two decades, numerous strains identified as P. tuberum or P. tuberum-like were isolated from several papilionoid legumes in South Africa, as well as from South and Central American Mimosa species. These two groups of isolates were found to contain different nodulation and nitrogen-fixation genes, suggesting that they might belong to different species. The main aim of this study was, therefore, to investigate the taxonomic status of these presumed P. tuberum isolates previously recovered from the root nodules of diverse legumes from the Core Cape Region (CCR) of South Africa, from the Caatinga, the Cerrado and the Pantanal of Brazil, and from western Mexico. The South African isolates associate with several genera in the Papilionoideae (e.g., Cyclopia, Virgilia, Hypocalyptus, Podalyria and Aspalathus) and with Vachellia karroo from the mimosoid clade. The Brazilian and Mexican isolates associate with several Mimosa species from the mimosoid clade in the Caesalpinioideae. A set of 31 South African, 28 South American and 2 Central American isolates were assigned to potential species using genealogical concordance analysis. This was accomplished by identifying unique and consistent clades across the genealogies inferred from the nucleotide sequences of independent housekeeping genes (i.e., atpD, gyrB, gltB, rpoB, acnA, pab and 16S rRNA). Subsequently, overall genome relatedness data and phenotypic characteristics were determined to seek support for the putative species. In this way, three species of rhizobial Paraburkholderia were discovered and described. The first is indigenous to South Africa, for which we propose the name P. podalyriae sp. nov. with the type strain WC7.3bT (= LMG 31413T; SARCC 750T). The other two species have Brazilian origins, and we propose the names P. simonii sp. nov. with the type strain JPY169T (= LMG 31411T; SARCC751T) and P. youngii sp. nov. with the type strain JPY251T (= LMG 31412T; SARCC752T).