Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Sun, 04 Aug 2019 05:16:33 Paraburkholderia piptadeniae sp. nov. and Paraburkholderia ribeironis sp. nov., two root-nodulating symbiotic species of Piptadenia gonoacantha in Brazil Caroline Bournaud, 1 † Lionel Moulin, 1,2, * Margo Cnockaert, 3 Sergio de Faria, 4 Yves Prin, 1 Dany Severac 5 and Peter Vandamme 3 Abstract During a survey of root-nodulating symbionts of Mimosoid species in the south-east region of Brazil, eight Paraburkholderia isolates were obtained from nodules of the legume species Piptadenia gonoacantha, either from the field or following a soil trapping method with the same plant host. 16S rRNA gene as well as recA and gyrB phylogenetic markers placed these strains in two new clades within the genus Burkholderia sensu lato. DNA–DNA hybridization values and analyses of average nucleotide identities of the whole genome sequence of selected strains in each clade (STM 7183 and STM 7296) showed that the two clades represented novel species of the genus Paraburkholderia. All eight isolates were further characterized using DNA base content determination, chemotaxonomic and biochemical profiling and symbiotic properties, which allowed to distinguish the novel species from known diazotrophic species of the genus Paraburkholderia. Based on genomic and phenotypic data, the names Paraburkholderia piptadeniae sp. nov. with type strain STM 7183 T (=DSM 101189 T =LMG 29163 T ) and Paraburkholderia ribeironis sp. nov. with type strain STM 7296 T (=DSM 101188 T =LMG 29351 T ) are proposed. The genus Burkholderia belongs to the class Betaproteobacte- ria and comprises more than 100 species with validly pub- lished names (www.bacterio.net/burkholderia.html) with new species being frequently described. Recently, two studies have proposed the split of the genus into three genera, with Bur- kholderia sensu stricto encompassing the majority of species causing infections in humans [i.e. Burkholderia cepacia com- plex (BCC) and Burkholderia pseudomallei and close rela- tives], and Paraburkholderia and Caballeronia which both include mainly species that do not cause infections in humans [1, 2]. Yet, both the Paraburkholderia [3] and Caballeronia [4] clades include several species that were reported to cause sporadic human infections. Strains representing the different species of Burkholderia (sensu lato) have been isolated from a wide variety of habitats such as terrestrial and aquatic envi- ronments, and form diverse associations with plants [5]. Among these associations, some species (all belonging to the new genus Paraburkholderia) form nitrogen-fixing nodules with legumes (for review, see [6]) and are therefore consid- ered as rhizobia (i.e. the so-called b-rhizobia). These species harbour nodulation (nod) and nitrogen fixation (nif) genes and form effective N 2 -fixing symbioses with specific clades of legumes, in particular in the large sub-tropical genus Mimosa (tribe Mimoseae) found in the Caatinga and Cerrado biomes in Brazil [7–9]. Currently, 14 species of the genus Parabur- kholderia have been described as containing legume- nodulating strains, including Paraburkholderia aspalathi [10], P. caballeronis [11], P. caribensis [12], P. diazotrophica [13], P. dilworthii [14], P. mimosarum [15], P. nodosa [16], P. phe- noliruptrix [17], P. phymatum and P. tuberum [18], P. rhyn- chosiae [19], P. sabiae [20], P. sprentiae [21] and P. symbiotica [22]. These species can be distinguished through their host spectrum and origin of nodulation genes, as Para- burkholderia strains isolated from nodules of endemic African Author affiliations: 1 Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et M editerran eennes, 34398 Montpellier, France; 2 IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; 3 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; 4 EMBRAPA- Agrobiologia, Km 47 Seropedica, 23851-970 Rio de Janeiro, Brazil; 5 Montpellier GenomiX, c/o Institut de G enomique Fonctionnelle, 141 rue de la Cardonille, 34094 Montpellier Cedex, France. *Correspondence: Lionel Moulin, lionel.moulin@ird.fr Keywords: Burkholderia; rhizobia; legumes; mimosoids; symbiosis; genomes. Abbreviations: ANI, average nucleotide identity; DDH, DNA-DNA hybridization; ML, maximum-likelihood. †Present address: Embrapa Genetic Resources and Biotechnology, Pest-Plant Molecular Interaction Laboratory, Brasilia, Distrito Federal, Brazil. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene, recA and gyrB sequences of P. piptadeniae STM 7183 T are LN875219, LN875227 and LN875234 ,respectively, and for the 16S rRNA gene and gyrB sequences of P. ribeironis STM 7296 T are LN875221 and LN875236, respectively; accession numbers for the 16S rRNA gene, recA and gyrB sequences of other strains of these two species are given in Fig. 1. The genome sequencing data for P. ribeironis STM 7296 T and P. piptadeniae STM 7183 T are under project accession numbers PRJEB10534 and PRJEB10535, respectively; with contigs CYGX01000001–CYGX01000228 and CYGY01000001-CYGY01000281, respectively. NOTE Bournaud et al., Int J Syst Evol Microbiol 2017;67:432–440 DOI 10.1099/ijsem.0.001648 001648 ã 2017 IUMS 432