Nitrogen (N), the nutrient most required for plant growth, is key for good yield of agriculturally important crops. Common bean (Phaseolus vulgaris L.) can benefit from bacteria collectively called rhizobia, which are capable of fixing atmospheric nitrogen (N2) in root nodules and supplying it to the plant. Common bean is amongst the most promiscuous legume hosts; several described species, in addition to putative novel ones have been reported as able to nodulate this legume, although not always effectively in terms of fixing N2. In this study, we present data indicating that Brazilian strains PRF 35T, PRF 54, CPAO 1135 and H 52, currently classified as Rhizobium tropici, represent a novel species symbiont of common bean. Morphological, physiological and biochemical properties differentiate these strains from other species of the genus Rhizobium, as do BOX-PCR profiles (less than 60 % similarity), multilocus sequence analysis with recA, gyrB and rpoA (less than 96.4 % sequence similarity), DNA–DNA hybridization (less than 50 % DNA–DNA relatedness), and average nucleotide identity of whole genomes (less than 92.8.%). The novel species is effective in nodulating and fixing N2 with P. vulgaris, Leucaena leucocephala and Leucaena esculenta. We propose the name Rhizobium paranaense sp. nov. for this novel taxon, with strain PRF 35T ( = CNPSo 120T = LMG 27577T = IPR-Pv 1249T) as the type strain.
Published Online:
Funding
This study was supported by the:
CNPq (National Council for Scientific and Technological Development, Brazil)
Project Repensa
(Award 562008/2010-1)
UNAM, Mexico
(Award PAPIIT IN205412)
CAPES (National Council for the Improvement of Higher Education)
CardosoJ. D.,
HungriaM.,
AndradeD. S.(2012). Polyphasic approach for the characterization of rhizobial symbionts effective in fixing N(2) with common bean (Phaseolus vulgaris L.). . Appl Microbiol Biotechnol93, 2035–2049. [View Article][PubMed]
ChueireL. M. O.,
BangelE. V.,
MostassoF. L.,
CampoR. J.,
PedrosaF. O.,
HungriaM.(2003). Classificação taxonômica das estirpes de rizóbio recomendadas para as culturas da soja e do feijoeiro baseada no seqüenciamento do gene 16S rRNA. . Rev Bras Ci Solo27, 833–840. [View Article]
CoenyeT.,
VandammeP.,
GovanJ. R. W.,
LiPumaJ. J.(2001). Taxonomy and identification of the Burkholderia cepacia complex. . J Clin Microbiol39, 3427–3436. [View Article][PubMed]
Dall’AgnolR. F.,
RibeiroR. A.,
Ormeño-OrrilloE.,
RogelM. A.,
DelamutaJ. R.,
AndradeD. S.,
Martínez-RomeroE.,
HungriaM.(2013).Rhizobium freirei sp. nov., a symbiont of Phaseolus vulgaris that is very effective at fixing nitrogen. . Int J Syst Evol Microbiol63, 4167–4173. [View Article][PubMed]
HallT. A.(1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser41, 95–98.
HungriaM.,
AndradeD. S.,
ChueireL. M. O.,
ProbanzaA.,
Guttierrez-MañeroF. J.,
MegíasM.(2000). Isolation and characterization of new efficient and competitive bean (Phaseolus vulgaris L.) rhizobia from Brazil. . Soil Biol Biochem32, 1515–1528. [View Article]
HungriaM.,
CampoR. J.,
MendesI. C.(2003). Benefits of inoculation of the common bean (Phaseolus vulgaris) crop with efficient and competitive Rhizobium tropici strains. . Biol Fert Soils39, 88–93. [View Article]
JordanD. C.(1984). Family III. Rhizobiaceae Conn 1938. . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 234–235. Edited by
KriegN. R.,
HoltJ. G.
. Baltimore:: Williams & Wilkins;.
KimuraM.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol16, 111–120. [View Article][PubMed]
KonstantinidisK. T.,
RametteA.,
TiedjeJ. M.(2006). Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. . Appl Environ Microbiol72, 7286–7293. [View Article][PubMed]
MartensM.,
DelaereM.,
CoopmanR.,
De VosP.,
GillisM.,
WillemsA.(2007). Multilocus sequence analysis of Ensifer and related taxa. . Int J Syst Evol Microbiol57, 489–503. [View Article][PubMed]
Martínez-RomeroE.,
SegoviaL.,
MercanteF. M.,
FrancoA. A.,
GrahamP.,
PardoM. A.(1991).Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. . Int J Syst Bacteriol41, 417–426. [View Article][PubMed]
MennaP.,
BarcellosF. G.,
HungriaM.(2009). Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes. . Int J Syst Evol Microbiol59, 2934–2950. [View Article][PubMed]
MostassoL.,
MostassoF. L.,
DiasB. G.,
VargasM. A. T.,
HungriaM.(2002). Selection of bean (Phaseolus vulgaris L.) rhizobial strains for the Brazilian Cerrados. . Field Crops Res73, 121–132. [View Article]
MousaviS. A.,
ÖstermanJ.,
WahlbergN.,
NesmeX.,
LavireC.,
VialL.,
PaulinL.,
de LajudieP.,
LindströmK.(2014). Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov.. Syst Appl Microbiol37, 208–215. [View Article][PubMed]
Ormeño-OrrilloE.,
MennaP.,
AlmeidaL. G. P.,
OlleroF. J.,
NicolásM. F.,
Pains RodriguesE.,
Shigueyoshi NakataniA.,
Silva BatistaJ. S.,
Oliveira ChueireL. M.& other authors (2012). Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.). . BMC Genomics13, 735. [View Article][PubMed]
RibeiroR. A.,
BarcellosF. G.,
ThompsonF. L.,
HungriaM.(2009). Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity. . Res Microbiol160, 297–306. [View Article][PubMed]
RibeiroR. A.,
RogelM. A.,
López-LópezA.,
Ormeño-OrrilloE.,
BarcellosF. G.,
MartínezJ.,
ThompsonF. L.,
Martínez-RomeroE.,
HungriaM.(2012). Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov.. Int J Syst Evol Microbiol62, 1179–1184. [View Article][PubMed]
RichterM.,
Rosselló-MóraR.(2009). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A106, 19126–19131. [View Article][PubMed]
SlaterS. C.,
GoldmanB. S.,
GoodnerB.,
SetubalJ. C.,
FarrandS. K.,
NesterE. W.,
BurrT. J.,
BantaL.,
DickermanA. W.& other authors (2009). Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. . J Bacteriol191, 2501–2511. [View Article][PubMed]
TigheS. W.,
de LajudieP.,
DipietroK.,
LindströmK.,
NickG.,
JarvisB. D. W.(2000). Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. . Int J Syst Evol Microbiol50, 787–801. [View Article][PubMed]
WangE. T.,
Martínez-RomeroE.(2000). Phylogeny of root- and stem-nodule bacteria associated with legumes. . In Prokaryotic Nitrogen Fixation: a Model System for Analysis of a Biological Process, pp. 177–186. Edited by
TriplettE. W.
. Wymondham:: Horizon Scientific;.