Rhizobium altiplani sp. nov., isolated from effective nodules on Mimosa pudica growing in untypically alkaline soil in central Brazil

Abstract

Root nodule bacteria were isolated from nodules on Mimosa pudica L. growing in neutral-alkaline soils from the Distrito Federal in central Brazil. The 16S rRNA gene sequence analysis of 10 strains placed them into the genus Rhizobium with the closest neighbouring species (each with 99 % similarity) being Rhizobium grahamii, Rhizobium cauense, Rhizobium mesoamericanum and Rhizobium tibeticum. This high similarity, however, was not confirmed by multi-locus sequence analysis (MLSA) using three housekeeping genes (recA, glnII and rpoB), which revealed R. mesoamericanum CCGE 501T to be the closest type strain (92 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with majority being C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c)], DNA G+C content (57.6 mol%), and carbon compound utilization patterns supported the placement of the novel strains in the genus Rhizobium. Results of average nucleotide identity (ANI) differentiated the novel strains from the closest species of the genus Rhizobium, R. mesoamericanum, R. grahamii and R. tibeticum with 89.0, 88.1 and 87.8 % similarity, respectively. The symbiotic genes essential for nodulation (nodC) and nitrogen fixation (nifH) were most similar (99-100 %) to those of R. mesoamericanum, another Mimosa-nodulating species. Based on the current data, these 10 strains represent a novel species of the genus Rhizobium for which the name Rhizobium altiplani sp. nov. is proposed. The type strain is BR 10423T (=HAMBI 3664T).

Soil characteristics determine the rhizobia in association with different species of Mimosa in central Brazil

“…Rhizobium strains that predominated in Posse were recovered in our phylogenetic analyses as closely related to R. altiplani and to other Rhizobium strains isolated from Mimosa species. R. altiplani was recorded associated with M. pudica growing in an anthropogenic neutral to alkaline soil (pH 7.7) in the Distrito Federal in central Brazil (Baraúna et al 2016). Isolates obtained from nodules of Mimosa spp.…”

“…One possible reason for such high prevalence of Paraburkholderia is that previous studies have mainly sampled in sites of low fertility acidic soils, which are more typical in the Cerrado region, the main centre of Mimosa diversity (Simon and Proença 2000). For the very few previous records of Rhizobium isolation from Mimosa carried out in this biome, there is no specific information on soil characteristics, except for that of R. altiplani, which was isolated from M. pudica growing in an alkaline soil substrate in a disturbed area close to Brasília (Baraúna et al 2016). It is important to consider that several patches of highly-fertile limestone soil associated with seasonally dry forests, such as those found in Posse, occur in central Brazil.…”

“…Evaluation of nodulation capacity Confirmation of nodulation capacity was verified by means of an authentication experiment. The species M. pudica L. was chosen as a Bmodel host^because it is a fast-growing species and has an ability to nodulate with a wide range of rhizobia, mainly β-proteobacteria (Chen et al 2005a;Bontemps et al 2010;Mishra et al 2012), but also some Rhizobium species (Elliott et al 2009; Baraúna et al 2016). Seeds were sterilized and their dormancy was broken as cited before.…”

“…The α-proteobacteria isolates grouped in a clade containing three Rhizobium strains from the study of Bontemps et al (2016) and with R. altiplani, a newly-described species of Rhizobium associated with M. pudica in central Brazil (Baraúna et al 2016) (Fig. 2).…”

Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil

“…The ANI approach has recently been accepted as an alternative to the traditional DNA: DNA hybridization method (Delamuta et al 2016;Baraúna et al 2016) and similarity values >95-96% are considered as the threshold to determine if two bacterial strains belong to the same species (Richter and Rosselló-Mora 2009).…”