Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils

Abstract

Root nodule bacteria were trapped within cowpea (Vigna unguiculata) in soils with different cultivation histories collected from the Amazonian rainforest in northern Brazil. Analysis of the 16S rRNA gene sequences of six strains (BR 3351 T , BR 3307, BR 3310, BR 3315, BR 3323 BR and BR 3361) isolated from cowpea nodules showed that they formed a distinct group within the genus Bradyrhizobium, which was separate from previously identified type strains. Phylogenetic analyses of three housekeeping genes (glnII, recA and rpoB) revealed that Bradyrhizobium huanghuaihaiense CCBAU 23303 T was the most closely related type strain (96 % sequence similarity or lower). Chemotaxonomic data, including fatty acid profiles (predominant fatty acids being C 16 : 0 and summed feature 8), the slow growth rate and carbon compound utilization patterns supported the assignment of the strains to the genus Bradyrhizobium. The results of DNA-DNA hybridizations, antibiotic resistance and physiological tests differentiated these novel strains from the most closely related species of the genus Bradyrhizobium with validly published names. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped the novel strains of the genus Bradyrhizobium together with Bradyrhizobium iriomotense strain EK05 T , with 94 % and 96 % sequence similarity, respectively. Based on these data, these six strains represent a novel species for which the name Brabyrhizobium manausense sp. nov. (BR 3351 T 5HAMBI 3596 T ), is proposed.The family Leguminosae is one of the most abundant plant families in the Amazonian rainforest (AR) with more than 1240 species and 140 genera of all three subfamilies (Caesalpinioideae, Mimosoideae and Papilionoideae) catalogued (Ducke, 1949;Silva et al., 1988). This family is ecologically and economically important to the biome, because it contains pioneer species that revegetate bare soils, species that produce grain for food and species used for timber production. Many legume species are capable of forming root (or sometimes stem) nodules, which contain nitrogen-fixing bacterial symbionts, collectively known as 'rhizobia ' (Sprent, 1995). The capacity to nodulate appears to be the rule for leguminous plants within the AR, since more than 80 % of species of the subfamilies Papilionoideae and Mimosoideae do it; however, only about 20 % of the Caesalpinioideae are capable of forming nodules (de Faria, et al., 1989(de Faria, et al., , 2010Moreira, et al., 1993). Legumes contribute significantly to the AR N-balance, with more than 1006 10 8 kg of nitrogen being fixed annually (Salati et al., 1982;Martinelli et al., 1992;Gehring, et al., 2005).Bacteria of the genus Bradyrhizobium have been reported to comprise the majority of root nodule bacteria isolated from The GenBank/EMBL/DDBJ accession number for the 16S rRNA, glnII, recA, rpoB, dnaK, gyrB, nodC and nifH gene sequences of BR3351 T are HQ641226, KF785986, KF785992, KF785998, KF786000, KF786001, KF786002 and KF786003, respectively. Abbreviation: AR, Amazonian ra...

Phylogenetic Analysis of Symbiotic Bacteria Associated with Two <i>Vigna</i> Species under Different Agro-Ecological Conditions in Venezuela

“…In Venezuela, these types of soils are common in traditional cropping systems, such as in Trujillo where CaCO 3 is added before and during Vigna cultivation (Casanova, 2005). Silva et al (2014) reported that in the Brazilian rainforest, Vigna was mainly nodulated by Bradyrhizobium, which is consistent with the present results. However, the isolates classified as Ensifer and Bradyrhizobium showed more biogeographic specificity than Rhizobium.…”

“…In the case of β-rhizobia, Venezuelan Paraburkholderia displayed nodulation, whereas ARA was not detected, which is consistent with previous findings in Brazil (Ferreira et al, 2012;Silva et al, 2014). Brazilian isolates related to P. fungorum were found in Amazonian soil (Brazil) using P. vulgaris (Ferreira et al, 2012;Silva et al, 2014), and explains the result obtained with LaV14 suggesting the presence of horizontal gene transfer between α-and β-rhizobia isolates in Venezuelan soils. B. elkanii was previously reported to be widely distributed in tropical soils (Barcellos et al, 2007;Radl et al, 2014).…”

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil

“…Cowpea ( Vigna unguiculata L. Walp) is a leguminous species able to nodulate and fix nitrogen with various rhizobium species in different continents. 1 , 2 , 3 , 4 Besides that, it is an important protein source for peoples’ nutrition and its cultivation is increasing in Brazil, being the cerrado biome the new agricultural frontier. BR 3262 is on the list of recommended strains for cowpea inoculation in Brazil and it was assigned as Bradyrhizobium member.…”

Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut

“…S2) methods. The level of similarity of concatenated partial sequences of the glnII , recA , gyrB and dnaK genes (1710 nt) was 100 % for the four Group A isolates, and they showed highest sequence similarity of 94, 93.4, 92.3 and 94.9 %, respectively, with Bradyrhizobium manausense BR 3351 T (Silva et al , 2014) (, Table S2), which is also their sister taxon in the 16S rRNA gene tree, although B. ganzhouense RITF806 T showed fewer nucleotide differences (). The three strains of Group B also had identical combined sequence for the core genes and shared highest similarity of 91.4, 94.5, 94.6 and 97.7 %, respectively, with Bradyrhizobium yuanmingense CCBAU 10071 T (Yao et al , 2002) (, Table S2), although the closest neighbour was B. diazoefficiens USDA 110 T in the 16S rRNA gene sequence tree ().…”