Samuel Ribeiro Passos

Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil

16S rRNA gene sequence analysis of eight strains (BR 3299(T), BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus Microvirga. Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA-DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus Microvirga. Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera Rhizobium and Mesorhizobium, which are not immediate relatives of the genus Microvirga, as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species, Microvirga lotononidis, Microvirga zambiensis and Microvirga lupini. Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299(T) ( = HAMBI 3457(T)).

Biodiversity of rhizobia associated with cowpea cultivars in soils of the lower half of the São Francisco River Valley

The biodiversity of rhizobium in soils of the Sao Francisco Valley is unknown and can be studied using cowpea as trap plants. The objective of this study was to verify the diversity of diazotrophic bacteria that nodulate cowpea in soils of the lower half of the Sao Francisco River Valley by morphological and genotypic characterization. Seven soil samples (A1, A2, A3, A4, C1, C2 and MC) were collected to capture bacteria associated to five cowpea cultivars (IPA 206, BRS Pujante, BRS Marataoa, Canapu Roxo, and Sempre Verde), in a 5x7 factorial design with three replications. Thirty days after plant emergence, the nodules were collected and the bacteria isolated and analyzed in relation to their growth characteristics in YMA medium. The 581 isolates were grouped in 49 morphologic groups. Of this total, 62.3 % formed colonies in up to three days, 33.4 % grew from the 6 th day on, and 4.3 % began to grow 4 to 5 days after incubation. Regarding the formation of acids and alkalis, 63 % acidified the medium, 12 % made it alkaline and 25 % maintained the medium at neutral pH. The highest diversity was observed in the A3 sample and in isolates associated with the cultivars Canapu Roxo and BRS Pujante. Thirty-eight representative isolates were chosen for the genotypic characterization, clustered in four groups based on the restriction analysis of 16s rDNA. This grouping was strongly correlated with the sampling site; 13 rhizobium isolates had an electrophoretic profile distinct from the standard rhizobium strains used in this study.

Diversidade e capacidade simbiótica de rizóbios isolados de nódulos de Mucuna-Cinza e Mucuna-Anã

Mucuna species are widely used as green manure, and little information is available about rhizobia that can nodulate them. The objective of this study was to evaluate the diversity and ability of bacteria isolated from symbiotic nodules of velvet bean (Mucuna pruriens (L.) DC.) and Mucuna deeringiana (Bort.) Merr. From the nodules of either mucuna species, grown in pots with soils from an agroecological system, 80 bacteria were isolated. The selected bacteria were classified and used to assess the symbiotic capacity. The diversity assessment of the isolates was based on cultural characteristics on YMA medium and the technique of restriction analysis of PCR products of 16S rDNA. The inoculation of Mucuna pruriens with five and Mucuna deeringiana with two isolates increased the aboveground biomass. Most isolates grew rapidly and acidified the culture medium. Restriction analysis showed low similarity of the reference strains with the bacterial isolates, suggesting the existence of isolates belonging to new groups that are able to nodulate the two mucuna species.

Produção e comportamento reológico de exopolissacarídeos sintetizados por rizóbios isolados de guandu

The objective of this work was to evaluate the production and the rheological behavior of exopolysaccharides (EPS) produced by pigeonpea [Cajanus cajan (L.) Millsp.] rhizobia isolates, as well as to evaluate the similarity of these isolates through amplified ribosomal DNA restriction analysis technique. The bacteria were cultured in YM liquid media and the EPS were precipited with cold ethanol from culture broth. After that, they were vacuum dried, weighted, stored and resuspended in water to rheological evaluations. The three evaluated isolates showed differences on the production and productivity of EPS, and the isolate 8.1c stood out, with higher relative efficiency. The evaluated EPS showed non-newtonian and pseudoplastic behavior, however they also presented differences as to the apparent viscosity at the same shear rate. At the shear rate of 1 s-1 all isolates were different, while at the shear rate of 40 s-1 the isolates 53.5 and 30.6a2 were the same, differing from the isolate 8.1c. Genetic similarity of the isolates was in agreement with the rheology results, where bacteria that synthesized EPS with lower apparent viscosity presented the higher similarity

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

Thirteen Gram-negative, aerobic, motile with polar flagella, rod-shaped bacteria were isolated from root nodules of Centrolobium paraense Tul. grown in soils from the Amazon region of Brazil. Growth of strains was observed at temperature range 20–36 °C (optimal 28 °C), pH ranges 5–11 (optimal 6.0–7.0), and 0.1–0.5%NaCl (optimal 0.1–0.3%). Analysis of 16S rRNA gene placed the strains into two groups within Bradyrhizobium. Closest neighbouring species (98.8%) for group I was B. neotropicale while for group II were 12 species with more than 99% of similarity. Multi-locus sequence analysis (MLSA) with dnaK, glnII, recA, and rpoB confirmed B. neotropicale BR 10247T as the closest type strain for the group I and B. elkanii USDA 76T and B. pachyrhizi PAC 48T for group II. Average Nucleotide Identity (ANI) differentiated group I from the B. neotropicale BR 10247T (79.6%) and group II from B. elkanii USDA 76T and B. pachyrhizi PAC 48T (88.1% and 87.9%, respectively). Fatty acid profiles [majority C16:0 and Summed feature 8 (18:1ω6c/18:1ω7c) for both groups], DNA G + C content, and carbon compound utilization supported the placement of the novel strains in the genus Bradyrhizobium. Gene nodC and nifH of the new strains have in general low similarity with other Bradyrhizobium species. Both groups nodulated plants from the tribes Crotalarieae, Dalbergiae, Genisteae, and Phaseoleae. Based on the presented data, two novel species which the names Bradyrhizobium centrolobii and Bradyrhizobium macuxiense are proposed, with BR 10245T (=HAMBI 3597T) and BR 10303T (=HAMBI 3602T) as the respective-type strains.

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

The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp) growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178 bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems.

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil

The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an “eco-friendly agricultural practice”. Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA–DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.

Draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite strain recommended for cowpea inoculation in Brazil.

The strain BR 3267 is a nitrogen-fixing symbiotic bacteria isolated from soil of semi-arid area of Brazilian Northeast using cowpea as the trap plant. This strain is used as commercial inoculant for cowpea and presents high efficient in nitrogen fixation as consequence of its adaptation potential to semi-arid conditions. We report here the draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite bacterium used as inoculant for cowpea. Whole genome sequencing of BR 3267 using Illumina MiSeq sequencing technology has 55 scaffolds with a total genome size of 7,904,309 bp and C+G 63%. Annotation was added by the RAST prokaryotic genome annotation service and has shown 7314 coding sequences and 52 RNA genes.

Draft Genome Sequence of Microvirga vignae Strain BR 3299T, a Novel Symbiotic Nitrogen-Fixing Alphaproteobacterium Isolated from a Brazilian Semiarid Region

ABSTRACT Microvirga vignae is a recently described species of root-nodule bacteria isolated from cowpeas grown in a Brazilian semiarid region. We report here the 6.4-Mb draft genome sequence and annotation of M. vignae type strain BR 3299. This genome information may help to understand the mechanisms underlying the ability of the organism to grow under drought and high-temperatures conditions.

Estrutura metabólica e genética de comunidades bacterianas em solo de cerrado sob diferentes manejos

O objetivo deste trabalho foi avaliar a estrutura metabolica e genetica de comunidades bacterianas em Latossolo de cerrado sob vegetacao nativa ou cultivado em sistema de rotacao soja/milho sob preparo convencional e plantio direto. Foram utilizadas microplacas EcoPlate para determinar o perfil e a diversidade metabolica das comunidades bacterianas, e eletroforese em gel com gradiente desnaturante (DGGE) para avaliar a estrutura genetica. O teste estatistico de Mantel foi utilizado para avaliar a relacao entre a estrutura metabolica e a genetica. A comunidade bacteriana sob vegetacao nativa apresentou perfil metabolico diferente do encontrado em solos cultivados. No solo cultivado com soja sob preparo convencional, o padrao de utilizacao das fontes de carbono diferenciou-se dos demais tratamentos. Com base nos resultados de DGGE, a comunidade bacteriana sob vegetacao nativa apresentou 35% de similaridade com as de areas cultivadas. Foram formados grupos distintos de comunidades bacterianas do solo entre as areas sob preparo convencional e plantio direto. Houve correlacao significativa de 62% entre as matrizes geradas pelas microplacas EcoPlate e pela DGGE. Variacoes no perfil metabolico estao relacionadas as variacoes na estrutura genetica das comunidades bacterianas do solo.