Developing a genomic-based strategy to confirm microbial identity in bio-inputs containing multiple strains: an easy, fast, and low-cost multiplex PCR applied to inoculants carrying soybean Bradyrhizobium.

Brazil stands out in research, industrial development, and farmers' use of microbial inoculants, with an emphasis on getting benefits from the biological nitrogen fixation process with the soybean crop. Nowadays, about 140 million doses of inoculants are commercialized annually for the soybean in the country, and strain identification is achieved by rep-PCR, an effective but time-consuming method. Aiming to develop an easy, low-cost, and low-time-consuming method, we used a complete genome-based approach based on the unequivocal identification of unique genes present in the genomes of each of the four Bradyrhizobium strains used in commercial inoculants: Bradyrhizobium elkanii strains SEMIA 587 and SEMIA 5019, Bradyrhizobium japonicum SEMIA 5079, and Bradyrhizobium diazoefficiens SEMIA 5080.

Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417.

Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.

Unlocking the growth-promoting and antagonistic power: A comprehensive whole genome study on Bacillus velezensis strains.

Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B.

The outstanding diversity of rhizobia microsymbionts of common bean (Phaseolus vulgaris L.) in Mato Grosso do Sul, central-western Brazil, revealing new Rhizobium species.

Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization.

Genomes of two type strains of the group: CCGE524 and CCGE526.

The genome sequences of two nitrogen-fixing type strains of the group were obtained: CCGE524 and CCGE526. Genomic analyses confirmed their taxonomic position and identified three complete sequences of the genes, indicative of three plasmids, one of them carrying symbiotic genes.

Genome Sequencing of Efficient Plant Growth-Promoting Bacteria for Lowland Rice.

The genomes of five elite strains identified as growth promoters of lowland rice (Oryza sativa L.) in Brazil were sequenced. They ranged in size from 3,695,387 bp to 5,682,101 bp, encompassing genes of saprophytic ability and stress tolerance.

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation.

Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N, and a major example relies on the high contribution associated with the soybean (, contrasting with the low rates reported with the common bean () crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances.

Genetic variation in symbiotic islands of natural variant strains of soybean and differing in competitiveness and in the efficiency of nitrogen fixation.

Soybean is the most important legume cropped worldwide and can highly benefit from the biological nitrogen fixation (BNF) process. Brazil is recognized for its leadership in the use of inoculants and two strains, CPAC 15 (=SEMIA 5079) and CPAC 7 (=SEMIA 5080) compose the majority of the 70 million doses of soybean inoculants commercialized yearly in the country. We studied a collection of natural variants of these two strains, differing in properties of competitiveness and efficiency of BNF.

Microbiological quality analysis of inoculants based on Bradyrhizobium spp. and Azospirillum brasilense produced "on farm" reveals high contamination with non-target microorganisms.

The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L.

Genomic Insights Into the Antifungal Activity and Plant Growth-Promoting Ability in CMRP 4490.

The main objective of this study was to evaluate strain CMRP 4490 regarding its ability to inhibit soil-borne plant pathogens and to increase plant growth. The study included evaluation of antifungal control, sequencing the bacterial genome, mining genes responsible for the synthesis of secondary metabolites, root colonization ability, and greenhouse studies for the assessment of plant growth-promoting ability. The strain was obtained from soil samples in the north of Paraná in Brazil and was classified as a , which is considered a promising biological control agent.

Whole-Genome Sequence of Bioactive Compound-Producing Pseudomonas aeruginosa Strain LV.

is known for a high adaptive capacity due to the ability to synthesize several compounds that give advantages for competing with other microorganisms in the environment. The LV strain synthesizes bioactive compounds, mainly by secondary metabolism, with antitumor and antimicrobial activities against microbial pathogens.

Phylogeny of symbiotic genes reveals symbiovars within legume-nodulating Paraburkholderia species.

Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes.

Genetic diversity of species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species sp. nov.

strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as , but with low phylogenetic resolution.

Paraburkholderia atlantica sp. nov. and Paraburkholderia franconis sp. nov., two new nitrogen-fixing nodulating species isolated from Atlantic forest soils in Brazil.

A polyphasic study was conducted with 11 strains trapped by Mimosa pudica and Phaseolus vulgaris grown in soils of the Brazilian Atlantic Forest. In the phylogenetic analysis of the 16S rRNA gene, one clade of strains (Psp1) showed higher similarity with Paraburkholderia piptadeniae STM7183 (99.6%), whereas the second (Psp6) was closely related to Paraburkholderia tuberum STM678 (99%).

sp. nov., a nitrogen-fixing lineage isolated from nodules of the caesalpinioid species and characterized by tolerance to high temperature .

The symbioses between legumes and nitrogen-fixing rhizobia make the greatest contribution to the global nitrogen input via the process of biological nitrogen fixation (BNF). stands out as the main genus nodulating basal Caesalpinioideae. We performed a polyphasic study with 11 strains isolated from root nodules of , an annual multi-functional native legume of the USA.

sp. nov., an effective nitrogen-fixing symbiont of partridge pea [ (Michx.) Greene], a native caesalpinioid legume broadly distributed in the USA.

Information about the symbionts of legumes of the Caesalpinioideae subfamily is still limited, and we performed a polyphasic approach with three strains-CNPSo 3448, CNPSo 3394 and CNPSo 3442-isolated from , a native legume broadly distributed in the USA. In the phylogenetic analysis of both the 16S rRNA gene and the intergenic transcribed spacer, the CNPSo strains were clustered within the superclade. Multilocus sequence analysis with six housekeeping genes-, , , , and -indicated that is the closest species, with 83 % of nucleotide identity.

Paraburkholderia guartelaensis sp. nov., a nitrogen-fixing species isolated from nodules of Mimosa gymnas in an ecotone considered as a hotspot of biodiversity in Brazil.

A polyphasic approach was used to infer the phylogenetic position of six nitrogen-fixing symbiotic bacteria isolated from Mimosa gymnas nodules grown in an ecotone between the Brazilian biomes of Atlantic Forest and Cerrado, considered as a hotspot of biodiversity. The 16S rRNA gene phylogeny indicated the highest similarity with Paraburkholderia oxyphila (98.7-98.

Draft Genome Sequence of Bradyrhizobium elkanii Strain SEMIA 938, Used in Commercial Inoculants for spp. in Brazil.

Due to its high capacity for nitrogen fixation, strain SEMIA 938 is used in commercial inoculants for lupins in Brazil. Its genome was estimated at 8,780,064 bp and indicates that it belongs to the species, while the analysis of nodulation genes classifies the strain in the symbiovar sojae.

Draft Genome Sequence of Strain CNPSo 3391, Isolated from a Soybean Nodule in Mozambique.

strain CNPSo 3391 was isolated from a soybean nodule in Mozambique. Its genome size was estimated at 4,926,588 bp. This isolate carries several coding sequences for stress tolerance, but no identifiable nodulation or virulence genes.

Draft Genome Sequence of Vancomycin-Resistant Enterococcus faecium UEL170 (Sequence Type 412), Isolated from a Patient with Urinary Tract Infection in a Tertiary Hospital in Southern Brazil.

Enterococcus faecium is a leading cause of health care-associated infections, with specific lineages circulating in hospital settings worldwide. Here, we report the draft genome sequence of the multidrug-resistant and biofilm-producing E. faecium UEL170, sequence type 412 (ST412), isolated from an inpatient with a urinary tract infection.

Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist of Fungal Plant Pathogens.

strain LABIM40 holds high potential for biological control of plant pathogens. Its complete genome contains one chromosome of 3,972,310 bp with 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in the suppression of fungal pathogens.

Draft Genome Sequences of Azospirillum brasilense Strains Ab-V5 and Ab-V6, Commercially Used in Inoculants for Grasses and Legumes in Brazil.

strains Ab-V5 and Ab-V6 are largely used in commercial inoculants for grasses and legumes in Brazil. Their genomes were estimated at 6,934,595 and 7,197,196 bp, respectively, and encompass genes related to nitrogen fixation, synthesis of phytohormones, and environmental adaptation. Although the strains differ in phenotypic properties, their genomes are highly similar.

Draft Genome Sequence of Strain 1.38, a Bacterium Isolated from the Rhizosphere of var. Puntal That Shows Biotechnological Potential as an Inoculant.

1.38 is a strain isolated from the rhizosphere of irrigated rice in southern Spain. Its genome was estimated at 4,869,281 bp, with 4,644 coding sequences (CDSs).