Genome Insights into the Novel Species Microvirga brassicacearum, a Rapeseed Endophyte with Biotechnological Potential.

Jiménez-Gómez Jiménez-Gómez,García-Fraile García-Fraile,Saati-Santamaría Saati-Santamaría,Igual Igual,Mateos Mateos,Rivas Rivas

doi:10.3390/microorganisms7090354

Jiménez-Gómez Jiménez-Gómez, García-Fraile García-Fraile + Show 4 more

Open Access

https://doi.org/10.3390/microorganisms7090354

Copy DOI

Abstract

Plants harbor a diversity of microorganisms constituting the plant microbiome. Many bioinoculants for agricultural crops have been isolated from plants. Nevertheless, plants are an underexplored niche for the isolation of microorganisms with other biotechnological applications. As a part of a collection of canola endophytes, we isolated strain CDVBN77T. Its genome sequence shows not only plant growth-promoting (PGP) mechanisms, but also genetic machinery to produce secondary metabolites, with potential applications in the pharmaceutical industry, and to synthesize hydrolytic enzymes, with potential applications in biomass degradation industries. Phylogenetic analysis of the 16S rRNA gene of strain CDVBN77T shows that it belongs to the genus Microvirga, its closest related species being M. aerophila DSM 21344T (97.64% similarity) and M. flavescens c27j1T (97.50% similarity). It contains ubiquinone 10 as the predominant quinone, C19:0 cycloω8c and summed feature 8 as the major fatty acids, and phosphatidylcholine and phosphatidylethanolamine as the most abundant polar lipids. Its genomic DNA G+C content is 62.3 (mol %). Based on phylogenetic, chemotaxonomic, and phenotypic analyses, we suggest the classification of strain CDVBN77T within a new species of the genus Microvirga and propose the name Microvirga brassicacearum sp. nov. (type strain CDVBN77T = CECT 9905T = LMG 31419T).

Highlights

After millions of years of evolution, microorganisms have compiled a noteworthy genetic diversity with biotechnological potential, which can be enhanced by tools, such as genetic engineering or heterologous gene expression
The comparison of the 16S rRNA gene sequence with those of type strains of described species available in GenBank and EzBiocloud databases showed that all strains but CDVBN77T showed similarities higher than 98% with their closest related type strains, whereas the similarity of strain CDVBN77T with M. aerophila DSM 21344T, its closest related type strain, was only 97.64%, which according to the threshold value of 98.7% in the 16S rRNA gene sequence with the closest related species indicated by Jongsik and collaborators [2] indicates that the strain constitutes a new species within the genus Microvirga
We performed a phylogenetic analysis of the 16S rRNA gene sequence of strain CDVBN77T and those of the type strains of all species included within the genus Microvirga

Summary

Introduction

After millions of years of evolution, microorganisms have compiled a noteworthy genetic diversity with biotechnological potential, which can be enhanced by tools, such as genetic engineering or heterologous gene expression. According to recent estimations, potentially 99.999% of microbial taxa remain undiscovered [1], so there is a huge genetic potential yet undiscovered. In the last couple of decades, the extensive use of the PCR and sequencing of the 16S rRNA gene has allowed a more accurate bacterial identification and served as the base for the discovery of new taxa, being the gold standard for prokaryote identification. The quick development of DNA sequencing platforms that generate rapid and low-cost high-throughput sequencing data has spearheaded the widespread sequencing of bacterial genomes which, together with the development of bioinformatics tools for genome sequence comparisons, facilitates the process of new species identification, by means of genome-to-genome sequence comparison [2]

Methods

Results

Conclusion