Abstract
Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015–6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively. The three genomes encode for secondary metabolites, with 38, 33 and 46 genes found to be associated with polyketide synthases/non-ribosomal peptide synthases and nine, seven and ten genes encoding for bacteriocins, respectively. The genome of strain AB308 encodes for one questionable prophage and three incomplete prophages, while only incomplete prophages were predicted in AB215 and AB57 genomes. Genetic and genomic data indicate that strains AB308, AB215 and AB57 are each representative of a new Mycobacterium species that we respectively named Mycobacterium terramassiliense, Mycobacterium numidiamassiliense and Mycobacterium rhizamassiliense.
Highlights
Non-tuberculous mycobacteria are known to belong to some rhizospheres
The matrix-assisted laser desorption/ionization time of flight (MALDI-TOF-MS) peptide profile derived from strains AB308, AB215 and AB57 did not match any of the profiles entered in the Bruker database; and differed from one strain to the two other ones
Phylogenetic tree based on the16S rDNA gene sequence indicated that these three isolates are distinguishable from their closest species belonging to the M. simiae complex (Fig. 2)
Summary
Non-tuberculous mycobacteria are known to belong to some rhizospheres. An Illumina-based analysis of core actinobacteriome revealed that organisms of the genus Mycobacterium were the organisms the most commonly detected in roots of rice plants after organisms of the genera Pseudonocardia and Dietzia; whereas mycobacteria were less frequent in stem and absent in seeds[1]. Mycobacterium phlei isolated from the wheat rhizosphere3,exhibited beneficial effects on wheat growth under saline conditions[4]. Using a drastic decontamination protocol and an improved culture medium for mycobacteria named MOD95 we isolated three endophytic mycobacteria closely associated with the roots of tomato plants; and characterized them as representative of three new Mycobacterium species; expanding the repertoire of cultured rhizosphere mycobacteria; and characterizing features unique to rhizosphere mycobacteria
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