Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots

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.

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth

“…The actinobacteria Mycobacterium genus is rather common in the rhizosphere and plant tissues ( Conn and Franco, 2004 ; Pirttila et al, 2005 ; Mano et al, 2007 ; Quambusch et al, 2014 ; Wang et al, 2016 ; Bouam et al, 2018 ) but its occurrence in plants has been underestimated due to the requirement for special media growth conditions ( Mano et al, 2007 ). A diversity of the Mycobacterium species has been documented for rice and tomato plants, as well as in vitro cultures ( Koskimaki et al, 2010 ; Wang et al, 2016 ; Bouam et al, 2018 ). Some species of Mycobacterium have been reported to suppress undifferentiated Scots pine tissue growth in vitro and reduce the length of hypocotyls of seedlings, but similar negative effects have not been observed for other species ( Laukkanen et al, 2000 ).…”

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

“…NTM are frequently isolated from plants. M. terramassiliense , M. rhizamassiliense , and M. numidiamassiliense were first described in tomato plant roots [ 210 ] and M. sarraceniae and M. helvum were first isolated in the pitcher plant in Minnesota sphagnum peat bogs [ 211 ]. M. avium was detected in the stems and leaves of different plant species after internalization into plant tissue through intact, as well as damaged, root systems, which can imply the role of plants in the spread and transmission of mycobacteria to other organisms in the environment [ 212 ].…”

Two New Cases of Pulmonary Infection by Mycobacterium shigaense, Japan

“…A core genes phylogenetic tree for genome sequences of 19 M. simiae complex and M. avium 104 was reconstructed by using Roary version 3.11.2 ( 10 ) ( Figure 2 ). M. shigaense strains were most closely related to M. rhizamassiliense ( 11 ); KC8 was less related to M. shigaense JCM 32072 T than to M. shigaense SCY. Raw sequence reads of M. shigaense KC8 and M. shigaense KC354 were deposited in the DNA Data Bank of Japan Sequence Read Archive (DNA Sequence Read Archive, https://www.ddbj.nig.ac.jp/dra/index.html ) under study accession no.…”