Massilia arenosa sp. nov., isolated from the soil of a cultivated maize field

Abstract

<jats:p>Strain MC02<jats:sup>T</jats:sup>, a Gram-stain-negative, rod-shaped bacterium, was isolated from field soil collected from California, USA. To examine if MC02<jats:sup>T</jats:sup> represents a novel species, we compared its colony morphology, 16S rRNA gene and whole genome sequence, and its metabolic phenotype using Biolog GenIII and MALDI-TOF analyses compared to reference strains. Based on 16S rRNA gene and whole genome sequencing, MC02<jats:sup>T</jats:sup> belongs to the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1713" xlink:type="simple">Massilia</jats:ext-link> </jats:named-content> </jats:italic> and <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.30550" xlink:type="simple">Massilia agri</jats:ext-link> </jats:named-content> </jats:italic> K-3–1<jats:sup>T</jats:sup> is the most similar strain with 96.97 % 16S rRNA gene sequence identity. MALDI-TOF analysis revealed that <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.13412" xlink:type="simple">Massilia aerilata</jats:ext-link> </jats:named-content> </jats:italic> DSM19289<jats:sup>T</jats:sup> is the closest match, but the similarity score was much lower than the ≥1.7 threshold for a reliable identification at the genus level. The predominant fatty acids were summed feature 3 (C<jats:sub>16 : 1</jats:sub>⍵7<jats:italic>c</jats:italic> and/or C<jats:sub>16 : 1</jats:sub>⍵6<jats:italic>c</jats:italic>; 49.07 %) and C<jats:sub>16 : 0</jats:sub> (30.01 %). The genome is 5.02 Mbp and the G+C content is 66.2 mol%. Whole genome comparisons to the closest related strains revealed an average amino acid identity value of 67.4 %, an OrthoANI similarity of 77.1 %, and a DNA–DNA-hybridization probability ≥70 %, confirming that MC02<jats:sup>T</jats:sup> represents a novel species. Strain MC02<jats:sup>T</jats:sup> can grow at pH 6 but not at pH 5, and a salt concentration of ≥1 % inhibits its growth. In contrast to other <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1713" xlink:type="simple">Massilia</jats:ext-link> </jats:named-content> </jats:italic> strains, MC02<jats:sup>T</jats:sup> can utilize turanose, inosine and <jats:sc>l</jats:sc>-serine. The genome of MC02<jats:sup>T</jats:sup> shows putative endophyte genes such as a nitrate reductase, several phosphatases, and biotin biosynthesis genes, 26 flagellar motility genes and 14 invasion and intracellular resistance genes. Based on its metabolic, physiological and genomic characteristics, we propose that strain MC02<jats:sup>T</jats:sup> (NRRL B-65554<jats:sup>T</jats:sup>=ATCC TSD-200<jats:sup>T</jats:sup>=LMG 31737<jats:sup>T</jats:sup>) represents a novel species of the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1713" xlink:type="simple">Massilia</jats:ext-link> </jats:named-content> </jats:italic> with the name <jats:italic>Massilia arenosa</jats:italic> sp. nov.</jats:p>

Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae

“…Based on this analysis, strains ONC3 T and M1 T show similarities in their metabolic profile and are both most closely positioned to M. arenosa MC02 T [53] (Fig. 3).…”

“…Based on this analysis, strains ONC3 T and M1 T show similarities in their metabolic profile and are both most closely positioned to M. arenosa MC02 T [53] (). Strain M1 T does not cluster with N. denitrificans TSA40 and differs particularly in its ability to utilize several amino acids from this strain (Table S2).…”

Novel Effects of Leonardite-Based Applications on Sugar Beet

“…belongs to the Oxalobacteraceae family, and among this family, we detected also the genus Massilia. Massilia is the richest genus of the Oxalobacteraceae family, isolated from roots and leaves, with plant growth-promoting activity and diseasesuppressive abilities, while Oxalicibacterium is considered the most specialized oxalate degrader (Bonanomi et al, 2018;Raths et al, 2020). Oxalate is a secondary metabolite, widely reported in plants and soils, and a major component of root exudate with a key role in the recruitment of soil microbial species (Martin et al, 2012;Baldani et al, 2014).…”

Massilia soli sp. nov., isolated from soil

“…The draft genome size of strain R798 T was 4 990 115 bp and 4597 total genes, 4527 protein coding genes and 58 tRNA genes were predicted from the genome sequence. The G+C content of strain R798 T calculated from the draft whole genome sequence was 63.3 mol%, which was within the range (62.6 to 66.7 mol%) of the G+C contents of Massilia members [1–13]. The draft genome sequence of strain R798 T was deposited to GenBank with the accession number JAFBIL000000000.…”

“…Cells of Massilia members are generally aerobic, Gram-negative, catalase-positive, oxidasevariable and motile or non-motile rods containing ubiquinone-8 (Q-8) as the major respiratory quinone and summed feature 3 (comprising C 16 : 1 ω7c and/or iso-C 15 : 0 2-OH) and C 16 : 0 as the major fatty acids. Massilia members have a very wide range of genome size (3.46-8.49 Mb) with 62.7-66.7 mol% G+C contents [1][2][3][4][5][6][7][8][9][10][11][12][13]. Analysis of ecologically meaningful bacteria is essential for understanding the function of soil bacterial communities.…”