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. 2020 Sep;9(9):e1101.
doi: 10.1002/mbo3.1101. Epub 2020 Jul 12.

Pseudomonas glycinae sp. nov. isolated from the soybean rhizosphere

Jiayuan Jia  1 , Xiaoqiang Wang  1   2 , Peng Deng  1 , Lin Ma  1   3 , Sonya M Baird  1 , Xiangdong Li  4 , Shi-En Lu  1
Affiliations

Pseudomonas glycinae sp. nov. isolated from the soybean rhizosphere

Jiayuan Jia et al. Microbiologyopen. 2020 Sep.

Abstract

Strains MS586T and MS82, which are aerobic, Gram-negative, rod-shaped, and polar-flagellated bacteria, were isolated from the soybean rhizosphere in Mississippi. Taxonomic positions of MS586T and MS82 were determined using a polyphasic approach. 16S rRNA gene sequence analyses of the two strains showed high pairwise sequence similarities (>98%) to some Pseudomonas species. Analysis of the concatenated 16S rRNA, rpoB, rpoD, and gyrB gene sequences indicated that the strains belonging to the Pseudomonas koreensis subgroup (SG) shared the highest similarity with Pseudomonas kribbensis strain 46-2T . Analyses of average nucleotide identity (ANI), genome-to-genome distance, delineated MS586T and MS82 from other species within the genus Pseudomonas. The predominant quinone system of the strain was ubiquinone 9 (Q-9), and the DNA G+C content was 60.48 mol%. The major fatty acids were C16:0 , C17:0 cyclo, and the summed features 3 and 8 consisting of C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c, respectively. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. Based on these data, it is proposed that strains MS586T and MS82 represent a novel species within the genus Pseudomonas. The proposed name for the new species is Pseudomonas glycinae, and the type strain is MS586T (accession NRRL B-65441 = accession LMG 30275).

Keywords: Pseudomonas glycinae; average nucleotide identity; rhizosphere; soybean.

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Conflict of interest statement

None declared.

Figures

FIGURE 1
FIGURE 1
Maximum‐likelihood tree illustrating the phylogenetic position of strain MS586T and related members of the genus Pseudomonas using four concatenated gene sequences (3696 bp): 16S rRNA (1326 bp), rpoB (905 bp), rpoD (802 bp), and gyrB (663 bp). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. A. baumannii strain ATCC 19606T was used as the outgroup. Only bootstrap values above 50% are indicated. The colored bar designates groups of Pseudomonas spp. Accession numbers of sequences used in this study are summarized in Table A2
FIGURE 2
FIGURE 2
Whole‐genome sequence tree generated with TYGS for strain MS586T and its closely related species of the genus Pseudomonas. Tree inferred with FastME from GBDP distances was calculated from genome sequences. Branch lengths are scaled in terms of GBDP distance formula d5; numbers above branches are GBDP pseudo‐bootstrap support values from 100 replications. The colored squares designate species cluster. Accession numbers of sequences used in this study are summarized in Table A3
FIGURE A1
FIGURE A1
The cellular morphology of strain MS586T was observed by transmission electron microscopy
FIGURE A2
FIGURE A2
Fingerprinting analysis of strain MS586T and strain MS82 based on analysis of BOX‐PCR: 1, strain MS586T; 2, strain MS82; Mk: 1‐kb DNA ladder (GoldBio) was used with markers
FIGURE A3
FIGURE A3
Two‐dimensional TLC of polar lipids of strain MS586T. DPG, diphosphatidylglycerol; L, lipid; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PL, phospholipid
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