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Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China

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Abstract

During characterization of rhizobacteria, strain DBTS2T was isolated from the rhizosphere soil samples of healthy tomato plants and characterized using a polyphasic taxonomic approach. Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Rhizobium and was most closely related to Rhizobium subbaraonis JC85T (99.1%) and Rhizobium daejeonense CCBAU 10050T (97%). Cells of strain DBTS2T were Gram-negative, short rod, aerobic and non-motile. This novel strain was found to grow at 20–45 °C (optimum 25–37 °C), pH 5–9 (optimum 8) and in the presence of 4% NaCl. It was positive for catalase and oxidase. The predominant cellular fatty acids were Summed Feature 8 (52.7%) and C19:0 cyclo ω8c (23.3%). The polar lipids of strain DBTS2T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid, unidentified aminolipid, four unidentified phospholipids, unidentified lipid, phosphatidylcholine, unknown glycolipid and unknown aminophosphoglycolipids. Q-10 was the major quinone. The DNA–DNA hybridization similarity values between the strain DBTS2T and R. subbaraonis JC85T, R. daejeonense CCBAU 10050T and Rhizobium azooxidifex DSM100211T were 46.4%, 20.7% and 25.5%, respectively. The ANI value was 91.96% between strain DBTS2T and R. subbaraonis JC85T and 75.18% between strain DBTS2T and R. daejeonense CCBAU 10050T. The DNA G+C content of the genomic DNA was 63.1 mol%. Based on these results, it was concluded that the isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium rhizolycopersici sp. nov. is proposed, with DBTS2T (= CICC 24887T = ACCC61707 = JCM 34245) as the type strain.

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Abbreviations

ANI:

Average nucleotide identity

DDH:

DNA–DNA hybridization

GGDC:

Genome-to-genome distance calculator

YMA:

Yeast mannitol agar

R2A:

Reasoner’s 2A agar

NA:

Nutrient agar

NJ:

Neighbor-joining

ML:

Maximum-likelihood

MP:

Maximum-parsimony

HPLC:

High-performance liquid chromatography

TLC:

Thin-layer chromatography; Q-10, ubiquinone 10

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Funding

Funding was provided by Key Technologies Research and Development Program of China (CN) (2019YFD1002001), the Program of Science and Technology of Beijing (Z191100004019025) and Fundamental Research Funds for Central Non-profit Scientific Institution (No. 1610132019015).

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Correspondence to Xiaoxia Zhang.

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The GenBank/ENA/DDBJ accession numbers for the 16S rRNA gene sequence of strain DBTS2T is MT703880. The whole-genome sequence of strains DBTS2T has been deposited into GenBank/ ENA /DDBJ under accession number JABXYK000000000.

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Thin, K.K., He, SW., Wang, X. et al. Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China. Curr Microbiol 78, 830–836 (2021). https://doi.org/10.1007/s00284-020-02323-6

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