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Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants

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Abstract

A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4–95.6%), Aquabacterium (95.9–95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30 °C in the presence of 1–6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8–76.3% and 19.4–21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711 T = NBRC 114717 T).

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Abbreviations

ANI:

Average amino acid identity

IAA:

Indole acetic acid

KCTC:

Korean Collection for Type Cultures

NBRC:

Biological resource Centre, NITE

MEGA:

Molecular Evolutionary Genetics Analysis

NJ:

Neighbour-joining

ML:

Maximum-likelihood

MP:

Maximum-parsimony

UBCG:

Up-to-date bacterial core gene

DPG:

Diphosphatidylglycerol

PE:

Phosphatidylethanolamine

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Funding

This work was supported by the National Institute of Biological Resources (NIBR) grant, funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202002203), and by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020R1F1A1072647).

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Authors and Affiliations

  1. Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea

    Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Minchung Kang, Yoonseop So & Taegun Seo

Authors
  1. Geeta Chhetri
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  2. Jiyoun Kim
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  3. Inhyup Kim
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  4. Minchung Kang
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  5. Yoonseop So
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  6. Taegun Seo
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Contributions

GC isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, and wrote the original draft; MK, JK, IK, YS helped with the analysis of taxonomic data; TS designed and supervised the study, and edited the original draft.

Corresponding author

Correspondence to Taegun Seo.

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This study does not describe any experimental work related to human.

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Repositories The draft genome and 16S rRNA gene sequences of strain ROOL2T have been deposited in GenBank/EMBL/DDBJ under accession numbers JACVVX000000000 and MN904860 respectively.

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Chhetri, G., Kim, J., Kim, I. et al. Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants. Antonie van Leeuwenhoek 114, 1925–1934 (2021). https://doi.org/10.1007/s10482-021-01651-2

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