Limnohabitans radicicola sp. nov., a slow-growing bacterium isolated from rhizosphere of rice plant and emended description of the genus Limnohabitans

Abstract

In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859(T) (98.2%) followed by Limnohabitans curvus KCTC 42562(T) (98%), Limnohabitans planktonicicus II-D5(T) (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2D(T) (97.4%). Growth of strain JUR4(T) occurred at 10-37 degrees C (optimum, 30 degrees C), at pH 5.5-8.0 (optimum, 6.5-7) and in the presence of 0-0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4(T) was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4(T) and closely related reference strains were 21.0-24.8% and 74.7-81.4%, respectively. Strain JUR4(T) contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C-16:0 and summed feature 3 (comprising C-16:1 omega 7c and/or C-16:1 omega 6c), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4(T) represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4(T) (=KACC 21745(T)=NBRC 114484(T)).