Enterobacter oligotrophica sp. nov., a novel oligotroph isolated from leaf soil

Abstract

A novel oligotrophic bacterium, designated strain CCA6, was isolated from leaf soil collected in Japan. Cells of the strain were found to be a Gram-negative, non-sporulating, motile, rod-shaped bacterium. Strain CCA6 grew at 10-45°C (optimum 20°C) and pH 4.5-10.0 (optimum pH 5.0). The strain was capable of growth in poor-nutrient (oligotrophic) medium, and growth was unaffected by high-nutrient medium. The major fatty acid and predominant quinone system were C_16:0 and ubiquinone-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain CCA6 presented as a member of the family Enterobacteriaceae. Multilocus sequence analysis (MLSA) based on fragments of the atpD, gyrB, infB, and rpoB gene sequences was performed to further identify strain CCA6. The MLSA showed clear branching of strain CCA6 with respect to Enterobacter type strains. The complete genome of strain CCA6 consisted of 4,476,585 bp with a G+C content of 54.3% and comprising 4,372 predicted coding sequences. The genome average nucleotide identity values between strain CCA6 and the closest related Enterobacter type strain were <88.02%. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain CCA6 (=HUT 8142^T =KCTC 62525^T ) can be considered as a novel species within the genus Enterobacter with the proposed name Enterobacter oligotrophica.

Keywords: Enterobacter; Voges-Proskauer test; average nucleotide identity value analysis; genome sequence; multilocus sequence analysis; oligotroph.

Figure 1

Phylogenetic tree constructed from analysis of 16S rRNA gene sequences showing the relationships between strain CCA6 and the related type strains. The bar indicates a 0.02% nucleotide substitution rate. The tree was rooted using Xenorhabdus nematophila ATCC 19061^T as the outgroup

Figure 2

Phylogenetic tree reconstructed from analysis of the sequences of four housekeeping genes (atpD, gyrB, infB, and rpoB) and showing the relationships between strain CCA6 and the related type strains. The bar indicates a 0.1% nucleotide substitution rate. The tree was rooted using X. nematophila ATCC 19061^T as the outgroup

Figure A1

Growth rates at 30°C of strain CCA6 and E. coli MG1655. The results for strain CCA6 and E. coli MG1655 are shown as filled and open symbols, respectively. The media are indicated as follows: circles, Nutrient Broth (pH 7.0) and squares, LB media (pH 7.0). The OD₆₀₀ was measured using a Bio Microplate Reader HiTS (Scinics, Tokyo, Japan). Experiments were performed in triplicate

Figure A2

Effects of culture conditions on growth of strain CCA6. (a) Effects of culture temperature. Cells were cultured in Nutrient Broth (pH 7.0). (b) Effects of culture pH. Cells were cultured in Nutrient Broth at 30°C. (c) Effect of NaCl concentration. Cells were cultured in Nutrient Broth (pH 7.0) at 30°C. Error bars indicate SE (n = 3)