Taxonomic description and draft genome of Pseudomonas sediminis sp. nov., isolated from the rhizospheric sediment of Phragmites karka

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11^T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11^T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11^T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246^T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045^T (99.29%), Pseudomonas toyotomiensis JCM 15604^T (99.15%), Pseudomonas chengduensis DSM 26382^T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016^T (99.08%), and Pseudomonas alcaliphila JCM 10630^T (99.01%). Experimental DNA-DNA relatedness between strain PI11^T and P. indoloxydans JCM 14246^T was 49.4%. The draft genome of strain PI11^T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11^T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C_18:1ω6c/ω7c, C_16:1ω6c/ω7c, and C_16:0. The DNA G + C content of strain PI11^T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11^T was delineated from other closely related type strains. It is proposed that strain PI11^T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11^T (= KCTC 42576^T = DSMZ 100245^T).