Pseudogemmobacter sonorensis sp. nov., a new alphaproteobacterium isolated from the slime flux of a tree (Populus fremontii) in the Sonoran Desert (Arizona, USA).

Abstract

The bacterial strain PA1-206B^T is a Gram-stain-negative, aerobic, non-motile and non-spore-forming bacterium with an irregular rod shape. It was isolated from a tree wound exudate of the Populus fremontii trunk in the Sonoran Desert (USA), and its taxonomic position was investigated by a polyphasic approach. Strain PA1-206B^T grew optimally at 28-30 °C and from pH 6 to 10 without NaCl. Based on 16S rRNA gene sequence analysis, this isolate showed only 96.0% sequence similarity to the type strain of Pseudogemmobacter hezensis and similarity of 94.4-95.7% to other species of the genus. Phylogenetic analysis based on whole-proteome comparisons placed strain PA1-206B^T within the genus Pseudogemmobacter but, on a distinct branch, clearly separated from its closest relatives. The major isoprenoid quinone of the strain was ubiquinone Q-10. The predominant fatty acids (>5%) were C_18:1  ω7c, C_16:0 and 11-methyl-C_18:1  ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids were present. The assembled draft genome of strain PA1-206B^T had 115 contigs with a total length of 4.5 Mb and a G+C content of 67.4 mol%. The overall genome-related indices (average nucleotide identity <80.4%, average amino acid identity <70.6%, digital DNA-DNA hybridization <21.6%) with respect to close relatives were below the corresponding threshold to demarcate bacterial species. Strain PA1-206B^T (=DSM 115559^T=NCAIM B.02680^T) is suggested as the type strain of a novel Pseudogemmobacter species, for which the name Pseudogemmobacter sonorensis sp. nov. is proposed.