Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum

To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242 T , was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242 T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242 T grew at pH 6.0–9.0 (optimum, pH 7.0) and 10–45 °C (optimum 37 °C), in the presence of 0–8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242 T clustered with Sinomicrobium pectinilyticum 5DNS001 T and S. oceani SCSIO 03483 T , and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001 T , S. oceani SCSIO 03483 T and all the other current type strains. Strain HD2P242 T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C 17 : 0 , iso-C 16 : 0 3-OH, anteiso-C 17 : 0 and summed feature 6 (C 19 : 1 ω 9 c and/or C 19 : 1 ω 11 c ). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA–DNA hybridization values of strain HD2P242 T with S. oceani SCSIO 03483 T and S. pectinilyticum 5DNS001 T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242 T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d -glucose by the glycolysis–gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242 T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242 T (=CGMCC 1.19025 T =KCTC 92136 T ).