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

Abstract

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 HD2P242T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242T 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 HD2P242T clustered with Sinomicrobium pectinilyticum 5DNS001T and S. oceani SCSIO 03483T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001T, S. oceani SCSIO 03483T and all the other current type strains. Strain HD2P242T 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-C17 : 0, iso-C16 : 0 3-OH, anteiso-C17 : 0 and summed feature 6 (C19 : 1  ω9c and/or C19 : 1  ω11c). 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 HD2P242T with S. oceani SCSIO 03483T and S. pectinilyticum 5DNS001T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242T 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 HD2P242T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242T (=CGMCC 1.19025T=KCTC 92136T).