Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root

• Published in: Antonie van Leeuwenhoek 2021-08, Vol.114 (8), p.1213-1224
• Main Authors: Gao, Jun-lian, Sun, Pengbo, Sun, Yu-chen, Xue, Jing, Wang, Guoliang, Wang, Li-wei, Du, Yunpeng, Zhang, Xiuhai, Sun, Jian-guang
• Format: Article
• Language: English
• Subjects: Acetic acid; Bacteria; Biomedical and Life Sciences; Corn; Deoxyribonucleic acid; DNA; Endophytes; Fatty acids; Flagella; Gene clusters; Genes; Genomes; Glycerol; Glycolipids; Gram stain; Hybridization; Indoleacetic acid; Life Sciences; Lipids; Medical Microbiology; Microbiology; New species; Nucleotide sequence; Nucleotides; Original Paper; Peptides; Phylogeny; Plant Sciences; Quinones; rRNA 16S; Sequence analysis; Soil Science & Conservation; Ubiquinone
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-021-01593-9

A novel Gram-stain-negative, aerobic and rod-shaped bacterium with a single polar flagellum or a stalk at the end of the cell, was isolated from maize roots in the Fangshan District of Beijing, People’s Republic of China. The new strain designated 774 T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774 T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3 T , Caulobacter zeae 410 T and Caulobacter radices 695 T , all with sequence similarities of 99.9%. The genome size of strain774 T was 5.4 Mb, comprising 5042 predicted genes with a DNA G+C content of 68.7%.Three striking lasso peptide biosynthetic gene clusters and two IAA synthesis genes belonging to the TPM pathway were also found in the genome of strain 774 T . The average nucleotide identity values and digital DNA–DNA hybridization values of the strain774 T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774 T were identified as C16: 0 (27.7%), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) (12.6%) and summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) (42.9%).The major polar lipids consisted of phosphatidyl–glycerol and glycolipids. The predominant ubiquinone was identified as Quinone 10. Based on the polyphasic characterization, strain 774 T represents a novel species of the genus Caulobacter , for which the name Caulobacter endophyticus sp. nov. is proposed with 774 T (= CGMCC 1.16558 T  = DSM 106777 T ) as the type strain.