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

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Abstract

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 774T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3T, Caulobacter zeae 410Tand Caulobacter radices 695T, all with sequence similarities of 99.9%. The genome size of strain774T 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 774T. The average nucleotide identity values and digital DNA–DNA hybridization values of the strain774T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774T 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 774T represents a novel species of the genus Caulobacter, for which the name Caulobacter endophyticus sp. nov. is proposed with 774T (= CGMCC 1.16558T = DSM 106777T) as the type strain.

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Acknowledgements

This research work was supported financially by the National Natural Science Foundation of China (No. 31870003), Science & Technology Innovation Project of Beijing Academy of Agricultural and Forestry Sciences (KJCX20200426), Science & Technology Innovation Project of Beijing Academy of Agricultural and Forestry Sciences (KJCX20200110) and Beijing Postdoctoral Research Foundation (2020-ZZ-106).

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  1. Jun-lian Gao and Pengbo Sun have contributed equally to this work.

Authors and Affiliations

  1. Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People’s Republic of China

    Jun-lian Gao, Yu-chen Sun, Jing Xue, Guoliang Wang, Li-wei Wang, Yunpeng Du & Xiuhai Zhang

  2. Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Pengbo Sun & Jian-guang Sun

  3. Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany

    Pengbo Sun

  4. College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People’s Republic of China

    Yu-chen Sun

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Contributions

JGS and XHZ designed research and project outline. JLG, PBS, YCS, LWW and JX performed isolation, deposition and polyphasic taxonomy. PBS, GLW and YPD performed genome analysis. JLG and YCS drafted the manuscript. PBS, JGS and XHZ revised the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Xiuhai Zhang or Jian-guang Sun.

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Gao, Jl., Sun, P., Sun, Yc. et al. Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root. Antonie van Leeuwenhoek 114, 1213–1224 (2021). https://doi.org/10.1007/s10482-021-01593-9

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