Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)

Petra Patakova; Maryna Vasylkivska; Karel Sedlar; Katerina Jureckova; Matej Bezdicek; Petra Lovecka; Barbora Branska; Petr Kastanek; Karel Krofta

doi:10.3389/fmicb.2024.1305338

Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)

Front Microbiol. 2024 Feb 8:15:1305338. doi: 10.3389/fmicb.2024.1305338. eCollection 2024.

Authors

Petra Patakova¹, Maryna Vasylkivska¹, Karel Sedlar^{2

3}, Katerina Jureckova², Matej Bezdicek^{4

5}, Petra Lovecka⁶, Barbora Branska¹, Petr Kastanek⁷, Karel Krofta⁸

Affiliations

¹ Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia.
² Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia.
³ Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany.
⁴ Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czechia.
⁵ Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czechia.
⁶ Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia.
⁷ Ecofuel Laboratories s.r.o., Prague, Czechia.
⁸ Hop Research Institute, Co. Ltd., Zatec, Czechia.

Abstract

Background: This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.

Methods: P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.

Results and discussion: The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.

Keywords: Pantoea agglomerans; genome characterization; gluconic acid; hops endophyte; plant growth promotion.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research was supported by the TACR NPO project no. TN02000044/01. This work is a part of the project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 101023766.