Publication detail

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

PATÁKOVÁ, P. VASYLKIVSKA, M. SEDLÁŘ, K. JUREČKOVÁ, K. BEZDÍČEK, M. LOVECKÁ, P. BRANSKÁ, B. KAŠTÁNEK, P. KROFTA, K.

Original Title

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

Type

journal article in Web of Science

Language

English

Original 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 DBM 3797; Humulus lupulus L.; whole genome sequencing

Authors

PATÁKOVÁ, P.; VASYLKIVSKA, M.; SEDLÁŘ, K.; JUREČKOVÁ, K.; BEZDÍČEK, M.; LOVECKÁ, P.; BRANSKÁ, B.; KAŠTÁNEK, P.; KROFTA, K.

Released

8. 2. 2024

Publisher

FRONTIERS MEDIA SA

ISBN

1664-302X

Periodical

Frontiers in Microbiology

Year of study

15

Number

Neuvedeno

State

Swiss Confederation

Pages from

1

Pages to

15

Pages count

15

URL

https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305338/full

BibTex

@article{BUT188076,
  author="Petra {Patáková} and Maryna {Vasylkivska} and Karel {Sedlář} and Kateřina {Šabatová} and Matěj {Bezdíček} and Petra {Lovecká} and Barbora {Branská} and Petr {Kaštánek} and Karel {Krofta}",
  title="Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)",
  journal="Frontiers in Microbiology",
  year="2024",
  volume="15",
  number="Neuvedeno",
  pages="1--15",
  doi="10.3389/fmicb.2024.1305338",
  issn="1664-302X",
  url="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305338/full"
}