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

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dc.contributor.authorPatáková, Petracs
dc.contributor.authorVasylkivska, Marynacs
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorŠabatová, Kateřinacs
dc.contributor.authorBezdíček, Matějcs
dc.contributor.authorLovecká, Petracs
dc.contributor.authorBranská, Barboracs
dc.contributor.authorKaštánek, Petrcs
dc.contributor.authorKrofta, Karelcs
dc.coverage.issue2cs
dc.coverage.volume15cs
dc.date.accessioned2025-02-03T14:40:07Z
dc.date.available2025-02-03T14:40:07Z
dc.date.issued2024-02-08cs
dc.description.abstractBackground 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.en
dc.formattextcs
dc.format.extent1-15cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationFrontiers in Microbiology. 2024, vol. 15, issue 2, p. 1-15.en
dc.identifier.doi10.3389/fmicb.2024.1305338cs
dc.identifier.issn1664-302Xcs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.orcid0000-0001-5143-9521cs
dc.identifier.other188076cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.researcheridAAC-2736-2019cs
dc.identifier.scopus56309904900cs
dc.identifier.scopus57205673155cs
dc.identifier.urihttps://hdl.handle.net/11012/249903
dc.language.isoencs
dc.publisherFrontierscs
dc.relation.ispartofFrontiers in Microbiologycs
dc.relation.urihttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305338/fullcs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1664-302X/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectPantoea agglomerans DBM 3797en
dc.subjectHumulus lupulus L.en
dc.subjectwhole genome sequencingen
dc.titleWhole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)en
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-188076en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:40:07en
sync.item.modts2025.01.17 15:16:13en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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