Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Motyka-Pomagruk, Agata; Żołędowska, Sabina; Misztak, Agnieszka; Śledź, Wojciech; Mengoni, Alessio; Łojkowska, Ewa

doi:10.1186/s12864-020-06863-w

Cited by 18 publications

(28 citation statements)

References 107 publications

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“…The second most abundant category of genes in the pan-genome was general function predicted only including 989 genes and then by genes related to transcription (K) including 803 genes. The over representation of "poorly characterized genes" and "general function predicted only" in the COG categories is similar to what has been observed in other pan-genome studies (Sood et al, 2019;Gaba et al, 2020;Motyka-Pomagruk et al, 2020). Regulation at the transcriptional initiation level is probably the most common scenario for metabolic adaptation in bacteria (Leyn et al, 2013;Arrieta-Ortiz et al, 2015).…”

Section: The Pan-genome Of the Bp Bacteriasupporting

confidence: 83%

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Gong

Liu

et al. 2021

Front. Microbiol.

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BackgroundMembers of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.ResultsPhylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair.ConclusionOur results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strain’s adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.

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Section: The Pan-genome Of the Bp Bacteriasupporting

confidence: 83%

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Gong

Liu

et al. 2021

Front. Microbiol.

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“…Finally, augmentation in the concentration of NH4NO3 in the FLC solution led to a linear increase in σ, likely as a result of the elevation in the concentration of electric charge carriers in the liquid. It is worth noticing that both species selected for this study, namely P. atrosepticum and D. solani, belong to the highly homogenous [52][53][54][55] representatives of the Pectobacteriaceae family. P. atrosepticum strains have been commonly isolated from seed potato fields in temperate climate regions for more than a century [56], while D. solani is believed to be an emerging pathogen of high economic importance [7].…”

Section: Selection Of the Optimal Experimental Conditions For Production Of The Nh 4 No 3 -Based Pals Of The Highest Electrical Conductivmentioning

confidence: 99%

Multivariate Optimization of the FLC-dc-APGD-Based Reaction-Discharge System for Continuous Production of a Plasma-Activated Liquid of Defined Physicochemical and Anti-Phytopathogenic Properties

Dzimitrowicz

Jamróz

Babinska

et al. 2021

IJMS

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To the present day, no efficient plant protection method against economically important bacterial phytopathogens from the Pectobacteriaceae family has been implemented into agricultural practice. In this view, we have performed a multivariate optimization of the operating parameters of the reaction-discharge system, employing direct current atmospheric pressure glow discharge, generated in contact with a flowing liquid cathode (FLC-dc-APGD), for the production of a plasma-activated liquid (PAL) of defined physicochemical and anti-phytopathogenic properties. As a result, the effect of the operating parameters on the conductivity of PAL acquired under these conditions was assessed. The revealed optimal operating conditions, under which the PAL of the highest conductivity was obtained, were as follows: flow rate of the solution equaled 2.0 mL min−1, the discharge current was 30 mA, and the inorganic salt concentration (ammonium nitrate, NH4NO3) in the solution turned out to be 0.50% (m/w). The developed PAL exhibited bacteriostatic and bactericidal properties toward Dickeya solani IFB0099 and Pectobacterium atrosepticum IFB5103 strains, with minimal inhibitory and minimal bactericidal concentrations equaling 25%. After 24 h exposure to 25% PAL, 100% (1−2 × 106) of D. solani and P. atrosepticum cells lost viability. We attributed the antibacterial properties of PAL to the presence of deeply penetrating, reactive oxygen and nitrogen species (RONS), which were, in this case, OH, O, O3, H2O2, HO2, NH, N2, N2+, NO2−, NO3−, and NH4+. Putatively, the generated low-cost, eco-friendly, easy-to-store, and transport PAL, exhibiting the required antibacterial and physicochemical properties, may find numerous applications in the plant protection sector.

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“…1 , G C A _ 0 0 3 6 2 8 0 2 5 . 1 , JABAOP000000000 and JABAOQ000000000 (Zoledowska et al 2018a;Motyka-Pomagruk et al 2020).…”

Section: Plant Materialsunclassified

The occurrence of bacteria from different species of Pectobacteriaceae on seed potato plantations in Poland

et al. 2020

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Bacteria from the genera Dickeya and Pectobacterium, the causative agents of soft rot and blackleg, trigger significant economic losses in potato production worldwide. Efficient struggle with these phytopathogens is highly challenging taking into consideration the lack of available control procedures. As only preventive measures are accessible, we decided to provide insight into the soft rot Pectobacteriaceae (SRP) present in Poland. During the growing seasons of 2013 and 2014, altogether 531 potato plants were collected from 138 seed potato fields and 23 storage facilities. Plant origin of the isolated bacteria, frequencies of coinfections with different species, the affected potato cultivars in addition to seasonal variation in the occurrence of SRP were studied. It was shown that bacteria from the Pectobacterium genus were abundant and outnumbered the ones classified to Dickeya spp. The vast majority of strains was isolated from the plant samples collected in July 2013 or in June–July 2014. The presence of all taxa of interest: Pectobacterium atrosepticum, Pectobacterium carotovorum, Pectobacterium parmentieri, Dickeya dianthicola and Dickeya solani were confirmed in July each year. We were able to isolate bacteria from the genus Dickeya and Pectobacterium from 35 out of 58 potato cultivars tested. The majority of SRP was isolated from potato stems, not from potato tubers. In four cases, coinfections of potato samples with even three diverse species of SRP, i.e. P. atrosepticum, P. carotovorum and P. parmentieri, were noted. It seems that since the first documented appearance of Dickeya solani in Poland in 2005, this pathogen has not played a dominating role in our country. The reported data describing the appearance and distribution of SRP in Poland might allow for prediction of the risks associated with infections initiated by these bacteria.

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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Cited by 18 publications

References 107 publications

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Multivariate Optimization of the FLC-dc-APGD-Based Reaction-Discharge System for Continuous Production of a Plasma-Activated Liquid of Defined Physicochemical and Anti-Phytopathogenic Properties

The occurrence of bacteria from different species of Pectobacteriaceae on seed potato plantations in Poland

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