Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Pritchard, Leighton; Glover, R.; Humphris, Sonia; Elphinstone, J. G.; Toth, Ian K.

doi:10.1039/c5ay02550h

Cited by 1,080 publications

(897 citation statements)

References 66 publications

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“…Therefore, all incorporated genomes share less than 98% average ANI. ANI was calculated with pyani (Pritchard et al, 2016). All included genomes and relevant information are presented in Supporting Information Table S1.…”

Section: Incorporated Reference Genomesmentioning

confidence: 99%

Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Lee

Ahlgren

Kling

et al. 2019

Environmental Microbiology

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Summary Synechococcus, a genus of unicellular cyanobacteria found throughout the global surface ocean, is a large driver of Earth's carbon cycle. Developing a better understanding of its diversity and distributions is an ongoing effort in biological oceanography. Here, we introduce 12 new draft genomes of marine Synechococcus isolates spanning five clades and utilize ~100 environmental metagenomes largely sourced from the TARA Oceans project to assess the global distributions of the genomic lineages they and other reference genomes represent. We show that five newly provided clade‐II isolates are by far the most representative of the recovered in situ populations (most ‘abundant’) and have biogeographic distributions distinct from previously available clade‐II references. Additionally, these isolates form a subclade possessing the smallest genomes yet identified of the genus (2.14 ± 0.05Mbps; mean ± 1SD) while concurrently hosting some of the highest GC contents (60.67 ± 0.16%). This is in direct opposition to the pattern in Synechococcus’s nearest relative, Prochlorococcus – wherein decreasing genome size has coincided with a strong decrease in GC content – suggesting this new subclade of Synechococcus appears to have convergently undergone genomic reduction relative to the rest of the genus, but along a fundamentally different evolutionary trajectory.

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Section: Incorporated Reference Genomesmentioning

confidence: 99%

Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Lee

Ahlgren

Kling

et al. 2019

Environmental Microbiology

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“…Bacterial soft rot, caused by pectinolytic Pectobacterium and Dickeya species (soft rot Pectobacteriaceae, SRP), is one of the major diseases of potato (Solanum tuberosum) and remains a concern of the seed potato production sector in many potato-growing regions of the world (Czajkowski et al, 2015;Pritchard et al, 2016). In western and northern Europe, a D. solani outbreak was identified in 2004, and since then the presence of D. solani isolates has been reported in a number of countries, with significant economic and yield losses due to the easy spread of D. solani through the seed potato trade and survival under the temperate climate (Laurila et al, 2008;Potrykus et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Dickeya solani is considered to be more aggressive than D. dianthicola or Pectobacterium species, with lower inoculum level as infection threshold (Toth et al, 2011). The most distinctive feature of the pathogenicity of D. solani and other soft rot bacteria is the production of diverse plant cell wall-degrading enzymes (PCWDEs), including pectinases, cellulases and protease, which results in rotting of the tissue and release of nutrients for the bacterial growth (Pritchard et al, 2016). During harvest, storage or transit, rotting of tubers is promoted by wounding, poor ventilation and high humidity.…”

Section: Introductionmentioning

confidence: 99%

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

et al. 2018

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Dickeya and Pectobacterium are responsible for causing blackleg of plants and soft rot of tubers in storage and in the field, giving rise to losses in seed potato production. In an attempt to improve potato health, biocontrol activity of known and putative antagonists was screened using in vitro and in planta assays, followed by analysis of their persistence at various storage temperatures. Most antagonists had low survival on potato tuber surfaces at 4 °C. The population dynamics of the best low‐temperature tolerant strain and also the most efficient antagonist, Serratia plymuthica A30, along with Dickeya solani as target pathogen, was studied with TaqMan real‐time PCR throughout the storage period. Tubers of three potato cultivars were treated in the autumn with the antagonist and then inoculated with D. solani. Although the cell densities of both strains decreased during the storage period in inoculated tubers, the pathogen population was always lower in the presence of the antagonist. The treated tubers were planted in the field the following growing season to evaluate the efficiency of the bacterial antagonist for controlling disease incidence. The potato endophyte S. plymuthica A30 protected potato plants by reducing blackleg development on average by 58.5% and transmission to tuber progeny as latent infection by 47–75%. These results suggest that treatment of potato tubers with biocontrol agents after harvest can reduce the severity of soft rot disease during storage and affect the transmission of soft rot bacteria from mother tubers to progeny tubers during field cultivation.

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“…recently introduced to Europe from outside (Khayi et al 2016). Lately, it has been proposed to phylogenetically separate P. wasabiae strains isolated from potato and other hosts and collected in USA, Europe and Canada from strains infecting horseradish in Asia (Yuan et al 2014;Pritchard et al 2016). What is more, last year Khayi and co-workers (Khayi et al 2016) reclassified potato-associated P. wasabiae strains to a new taxon named P. parmentieri (Khayi et al 2016) -a distinct cluster from the one grouping P. wasabiae strains isolated from horseradish plants.…”

mentioning

confidence: 99%

Isolation and phenotypic and morphological characterization of the first Podoviridae lytic bacteriophages ϕA38 and ϕA41 infecting Pectobacterium parmentieri (former Pectobacterium wasabiae)

et al. 2017

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Two bacteriophages, ϕA38 and ϕA41, infecting Pectobacterium parmentieri strain SCC 3193 (former Pectobacterium wasabiae strain SCC 3193) were isolated from arable soil samples collected in different regions of Poland. ϕA38 and ϕA41 have a typical morphology of the members of the family Podoviride and order Caudovirales, with a head diameter of ca. 60 nm and tail length of ca. 20 nm. Phages ϕA38 and ϕA41 exhibited a similar RFLP pattern with Csp6I restriction endonuclease. They were stable in a range of pHs, temperatures and osmolarities but were rapidly inactivated by UV light. During the first 20 min., 74 and 69% of ϕA38 and ϕA41 phages, respectively, were adsorbed to SCC 3193 cells. In one-step growth experiments, ϕA38 and ϕA41 showed latent period of ca. 20-30 min and burst size of 102 and 141 phages, respectively. The optimal multiplicity of infection (MOI) was calculated to be 0.01 for both bacteriophages. In the host range experiments, both phages were able to infect six from 21 of the tested P. parmentieri isolates but the phages were unable to infect other members of the Pectobacterium spp. or Dickeya spp. In the proof-of-concept experiments, ϕA38 and ϕA41 were able to inhibit the growth of P. parmentieri strain SCC 3193 and to protect potato tuber tissue maceration caused by the bacterium. The potential use of ϕA38 and ϕA41 bacteriophages for the biocontrol of P. parmentieri in potato is discussed.

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Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

Abstract: Whole genome comparisons provide a quantitative, objective basis for taxonomic classification of bacterial pathogens important to food security.

Cited by 1,080 publications

References 66 publications

Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

Isolation and phenotypic and morphological characterization of the first Podoviridae lytic bacteriophages ϕA38 and ϕA41 infecting Pectobacterium parmentieri (former Pectobacterium wasabiae)

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