Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe

• Published in: BMC genomics 2020-07, Vol.21 (1), p.505-505, Article 505
• Main Authors: Taparia, Tanvi, Krijger, Marjon, Haynes, Edward, Elphinstone, John G, Noble, Ralph, van der Wolf, Jan
• Format: Article
• Language: English
• Subjects: Agaricus; Agaricus - genetics; Agaricus bisporus; Average nucleotide identity; Bacteria; Basidiocarps; Belgium; Blotch; Cultivation; Deoxyribonucleic acid; Diagnostic software; Diagnostic systems; Disease; DNA; Economic conditions; Epidemics; Europe; Farms; Fungiculture; Gene sequencing; Genetic aspects; Genetic diversity; Genomes; Genomics; Humidity; Hybridization; In-silico DNA DNA hybridization; Multilocus sequence alignment; Mushrooms; Nomenclature; Nucleotide sequence; Nucleotides; Pathogenicity; Pathogens; Phylogenetics; Phylogeny; Physiological aspects; Pseudomonas; Pseudomonas - genetics; Pseudomonas gingeri; Pseudomonas sp. NC02; Serratia spp; Taxonomy; United Kingdom; Virulence
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-06905-3

Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe. In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses. The known pathogens "Pseudomonas gingeri", P. tolaasii, "P. reactans" and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated. A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.