Species' identification and microarray‐based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway

Abstract

Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequencing of the 16S rRNA gene identified 14 nonmelanin-producing strains to S. turgidiscabies. Fourteen melanin-producing strains were detected with primers specific to S. scabies, but whole-genome microarray analysis, based on 12 766 probes designed for 8848 predicted open reading frames (ORFs) of S. scabies, showed that the 14 strains were different from S. scabies. They were subsequently identified to be S. europaeiscabiei based on the internal transcribed spacer (ITS) sequences of the rRNA genes. This is the first report of the occurrence of S. turgidiscabies and S. europaeiscabiei in Norway. The putative 762 genes exhibiting the highest sequence differences between strains of S. europaeiscabiei and S. scabies according to microarray analysis were concentrated in relatively few gene ontology (GO) categories, including 'symbiosis and mutualism through parasitism', 'cell death' and 'responses to biotic stimulus', whereas genes related to primary metabolism appeared to be more conserved. Microarray data and 16S rRNA gene phylogeny showed, consistently, that there were two genetically distinguishable groups of S. europaeiscabiei on the basis of differences in 131 genes. The results provide novel information about the genetic variability of S. europaeiscabiei and the gene-specific variability between the genomes of S. europaeiscabiei and S. scabies. The usefulness of a custom-designed, whole-genome oligonucleotide microarray in a survey of bacterial plant pathogens was demonstrated.

Diversity of Plant Associated Actinobacteria

“…Such improvement is enabled by Soil DNA Isolation kits (MoBio Laboratories Inc., Solana Beach, CA) (Gonzalez-Franco et al 2009). Also, improvement of the use of specific primers and environmental clone libraries (McCaig et al 1999;Rintala et al 2001), DNA hybridization (Zaluga et al 2013), whole-genome microarray analysis (Dees et al 2012) and the 16S rRNA gene Microarrays PhyloChip technology (Weinert et al 2011) which proved to reveal more bacterial diversity in environmental samples than clone library (DeSantis et al 2007) will constitute a powerful approach for studying the Actinobacterial diversity. Still, a great development of the diversity knowledge could be the result of the great ongoing progress in their taxonomy.…”

“…Hence, these authors concluded that ITS RFLP could be used as an alternative to the laborious DNA-DNA hybridization. This technique was used to assess diversity within populations of Actinobacteria (Song et al 2004b;Wanner 2009;de Leon et al 2009;Dees et al 2012). Many researches focused on the IGS between functional genes in Actinobacteria such as nif gene (Jamann et al 1993;Navarro et al 1997;Hahn et al 1999;Dai et al 2004).…”

“…Recent works described other new potato scab disease causing agents, S. luridiscabiei, S. puniciscabiei and S. niveiscabiei in Korea (Park et al 2003). Since it was discovered in France by Bouchek-Mechiche et al (1998), S. europaeiscabiei was reported in other areas in Europe (Dees et al 2012;Leiminger et al 2013) and USA (Wanner 2009) suggesting that this species may be as worldwidly distributed as S. scabiei. Aiming to investigate internal transcribed spacer (ITS) region could be used as alternative to 16S rRNA sequences.…”

“…It was advocated that production of melanoid pigments is associated with pathogenicity in S. scabiei (Lambert and Loria 1989b). However, the discovery of pathogenic strains with no production of such pigments (Takeuchi et al 1996;Dees et al 2012) and their production by non-pathogens ascertain that their production is not essential for the pathogenicity. Lambert and Loria (1989a, b) used phenotypic traits to characterize streptomyces that cause common potato scab disease responsible of potato common scab disease (Locci 1994).…”

“…Thaxtomins are considered as pathogenicity determinants. Dees et al (2012) showed that the txtAB sequences of different species including S. scabiei and S. turgidiscabiei are divergent. However, the presence of this gene is well correlated with the pathogenicity (Wanner 2009).…”