Dissimilar gene repertoires of Dickeya solani involved in the colonization of lesions and roots of Solanum tuberosum

Abstract

Dickeya and Pectobacterium species are necrotrophic pathogens that macerate stems (blackleg disease) and tubers (soft rot disease) of Solanum tuberosum. They proliferate by exploiting plant cell remains. They also colonize roots, even if no symptoms are observed. The genes involved in pre-symptomatic root colonization are poorly understood. Here, transposon-sequencing (Tn-seq) analysis of Dickeya solani living in macerated tissues revealed 126 genes important for competitive colonization of tuber lesions and 207 for stem lesions, including 96 genes common to both conditions. Common genes included acr genes involved in the detoxification of plant defense phytoalexins and kduD, kduI, eda (=kdgA), gudD, garK, garL, and garR genes involved in the assimilation of pectin and galactarate. In root colonization, Tn-seq highlighted 83 genes, all different from those in stem and tuber lesion conditions. They encode the exploitation of organic and mineral nutrients (dpp, ddp, dctA, and pst) including glucuronate (kdgK and yeiQ) and synthesis of metabolites: cellulose (celY and bcs), aryl polyene (ape), and oocydin (ooc). We constructed in-frame deletion mutants of bcsA, ddpA, apeH, and pstA genes. All mutants were virulent in stem infection assays, but they were impaired in the competitive colonization of roots. In addition, the ΔpstA mutant was impaired in its capacity to colonize progeny tubers. Overall, this work distinguished two metabolic networks supporting either an oligotrophic lifestyle on roots or a copiotrophic lifestyle in lesions. This work revealed novel traits and pathways important for understanding how the D. solani pathogen efficiently survives on roots, persists in the environment, and colonizes progeny tubers.

Genetic Loci of Plant Pathogenic Dickeya solani IPO 2222 Expressed in Contact with Weed-Host Bittersweet Nightshade (Solanum dulcamara L.) Plants

“…Tn-seq involves the integration of transposon mutagenesis with high-throughput sequencing technologies, facilitating a systematic interrogation of the bacterial genome for genes essential for a particular process. Tn-seq has already proven to be a useful approach to studying D. dadantii genes required for colonization and survival in chicory plants [ 65 ], D. solani genes involved in colonization of lesions and roots of potato plants [ 66 ], as well as D. dadantii and D. dianthicola genes important for the bacterial growth in potato tubers [ 67 ].…”

Shedding light on bacteria–host interactions with the aid of TnSeq approaches

“…The recovered library can be enriched (outgrown, amplified) by cultivation. Some authors have done so in rich media after collecting the mutants from the host ( 40 , 76 , 77 ). This allows to increase the total mass of mutants, facilitating DNA recovery for subsequential steps.…”

“…TnSeq has also been conducted in bacteria with different lifestyles, like the human pathogen Staphylococcus aureus ( 82 ), the plant pathogen Agrobacterium tumefaciens ( 40 ), the opportunistic pathogen S. pneumoniae ( 83 ), the plant mutualistic species Pseudomonas simiae ( 84 ), or the insect symbiont Snodgrassella alvi ( 85 ), among others. Interestingly, some TnSeq studies have used different hosts in which a target bacterium develops disparate lifestyles (pathogenic and non-pathogenic) ( 40 , 76 ). A major driver for the development of genome-wide approaches such as TnSeq has been the analysis of detrimental interactions of pathogens with their hosts.…”