Genomic analysis of the biocontrol strain <i> <scp>P</scp> seudomonas fluorescens </i> <scp>Pf</scp> 29 <scp>Arp</scp> with evidence of <scp>T</scp> 3 <scp>SS</scp> and <scp>T</scp> 6 <scp>SS</scp> gene expression on plant roots

Abstract

Summary Several bacterial strains of the P seudomonas genus provide plant growth stimulation, plant protection against pests or bioremediation. Among these bacteria, P . fluorescens Pf 29 Arp reduces the severity of take‐all, a disease caused by the pathogenic fungus G aeumannomyces graminis var. tritici ( Ggt ) on wheat roots. In this study, we obtained a draft genome of Pf 29 Arp and subsequent comparative genomic analyses have revealed that this bacterial strain is closely related to strains of the ‘ P . brassicacearum ‐like’ subgroup including P . brassicacearum ssp. brassicacearum NFM 421 and P . fluorescens F 113. Despite an overall chromosomal organization similar to these strains, a number of features including antibiotic synthesis gene clusters from secondary metabolism are not found in the Pf 29 Arp genome. But Pf 29 Arp possesses different protein secretion systems including type III ( T 3 SS ) and type VI ( T 6 SS ) secretion systems. Pf 29 Arp is the first P seudomonas sp. strain described with four T 6 SS clusters (cluster I , II , III and IV ). In addition, some protein‐coding genes involved in the assembly of these secretion systems are basally expressed during Pf 29 Arp colonization of healthy wheat roots and display different expression patterns on necrotized roots caused by Ggt . These data suggest a role of T 3 SS and T 6 SS in the Pf 29 Arp adaptation to different root environments.