title: Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm.
abstract: The rhizosphere-colonizing bacterium Pseudomonas chlororaphis 30-84 is an effective biological control agent against take-all disease of wheat. In this study, we characterize a small-colony variant (SCV) isolated from a P. chlororaphis 30-84 biofilm. The SCV exhibited pleiotropic phenotypes, including small cell size, slow growth and motility, low levels of phenazine production, and increased biofilm formation and resistance to antimicrobials. To better understand the genetic alterations underlying these phenotypes, RNA and whole-genome sequencing analyses were conducted comparing an SCV to the wild-type strain. Of the genome's 5,971 genes, transcriptomic profiling indicated that 1,098 (18.4%) have undergone substantial reprograming of gene expression in the SCV. Whole-genome sequence analysis revealed multiple alterations in the SCV, including mutations in yfiR (cyclic-di-GMP production), fusA (elongation factor), and cyoE (heme synthesis) and a 70-kb deletion. Genetic analysis revealed that the yfiR locus plays a major role in controlling SCV phenotypes, including colony size, growth, motility, and biofilm formation. Moreover, a point mutation in the fusA gene contributed to kanamycin resistance. Interestingly, the SCV can partially switch back to wild-type morphologies under specific conditions. Our data also support the idea that phenotypic switching in P. chlororaphis is not due to simple genetic reversions but may involve multiple secondary mutations. The emergence of these highly adherent and antibiotic-resistant SCVs within the biofilm might play key roles in P. chlororaphis natural persistence.
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA dwang22@lanl.gov eapierson@tamu.edu.
authors.forename: Dongping
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dorosky
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Cliff S
authors.initials: CS
authors.lastname: Han
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Chien-Chi
authors.initials: CC
authors.lastname: Lo
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Armand E K
authors.initials: AE
authors.lastname: Dichosa
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Chain
authors.affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA.
authors.forename: Jun Myoung
authors.initials: JM
authors.lastname: Yu
authors.affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA.
authors.forename: Leland S
authors.initials: LS
authors.lastname: Pierson
authors.affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA Department of Horticultural Sciences, Texas A&M University, College Station, Texas, USA dwang22@lanl.gov eapierson@tamu.edu.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Pierson
mesh_terms: D000220:Adaptation, Biological; D000900:Anti-Bacterial Agents / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development*; D004361:Drug Tolerance; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D023281:Genomics; D008124:Locomotion; D008969:Molecular Sequence Data; D010619:Phenazines / Q000378:metabolism; D018517:Plant Roots / Q000382:microbiology; D011549:Pseudomonas / Q000187:drug effects / Q000254:growth & development / Q000378:metabolism / Q000502:physiology*; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014908:Triticum / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents; D010619:Phenazines; C000598831:phenazine