title: Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers.
abstract: Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community.
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Viia
authors.initials: V
authors.lastname: Kõiv
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Märt
authors.initials: M
authors.lastname: Roosaare
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Eve
authors.initials: E
authors.lastname: Vedler
authors.affiliation: Estonian Genome Center, University of Tartu, Riia 23 B, 51010 Tartu, Estonia.
authors.forename: Paula Ann
authors.initials: PA
authors.lastname: Kivistik
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Kristel
authors.initials: K
authors.lastname: Toppi
authors.affiliation: Institute of Technology, University of Tartu, 1 Nooruse Street, Tartu 50411, Estonia.
authors.forename: David W
authors.initials: DW
authors.lastname: Schryer
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Maido
authors.initials: M
authors.lastname: Remm
authors.affiliation: Institute of Technology, University of Tartu, 1 Nooruse Street, Tartu 50411, Estonia.
authors.forename: Tanel
authors.initials: T
authors.lastname: Tenson
authors.affiliation: Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Mäe
mesh_terms: D001483:Base Sequence; D060026:Endophytes; D059014:High-Throughput Nucleotide Sequencing; D064307:Microbiota / Q000235:genetics; D044043:Pectobacterium / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification / Q000502:physiology*; D010641:Phenotype; D010802:Phylogeny; D035281:Plant Tubers / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011198:Solanum tuberosum / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S