title: Unifying bacteria from decaying wood with various ubiquitous Gibbsiella species as G. acetica sp. nov. based on nucleotide sequence similarities and their acetic acid secretion.
abstract: Bacteria were isolated from necrotic apple and pear tree tissue and from dead wood in Germany and Austria as well as from pear tree exudate in China. They were selected for growth at 37 °C, screened for levan production and then characterized as Gram-negative, facultatively anaerobic rods. Nucleotide sequences from 16S rRNA genes, the housekeeping genes dnaJ, gyrB, recA and rpoB alignments, BLAST searches and phenotypic data confirmed by MALDI-TOF analysis showed that these bacteria belong to the genus Gibbsiella and resembled strains isolated from diseased oaks in Britain and Spain. Gibbsiella-specific PCR primers were designed from the proline isomerase and the levansucrase genes. Acid secretion was investigated by screening for halo formation on calcium carbonate agar and the compound identified by NMR as acetic acid. Its production by Gibbsiella spp. strains was also determined in culture supernatants by GC/MS analysis after derivatization with pentafluorobenzyl bromide. Some strains were differentiated by the PFGE patterns of SpeI digests and by sequence analyses of the lsc and the ppiD genes, and the Chinese Gibbsiella strain was most divergent. The newly investigated bacteria as well as Gibbsiella querinecans, Gibbsiella dentisursi and Gibbsiella papilionis, isolated in Britain, Spain, Korea and Japan, are taxonomically related Enterobacteriaceae, tolerate and secrete acetic acid. We therefore propose to unify them in the species Gibbsiella acetica sp. nov.
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany. Electronic address: Klaus.Geider@jki.bund.de.
authors.forename: Klaus
authors.initials: K
authors.lastname: Geider
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany. Electronic address: marina_gernold@yahoo.de.
authors.forename: Marina
authors.initials: M
authors.lastname: Gernold
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany. Electronic address: Susanne.Epple@jki.bund.de.
authors.forename: Susanne
authors.initials: S
authors.lastname: Jock
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany. Electronic address: Annette.Wensing@jki.bund.de.
authors.forename: Annette
authors.initials: A
authors.lastname: Wensing
authors.affiliation: FSU Jena, Institute of Microbiology, Microbial Phytopathology, Neugasse 25, Jena, Germany. Electronic address: Beate.Voelksch@uni-jena.de.
authors.forename: Beate
authors.initials: B
authors.lastname: Völksch
authors.affiliation: Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221 Dossenheim, Germany. Electronic address: Juergen.Gross@jki.bund.de.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Gross
authors.affiliation: Max-Planck-Institute for Chemical Ecology, Bioorganic Chemistry, Jena and Chemical Ecology/Biological Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany. Electronic address: dieter.spiteller@uni-konstanz.de.
authors.forename: Dieter
authors.initials: D
authors.lastname: Spiteller
mesh_terms: D019342:Acetic Acid / Q000378:metabolism; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D004755:Enterobacteriaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D005798:Genes, Bacterial; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014197:Trees / Q000382:microbiology; D014934:Wood / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D019342:Acetic Acid
keywords: Acetic acid; GC/MS analysis; Gibbsiella quercinecans; NMR; PCR detection; Taxonomy