title: Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil.
abstract: Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases.
authors.affiliation: Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.
authors.forename: Ondrej
authors.initials: O
authors.lastname: Uhlik
authors.forename: Michal
authors.initials: M
authors.lastname: Strejcek
authors.forename: Petra
authors.initials: P
authors.lastname: Junkova
authors.forename: Miloslav
authors.initials: M
authors.lastname: Sanda
authors.forename: Miluse
authors.initials: M
authors.lastname: Hroudova
authors.forename: Cestmir
authors.initials: C
authors.lastname: Vlcek
authors.forename: Martina
authors.initials: M
authors.lastname: Mackova
authors.forename: Tomas
authors.initials: T
authors.lastname: Macek
mesh_terms: D031215:Armoracia; D001419:Bacteria / Q000737:chemistry* / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D015373:Bacterial Typing Techniques / Q000379:methods*; D044822:Biodiversity; D001713:Biphenyl Compounds / Q000378:metabolism*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D001713:Biphenyl Compounds; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; C010574:biphenyl