MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 2006, p. 510–547 Vol. 70, No. 2 1092-2172/06/$08.00+0 doi:10.1128/MMBR.00047-05 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Biology of Pseudomonas stutzeri Jorge Lalucat, 1,2 * Antoni Bennasar, 1 Rafael Bosch, 1 Elena Garcı ´a-Valde ´s, 1,2 and Norberto J. Palleroni 3 Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain 1 ; Institut Mediterrani d’Estudis Avanc ¸ats (CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain 2 ; and Department of Biochemistry and Microbiology, Rutgers University, Cook Campus, New Brunswick, New Jersey 08901-8520 3 INTRODUCTION .......................................................................................................................................................511 DEFINITION OF THE SPECIES AND DIFFERENTIATION FROM OTHER PSEUDOMONAS SPECIES ....511 Definition .................................................................................................................................................................511 Differentiation from Other Species ......................................................................................................................511 DISCOVERY AND NOMENCLATURAL PROBLEMS ........................................................................................512 OCCURRENCE AND ISOLATION PROCEDURES ............................................................................................512 PHENOTYPIC PROPERTIES ..................................................................................................................................514 Colony Structures/Types ........................................................................................................................................514 Morphological Characterization (Cells, Reserve Materials, Flagella, and Pili) and Chemotaxis ..............515 Chemical Characterization and Chemotaxonomy ..............................................................................................515 DNA base composition .......................................................................................................................................515 Protein patterns ..................................................................................................................................................515 LPS and immunological characteristics ..........................................................................................................515 Fatty acid composition .......................................................................................................................................516 Quinone and polyamine composition...............................................................................................................516 PHA.......................................................................................................................................................................516 GENOMIC CHARACTERIZATION AND PHYLOGENY ....................................................................................516 DNA-DNA Hybridizations......................................................................................................................................516 Genome Size and Organization ............................................................................................................................517 Genotyping ...............................................................................................................................................................517 Genetic Diversity: MLEE .......................................................................................................................................518 Genetic Diversity: MLST .......................................................................................................................................518 Phylogeny .................................................................................................................................................................519 Clonality ...................................................................................................................................................................520 TAXONOMIC RANKS: GENOMOVARS ...............................................................................................................520 IDENTIFICATION .....................................................................................................................................................521 Phenotypic Identification .......................................................................................................................................521 Molecular DNA-Based Identification ...................................................................................................................521 Polyphasic Identification........................................................................................................................................521 PHYSIOLOGICAL PROPERTIES ...........................................................................................................................522 Temperature, Pressure, pH, and O 2 Relationships ...........................................................................................522 Denitrification .........................................................................................................................................................522 Structural gene clusters and the nature of denitrification genes ................................................................522 (i) nar genes .....................................................................................................................................................523 (ii) nir genes ....................................................................................................................................................524 (iii) nor genes ..................................................................................................................................................524 (iv) nos genes ...................................................................................................................................................524 Metalloenzymes involved in the denitrification process ................................................................................525 (i) Nitrate respiration and NaRs..................................................................................................................525 (ii) Properties of NarL and NarX proteins .................................................................................................526 (iii) Nitrite respiration and NiRs .................................................................................................................526 (iv) Nitric oxide respiration and NORs.......................................................................................................526 (v) Nitrous oxide respiration and N 2 ORs ...................................................................................................527 Chlorate and Perchlorate as Terminal Electron Acceptors ..............................................................................527 Organic Compounds Used as the Sole Carbon and Energy Source................................................................528 Inorganic Energy Sources (Thiosulfate) ..............................................................................................................528 Production of Siderophores ...................................................................................................................................529 Nitrogen Fixation ....................................................................................................................................................529 Phosphite and Hypophosphite Oxidation............................................................................................................530 * Corresponding author. Mailing address: Institut Mediterrani d’Estudis Avanc ¸ats (CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain. Phone: 34 971 173140. Fax: 34 971 173184. E-mail: jlalucat@uib.es. 510 on February 1, 2016 by guest http://mmbr.asm.org/ Downloaded from