Introduction Pseudomonas putida 2002 P. putida P. putida 2006 2003 2006 2006 2004 2005 2006 2006 P. putida 2003 2004 2002 2002 P. putida 1998 1990 2004 1998 2000 2002 P. putida 2003 2004 2004 2000 2005 Pseudomonas 2005 2006 P. putida Pseudomonas 2000 1996 1996 P. putida 1996 P. putida 2006 2007 2006 P. putida P. putida T P. putida Pseudomonas Materials and methods Strains, cultivation conditions, and DNA extraction Pseudomonas 1 1982 8 w v Table 1 Pseudomonas a b c P. putida DSMZ KT2440, ATCC 47054; NCIMB 11950 P. putida DSMZ mt-2, ATCC 23973; ATCC 33015; JCM 6156; NCIMB 12182 P. putida 1990 ATCC 700801 P. putida T DSMZ T T T T T T P. putida DSMZ ATCC 17453; ICPB 2563-77; JCM 6157; NCIMB 10007 P. putida DSMZ ATCC 17485; ICPB 2789-111; JCM 6158; NCIMB 12092 P. monteilii DSMZ ATCC 700476; CCUG 38736; LMG 21609; CIP 104883 P. fluorescens T DSMZ T T T T T T a b DSMZ c ATCC ICPB NCIMB NCTC JCM CIP CCUG LMG Preparation of biotin-labelled fragmented genomic DNAs 2003 w v Design of high-density oligonucleotide microarrays and hybridization with genomic DNAs P. putida http://www.affymetrix.com/support/technical/other/custom_design manual. pdf p p p τ P. putida 2 Table 2 Pseudomonas P. putida a Strain Present (absent) in percent (%) Putative genes and intergenic regions (7,781 probe sets) Putative genes (5,338 probe sets) Putative genes with assigned function (3,670 probe sets) P. putida b 97.6 (1.4) 99.6 (0.0) 99.8 (0.0) P. putida 98.6 (1.4) 99.9 (0.1) 100.0 (0.0) P. putida b 78.0 (16.9) 81.8 (13.9) 86.9 (9.7) P. putida T 60.5 (39.5) 64.2 (35.8) 69.3 (30.7) P. putida 56.2 (43.8) 60.7 (39.3) 66.5 (33.5) P. putida 58.8 (41.2) 62.6 (37.4) 67.8 (32.2) P. monteilii 57.7 (42.3) 61.7 (38.3) 66.8 (33.2) P. fluorescens T 22.0 (78.0) 27.2 (72.8) 30.7 (69.3) a p p τ b P. putida Calculation of dendrograms m n m n AFLP analysis 1996 1999 1995 P. putida P. monteilii Pseudomonas fluorescens Nla Csp Nla Csp 2004 m n m n Standard PCR and sequencing P. putida 1977 Biological function-derived phylogenetic analysis 1997 2003 Pseudomonas 3 1997 2003 P. putida http://www.ncbi.nlm.nih.gov/sutils/coxik.cgi?gi=266 3 Table 3 a P. putida b Description c COGs KT2440 in S12 F Nucleotide transport and metabolism 93 87 (93.5%) J Translation 194 178 (91.8%) H Coenzyme transport and metabolism 183 166 (90.7%) T Signal transduction mechanisms 427 387 (90.6%) I Lipid transport and metabolism 194 174 (89.7%) N Cell motility 130 116 (89.2%) G Carbohydrate transport and metabolism 264 232 (87.9%) P Inorganic ion transport and metabolism 368 322 (87.5%) U Intracellular trafficking and secretion 119 104 (87.4%) E Amino acid transport and metabolism 630 550 (87.3%) O Posttranslational modification, protein turnover, chaperones 194 169 (87.1%) C Energy production and conversion 321 276 (86.0%) Q Secondary metabolites biosynthesis, transport and catabolism 161 138 (85.7%) K Transcription 499 426 (85.4%) V Defense mechanisms 66 56 (84.8%) R′ General function prediction only 733 620 (84.6%) S Function unknown 442 365 (82.6%) M Cell membrane biogenesis 288 227 (78.8%) D Cell cycle control 56 41 (73.2%) – Not in COGs 853 544 (63.8%) L Replication, recombination and repair 269 158 (58.7%) a Materials and methods b c P. putida http://www.ncbi.nlm.nih.gov/ COG/ Results P. putida P. putida Pseudomonas 1 Materials and methods 2 2 P. putida 2 2 Microarray-based genomotyping 1 2 P. putida 1 P. fluorescens T Pseudomonas monteilii putida P. putida P. putida 1 1996 1999 1995 1 Fig. 1 Pseudomonas a 2 b  1997 2003 2 http://www.ncbi.nlm.nih.gov/ COG/ P. putida 2 3 2 Pseudomonas 2 T Fig. 2 Pseudomonas P. putida http://www.ncbi.nlm.nih.gov/sutils/coxik.cgi?gi=266 3  P. putida 2002 2003 P. putida 2002 2003 4 P. putida T T P. putida ben hmg, mai phh, tyrB catAB catR, pcaQ, pobR, phaNM catA2 4 catC vdh calB fcs Table 4 Comparison of the presence/absence designations of genes encoding metabolic pathways of aromatic compounds in different pseudomonads derived from Affymetrix decision matrix MAS 5.0 Strain a Genes of aromatic pathways not identified in hybridizations with genomic DNA P. putida 100.0  P. putida 100.0  P. putida 100.0  P. putida T 82.9 catC; fadAxB2x; fcs; pcaQ; phaDHMN; vdh; calB; catA2 P. putida 75.7 benE-1; catCR; ech; fadAxB2x; fcs; pcaDQ; phaGHMN; pobAR; vdh; catA2 P. putida 75.7 catCR; ech; fadAxB2x; pcaBCQ; phaDHJMN; phhR; pobR; vdh; calB; catA2 P. monteilii 74.3 benE-1; catCR; ech; fadB2x; fcs; pcaBDQ; phaEGHMN; pobAR; vdh; calB; catA2 P. fluorescens T 25.7 aat; acdA; benACDE-1E-2FKR; catABCR; fadAxBB1xB2xDx; fcs; hpd; pcaCDHIJKQT; pcm; phaAB-EG-ILMN; phhBR; pobAR; tyrB-2; vanAB; vdh; calB; ferR; catA2 a P. putida pcaBCDFGHIJKQRT catABCRA2 hmgA, mai meta pcm pobAR benABCDE-1E-2FKR phaABCDEFGHIJKLMNJ1 fadABDHAxB1xB2xD2Dx vanAB, vdh, calB, ferR, fcs, ech, aat, acdA phhABR, tyrB-1B-2, hpd, pcm Discussion P. putida P. putida P. fluorescens T P. putida 2005 2006 2005 P. aeruginosa 2002 2003 2001 Escherichia coli 2004 P. putida P. putida P. putida P. putida 2002 P. putida T 2002 Pseudomonas 1994 T P. putida T T P. putida 1996 1996 1996 P. monteilii P. fluorescens P. fluorescens T Pseudomonas P. monteilii P. putida T P. putida P. putida P. monteilii P. putida P. monteilii P. monteilii T T T m 1997 P. monteilii T T 2002 P. monteilii P. putida o m 2002 1997 In conclusion, the genomotyping of different pseudomonads using KT2440-based DNA microarrays yielded novel insights in their phylogenetic relationships and the underlying identification of genes and their distribution over different primary and secondary biological functions. This revealed the utility of KT2440-based microarrays in transcriptomics and classification studies of these strains.