Table 3. Common genes differentially expressed in P. fluorescens Pf0-1 during interspecific competition with three bacterial strains.

SEQ_ID	Gene description	Possible function	Fold change with Pedobacter V48	Fold change with Brevundimonas V52	Fold change with Bacillus V102
Pfl_0360	Urocanate hydratase	Amino acid transport and metabolism	6.3	3.9	19.3
Pfl_0651	Response regulator receiver domain protein (CheY)	Signal transduction mechanisms	3.3	2.3	2.6
Pfl_0657	Chemotaxis sensory transducer, cache sensor	Signal transduction mechanisms	3.4	2.4	3.2
Pfl_1499	Phenylalanine 4-monooxygenase	Amino acid transport and metabolism	30.5	4.9	4.4
Pfl_1529	Flagellar hook-associated 2-like	Cell motility and secretion	2.6	2.4	2.7
Pfl_1534	Two component, sigma-54 specific, transcriptional regulator	Signal transduction mechanisms	2.4	2.6	2.7
Pfl_1562	Cobyrinic acid a,c-diamide synthase	Cell motility and secretion	4.2	3.2	2.3
Pfl_1563	Flagellar biosynthesis sigma factor	Cell motility and secretion	3.3	2.9	2.3
Pfl_1702	Protein of unknown function DUF989	Unknown	3.4	2.7	2.5
Pfl_1703	Ureidoglycolate hydrolase	Nucleotide transport and metabolism	4.1	2.7	2.3
Pfl_2321	Ring hydroxylating dioxygenase, α-subunit	Energy production and conversion	3	6.6	2.1
Pfl_2322	2-chlorobenzoate 1,2-dioxygenase	Energy production and conversion	4.3	5.2	4.9
Pfl_2323	Benzoate 1,2-dioxygenase ferredoxin reductase subunit	Energy production and conversion	3.9	2.2	2.1
Pfl_2324	1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase	Energy production and conversion	5.8	2.2	2.7
Pfl_2601	Chemotaxis sensory transducer	Signal transduction mechanisms	3	2.8	5.4
Pfl_2964	Hypothetical protein	Unknown	7.6	2.3	2.3
Pfl_2968	Ring hydroxylating dioxygenase, α-subunit	Energy production and conversion	2.8	2.1	9.8
Pfl_3441	Dihydropyrimidinase	Nucleotide transport and metabolism	3.4	2.3	5.4
Pfl_3768	Chemotaxis sensory transducer	Signal transduction mechanisms	3.4	3.1	5.5
Pfl_4431	Chemotaxis sensory transducer, cache sensor	Signal transduction mechanisms	3.9	2.8	3.7
Pfl_5297	Phosphoribosyl-dephospho-CoA transferase	Lipid metabolism	6.1	2.2	10.5
Pfl_0193	Hypothetical protein	Unknown	−36.9	−6.5	−33.9
Pfl_0194	Thiosulphate-binding protein	Inorganic ion transport and metabolism	−45.6	−6.1	−49.5
Pfl_0221	Protein of unknown function DUF1234	Unknown	−6.3	−2.4	−9.6
Pfl_0223	NLPA lipoprotein	Inorganic ion transport and metabolism	−31.1	−2.1	−31.6
Pfl_0256	Taurine ABC transporter, periplasmic-binding protein	Inorganic ion transport and metabolism	−5.6	−3.2	−39.1
Pfl_0877	Sulfate adenylyltransferase subunit 2	Amino acid transport and metabolism	−15.6	−6.2	−5.7
Pfl_1610	Succinate dehydrogenase, cytochrome b subunit	Energy production and conversion	−3.4	−2.3	−2.6
Pfl_1611	Succinate dehydrogenase, hydrophobic membrane anchor protein	Energy production and conversion	−3.1	−2.6	−2.3
Pfl_2205	ABC transporter, periplasmic substrate-binding protein	Inorganic ion transport and metabolism	−3.5	−4.1	−3.3
Pfl_2346	Transcriptional regulator, XRE family with cupin sensor domain	Transcription	−4.8	−2.7	−2.7
Pfl_2801	Amino acid ABC transporter, permease protein, 3-TM region	Amino acid transport and metabolism	−5.2	−7.2	−9.4
Pfl_2802	Extracellular solute-binding protein, family 3	Cell envelope biogenesis, outer membrane	−9.4	−3.2	−23.1
Pfl_3594	Isocitrate dehydrogenase (NADP+)	Energy production and conversion	−6.5	−5.4	−2.9
Pfl_4370	Extracellular solute-binding protein, family 1	Carbohydrate transport and metabolism	−6.6	−2.7	−6.3
Pfl_4376	Glyceraldehyde-3-phosphate dehydrogenase	Carbohydrate transport and metabolism	−5.6	−4.7	−10.1
Pfl_4517	Argininosuccinate synthase	Amino acid transport and metabolism	−3.4	−2.3	−2.1
Pfl_5065	30s ribosomal protein S8	Translation, ribosomal structure and biogenesis	−2.7	−2.9	−2.5
Pfl_5621	Phosphoribosylaminoimidazole carboxylase ATPase subunit	Nucleotide transport and metabolism	−2.9	−2.2	−2.1
Pfl_5622	Phosphoribosylaminoimidazole carboxylase	Nucleotide transport and metabolism	−7.4	−3.1	−2.3
Pfl_5626	Sodium:alanine symporter	Amino acid transport and metabolism	−4.2	−2.5	−3.2
Pfl_5640	Acetyl-CoA carboxylase	Lipid metabolism	−12.3	−3.4	−5.4