Table 2. Differentially expressed genes of S. wittichii RW1 common to pair-wise comparisons in short contact sand experiments.

Gene	Annotation	Fold change in comparisona
		SAL-NOTHb vs ctrl SAL	SAL-DBF vs ctrl SAL	DBF-DBF vs ctrl DBF	Two-way ANOVAc
					1 h	EXPO	STAT
Swit_0061	Ribosomal large subunit pseudouridine synthase D	−5.3	−3.3	2	2.6	−1.9	1.0
Swit_0266	UspA domain-containing protein	−4.7	−5.7	−4.6	−1.7	−3.2	−1.1
Swit_0540	TonB-dependent receptor	−2.6	−2.3	3.5	2.6	−1.4	1.1
Swit_0652	Methylmalonate-semialdehyde dehydrogenase	4.2	4.5	6.5	1.1	6.2	1.9
Swit_0975	Muconate cycloisomerase	−21.7	−21.1	−6.3	1.5	−1.9	−1.1
Swit_0976	Muconolactone Delta-isomerase	−12.9	−11.9	−4.5	1.7	−5.4	1.2
Swit_0977	Catechol 1,2-dioxygenase	−11.4	−12.9	−9.8	−1.1	−2.6	1.6
Swit_1124	Glutaredoxin	3.7	4.3	2.7	1.8	2.2	33.9
Swit_1200	Globin	−21.8	−22.1	−3.3	−4.6	−1.3	−1.3
Swit_1327	30S ribosomal protein S11	−2.3	2.5	10.5	2.2	1.4	2.6
Swit_1328	30S ribosomal protein S13	−2.1	2.8	14.1	4.9	1.5	2.4
Swit_1336	30S ribosomal protein S5	−6.3	−2.3	35.2	7.7	−1.4	1.2
Swit_1346	50S ribosomal protein L16	−5.6	−2.2	22.2	4.6	−1.3	−1.0
Swit_1799	Cbb3-type cytochrome oxidase component	−4.4	−4.5	−3.5	−1.5	−2.8	−1.7
Swit_1800	Cytochrome c oxidase, cbb3-type, subunit II	−3.3	−3.9	−2.8	1.2	−2.4	−1.4
Swit_2401	5,10-Methylenetetrahydrofolate reductase	−14.3	−2.4	4.6	3.0	−3.1	−1.5
Swit_2914	FeS assembly SUF system protein	−6.2	−3.1	3.7	2.3	−1.1	1.4
Swit_3044	TonB-dependent receptor	−3.1	−8.8	−4.6	2.7	−4.0	−18.7
Swit_3144	TonB-dependent receptor	−3.1	−8.2	−17.8	−1.0	−1.4	3.4
Swit_3256	TonB-dependent receptor	−2.5	−8.2	−6.5	3.7	−1.6	1.6
Swit_3587	Alkyl hydroperoxide reductase	2.5	6.3	5.4	49.3	−1.1	7.4
Swit_3729	Hypothetical protein Swit_3729	−3	−3.9	−8.2	−1.2	−1.8	5.3
Swit_3904	Hypothetical protein Swit_3904	11.7	9.8	3.8	51.7	2.4	31.3
Swit_3960	Hypothetical protein Swit_3960	2.5	4.1	4.4	1.7	1.6	5.0
Swit_4364	Methylamine dehydrogenase accessory protein MauD	9	−2.2	−3.1	1.6	−1.1	−2.5
Swit_4662	BLUF domain-containing protein	−2.8	−7.9	−9.2	1.0	−3.1	1.8
Swit_5202	Hypothetical protein Swit_5202	−8.7	−5.6	−2.6	1.2	1.4	−2.5

Abbreviation: ANOVA, analysis of variance.

^aFold change (absolute) in condition compared with control, negative values indicate decreased expression in soil.

^bSample indications: Bare sand vs control cells growing in salicylate (SAL-NOTH vs ctrl SAL), sand contaminated with DBF vs control cells growing in salicylate (SAL-DBF vs ctrl SAL), and sand contaminated with DBF vs control cells growing in dibenzofuran (DBF-DBF vs ctrl DBF).

^cTwo-way ANOVA in the condition ‘growth phase' 1 h: DBF-DBF vs ctrl DBF, EXPO: SAND-DBF-EXPO vs wsDBF, and STAT: SAND-DBF-STAT vs LIQ-DBF-STAT.