Fig. S1. Properties of transposon insertion mutant library. (A) Genome-wide distribution of insertion sites in the mutant library. Chromosomal position and log10 lead counts of insertion sites are shown. Blue and grey bars represent insertions in cording sequences and non-coding sequences, respectively. (B) A histogram showing the number of insertion sites per gene. 


Fig. S2 .

 S2 Fig. S2. Comparison of gene detection frequencies with inoculated mutant library. Axes indicate the Log10 gene-level detection frequency. 


Fig. S3 .

 S3 Fig. S3. Determination of depleted and enriched genes of Aquitalea magnusonii H3. We determined depleted genes (blue plots) and enriched genes (red plots) based on effect size (> 2-fold) and significance (q < 0.05) between Plant and Control samples. Break lines represent threshold values. 


Fig. S4 .

 S4 Fig. S4. Relationship between number of insertion sites and statistical power to detect depleted/enriched genes. Each plot represents tested genes (insertion number ≥ 2), and obtained qvalue was plotted against insertion number. Results of 3-h and 7-d experiments were shown in the same figure (n = 6,724 genes). 


Fig. S5 .

 S5 Fig. S5. Comparison of the screening results of 3-h and 7-d experiments. The same plots as Fig. 1d are shown per functional category. 




  


Table S1

 S1 COG classification of depleted and enriched genes detected in the Tn-seq. Asterisks indicate the results of enrichment analysis (Fisher's exact test). 


	COG category	Number of genes >2 insertion sites	3 h Depleted Enriched	7 d Depleted Enriched
	Amino acid transport and metabolism (E)	350	21***	0	7	19***
	Transcription (K)	245	2	0	5	7
	Signal transduction mechanisms (T)	221	7	0	6	7
	Energy production and conversion (C)	192	5	0	7	1
	Cell wall/membrane/envelope biogenesis (M)	176	8	5***	6	10**
	Carbohydrate transport and metabolism (G)	169	3	0	2	1
	Inorganic ion transport and metabolism (P)	165	0	1	2	1
	Cell motility (N)	142	24***	1	28***	1
	Lipid transport and metabolism (I)	130	5	1	2	1
	Posttranslational modification, protein turnover, chaperones (O)	117	1	0	4	0
	Replication, recombination and repair (L)	103	0	0	1	2
	Coenzyme transport and metabolism (H)	99	1	0	3	2
	Other categories	913	8	2	9	11
	Unclassified to COG	537	0	0	1	2
	*, p < 0.05; **, p < 0.01; ***, p < 0.001