Table S1. Total number of sequences, OTU and diversity index on the basis of 16S rRNA amplicon analysis S. polyrhiza L. minor L. aequinoctialis Pond Sample fronds roots fronds roots fronds roots water Total sequences 79,776 117,708 105,574 99,732 105,003 84,173 79,911 OTU 1,971 2,680 1,580 2,351 1,537 1,341 1,986 Specific OTU 602 1,095 648 848 714 587 1,146 PIE index 0.962 0.981 0.973 0.978 0.956 0.961 0.915 200 0 Count −5 0 5 Value

unclassified Acidobacteria unclassified Chloracidobacteria1 unclassified Chloracidobacteria2 Acidobacteria unclassified Solibacterales1 unclassified Solibacterales2 Microbacteriaceae unclassified Acidimicrobiales1 unclassified Acidimicrobiales2 Actinobacteria unclassified Actinomycetales Armatimonadaceae Fimbriimonadaceae Armatimonadetes Chitinophagaceae Cryomorphaceae Cyclobacteriaceae Cytophagaceae Flavobacteriaceae Saprospiraceae Sphingobacteriaceae Bacteroidetes Weeksellaceae unclassified Bacteroidales unclassified Cytophagales unclassified Saprospirales unclassified Sphingobacteriales Rhabdochlamydiaceae Chlamydiae unclassified Chlorobi Chlorobi unclassified Anaerolineae unclassified Roseiflexales Chloroflexi Synechococcaceae unclassified Cyanobacteria Cyanobacteria Fusobacteriaceae unclassified Fibrobacteres Fibrobacteres unclassified GN02 Candidate phylum GN02 Gemmatimonadaceae unclassified Gemmatimonadales Gemmatimonadetes Gemmataceae Isosphaeraceae Pirellulaceae Planctomycetaceae unclassified Phycisphaerae Planctomycetes unclassified Phycisphaerales unclassified Planctomycetes1 unclassified Planctomycetes2 unclassified Planctomycetes3 Acetobacteraceae Caulobacteraceaeae Erythrobacteraceae Hyphomicrobiaceae Hyphomonadaceae Methylocystaceae Phyllobacteriaceae Rhizobiaceae Rhodobacteraceae Rhodospirillaceae Rickettsiaceae Alphaproteobacteria Sphingomonadaceae Xanthobacteraceae unclassified Alphaproteobacteria1 unclassified Alphaproteobacteria2 unclassified Alphaproteobacteria3 unclassified Rhizobiales1 unclassified Rhizobiales2 unclassified Rickettsiales unclassified Sphingomonadales1 unclassified Sphingomonadales2 Alcaligenaceae Comamonadaceae Methylophilaceae Oxalobacteraceae Procabacteriaceae Rhodocyclaceae unclassified Betaproteobacteria1 Betaproteobacteria unclassified Betaproteobacteria2 unclassified Betaproteobacteria3 unclassified Burkholderiales1 unclassified Burkholderiales2 unclassified Thiobacterales Bdellovibrionaceae Nannocystaceae Polyangiaceae unclassified Deltaproteobacteria1 unclassified Deltaproteobacteria2 unclassified Deltaproteobacteria3 Deltaproteobacteria unclassified Deltaproteobacteria4 unclassified Myxococcales1 unclassified Myxococcales2 unclassified Myxococcales3 unclassified Spirobacillales Aeromonadaceae Alteromonadaceae Chromatiaceae Crenotrichaceae Moraxellaceae Sinobacteraceae Gammaproteobacteria Xanthomonadaceae unclassified Chromatiales unclassified Gammaproteobacteria unclassified Legionellales unclassified Methylococcales unclassified Proteobacteria1 unclassified Proteobacteria2 unclassified Proteobacteria unclassified SR1 Candidate phylum SR1 Chthoniobacteraceae Opitutaceae Pedosphaeraceae Verrucomicrobiaceae Verrucomicrobia unclassified Pedosphaerales1 unclassified Pedosphaerales2 unclassified Pedosphaerales3 -f -r -f -f -r -r L.a L.a S.p S.p L.m L.m Water

Fig. S1 Iwashita et al. 24.024 -0.2780661S.p-f 7.8069849S.p-r 0.5522839L.m-f 10.2982774L.m-r 12.012 -2.4135442L.a-f 6.5800141L.a-r -22.5459501Pd

00 PCA2 (18.4%)

−12.0-12

−24.0-24 −24.0-24 −12.0-12 0 1212.0 24.024

PCA1 (60.1%)

Fig. S2 Iwashita et al. 100%100% AcidobacteriaAcidobacteria ActinobacteriaActinobacteria 90%90% ArmatimonadetesArmatimonadetes BacteroidetesBacteroidetes FirmicutesFirmicutes 80%80% ProteobacteriaProteobacteria VerrucomicrobiaVerrucomicrobia 70%70%

60%60%

50%50%

Abundance 40%40%

30%30%

20%20%

10%10%

0%0% Pond Root Root Root Frond Frond Frond Water S. polyrhiza L. minor L. aequinoctialis

Fig. S3 Iwashita et al. Fig. S1. Heat map for distribution of bacterial families in duckweed fronds, roots and pond water. Each sample name indicates as follows: S.p-f, fronds of S. polyrhiza; S.p-r, roots of S. polyrhiza; L.m-f, fronds of L. minor; L.m-r, roots of L. minor; L.a-f, fronds of L. aequinoctialis, L.a-r, roots of L. aequinoctialis; Water, pond water.

Fig. S2. Principal component analysis (PCA) based on microbial communities at the family level in duckweed fronds, roots, and pond water (abundance >0.1% in any samples).

Fig. S3. Phylogenetic distribution of the isolates from duckweed fronds, roots and the pond water at the phylum level.