Supplementary material for PLANT AND SOIL

Diversity and functional characterization of bacterial endophytes dwelling in various rice (Oryza sativaL.) tissues, and their seed-borne dissemination into rhizosphere under gnotobiotic P-stress

SupplementaryTable S1. Physicochemical properties of two soil-types used for rice cultivation

Soil-type / pH / EC
(μS cm–1) / OM
(%) / Total N
(g kg–1) / P / K / Ca / Mg / Fe / Mn / Cu / Zn
mg kg–1
Acidic / 5.5 / 337 / 1.8 / 0.9 / 150.8 / 112.8 / 1156.3 / 129.7 / 652.8 / 488.2 / 3.4 / 15.0
Near-neutral / 7.7 / 278 / 1.0 / 1.2 / 385.8 / 69.8 / 6485.5 / 389.0 / 882.0 / 338.0 / 6.0 / 22.9

EC: electric conductivity; OM: organic matter.

Supplementary Table S2.Recipe for modified sterile Hoagland solution used in the gnotobiotic rice cultivation

0P / XP / 1P
Ingredient* / Final concentration (mM)
KH2PO4 / – / – / 0.5
Ca3(PO4)2 / – / 0.5 / –
KNO3 / 5 / 5 / 5
Ca(NO3)2‧4H2O / 5 / 5 / 5
MgSO4‧7H2O / 2 / 2 / 2
NH4NO3 / 1 / 1 / 1
Fe(III)-EDTA / 0.0025 / 0.0025 / 0.0025
H3BO3 / 0.05 / 0.05 / 0.05
MnCl2‧7H2O / 0.007 / 0.007 / 0.007
ZnSO4‧7H2O / 0.00075 / 0.00075 / 0.00075
CuSO4‧5H2O / 0.0002 / 0.0002 / 0.0002
Na2MoO4‧2H2O / 0.0005 / 0.0005 / 0.0005

*, introduced to 10 mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer (pH 5.5)

0P, no phosphate; XP, insoluble phosphate; 1P, soluble phosphate.

SupplementaryTable S3. Summary of Venn’s plot derived for endophytic bacterial distribution in rice cultivars planted at acidic soil.

Cultivars / Endophytic bacterial genera / Total
TCN1 TCS10 TK8 TN71 / Bacillus / 1
TCN1 TCS10 TK8 / Sphingomonas, Pseudomonas / 2
TCN1 TK8 / Alcaligenes, Pantoea / 2
TCN1 TN71 / Staphylococcus / 1
TCN1 / Cedecea, Enterobacter, Acinetobacter, Herbaspirillum, Shigella / 5
TCS10 / Achromobacter, Rheinheimera / 2
TK8 / Rhizobium, Curtobacterium, Lysinibacillus / 3
TN71 / Burkholderia / 1

SupplementaryTable S4. Summary of Venn’s plot derived for endophytic bacterial distribution in rice cultivars planted at near-neutral soil.

Cultivars / Endophytic bacterial genera / Total
TCN1 TCS10 TK8 TN71 / Bacillus, Pantoea, Pseudomonas / 3
TCN1 TCS10 / Rhizobium / 1
TCN1 TN71 / Sphingomonas / 1
TCS10 / Enterococcus, Xanthomonas, Microbacterium, Enterobacter, Rheinheimera / 5
TK8 / Lysinibacillus, Achromobacter / 2

Supplementary Table S5. PCR-DGGE identification of seed-borne uncultured rice endophytes

DGGE / Accession / Closely related rice-associated taxa and accession number / % Query / Gap / Sequencea
Band No / number / coverage / identity
1 / KM065389 / Pantoea sp. LS-042 (KJ584027) / 100 / 0 / (100%) 484/484
Flavobacterium acidificum LMG 8364T (JX986959) / 98 / 0 / (100%) 479/479
Pantoea ananatis ATCC 19321T (U80209) / 95 / 0 / (100%) 464/464
Pantoea septica LMG 5345T (EU216734) / 84 / 0 / (100%) 408/408
Pantoea sp. LS-013 (KF870425) / 75 / 0 / (100%) 367/367
Uncultured Pantoea SHCB0588 (JN697822) / 71 / 0 / (100%) 346/346
Pantoea agglomerans DSM 3493T (AJ233423) / 98 / 0 / (99.8%) 474/475
Uncultured Pantoea sp. [DGGE gel band 10] (JN110455) / 63 / 0 / (99.7%) 304/305
Pantoea sp. LS-123 (KJ584033) / 100 / 1 / (99.6%) 482/484
2 / KM065390 / Uncultured Bacillus sp. [DGGE gel band 15] (JN110460) / 63 / 1 / (97.8%) 311/318
Bacillus sp. P-150 (AM412171) / 88 / 3 / (97.5%) 433/444
3 / KM065391 / Uncultured Bacillus sp. [DGGE gel band 15] (JN110460) / 63 / 1 / (97.8%) 317/324
Bacillus sp. P-150 (AM412171) / 88 / 3 / (97.6%) 440/451
4 / KM065392 / Bacillus sp. P-150 (AM412171) / 90 / 3 / (96.8%) 336/347
Uncultured Bacillus sp. [DGGE gel band 15] (JN110460) / 57 / 1 / (96.8%) 214/221
5 / KM065393 / Uncultured Bacillus sp. [DGGE gel band 15] (JN110460) / 61 / 1 / (97.6%) 287/294
Bacillus sp. P-150 (AM412171) / 88 / 3 / (97.4%) 409/420
6 / KM065394 / Uncultured Bacillus sp. [DGGE gel band 15] (JN110460) / 63 / 1 / (97.8%) 311/318
Bacillus sp. P-150 (AM412171) / 88 / 3 / (97.5%) 433/444
8 / KM065396 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 75 / 0 / (99.5%) 363/365
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 63 / 0 / (99.4%) 305/307
9 / KM065397 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 75 / 0 / (99.7%) 364/365
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 63 / 0 / (99.7%) 306/307
10 / KM065398 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 75 / 0 / (99.5%) 362/364
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 63 / 0 / (99.4%) 304/306
12 / KM065399 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 75 / 0 / (100%) 330/330
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 61 / 0 / (100%) 272/272
14 / KM065401 / Pseudomonas oryzihabitans IAM 1568T (AM262973) / 98 / 0 / (100%) 482/482
Pseudomonas sp. REICA_175 (JN697674) / 64 / 0 / (100%) 317/317
Pseudomonas sp. LS-037 (KF870434) / 82 / 0 / (99.8%) 405/406
Pseudomonas sp. LS-040 (KF870436) / 82 / 0 / (99.8%) 406/407
Uncultured Pseudomonas sp. [DGGE gel band 12] (JN110457) / 62 / 0 / (99.7%) 307/308
Uncultured Pseudomonas sp. [DGGE gel band 2] (JN110447) / 63 / 0 / (99.7%) 310/311
Pseudomonas sp. MDR7 (AM911672) / 68 / 0 / (98.8%)333/337
Pseudomonas sp. LS-011 (KF870423) / 76 / 1 / (98.4%) 368/374
Uncultured Pseudomonas sp. [DGGE gel band 14] (JN110459) / 62 / 0 / (98.4%) 304/309
Uncultured Pseudomonas SHCB0777 (JN697940) / 75 / 0 / (97.8%) 363/371
15 / KM065402 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 75 / 0 / (99.5%) 362/364
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 63 / 0 / (99.4%) 304/306
17 / KM065403 / Pseudomonas oryzihabitans IAM 1568T (AM262973) / 98 / 0 / (100%) 481/481
Pseudomonas sp. REICA_175 (JN697674) / 64 / 0 / (100%) 316/316
Pseudomonas sp. LS-037 (KF870434) / 82 / 0 / (99.8%) 404/405
Pseudomonas sp. LS-040 (KF870436) / 82 / 0 / (99.8%) 405/406
Pseudomonas sp. MDR7 (AM911672) / 68 / 0 / (98.8%) 333/337
Uncultured Pseudomonas sp. [DGGE gel band 2] (JN110447) / 63 / 0 / (99.7%) 309/310
Uncultured Pseudomonas sp. [DGGE gel band 12] (JN110457) / 62 / 0 / (99.7%) 307/308
Uncultured Pseudomonas sp. [DGGE gel band 14] (JN110459) / 62 / 0 / (98.7%) 301/305
Pseudomonas sp. LS-011 (KF870423) / 75 / 1 / (98.7%) 365/370
Uncultured Pseudomonas SHCB0777 (JN697940) / 74 / 0 / (98.1%) 360/367
18 / KM065404 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 80 / 0 / (99.7%) 364/365
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 68 / 0 / (99.7%) 306/307
19 / KM065405 / Uncultured Stenotrophomonas SHCB1148 (JN698214) / 74 / 0 / (99.7%) 364/365
Uncultured Stenotrophomonas sp.[DGGE gel band 9] (JN110454) / 62 / 0 / (99.7%) 306/307

Bands 1, 2 and 3 were originated from seed endosphere of Oryza sativa ssp. indica cv. TCN1

Bands 4–6 and 8–10 were originated from seed endosphere of O. sativa ssp. indica cv. TCS10

Bands 12, 14 and 15 were originated from seed endosphere of O. sativa ssp. japonica cv. TK8

Bands 17, 18 and 19 were originated from seed endosphere of O. sativa ssp. japonica cv. TN71

a16S rRNA gene

(a)

(b)

SupplementaryFig. S1 Class-wise distribution of cultured rice-endophytic bacterial strains (CREBS) in whole plants of different cultivars planted at acidic (a) and near-neutral (b) soils.

(a)

(b)

SupplementaryFig. S2 CREBS-derived plant-probiotic functionality distribution in the whole plants of different cultivars planted at acidic (a) and near-neutral (b) soils.