Supporting Information Tables S1–S5 and Figures S1–S9.
Table S1 The characteristics of 12cucumber soils used in this study
Soils / Soil / Area / Geographical / Land Use / Organic Matter / Total N / NH4+_N / NO3−_N / Inorganic-N / Olsen-P / NH4OAc-K / pH / ECCodes / Information / History / (g kg-1) / (g kg-1) / (mg kg-1) / (mg kg-1) / (mg kg-1) / (mg kg-1) / (mg kg-1) / (mS cm-1)
Soil-1 / S1 / Shunyi / 40°10´N, 116°33´E
35 m a.s.l. / Cucumber,
20 years / 25.6 / 1.57 / 6.63 / 50.75 / 57.39 / 143.78 / 598.53 / 7.09 / 0.50
Soil-2 / S2 / Shunyi / 40°11´N, 116°38´E
35 m a.s.l. / Cucumber,
16 years / 9.1 / 0.55 / 12.41 / 60.46 / 72.87 / 147.56 / 449.80 / 7.16 / 0.39
Soil-3 / S3 / Shunyi / 40°14´N, 116°47´E
35 m a.s.l. / Cucumber,
10 years / 19.0 / 1.16 / 16.84 / 285.79 / 302.63 / 113.12 / 500.26 / 7.15 / 1.30
Soil-4 / S4 / Shunyi / 40°16´N, 116°52´E
35 m a.s.l. / Cucumber,
4 years / 25.6 / 1.89 / 8.40 / 96.09 / 104.49 / 66.07 / 373.63 / 7.31 / 0.61
Soil-5 / S5 / Daxing / 39°29´N, 116°18´E
33 m a.s.l. / Cucumber,
22years / 29.3 / 2.66 / 11.23 / 33.58 / 44.80 / 104.30 / 313.87 / 7.52 / 0.50
Soil-6 / S6 / Daxing / 39°34´N, 116°23´E
33 m a.s.l. / Cucumber,
15 years / 11.8 / 0.76 / 10.43 / 142.63 / 153.06 / 130.76 / 238.18 / 7.51 / 0.76
Soil-7 / S7 / Daxing / 39°43´N, 116°34´E
33 m a.s.l. / Cucumber,
7 years / 13.7 / 0.84 / 7.22 / 41.96 / 49.18 / 79.09 / 31.01 / 7.46 / 0.40
Soil-8 / S8 / Daxing / 39°49´N, 116°37´E
33 m a.s.l. / Cucumber,
1 year / 15.3 / 0.93 / 7.32 / 64.86 / 72.18 / 166.89 / 48.27 / 7.44 / 0.57
Soil-9 / S9 / Miyun / 40°24´N, 116°45´E
73 m a.s.l. / Cucumber,
18 years / 20.8 / 1.27 / 12.80 / 240.99 / 253.79 / 340.79 / 292.63 / 6.28 / 1.75
Soil-10 / S10 / Miyun / 40°30´N, 116°58´E
73 m a.s.l. / Cucumber,
12 years / 27.8 / 2.90 / 27.12 / 656.80 / 683.93 / 358.02 / 687.11 / 5.87 / 5.52
Soil-11 / S11 / Miyun / 40°33´N, 117°14´E
73 m a.s.l. / Cucumber,
5 years / 20.3 / 1.21 / 14.85 / 162.33 / 177.18 / 136.64 / 230.21 / 6.41 / 1.17
Soil-12 / S12 / Miyun / 40°40´N, 117°27´E
73 m a.s.l. / Cucumber,
3 years / 19.2 / 1.18 / 8.02 / 70.25 / 78.27 / 175.71 / 131.94 / 6.75 / 0.84
Compost / 297.92 / 17.11 / 170 / 1900 / 2070 / 3580 / 16350 / 6.25 / 4.05
Table S2Alpha-diversity (i.e. estimated OTUs, Shannon diversity and the Chao-1 estimator of total species richnessidentifiedfromcucumber rhizosphere soils) as affected by soil environment, compost addition, bacterial inoculation, and compost addition by bacterial inoculation interaction.
Factor / Level / 100 reads / 800 reads / 1500 reads / 2200 readsShannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness
Soil environment / Soil-1 / 3.77 / 266 / 98 / 6.38 / 1914 / 667 / 6.72 / 2911 / 1073 / 6.88 / 3422 / 1358
Soil-2 / 3.77 / 232 / 97 / 6.40 / 1728 / 674 / 6.75 / 2625 / 1087 / 6.91 / 3143 / 1388
Soil-3 / 3.74 / 243 / 98 / 6.31 / 1718 / 647 / 6.54 / 2546 / 1021 / 6.83 / 2994 / 1268
Soil-4 / 3.78 / 272 / 99 / 6.42 / 1989 / 680 / 6.77 / 3018 / 1107 / 6.93 / 3624 / 1416
Soil-5 / 3.85 / 198 / 99 / 6.63 / 1615 / 742 / 6.99 / 2720 / 1307 / 7.17 / 3412 / 1814
Soil-6 / 3.84 / 226 / 99 / 6.59 / 1784 / 729 / 6.96 / 2943 / 1275 / 7.13 / 3683 / 1756
Soil-7 / 3.86 / 284 / 99 / 6.63 / 2304 / 742 / 7.00 / 3850 / 1303 / 7.17 / 4823 / 1799
Soil-8 / 3.80 / 607 / 99 / 6.49 / 4549 / 707 / 6.86 / 7249 / 1206 / 6.99 / 8864 / 1623
Soil-9 / 3.79 / 628 / 98 / 6.42 / 4403 / 674 / 6.77 / 6666 / 1112 / 6.92 / 7815 / 1442
Soil-10 / 3.75 / 272 / 96 / 6.34 / 1930 / 648 / 6.65 / 2919 / 1027 / 6.79 / 3391 / 1295
Soil-11 / 3.80 / 218 / 98 / 6.46 / 1623 / 684 / 6.80 / 2572 / 1140 / 6.97 / 3102 / 1499
Soil-12 / 3.82 / 198 / 99 / 6.54 / 1544 / 715 / 6.91 / 2495 / 1222 / 7.07 / 3077 / 1640
Compost addition / Not added / 3.81 / 321 / 98 / 6.51 / 2309 / 706 / 6.87 / 3556 / 1196 / 7.03 / 4390 / 1600
Added / 3.78 / 286 / 98 / 6.43 / 2208 / 679 / 6.75 / 3530 / 1117 / 6.93 / 4168 / 1449
Bacterial inoculation / Not inoculated / 3.80 / 316 / 98 / 6.48 / 2314 / 695 / 6.81 / 3564 / 1168 / 6.99 / 4285 / 1549
Inoculated / 3.79 / 292 / 98 / 6.46 / 2203 / 689 / 6.81 / 3522 / 1144 / 6.97 / 4273 / 1500
Compost addition by / Soil / 3.81 / 359 / 98 / 6.52 / 2561 / 709 / 6.88 / 3869 / 1210 / 7.03 / 4805 / 1628
bacterial inoculation / Soil + compost / 3.79 / 284 / 98 / 6.44 / 2067 / 682 / 6.75 / 3258 / 1127 / 6.94 / 3765 / 1471
interaction / Soil + compost + inoculation / 3.78 / 273 / 98 / 6.41 / 2057 / 676 / 6.76 / 3191 / 1106 / 6.91 / 4571 / 1428
Soil + inoculation / 3.81 / 295 / 98 / 6.50 / 2349 / 703 / 6.85 / 3853 / 1183 / 7.02 / 3975 / 1573
Table S3Alpha-diversity (i.e. estimated OTUs, Shannon diversity and the Chao-1 estimator of total species richnessidentifiedfromcucumber rhizosphere soils) for each treatment in soils 1-6.
Soils / Treatments / 100 reads / 800 reads / 1500 reads / 2200 readsShannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness
Soil-1 / Soil / 3.84 / 160 / 99 / 6.57 / 1260 / 719 / 6.93 / 2055 / 1240 / 7.09 / 2507 / 1679
Soil + compost / 3.75 / 391 / 98 / 6.32 / 2718 / 647 / 6.66 / 4002 / 1021 / 6.82 / 4703 / 1260
Soil + compost + inoculation / 3.71 / 150 / 97 / 6.25 / 1020 / 630 / 6.59 / 1507 / 961 / 6.72 / 1640 / 1143
Soil + inoculation / 3.77 / 364 / 98 / 6.38 / 2659 / 672 / 6.72 / 4079 / 1068 / 6.88 / 4838 / 1348
Soil-2 / Soil / 3.76 / 275 / 96 / 6.42 / 2103 / 679 / 6.77 / 3275 / 1105 / 6.93 / 3876 / 1416
Soil + compost / 3.82 / 181 / 99 / 6.54 / 1379 / 710 / 6.88 / 2195 / 1199 / 7.06 / 2679 / 1607
Soil + compost + inoculation / 3.71 / 169 / 97 / 6.25 / 1165 / 631 / 6.59 / 1657 / 962 / 6.74 / 1950 / 1155
Soil + inoculation / 3.77 / 302 / 97 / 6.40 / 2265 / 674 / 6.74 / 3372 / 1080 / 6.91 / 4067 / 1374
Soil-3 / Soil / 3.81 / 193 / 98 / 6.47 / 1483 / 693 / 6.82 / 2225 / 1147 / 6.97 / 2753 / 1491
Soil + compost / 3.68 / 154 / 96 / 6.20 / 1051 / 615 / 6.09 / 1517 / 931 / 6.76 / 1713 / 1121
Soil + compost + inoculation / 3.73 / 215 / 98 / 6.26 / 1426 / 627 / 6.60 / 2194 / 980 / 6.76 / 2445 / 1198
Soil + inoculation / 3.74 / 412 / 98 / 6.32 / 2909 / 652 / 6.67 / 4249 / 1025 / 6.82 / 5065 / 1263
Soil-4 / Soil / 3.80 / 230 / 99 / 6.47 / 1715 / 692 / 6.82 / 2695 / 1151 / 6.99 / 3193 / 1498
Soil + compost / 3.76 / 306 / 98 / 6.36 / 2188 / 665 / 6.72 / 3326 / 1059 / 6.88 / 3980 / 1328
Soil + compost + inoculation / 3.81 / 171 / 99 / 6.48 / 1312 / 696 / 6.82 / 1979 / 1154 / 6.97 / 2418 / 1499
Soil + inoculation / 3.76 / 381 / 98 / 6.37 / 2741 / 666 / 6.72 / 4071 / 1062 / 6.88 / 4905 / 1337
Soil-5 / Soil / 3.86 / 270 / 99 / 6.70 / 2254 / 761 / 7.07 / 3931 / 1368 / 7.24 / 4858 / 1935
Soil + compost / 3.83 / 147 / 98 / 6.57 / 1146 / 721 / 6.93 / 1891 / 1255 / 7.09 / 2345 / 1714
Soil + compost + inoculation / 3.88 / 203 / 98 / 6.69 / 1724 / 758 / 7.06 / 2881 / 1356 / 7.23 / 3762 / 1912
Soil + inoculation / 3.81 / 171 / 99 / 6.57 / 1335 / 726 / 6.92 / 2177 / 1249 / 7.10 / 2681 / 1693
Soil-6 / Soil / 3.85 / 188 / 99 / 6.66 / 1557 / 747 / 7.03 / 2615 / 1333 / 7.21 / 3354 / 1865
Soil + compost / 3.88 / 234 / 100 / 6.69 / 1895 / 754 / 7.05 / 3318 / 1356 / 7.22 / 4129 / 1902
Soil + compost + inoculation / 3.74 / 274 / 96 / 6.29 / 1957 / 640 / 6.64 / 2807 / 999 / 6.80 / 3288 / 1234
Soil + inoculation / 3.90 / 209 / 100 / 6.74 / 1726 / 774 / 7.11 / 3034 / 1411 / 7.29 / 3961 / 2023
Table S4 Alpha-diversity (i.e. estimated OTUs, Shannon diversity and the Chao-1 estimator of total species richnessidentifiedfromcucumber rhizosphere soils) for each treatment in soils 7-12.
Soils / Treatments / 100 reads / 800 reads / 1500 reads / 2200 readsShannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness / Shannon / Chao-1 / Species richness
Soil-7 / Soil / 3.89 / 514 / 100 / 6.72 / 4282 / 768 / 7.09 / 7251 / 1394 / 7.27 / 9375 / 1983
Soil + compost / 3.87 / 185 / 99 / 6.67 / 1487 / 756 / 7.05 / 2620 / 1347 / 7.23 / 3218 / 1885
Soil + compost + inoculation / 3.87 / 166 / 99 / 6.64 / 1367 / 740 / 6.99 / 2213 / 1297 / 7.16 / 2745 / 1795
Soil + inoculation / 3.80 / 273 / 99 / 6.49 / 2082 / 703 / 6.85 / 3315 / 1172 / 7.02 / 3956 / 1533
Soil-8 / Soil / 3.88 / 739 / 99 / 6.66 / 6262 / 782 / 7.12 / 10975 / 1439 / 7.20 / 14586 / 2082
Soil + compost / 3.70 / 928 / 98 / 6.26 / 6374 / 633 / 6.58 / 9430 / 975 / 6.69 / 10589 / 1171
Soil + compost + inoculation / 3.73 / 557 / 98 / 6.28 / 3785 / 636 / 6.62 / 5562 / 983 / 6.76 / 6357 / 1185
Soil + inoculation / 3.90 / 203 / 99 / 6.75 / 1774 / 776 / 7.13 / 3028 / 1425 / 7.31 / 3924 / 2055
Soil-9 / Soil / 3.75 / 264 / 98 / 6.31 / 1797 / 646 / 6.64 / 2727 / 1012 / 6.78 / 3206 / 1250
Soil + compost / 3.84 / 182 / 98 / 6.55 / 1399 / 714 / 6.91 / 2379 / 1226 / 7.08 / 2878 / 1647
Soil + compost + inoculation / 3.73 / 1883 / 97 / 6.27 / 13008 / 634 / 6.62 / 19242 / 986 / 6.78 / 22238 / 1203
Soil + inoculation / 3.85 / 183 / 98 / 6.53 / 1409 / 702 / 6.89 / 2315 / 1222 / 7.06 / 2936 / 1669
Soil-10 / Soil / 3.69 / 391 / 96 / 6.24 / 2624 / 623 / 6.56 / 3862 / 944 / 6.67 / 4365 / 1140
Soil + compost / 3.74 / 213 / 95 / 6.29 / 1528 / 626 / 6.58 / 2175 / 976 / 6.74 / 2562 / 1228
Soil + compost + inoculation / 3.79 / 170 / 95 / 6.44 / 1309 / 677 / 6.75 / 2029 / 1117 / 6.87 / 2470 / 1440
Soil + inoculation / 3.78 / 314 / 96 / 6.39 / 2258 / 666 / 6.72 / 3611 / 1072 / 6.88 / 4165 / 1372
Soil-11 / Soil / 3.79 / 180 / 97 / 6.39 / 1297 / 659 / 6.72 / 2046 / 1080 / 6.89 / 2441 / 1392
Soil + compost / 3.78 / 298 / 97 / 6.36 / 2111 / 654 / 6.69 / 3283 / 1055 / 6.84 / 3792 / 1341
Soil + compost + inoculation / 3.80 / 180 / 98 / 6.55 / 1387 / 713 / 6.90 / 2244 / 1219 / 7.07 / 2809 / 1643
Soil + inoculation / 3.83 / 216 / 99 / 6.53 / 1696 / 709 / 6.89 / 2715 / 1204 / 7.06 / 3365 / 1619
Soil-12 / Soil / 3.86 / 189 / 99 / 6.63 / 1550 / 737 / 6.99 / 2576 / 1301 / 7.16 / 3150 / 1800
Soil + compost / 3.79 / 187 / 98 / 6.44 / 1410 / 683 / 6.80 / 2161 / 1128 / 6.94 / 2587 / 1447
Soil + compost + inoculation / 3.85 / 164 / 99 / 6.59 / 1268 / 728 / 6.95 / 2111 / 1258 / 7.11 / 2735 / 1723
Soil + inoculation / 3.79 / 250 / 98 / 6.52 / 1947 / 710 / 6.89 / 3133 / 1200 / 7.05 / 3837 / 1588
Table S5
Pearson correlation coefficient (r) among soil environmental factors.
OM / TN / pH / EC / AN / IN / NN / AP / AKOrganic matter (OM) / -
Total N (TN) / 0.972*** / -
pH / -0.595*** / -0.580*** / -
EC / 0.810*** / 0.761*** / -0.611*** / -
Ammonium N (AN) / 0.299* / 0.234 / -0.035 / 0.277 / -
Nitrate N (NN) / 0.446** / 0.361** / -0.510*** / 0.679*** / 0.029 / -
Inorganic N (IN) / 0.479** / 0.386** / -0.509*** / 0.706*** / 0.156 / 0.992*** / -
Available P (AP) / 0.706*** / 0.633*** / -0.628*** / 0.701*** / 0.126 / 0.533*** / 0.543*** / -
Available K (AK) / 0.848*** / 0.794*** / -0.728*** / 0.908*** / 0.202 / 0.690*** / 0.707*** / 0.749*** / -
*, ** and ***Correlation is significant at the 0.05, 0.01 and 0.001 levels, respectively; n = 48.
Figure S1Rarefaction curvesdepicting theeffect of bacterial16S rRNA sequence number on the number of operational taxonomic units (OTUs) identifiedfromcucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1.
Figure S2Relative abundances of bacterial phyla inthe cucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S3Relative abundances of bacterial classes inthe cucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S4Relative abundances of the 22 most abundant bacterial orders inthe cucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S5Relative abundances of the 22 most abundant bacterial families inthe cucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S6Relative abundances of the 22 most abundant bacterial genera inthe cucumber rhizosphere soils (S1-S12) with four treatments, untreated soil (S), soil plus compost (SC), soil plus compost plus inoculation (SCI), and soil plus inoculation (SI). Soil codes (S1-S12) are the same as in Table S1. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S7Gammaproteobacteria(a) and Alphaproteobacteria (b) order level distribution inthe cucumber rhizosphere soils as affected bysoil environment, compost addition, bacterial inoculation, and compost addition by bacterial inoculation interaction. Relative abundances were estimated from the proportional abundances ofclassifiable sequences.
Figure S8Relative abundances of the predominant bacterial genera (more than 0.5%)found inthe cucumber rhizosphere soils.
Figure S9Pearson correlation coefficient among soil organic matter (OM) and the relative abundances of bacterial phyla. PValues in bold are statistically significant at P < 0.05.