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Sample Bacteria
Raw(x2) Processed Chimera Plant
NNNN
FB_MI_1_Lv 92195 29614 29246 220
FB_MI_1_Rt 34253 9484 9355 587
FB_MI_1_Rz 55128 14767 9814 9479
FB_MI_2_Lv 43157 12589 12546 82
FB_MI_2_Rt 41600 10936 10748 939
FB_MI_2_Rz 62505 15940 8080 7748
FB_MI_3_Lv 48429 15864 13719 597
FB_MI_3_Rt 74096 13661 12689 3843
FB_MI_3_Rz 49262 10684 5989 5739
FB_MI_4_Lv 14722 5142 5134 4
FB_MI_4_Rt 55562 14237 13608 1598
FB_MI_4_Rz 58411 15495 7505 7175
FB_MI_5_Lv 30723 6866 6611 6546
FB_MI_5_Rt 84066 17286 16381 3110
FB_MI_5_Rz 120579 31813 15829 15156
FBM_1_Bs 208952 55303 32308 30936
FBM_1_Lv 61058 20291 17495 13052
FBM_1_Rz 116927 21953 17499 16712
FBM_2_Bs 39244 12313 10246 10015
FBM_2_Lv 604374 16379 10480 7256
FBM_2_Rt 46838 13318 12903 1105
FBM_2_Rz 41534 11426 7904 7665
FBM_3_Bs 106733 31582 17573 16861
FBM_3_Lv 73090 12369 12333 127
FBM_3_Rt 30216 8733 8344 852
FBM_3_Rz 37999 8727 4884 4722
FBM_4_Bs 54035 14167 8987 8693
FBM_4_Lv 203913 64096 47225 26658
FBM_4_Rt 127510 34332 22236 14298
FBM_4_Rz 112005 26070 13761 12944
FBM_5_Bs 32527 9951 7378 7139
FBM_5_Lv 29473 9019 8983 148
FBM_5_Rt 28412 7148 7019 380
FBM_5_Rz 195833 47431 30810 29654
FB_RI_1_Lv 155980 44384 31488 5819
FB_RI_1_Rt 37296 7867 6838 2058
FB_RI_1_Rz 33987 9881 5698 5545
FB_RI_2_Lv 148076 43202 42810 1831
FB_RI_2_Rt 729385 31460 26419 3232
FB_RI_2_Rz 116372 34039 26536 25606
FB_RI_3_Lv 61754 18825 18668 1572
FB_RI_3_Rt 28189 6807 6601 3431
FB_RI_3_Rz 41485 11844 10559 10405
Table S7. Sequence statistics. FBM/WM = faba bean/wheat monoculture, FB_RI/W_RI = faba bean/wheat row intercropping, FB_MI/W_MI = faba bean/wheat mixed
intercropping; 1-5 = replicate 1-5; Bs = bulk soil, Rz = rhizosphere soil, Rt = root endosphere, Lv = leaf endosphere.
FB_RI_4_Lv 63217 20059 19945 276
FB_RI_4_Rt 74761 21953 21506 1183
FB_RI_4_Rz 5054 1426 1356 1337
FB_RI_5_Lv 117349 36154 22024 21603
FB_RI_5_Rt 74255 18300 17695 1347
FB_RI_5_Rz 34126 8956 6025 5848
W_MI_1_Lv 127456 31948 14363 10146
W_MI_1_Rt 134583 37333 21312 21058
W_MI_1_Rz 29401 7252 5709 5014
W_MI_2_Lv 23446 5898 3607 3581
W_MI_2_Rt 69820 18448 17772 7426
W_MI_2_Rz 42330 9909 3518 3361
W_MI_3_Lv 42462 9560 7446 6422
W_MI_3_Rt 52771 15760 14969 3989
W_MI_3_Rz 88612 20498 14898 14385
W_MI_4_Lv 121964 29246 17182 13700
W_MI_4_Rt 54396 16493 15528 3218
W_MI_5_Lv 47996 11542 8036 7156
W_MI_5_Rt 51004 14399 13926 3265
W_MI_5_Rz 118080 27839 15266 14625
WM_1_Bs 29711 8218 5547 5351
WM_1_Lv 98246 12114 8382 7947
WM_1_Rt 124897 28138 26433 9994
WM_1_Rz 153171 34795 24974 24139
WM_2_Bs 46740 12545 9274 8984
WM_2_Lv 257198 8154 4965 4840
WM_2_Rt 54574 12218 11137 4713
WM_2_Rz 81839 21869 16143 15575
WM_3_Bs 164911 48135 25658 24378
WM_3_Lv 61043 14138 11908 10174
WM_3_Rt 55085 15162 14157 4991
WM_3_Rz 88930 24810 14518 13872
WM_4_Bs 53478 13329 9949 9477
WM_4_Lv 155359 33942 19844 9207
WM_4_Rt 78885 21332 20625 1435
WM_4_Rz 25387 6988 4177 4007
WM_5_Bs 54055 14160 8952 8491
WM_5_Lv 53334 14868 8855 8040
WM_5_Rt 31169 8582 8180 1611
WM_5_Rz 81980 20400 11306 10844
W_RI_1_Lv 32881 10609 7579 6116
W_RI_1_Rt 121120 28222 26182 14232
W_RI_1_Rz 169060 38604 24320 23327
W_RI_2_Lv 115807 35133 25659 23794
W_RI_2_Rt 288870 17526 14623 7898
W_RI_2_Rz 64846 16459 11879 11476
W_RI_3_Lv 108758 30898 20635 20183
W_RI_3_Rt 35940 11827 11634 1283
W_RI_3_Rz 36284 9786 6832 6671
W_RI_4_Lv 195613 52194 29354 26114
W_RI_4_Rt 132081 37474 35510 6512
W_RI_4_Rz 66603 11210 8818 8560
W_RI_5_Lv 88007 26543 17087 16050
W_RI_5_Rt 83544 26449 25229 3665
W_RI_5_Rz 38373 9096 3532 3374
X_MI_1_Bs 31373 4686 2804 2697
X_MI_2_Bs 16451 3631 2794 2641
X_MI_3_Bs 99489 18797 9983 9503
X_MI_4_Bs 7817 2017 1140 1109
X_MI_5_Bs 17839 4107 3205 3067
X_RI_1_Bs 12801 3610 2376 2282
X_RI_2_Bs 34541 9786 7177 6970
X_RI_3_Bs 11492 3128 2745 2416
X_RI_4_Bs 48351 13050 8447 8129
X_RI_5_Bs 79417 22415 11767 11206
Sum 9428318 2041422 1499617 897824
Fungi
Raw(x2) Processed Chimera Plant
N N N N
745 26 25 8
32025 1423 1395 71
49931 3936 3581 2003
5627 186 179 24
23033 490 482 54
14306 708 645 547
4216 87 86 20
17466 687 680 20
20322 1473 1330 1210
1071 45 45 12
163166 5911 5784 751
11869 583 504 437
3816 256 248 124
19290 742 705 52
7061 486 443 392
25028 1497 1376 1269
204852 9016 8883 23
23930 1085 965 736
72164 4048 3681 3419
6951 346 339 2
93460 3179 2801 794
19334 816 712 596
39592 2182 2009 1555
1301 72 70 4
512982 51604 48524 42049
3217 182 162 148
27243 2078 1942 1491
13519 618 607 3
42290 2600 2379 82
15507 842 739 496
60291 6427 5467 1742
7373 407 330 204
289829 33183 29626 1719
2747 165 143 90
10728 581 578 28
25265 882 872 19
9532 222 196 181
46134 2451 2411 336
11653 391 373 11
19273 561 479 388
13811 800 785 134
47690 1605 1487 534
2787 101 85 64
FBM/WM = faba bean/wheat monoculture, FB_RI/W_RI = faba bean/wheat row intercropping, FB_MI/W_MI = faba bean/wheat mixed
intercropping; 1-5 = replicate 1-5; Bs = bulk soil, Rz = rhizosphere soil, Rt = root endosphere, Lv = leaf endosphere.
8957 520 488 122
13714 684 677 21
6410 263 243 193
19527 555 549 121
20933 823 811 30
9980 630 531 325
2087 85 83 68
82259 1875 1773 1141
21376 1096 951 882
10225 678 639 582
44250 1849 1665 799
41710 2386 2172 2009
19072 594 578 101
31796 1358 1194 470
178824 15851 14419 13372
33400 1958 1884 346
16369 365 307 101
16497 408 384 143
16839 846 772 418
62135 4378 3847 2882
40215 5863 5262 5120
573104 35896 34345 27353
36762 1981 1819 0
124731 8881 8093 7211
41817 3369 2972 2752
31324 1937 1898 1642
50453 1224 1164 157
18639 524 455 382
15031 360 310 294
26722 2229 2101 1761
47045 1121 1018 93
29734 2369 2227 1908
6690 524 451 412
10663 615 562 477
400018 5706 5408 2487
10719 546 472 429
3776 271 248 235
29681 2569 2428 2113
46766 1157 1041 472
667681 46571 42697 39913
19775 669 651 344
93344 2209 1593 899
4147 328 307 281
5635 440 425 388
25064 2616 2430 2124
17799 1451 1331 1244
22511 669 618 369
26521 903 863 27
37626 2708 2539 2331
10382 637 624 534
42434 1090 968 147
15361 1127 1023 956
10469 2982 2950 2879
49040 1376 1250 408
5922 68 48 26
46628 4609 4247 1897
56663 4854 4465 4166
35955 3402 3187 2948
40860 2263 2051 1782
82130 6334 5506 5216
168157 15262 13863 12961
63857 3409 3134 2860
540574 55780 49779 48421
48831 1771 1590 1453
56679 6605 5820 4369
6416722 429457 394353 282209