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Supplementary Figure 1. Bayesian dendrogram showing the relationships among the 16S rDNA sequences of 47 isolates belonging to the genus Bacillus and those of reference type strains. Posterior probability values are indicated at the node. Nodes are collapsed at 70% probability. LT = bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem.
0.4
S000446621_Bacillus_decoloration
S000133610_Bacillus_barbaricus_V
LT86
S000979521_Bacillus_megaterium_I
S000543426_Bacillus_boroniphilus
S000501792_Bacillus_bogoriensis_
S000429574_Bacillus_aquimaris_TF
S000805894_Bacillus_butanolivora
S000278327_Bacillus_methanolicus
S000437736_Bacillus_sporothermod
S000102217_Bacillus_acidicola_10
S000366467_Bacillus_gelatini_LMG
S000428475_Bacillus_subtilis_NRR
LT19
S001098928_Bacillus_nealsonii_DS
S000903108_Bacillus_solisalsi_YC
S001020552_Escherichia_coli_J016
LT78
LT60
LT10
S002291145_Bacillus_cereus_ATCC_
S000362993_Bacillus_taeanensis_B
LT11
LT46
S001014162_Bacillus_aerophilus
S000434839_Bacillus_circulans_AY
LT31
LT36
LT23
S000481068_Bacillus_pumilus_ATCC
S000446644_Bacillus_murimartini_
S000383283_Bacillus_mannanilytic
S001152386_Bacillus_qingdaonensi
S001014161_Bacillus_stratospheri
S000001855_Bacillus_mycoides_ATC
S000006950_Bacillus_gibsonii_DSM
S000473524_Bacillus_patagoniensi
LT14
S000469513_Bacillus_asahii_MA001
S000373335_Bacillus_salarius_BH1
S000408851_Bacillus_macauensis_Z
S000383277_Bacillus_akibai_1139_
S000414555_Bacillus_thermoamylov
S000843929_Bacillus_infernus_TH-
LT25
S002234727_Bacillus_tequilensis_
LT26
S000439486_Bacillus_vietnamensis
LT62
S000147238_Bacillus_krulwichiae_
LT71
S000323277_Bacillus_bataviensis_
S000373337_Bacillus_koreensis_BR
S000842016_Bacillus_isabeliae_CV
S000995279_Bacillus_acidiproduce
S000376345_Bacillus_anthracis_AT
S000649848_Bacillus_acidiceler_C
S000496869_Bacillus_oshimensis_K
S001098353_Bacillus_marmarensis
S000016369_Bacillus_badius_ATCC_
S000485127_Bacillus_fordii_R-719
S000003470_Bacillus_clausii_DSM_
S000447571_Bacillus_herbersteine
LT96
S000390853_Bacillus_endophyticus
LS8
S000008091_Bacillus_alcalophilus
LT22
S000323282_Bacillus_soli_LMG_218
LS1
S000644546_Bacillus_idriensis_SM
S000021968_Bacillus_psychrosacch
S000649704_Bacillus_thioparans_B
LT84
S000842524_Bacillus_canaveralius
S000351293_Bacillus_hwajinpoensi
LT24
S000021836_Bacillus_fumarioli_LM
S000013858_Bacillus_pseudofirmus
LR39
S002034580_Bacillus_nanhaiensis_
S000129063_Bacillus_fastidiosus_
S000503246_Bacillus_cibi_JG-30_A
S000484380_Bacillus_plakortidis_
S000083979_Bacillus_okuhidensis
S000701172_Bacillus_selenatarsen
S000001560_Bacillus_smithii_DSM_
LT27
S000417318_Bacillus_altitudinis4
S000768919_Bacillus_coahuilensis
S000014510_Bacillus_niacini_IFO1
S000622315_Bacillus_kribbensis_B
LT34
S000598282_Bacillus_niabensis_4T
S000007628_Bacillus_carboniphilu
S000131291_Bacillus_shackletonii
S000627913_Bacillus_pocheonensis
S001265319_Bacillus_galliciensis
S000010351_Bacillus_halodurans_D
S000000169_Bacillus_lentus_NCIMB
S001744238_Bacillus_nanhaiisedim
S000653122_Bacillus_okhensis_Kh1
LT61
S000389386_Bacillus_jeotgali_YKJ
S000548368_Bacillus_alveayuensis
LT20
S000383485_Bacillus_funiculus_NA
S001264210_Bacillus_chungangensi
S000428419_Bacillus_siralis_1715
S000824850_Bacillus_alkalinitril
S000008098_Bacillus_cohnii_DSM_6
S001577240_Bacillus_oceanisedimi
S000276014_Bacillus_galactosidil
S000016025_Bacillus_thermocloaca
S000485126_Bacillus_fortis_R-651
LT93
S000108528_Bacillus_aeolius_4-1_
S000323275_Bacillus_drentensis_L
LR37
LR89
LT18
S000457154_Bacillus_alkalitellur
S000627914_Bacillus_ginsengihumi
S000130255_Bacillus_benzoevorans
LT39
S000734915_Bacillus_amyloliquefa
S000012241_Bacillus_vallismortis
S000383265_Bacillus_hemicellulos
S000117161_Bacillus_algicola_KMM
LT33
LT40
S000366697_Bacillus_indicus_Sd3
S001098152_Bacillus_korlensis
S000001559_Bacillus_halmapalus_D
S001187364_Bacillus_lehensis_MLB
LT30
S001156575_Bacillus_rigui_WPCB07
LT97
S000383284_Bacillus_horikoshii_D
LT57
S000331995_Bacillus_litoralis_SW
S000458519_Bacillus_safensis_FO-
S000528024_Bacillus_oleronius_AT
LR40
S000979524_Bacillus_thuringiensi
LT63
S000323278_Bacillus_vireti_LMG_2
S000366852_Bacillus_humi_LMG_221
LT81
S000628319_Bacillus_cereus_ATCC_
S000003473_Bacillus_subtilis_DSM
S001199925_Bacillus_persepolensi
S001291460_Bacillus_trypoxylicol
S000323281_Bacillus_novalis_LMG_
S000644545_Bacillus_infantis_SMC
S000543964_Bacillus_arsenicus_co
S000130053_Bacillus_luciferensis
LT58
S000010355_Bacillus_pseudalcalip
LT98
S000711958_Bacillus_aidingensis_
S000435906_Bacillus_horti_K13_D8
S001576866_Bacillus_siamensis_PD
LT83
LT94
S000979519_Bacillus_firmus_IAM_1
LR90
LT16
S000014133_Bacillus_atrophaeus_J
S000390972_Bacillus_sonorensis_N
S001416952_Bacillus_horneckiae_1
S000858658_Bacillus_licheniformi
S000446637_Bacillus_muralis_LMG_
S000383270_Bacillus_wakoensis_N-
S000276781_Bacillus_ruris_R-6760
LT64
S000627916_Bacillus_panaciterrae
S001093971_Bacillus_halochares
S000424697_Bacillus_circulans_AT
S001239910_Bacillus_methylotroph
S000012966_Bacillus_flexus_IFO15
S000417319_Bacillus_aerius24K_AJ
S000005711_Bacillus_simplex_DSM_
S000727823_Bacillus_coagulans_NB
LT76
S000429573_Bacillus_marisflavi_T
S000006847_Bacillus_mojavensis_I
S000941821_Bacillus_azotoformans
S000373336_Bacillus_seohaeanensi
S000544167_Bacillus_foraminis_CV
S000016288_Bacillus_weihenstepha
S000485124_Bacillus_farraginis_R
0.9106
0.9724
1
0.8528
0.6017
0.9886
0.5762
0.798
0.5333
0.6656
0.7607
0.8966
0.9996
0.5526
0.9939
1
0.9768
1
0.6249
1
0.7375
0.6827
1
1
0.674
0.8089
0.9978
0.5145
1
0.8357
0.5399
0.8628
0.9991
1
1
0.9544
0.6854
0.7314
0.6595
1
1
1
0.7336
1
0.9965
1
0.5776
Supplementary Figure 2. Bayesian dendrogram showing the relationships among the 16S rDNA sequences of isolates belonging to the genus Pseudomonas and those of reference type strains. Posterior probability values are indicated at the node. Nodes are collapsed at 70% probability. LT= bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves.
0.9
LS97
S000858471_P_mohnii
LT59
S000001098_P_pertucinogena
S000008929_P_taetrolens
S000263191_P_fulva
S000495962_P_pachastrellae
S000543032_P_xanthomarina
S000145156_P_trivialis
LL4
LS21
S000824948_P_panipatensis
LT29
S000567747_P_azotifigens
LS5
LL73
LL21
S000427988_P_knackmussii
LL68
LS82
LS6
LS15
LS92
LS4
LS23
LR100
LS27
S000013342_P_rhodesiae
LS51
S000259962_P_vancouverensis
LR82
LS76
S000010427_P_aeruginosa
S000428888_P_thivervalensis
S000366447_P_proteolytica
S000428465_P_migulae
LS77
S000690384_P_japonica
LL97
S000366445_P_antarctica
S000541019_P_argentinensis
LT95
S000002018_P_fluorescens
LS53
S000269325_P_chlororaphis
LS79
LL58
LR14
LS66
S000002852_P_psychrophila
S001095516_P_taiwanensis
LS65
LL72
S001243670_P_fuscovaginae
S002221855_P_chlororaphis
LS32
LL74
LS89
LT69
LS78
LR58
S001171509_P_lini
LS37
S000016452_P_mendocina
S000964788_P_guineae
LS84
LT68
S000010434_P_corrugata
LL10
S001156249_P_pelagia
LL16
LS47
LS2
LL22
S000395042_P_koreensis
LS95
LS33
S000499371_P_costantinii
S000428332_P_cedrina
LT17
LS45
LL49
S000383942_P_cremoricolorata
LS90
S000009690_P_synxantha
S000444074_P_segetis
LL24
S001014073_P_marincola
S000858469_P_reinekei
LT89
LS57
LS71
LL50
S000010364_P_luteola
S000011992_P_marginalis
S000005892_P_cichorii
LT70
S000005898_P_azotoformans
LS35
S000428381_P_jessenii
LR87
LS38
S001043991_P_extremaustralis
LT15
S000006645_P_citronellolis
LT65
LL33
LR73
LR35
LS48
LR43
S000436974_P_flavescens
LS67
LS28
LL35
LL71
LT44
LT77
S000001334_P_mucidolens
S000558609_P_xiamenensis
LS29
S000260088_P_abietaniphila
LT54
LS56
S000006483_P_plecoglossicida
S000004324_P_oryzihabitans
LL42
S000022067_P_agarici
S000428331_P_orientalis
LT41
LS75
S000358323_P_lutea
S000428789_P_stutzeri
LS46
S000390413_P_brenneri
S000498899_P_tolaasii
LL36
LS83
LL79
LR1
LR42
LS19
S000145154_P_poae
LR85
LL20
LS63
S000392851_P_mediterranea
LT35
S000400225_P_viridiflava
LS39
LT9
S000575187_P_panacis
S001153684_P_cuatrocienegasensis
S000004663_P_veronii
LL11
LT51
LS43
S000390990_P_indica
LT55
LR3
S000145522_P_cannabina
S000903111_P_duriflava
LS60
S000428886_P_brassicacearum
LS42
LL12
LT50
S000428774_P_fragi
S001350578_P_oleovorans
S000516031_P_vranovensis
S000355057_P_salomonii
S000007012_P_resinovorans
LR33
LS96
S000366446_P_meridiana
LS44
S000146818_P_tremae
LL34
LS50
LS54
LS59
LT53
LS22
S000013175_P_frederiksbergensis
LR88
S001241637_P_taeanensis
S000003555_P_alcaligenes
LS18
S000651000_P_syringae
S000428466_P_gessardii
S001095875_P_brassicacearum
S000395038_P_jinjuensis
LL14
S000626936_P_nitroreducens
LS85
S000013965_P_graminis
LS68
S000004193_P_savastanoi
LR94
S001098319_P_caeni
LS17
S000395040_P_umsongensis
LT47
LS30
S002151284_P_arsenicoxydans
S000009281_P_pseudoalcaligenes
LS70
S000013341_P_monteilii
LT79
S000608925_P_peli
LT43
S000015943_P_asplenii
LR2
S000262316_P_parafulva
S000004781_P_caricapapayae
LS91
S000608918_P_borbori
LS49
S000008928_P_oleovorans
S000010130_P_alcaliphila
LS26
LR74
S000968494_P_xinjiangensis
LT82
LR83
S000516032_P_moraviensis
S000841838_P_mosselii
LS72
LR84
LR44
S000942753_P_sabulinigri
S000143918_P_lurida
S000000053_P_amygdali
LS81
S000146512_P_congelans
LL18
S000010260_P_ficuserectae
LR30
LR91
S000108891_P_kilonensis
S000499514_P_extremorientalis
LS98
S000639965_P_delhiensis
LL60
LT90
LT32
LS73
LR4
LS52
LL63
LL91
S000260543_P_anguilliseptica
S000390380_P_grimontii
LL23
LT4
LL65
LS34
LS62
LS31
S000003153_P_putida
S000416841_P_psychrotolerans
LS36
S000145155_P_cedrina
LS24
S000721984_P_chlororaphis
S000428211_P_mandelii
S000355056_P_palleroniana
S000000900_P_chlororaphis
LS20
LS16
LR38
LT45
LS13
S000437396_P_balearica
S000398317_P_rhizosphaerae
LS64
LS55
LS58
LS61
LS74
LS14
S000858470_P_moorei
LR36
S000639962_P_pohangensis
S000749691_P_simiae
S001020552_Escherichia_coli
LL15
LT72
S000011995_P_straminea
LS7
LR13
LS41
LT66
S000428195_P_libanensis
S000014863_P_lundensis
LS25
LS10
S000514601_P_otitidis
0.9
1
0.57
0.87
0.75
0.94
0.63
1
0.72
0.69
0.72
0.84
1
0.55
0.55
0.88
0.78
0.53
0.97
1
1
0.54
0.56
0.98
0.69
0.79
0.57
0.65
0.69
0.99
1
1
0.9
0.67
0.98
0.95
0.56
0.72
Supplementary Figure 3. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of 37 isolates belonging to the genus Stenotrophomonas and those of reference type strains. Bootstrap values are indicated at the node. LL= bacteria isolated from the leaves, LR = bacteria isolated from the roots (see Material and Methods and Suppl. Table 4 for details).
LR26
S000129976 S rhizophila e-p10
LRL93
LL44
LR98
LR99
LR95
LR79
LR75
LR61
LR60
LR48
LR32
LR31
LR29
S000559371 S ginsengisoli
S000386319 S koreensis TR6-01
S000390459 S acidaminiphila AMX19
S000003927 S nitritireducens L2
S000841904 S terrae R-32768
S000130243 P pictorum LMG 981
S000841903 S humi R-32729
LR8
LR34
LR41
LR71
LR72
LR76
LR80
LR86
LL13
LL17
LL37
LL76
LL38
LL39
LL43
LL45
LL75
LL77
LL88
LL94
LL96
LT48
S000007629 P geniculata ATCC 19374T
S000009493 P beteli ATCC 19861T6
S000010261 P hibiscicola ATCC 19867T
S000824093 S maltophilia IAM 12423
S001097383 S chelatiphaga LPM-5
S001576206 S daejeonensis MJ03
S001611233 S pavanii ICB 89
LR28
S001020552 Escherichia coli
86
76
74
74
70
Supplementary Figure 4. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of 46 isolates belonging to the genus Rhizobium and those of reference type strains. Bootstrap values are indicated at each node. Nodes are collapsed at 70% probability. LT= bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots (see Material and Methods and Suppl. Table 4 for details).
S000261905 R galegae S163
S000903294 R alkalisoli CCBAU 01393
S001098292 R huautlense CCBAU 65798
S000413447 R galegae ATCC 43677
S000444220 R vignae CCBAU 23084
S000967567 R tubonense CCBAU 85046
S000021974 S sp S009
S002233877 R helanshanense CCNWMQ14-1
S000434676 R loessense CCBAU 7190B
S000639628 S sp DAO10
S000824040 Amorphomonas oryzae B47
S000722695 R cellulosilyticum ALA10B2
S000967566 R cellulosilyticus CCBAU 8504
S002232356 R sphaerophysae CCNWQTX20
S003717524 Shinella sp M80
S000427818 R huautlense SO2
S000364391 R sp Esparseta 3
S003749510 A viscosum SDGD01
S001589495 R pongamiae VKLR-01
S003301457 A tumefaciens MM10
S002221963 R pusense NRCPB10
S000721046 R radiobacter IAM 12048
S001745941 R vignae CCBAU 05176
S001588055 Beijerinckia fluminensis UQM
S003717587 A tumefaciens KFB 233
S002228822 A larrymoorei BAC1011
S000021216 R larrymoorei 3-10
LT12
S000635884 A sp CCBAU 23089
S002958452 A tumefaciens B2
LR70
LT92
LR56
S000003864 A sp MSMC211
S003262687 A tumefaciens NBRC 15189
S003753424 Candidatus R massiliae MD 06
LR55
LT74
S000389830 BradyR japonicum PRY62
LR63
LR54
S001170532 A tumefaciens CCNWGS0221
LR51
S003289155 endophytic bacterium 90L-1
LR50
LR62
LT87
S000002681 A sp LMG 11936
LR47
LR65
LR57
LT73
LR45
LR52
S000431871 Candidatus R massiliae 90A
S001188792 endophytic bacterium HB03
LR22
S000444931 P viscosum CICC10215
S000015668 A sp LMG 11915
LR20
S000393816 R galegae DASA12028
LR11
S002229177 A tumefaciens RR5
LR49
S002958314 M sp CCNWGS0211
LR6
S003289156 endophytic bacterium 90L-2
LR53
S000127045 Azospirillum sp Z29621
S000017731 A vitis CFBP 2617
S002233057 R taibaishanense CCNWSX 0457
S000721033 A vitis G-Ag-19
S003262668 A vitis NBRC 15140
S000437650 R vitis NCPPB3554
S000021625 R aggregatum IFAM 1003
S000391412 A albertimagni AOL15
S001548991 R rosettiformans W3
S000456906 A vitis PHX1
S001241092 Blastobacter aggregatus RW7
S000421666 A larrymoorei ICMP 15237
S000721040 A tumefaciens MAFF 03-01224
S000964676 A fabrum str C58
S002445816 R skierniewicense AL93
S002408292 A rubi LMG 159
LR19
LR7
LR21
LR18
LR9
LR24
LR16
LR23
LR12
LR46
LR17
LR5
LR25
S000429561 A sp PB
S000140466 R daejeonense L61T KCTC 12121
S000942308 R selenitireducens B1
S000262203 S fredii S150
S002914131 Ensifer sp KJ018
S001328174 R cnuense KSW 4-12
S003287632 S sp MG-2011-4-AO
S000996028 R giardinii CCBAU 01209
S000330242 S sp S1-T-10
S000392228 S sp 9702-M4
S000635883 BradyR sp CCBAU 23024
S000438628 R giardinii H152
S000015022 R sp DUS470
S002411294 R undicola OURAN110
LR66
LR77
LR15
LR78
LR64
LR67
LT91
LR68
LR69
S000769199 R sp BSV16
S000967698 Mycoplana peli AN419
S000769681 R borbori DN316
S000388919 R yanglingense CCBAU 71462
S001168838 R oryzae Alt 505
S000323103 R sp TCK
S000806232 R soli DS-42
S000111802 R indigoferae CCBAU 71042
S000541167 R gallicum bv gallicum IE4770
S000967565 R sullae CCBAU 85011
S001096426 R loessense CCBAU 25159
S000438747 R mongolense USDA 1844
S000262741 R mongolense S110
S000559201 R mesosinicum CCBAU 25010
S000387012 R gallicum CbS-1
S000979020 R yanglingense SH22623
S001014241 R alamii GBV016
S000979022 R loessense CCBAU 7190B
S001294595 R phenanthrenilyticum F11
S000367571 R etli PRF51
S000769770 R phaseoli ATCC 14482
S000261327 R etli S1
S000635888 R mesosinicum CCBAU 41026
S000393807 R gallicum DASA12020
S000437446 R etli CFN 42 USDA 9032
S003284111 R vallis R3-65
S000265215 R pisi DSM 30132
S000776010 R fabae CCBAU 33202
S000055319 R sp WSM749
S000364392 R sullae DSM 14623
S002911602 R grahamii CCGE 502
S002961235 R genosp TUXTLAS-27 4m
S003284683 R endophyticum S6-260
S000967537 R tibeticum CCBAU 85039
S000262202 R mongolense S152
S003746557 M ciceri CPN7
S000364339 R tropici LMG 9518
S000926235 R multihospitium CCBAU 83401
S000752081 R miluonense CCBAU 41251
S000393812 R leguminosarum DASA23002
S000981736 R hainanense I66
S000413524 A sp K-Ag-3
S000364330 A rhizogenes LMG 152
S002290486 A radiobacter K84 ATCC BAA-86
S000421679 R rubi ICMP 11833
S002035399 A rubi F266
S000413521 R rhizogenes IFO 13257
S002034822 R lusitanum CCBAU 15087
S000000452 R genosp R BDV5365
S000979412 R indigoferae CCBAU 71042
S000014582 M sp N36
S000093085 R leguminosarum WSM1698
S001187435 R leguminosarum bv trifolii W
S000775995 R leguminosarum bv viciae CCB
S002222203 R leguminosarum bv phaseoli 3
S000379907 R mesoamericanum tpud40a
S000410286 R etli
Caulobacter/158-602 mirabilis T FWC38
89
84
81
77
76
73
70
70
Supplementary Figure 5. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of 25 isolates belonging to the genus Pantoea and those of reference type strains. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves (see Material and Methods and Suppl. Table 4 for details).
LS100
LL41
LS99
LS93
LS11
LS9
S001187644 Pantoea conspicua LMG 24534 EU216737
S001187642 Pantoea brenneri LMG 5343 EU216735
S001187456 Pantoea vagans LMG 24199 EF688012
S001187455 Pantoea deleyi LMG 24200 EF688011
S001187454 Pantoea anthophila LMG 2558 EF688010
S001187453 Pantoea eucalypti LMG 24197 EF688009
S000016079 Pantoea agglomerans DSM 3493 AJ233423
LL95
LL89
LL78
LL54
LL90
LL48
LL53
LL9
LL62
LL70
LL86
LL92
LL69
LL56
LL40
LL47
LL61
LL46
LL55
S000381168 Pantoea ananatis ATCC 33244 U80196
S000412194 Pantoea allii BD 390 1 AY530795
S001610452 Pantoea calida 1400/07 GQ367478
S000000125 Pantoea cypripedii DSM 3873 AJ233413
S001610453 Pantoea gaviniae A18/07 GQ367483
S000381179 Pantoea stewartii ATCC 8199 U80208
S000691510 Pantoea dispersa LMG2603 DQ504305
S001187641 Pantoea septica LMG 5345 EU216734
S001187643 Pantoea eucrina LMG 2781 EU216736
S001020552 Escherichia coli J01695
98
98
80
94
78
81
90
75
100
98
70
Supplementary Figure 6. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of 30 isolates belonging to the genus Microbacterium and those of reference type strains. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT = bacteria isolated from the rhizosphere, LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves (see Material and Methods and Suppl. Table 4 for details).
LT2
LT8
LL5
LT7
LT6
LT5
LT4
LL6
LT3
S000381732 M luteolum
S000381733 M saperdae
S000440800 M maritypicum
S000019591 M liquefaciens
S000007793 M oxydans
LT85
LL29
S000121408 M paraoxydans
S000901905 M aquimaris
S000020165 M testaceum
S000892535 M profundi
S000650697 M thalassium
LS87
S001014065 M hatanonis
S001417385 M pseudoresistens
S000381731 M keratanolyticum
S000427347 M halophilum
S000001703 M resistens
S000965858 M binotii
S000967183 M insulae
S000503539 M natoriense
S000440798 M xylanilyticum
S000083932 M aerolatum
S000014753 M foliorum
S000012860 M phyllosphaerae
S000381734 M terrae
S000381737 M ketosireducens
S000871546 M soli
S000843265 M kribbense
S000021147 M trichothecenolyticum
S000001603 M arabinogalactanolyticum
S000018525 M esteraromaticum
LL7
S001417386 M humi
S001155658 M lindanitolerans
S001351455 M agarici
S000002734 M arborescens
S000003131 M imperiale
S000650694 M hominis
S001577352 M radiodurans
S000473677 M halotolerans
S000000028 M flavescens
LL2
LL30
LL32
LL100
LL83
S000539538 M oleivorans
LL57
LL1
LL84
LL67
LL82
LL31
LT56
LT67
S000539539 M hydrocarbonoxydans
S000006251 M dextranolyticum
S000010831 M laevaniformans
LL59
LL8
LL81
LL85
S000381738 M chocolatum
S000469185 M kitamiense
S000427348 M aurantiacum
S000891240 M luticocti
S000727788 M ginsengisoli
S001577784 M mitrae
S001187351 M invictum
S000964148 M flavum
S000964147 M fluvii
S000541107 M koreense
S000006247 M aurum
S000013457 M lacticum
S000009659 M schleiferi
S000964146 M awajiense
S000622940 M aoyamense
S000711011 M pygmaeum
S000622938 M deminutum
S000711001 M terricola
S000381735 M terregens
S000622939 M pumilum
S000964149 M lacus
S000841857 M indicum
S000390332 M gubbeenense
S000022611 M barkeri
S001020552 Escherichia coli
99
92
Supplementary Figure 7. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of 47 isolates belonging to the genus Bacillus and those of reference type strains. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT = bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem (see Material and Methods and Suppl. Table 4 for details).
S000131291 Bacillus shackletonii LMG 18435 AJ250318
S000373336 Bacillus seohaeanensis BH724 AY667495
S000102217 Bacillus acidicola 105-2 AF547209
S000016369 Bacillus badius ATCC 14574 X77790
S000016288 Bacillus weihenstephanensis DSM11821 AB021199
S000014133 Bacillus atrophaeus JCM9070 AB021181
S000013858 Bacillus pseudofirmus DSM 8715 X76439
S000012241 Bacillus vallismortis DSM11031 AB021198
S000007628 Bacillus carboniphilus JCM9731 AB021182
S000006950 Bacillus gibsonii DSM 8722 X76446/
S000006847 Bacillus mojavensis IFO15718 AB021191
S000003473 Bacillus subtilis DSM10 AJ276351
S000001855 Bacillus mycoides ATCC6462 AB021192
S002291145 Bacillus cereus ATCC 14579 AE016877
S002234727 Bacillus tequilensis 10b HQ223107
S001576866 Bacillus siamensis PD-A10 GQ281299
S001239910 Bacillus methylotrophicus CBMB205 EU194897
S001098353 Bacillus marmarensis GMBE72 EU621902
S001098152 Bacillus korlensis ZLC-26 EU603328
S000995279 Bacillus acidiproducens SL213 EF379274
S000979524 Bacillus thuringiensis IAM 12077 D16281
LT86
LT84
LT83
LT81
LT78
LT64
LT62
LT61
LT60
LT58
LT57
LT46
LT40
LT33
LT30
LT25
LT24
LT20
LT19
LT18
LT16
LT14
LT11
LR40
LR39
LR37
LS8
LS1
S000979519 Bacillus firmus IAM 12464 D16268
S000858658 Bacillus licheniformis ATCC 14580 DSM 13 CP000002
S000842016 Bacillus isabeliae CVS-8 AM503357
S000734915 Bacillus amyloliquefaciens NBRC 15535 AB255669
S000727823 Bacillus coagulans NBRC 12583 AB271752
S000628319 Bacillus cereus ATCC 14579 AE016877
S000627914 Bacillus ginsengihumi Gsoil 114 AB245378
S000528024 Bacillus oleronius ATCC 700005 AY988598
S000485127 Bacillus fordii R-7190 AY443039
S000485126 Bacillus fortis R-6514 AY443038
S000484380 Bacillus plakortidis P203 AJ880003
S000446644 Bacillus murimartini LMG 21005 AJ316316
S000446621 Bacillus decolorationis LMG 19507 AJ315075
S000439486 Bacillus vietnamensis 15-1 AB099708
S000437736 Bacillus sporothermodurans M215 U49078
S000429573 Bacillus marisflavi TF-11 AF483624
S000428475 Bacillus subtilis NRRL B-23049 AF074970
S000417319 Bacillus aerius24K AJ831843
S000543964 Bacillus arsenicus con a/3 AJ606700
S002034580 Bacillus nanhaiensis JSM 082006 GU477780
S000001560 Bacillus smithii DSM 4216 Z26935
S000133610 Bacillus barbaricus VII-B3-A2 AJ422145
S000408851 Bacillus macauensis ZFHKF-1 AY373018
S000390972 Bacillus sonorensis NRRL B-23154 AF302118
S000376345 Bacillus anthracis ATCC 14578 AB190217
S000543426 Bacillus boroniphilus T-15Z AB198719
S000544167 Bacillus foraminis CV53 AJ717382
S000548368 Bacillus alveayuensis TM 1 AY605232
S000627913 Bacillus pocheonensis Gsoil 420 AB245377
S000644545 Bacillus infantis SMC 4352-1 AY904032
S000649704 Bacillus thioparans BMP-1 DQ371431
S000649848 Bacillus acidiceler CBD 119 DQ374637
S000701172 Bacillus selenatarsenatis SF-1 AB262082
S000805894 Bacillus butanolivorans K9 EF206294
S000824850 Bacillus alkalinitrilicus ANL-iso4 EF422411
S000842524 Bacillus canaveralius KSC SF8b DQ870688
S000941821 Bacillus azotoformans NBRC 15712 AB363732
S000000169 Bacillus lentus NCIMB8773 AB021189
LR89
LR90
S001098928 Bacillus nealsonii DSM 15077 EU656111
S001416952 Bacillus horneckiae 1P01SC EU861362
S001577240 Bacillus oceanisediminis H2 GQ292772
S000001559 Bacillus halmapalus DSM 8723 X76447
S000005711 Bacillus simplex DSM 1321T AJ439078
S000008098 Bacillus cohnii DSM 6307 T X76437
S000014510 Bacillus niacini IFO15566 AB021194
S000021968 Bacillus psychrosaccharolyticus ATCC23296 AB021195
S000130053 Bacillus luciferensis LMG 18422 AJ419629
S000130255 Bacillus benzoevorans NCIMB 12555 X60611
S000276781 Bacillus ruris R-6760 LMG 22866 AJ535639
S001265319 Bacillus galliciensis BFLP-1 FM162181
S000331995 Bacillus litoralis SW-211 AY608605
S000598282 Bacillus niabensis 4T19 AY998119
S000447571 Bacillus herbersteinensis D-15a AJ781029
S000429574 Bacillus aquimaris TF-12 AF483625
S000373337 Bacillus koreensis BR030 AY667496
S000435906 Bacillus horti K13 D87035
S000366697 Bacillus indicus Sd/3 AJ583158
S000383283 Bacillus mannanilyticus AM-001 AB043864
S000390853 Bacillus endophyticus 2DT AF295302
S000903108 Bacillus solisalsi YC1 EU046268
S000417318 Bacillus altitudinis41KF2b AJ831842
S000458519 Bacillus safensis FO-036b AF234854
S000481068 Bacillus pumilus ATCC 7061 AY876289
S001187364 Bacillus lehensis MLB2 AY793550
S000496869 Bacillus oshimensis K11 AB188090
S000503246 Bacillus cibi JG-30 AY550276
S000644546 Bacillus idriensis SMC 4352-2 AY904033
LT10
LT26
LT27
LT31
LT34
LT36
LT39
LT71
LT93
LT94
LT96
LT97
LT98
S001014161 Bacillus stratosphericus41KF2a AJ831841
S001014162 Bacillus aerophilus28K AJ831844
S000003470 Bacillus clausii DSM 8716 X76440
S000012966 Bacillus flexus IFO15715 AB021185
S000117161 Bacillus algicola KMM 3737 AY228462
S000351293 Bacillus hwajinpoensis SW-72 AF541966
S000434839 Bacillus circulans AY043084
S000276014 Bacillus galactosidilyticus LMG 17892 AJ535638
S000108528 Bacillus aeolius 4-1 AJ504797
S000278327 Bacillus methanolicus NCIMB 13113T AB112727
S000021836 Bacillus fumarioli LMG 17489 AJ250056
S000362993 Bacillus taeanensis BH030017 AY603978
S000622315 Bacillus kribbensis BT080 DQ280367
S001156575 Bacillus rigui WPCB074 EU939689
S000383485 Bacillus funiculus NAF001 AB049195
S000627916 Bacillus panaciterrae Gsoil 1517 AB245380
S000768919 Bacillus coahuilensis m4-4 EF014452
S000979521 Bacillus megaterium IAM 13418 D16273
LT22
LT23
LT76
S000129063 Bacillus fastidiosus DSM 91 X60615
S000473524 Bacillus patagoniensis PAT 05 AY258614
LT63
S000016025 Bacillus thermocloacae DSM 5250 Z26939
S001020552 Escherichia coli J01695
S001264210 Bacillus chungangensis CAU 348 FJ514932
S000485124 Bacillus farraginis R-6540 AY443036
S000843929 Bacillus infernus TH-23 (SMCC/W 479) U20385
S001093971 Bacillus halochares MSS4 AM982516
S001152386 Bacillus qingdaonensis CM1 DQ115802
S000414555 Bacillus thermoamylovorans CNCM I-1378 L27478
S000323275 Bacillus drentensis LMG 21831 AJ542506
S001744238 Bacillus nanhaiisediminis NH3 GQ292773
S000383277 Bacillus akibai 1139 AB043858
S000366467 Bacillus gelatini LMG 21880 AJ551329
S000383270 Bacillus wakoensis N-1 AB043851
S000653122 Bacillus okhensis Kh10-101 DQ026060
S000383265 Bacillus hemicellulosilyticus C-11 AB043846
S001291460 Bacillus trypoxylicola SU1 AB434284
S000008091 Bacillus alcalophilus DSM 485 T X76436
S000010351 Bacillus halodurans DSM 497T AJ302709
S000010355 Bacillus pseudalcaliphilus DSM 8725 X76449
S000083979 Bacillus okuhidensis AB047684
S000147238 Bacillus krulwichiae AM31D AB086897
S000501792 Bacillus bogoriensis LBB3 AY376312
S000373335 Bacillus salarius BH169 AY667494
S001199925 Bacillus persepolensis HS-136 FM244839
S000711958 Bacillus aidingensis 17-5 DQ504377
S000323277 Bacillus bataviensis LMG 21833 AJ542508
S000323278 Bacillus vireti LMG 21834 AJ542509
S000323281 Bacillus novalis LMG 21837 AJ542512
S000323282 Bacillus soli LMG 21838 AJ542513
S000366852 Bacillus humi LMG 22167 AJ627210
S000383284 Bacillus horikoshii DSM8719 AB043865
S000389386 Bacillus jeotgali YKJ-10 AF221061
S000424697 Bacillus circulans ATCC 4513 NCTC 2610 NCDO1775 AY724690
S000428419 Bacillus siralis 171544 AF071856
S000446637 Bacillus muralis LMG 20238 AJ316309
S000457154 Bacillus alkalitelluris BA288 AY829448
S000469513 Bacillus asahii MA001 AB109209
75
Supplementary Figure 8. Maximum parsimony dendrogram showing the relationships among the 16S rDNA sequences of isolates belonging to the genus Pseudomonas and those of reference type strains. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT= bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves (see Material and Methods and Suppl. Table 4 for details).
LS19
S001171509 P lini
S000858469 P reinekei
S000499371 P costantinii
S000428886 P brassicacearum
S000428331 P orientalis
S000395042 P koreensis
S000383942 P cremoricolorata
S000269325 P chlororaphis
S000146512 P congelans
S000013175 P frederiksbergensis
S000010130 P alcaliphila
S000006483 P plecoglossicida
S000003555 P alcaligenes
S000000053 P amygdali
LL71
LL49
LL23
LL14
LT89
LT68
LT51
LT41
LR83
LR42
LR13
LS96
LS84
LS76
LS68
LS61
LS54
LS47
LS39
LS25
LS18
LS7
S000543032 P xanthomarina
S000498899 P tolaasii
S000428211 P mandelii
S000395040 P umsongensis
S000366447 P proteolytica
S000263191 P fulva
S000145522 P cannabina
S000011995 P straminea
S000009690 P synxantha
S000005898 P azotoformans
LL97
LL68
LL42
LL22
LL12
LT82
LT66
LT50
LR94
LR82
LR38
LS95
LS83
LS75
LS67
LS60
LS53
LS46
LS38
LS31
LS24
LS17
LS6
S002221855 P chlororaphis
S000428195 P libanensis
S000395038 P jinjuensis
S000841838 P mosselii
S000262316 P parafulva
S000145156 P trivialis
S000015943 P asplenii
S000011992 P marginalis
S000009281 P pseudoalcaligenes
LL91
LL65
LL36
LL21
LL11
LT65
LT47
LT32
LR91
LR74
LR36
LR3
LS92
LS82
LS66
LS74
LS59
LS52
LS45
S000005892 P cichorii
S000541019 P argentinensis
LS37
S000022067 P agarici
LS30
LS23
LS16
LS5
S002151284 P arsenicoxydans
S000749691 P simiae
S000516032 P moraviensis
S000428466 P gessardii
S000392851 P mediterranea
S000145155 P cedrina
S000014863 P lundensis
S000942753 P sabulinigri
S000010434 P corrugata
LS2
LS15
LS4
S000146818 P tremae
S000004193 P savastanoi
S000000900 P chlororaphis
LL72
LL50
LL24
LL15
LT90
LT69
LT53
LT4
LT9
LR84
LR43
LR14
LS97
LS85
LS77
LS70
LS62
LS55
LS48
LS41
LS33
LS10
LS26
LS13
LS14
LS20
LS57
LS21
LS35
LS50
LS64
LS79
LR1
LR58
LT17
LT55
LL4
LL34
LL74
S000004663 P veronii
S000145154 P poae
S000358323 P lutea
LS22
S001350578 P oleovorans
LS27
LS28
LS90
LS29
LR35
LS34
LS36
LS42
LS43
LS44
LS49
LS51
LS56
S000002018 P fluorescens
S000013342 P rhodesiae
LS58
LS71
LS63
LS65
LS72
S000013965 P graminis
LL33
LS73
LS78
LS81
LL63
LS89
LS91
LS98
LR2
LR30
LL20
S000858471 P mohnii
LR33
LR44
LR73
S000499514 P extremorientalis
LR85
LR87
LR88
LT45
LR100
S001098319 P caeni
S000436974 P flavescens
LT15
S000001334 P mucidolens
LT29
S000390413 P brenneri
LT35
S000008929 P taetrolens
S000366446 P meridiana
S000964788 P guineae
S000366445 P antarctica
S000428774 P fragi
LT79
S000002852 P psychrophila
LT43
LT44
LT54
LT59
LT70
LT77
S000013341 P monteilii
S000004781 P caricapapayae
LT95
LL10
LL16
LL18
LL35
LL58
S000398317 P rhizosphaerae
LL73
LL60
LL79
S000001098 P pertucinogena
S000558609 P xiamenensis
S000968494 P xinjiangensis
S001156249 P pelagia
S000016452 P mendocina
S000004324 P oryzihabitans
S000010260 P ficuserectae
S000108891 P kilonensis
S000143918 P lurida
S000390380 P grimontii
S000400225 P viridiflava
S000259962 P vancouverensis
S001043991 P extremaustralis
S000355056 P palleroniana
S000355057 P salomonii
S000428332 P cedrina
S000428381 P jessenii
S000428465 P migulae
S000428888 P thivervalensis
S000516031 P vranovensis
S000575187 P panacis
S000651000 P syringae
S000690384 P japonica
S000721984 P chlororaphis
S000858470 P moorei
S001095516 P taiwanensis
S001095875 P brassicacearum
S001243670 P fuscovaginae
S000007012 P resinovorans
S000260543 P anguilliseptica
LT72
S000437396 P balearica
S000495962 P pachastrellae
S000903111 P duriflava
S000427988 P knackmussii
S000006645 P citronellolis
S000639965 P delhiensis
S000428789 P stutzeri
S000567747 P azotifigens
S000010364 P luteola
S000639962 P pohangensis
S000444074 P segetis
S000260088 P abietaniphila
S000514601 P otitidis
LR4
S000626936 P nitroreducens
S000390990 P indica
S000008928 P oleovorans
S000824948 P panipatensis
S000010427 P aeruginosa
S000416841 P psychrotolerans
S000608925 P peli
S001241637 P taeanensis
S001014073 P marincola
LS32
S000003153 P putida
S000608918 P borbori
S001153684 P cuatrocienegasensis
S001020552 Escherichia coli
75
64
Supplementary Figure 9. NJ dendrogram showing the relationships among the 16S rDNA sequences of 37 isolates belonging to the genus Stenotrophomans and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LL= bacteria isolated from the leaves, LR = bacteria isolated from the roots.
LR80
LR86
LR75
LL37
LL39
LL76
LR72
LL17
LL43
LR71
LL13
LL88
LR76
LL94
LR28
LL77
LL45
LL96
LL75
S001097383 Stenotrophomonas chelatiphaga LPM-5 EU573216
LL38
LR41
S001576206 Stenotrophomonas daejeonensis MJ03 GQ241320
LR34
LT48
LR8
S001611233 Stenotrophomonas pavanii ICB 89 FJ748683
S000007629 Pseudomonas geniculata ATCC 19374T AB021404
S000010261 Pseudomonas hibiscicola ATCC 19867T AB021405
S000009493 Pseudomonas beteli ATCC 19861T AB021406
S000824093 Stenotrophomonas maltophilia IAM 12423 AB294553
S000559371 Stenotrophomonas ginsengisoli DQ109037
S000386319 Stenotrophomonas koreensis TR6-01 AB166885
S000390459 Stenotrophomonas acidaminiphila AMX19 AF273080
S000003927 Stenotrophomonas nitritireducens L2 AJ012229
S000841904 Stenotrophomonas terrae type strain: R-32768 AM403589
S000130243 Pseudomonas pictorum LMG 981 AJ131116
S000841903 Stenotrophomonas humi type strain: R-32729 AM403587
S000129976 Stenotrophomonas rhizophila e-p10 AJ293463
LR26
LR29
LR60
LR79
LL44
LR32
LR31
LR61
LR95
LR48
LR98
LR99
LRL93
S001020552 Escherichia coli J01695
97
78
87
86
76
75
70
88
Supplementary Figure 10. NJ dendrogram showing the relationships among the 16S rDNA sequences of 46 isolates belonging to the genus Rhizobium and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at each node. Nodes are collapsed at 70% probability. LT= bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots.
S002232356 Rhizobium sphaerophysae CCNWQTX20 HM628695
S003717524 Shinella sp M80 KC464844
S000967566 Rhizobium cellulosilyticus CCBAU 85045 EU256433
S000639628 Sinorhizobium sp DAO10 DQ336178
S000824040 Amorphomonas oryzae B47 AB233494
S002233877 Rhizobium helanshanense CCNWMQ14-1 HQ132350
S000427818 Rhizobium huautlense SO2 AF025852
S000021974 Sinorhizobium sp S009 AF285965
S000261905 Rhizobium galegae S163 AY509213
S000444220 Rhizobium vignae CCBAU 23084 AY775170
S000967567 Rhizobium tubonense CCBAU 85046 EU256434
S001098292 Rhizobium huautlense CCBAU 65798 EU618032
S000413447 Rhizobium galegae ATCC 43677 D11343
S000434676 Rhizobium loessense CCBAU 7190B AY034026
S000903294 Rhizobium alkalisoli CCBAU 01393 EU074168
S000393816 Rhizobium galegae DASA12028 AF417566
S003717587 Agrobacterium tumefaciens KFB 233 KC466565
S000635884 Agrobacterium sp CCBAU 23089 DQ310793
S002229177 Agrobacterium tumefaciens RR5 HM367737
S002958314 Mesorhizobium sp CCNWGS0211 JN622153
S002958452 Agrobacterium tumefaciens B2 JN628031
S001745941 Rhizobium vignae CCBAU 05176 GU128881
S003289156 endophytic bacterium 90L-2 JF901344
S003749510 Agrobacterium viscosum SDGD01 JX987134
S000015668 Agrobacterium sp LMG 11915 AJ130720
S001188792 endophytic bacterium HB03 FJ205660
LT87
S001588055 Beijerinckia fluminensis UQM 1685 EU401907
LR70
S003262687 Agrobacterium tumefaciens NBRC 15189 AB680796
LR57
S001170532 Agrobacterium tumefaciens CCNWGS0221 FJ154085
LR54
LR55
S000002681 Agrobacterium sp LMG 11936 AJ130721
LR53
S000364391 Rhizobium sp Esparseta 3 Y10169
LR52
S003289155 endophytic bacterium 90L-1 JF901343
LR51
LT74
S000003864 Agrobacterium sp MSMC211 AJ004859
LR50
S000389830 Bradyrhizobium japonicum PRY62 AF239847
LR49
LT73
LT12
LR47
S001589495 Rhizobium pongamiae VKLR-01 GQ444136
LR45
S000444931 Agrobacterium viscosum CICC10215 AY794055
S000127045 Azospirillum sp Z29621
LR22
S000721046 Rhizobium radiobacter IAM 12048 AB247615
S000431871 Candidatus Rhizobium massiliae 90A AF531767
S003753424 Candidatus Rhizobium massiliae MD 06 KC247684
LR20
LT92
S003301457 Agrobacterium tumefaciens MM10 JX083962
S000964676 Agrobacterium fabrum str C58 AE007869
S002445816 Rhizobium skierniewicense AL93 HQ823553
S002408292 Agrobacterium rubi LMG 159 FR828341
S000722695 Rhizobium cellulosilyticum ALA10B2 DQ855276
LR19
LR62
S000421666 Agrobacterium larrymoorei ICMP 15237 AY626382
S000721040 Agrobacterium tumefaciens MAFF 03-01224 AB247609
S000017731 Agrobacterium vitis CFBP 2617 AJ389911
S002233057 Rhizobium taibaishanense CCNWSX 0457 HM776996
S000721033 Agrobacterium vitis G-Ag-19 AB247602
S003262668 Agrobacterium vitis NBRC 15140 AB680777
S000437650 Rhizobium vitis NCPPB3554 U45329
S000456906 Agrobacterium vitis PHX1 AY826796
S001548991 Rhizobium rosettiformans W3 EU781656
S000391412 Agrobacterium albertimagni AOL15 AF316615
S001241092 Blastobacter aggregatus RW7 FJ172041
S000021625 Rhizobium aggregatum IFAM 1003 X73041
LR18
LR46
LR23
LR24
LR11
LR56
LR9
LR17
LR7
LR21
LR65
LR6
S002221963 Rhizobium pusense NRCPB10 FJ969841
LR5
LR12
LR16
LR25
S000140466 Rhizobium daejeonense L61T KCTC 12121 AY341343
S000942308 Rhizobium selenitireducens B1 EF440185
S000429561 Agrobacterium sp PB AF482682
S000262203 Sinorhizobium fredii S150 AY509217
S002914131 Ensifer sp KJ018 JF904881
S001328174 Rhizobium cnuense type strain KSW 4-12 JBRI2114 AM498743
S003287632 Sinorhizobium sp MG-2011-4-AO FR872496
S000330242 Sinorhizobium sp S1-T-10 AY505133
S000996028 Rhizobium giardinii CCBAU 01209 EU399693
S000392228 Sinorhizobium sp 9702-M4 AF357225
S000635883 Bradyrhizobium sp CCBAU 23024 DQ310792
S000438628 Rhizobium giardinii H152 U86344
S002228822 Agrobacterium larrymoorei BAC1011 HM355602
S000021216 Rhizobium larrymoorei 3-10 Z30542
LR63
S000015022 Rhizobium sp DUS470 Y11084
S002411294 Rhizobium undicola OURAN110 HQ895844
LR66
LR77
LR15
LR78
LR64
LR67
LT91
LR68
LR69
S000769199 Rhizobium sp BSV16 EF101308
S000967698 Mycoplana peli AN419 EU258744
S000769681 Rhizobium borbori DN316 EF125187
S001168838 Rhizobium oryzae Alt 505 EU056823
S000388919 Rhizobium yanglingense CCBAU 71462 AF195031
S000111802 Rhizobium indigoferae CCBAU 71042 AF364068
S000379907 Rhizobium mesoamericanum tpud40a AY691399
S000410286 Rhizobium etli AY460185
S001294595 Rhizobium phenanthrenilyticum F11 FJ743436
S000014582 Mesorhizobium sp N36 AF282924
S001187435 Rhizobium leguminosarum bv trifolii WSM2304 CP00119
S000093085 Rhizobium leguminosarum WSM1698 AF533683
S000775995 Rhizobium leguminosarum bv viciae CCBAU 01253 DQ835291
S000979412 Rhizobium indigoferae CCBAU 71042 AY034027
S002222203 Rhizobium leguminosarum bv phaseoli 31c3 FN433080
S000000452 Rhizobium genosp R BDV5365 Z94803
S000413524 Agrobacterium sp K-Ag-3 D14504
S000981736 Rhizobium hainanense I66 U71078
S000364339 Rhizobium tropici LMG 9518 X67233
S000926235 Rhizobium multihospitium CCBAU 83401 EF035074
S000393812 Rhizobium leguminosarum DASA23002 AF417562
S000752081 Rhizobium miluonense CCBAU 41251 EF061096
S002035399 Agrobacterium rubi F266 GU580894
S000421679 Rhizobium rubi ICMP 11833 AY626395
S000364330 Agrobacterium rhizogenes LMG 152 X67224
S002034822 Rhizobium lusitanum CCBAU 15087 GU552881
S002290486 Agrobacterium radiobacter K84 ATCC BAA-868 CP000628
S000413521 Rhizobium rhizogenes IFO 13257 D14501
S003746557 Mesorhizobium ciceri CPN7 JX868851
S000262202 Rhizobium mongolense S152 AY509209
S000262741 Rhizobium mongolense S110 AY509212
S000387012 Rhizobium gallicum CbS-1 AF008126
S000541167 Rhizobium gallicum bv gallicum IE4770 AY998045
S001096426 Rhizobium loessense CCBAU 25159 EU532143
S001014241 Rhizobium alamii type strain:GBV016 AM931436
S000979022 Rhizobium loessense CCBAU 7190B AF364069
S000438747 Rhizobium mongolense USDA 1844 U89817
S000559201 Rhizobium mesosinicum CCBAU 25010 DQ100063
S000979020 Rhizobium yanglingense SH22623 AF003375
S000967565 Rhizobium sullae CCBAU 85011 EU256432
S000367571 Rhizobium etli PRF51 AY117629
S000769770 Rhizobium phaseoli ATCC 14482 EF141340
S002911602 Rhizobium grahamii CCGE 502 JF424608
S002961235 Rhizobium genosp TUXTLAS-27 4m JN703467
S003284683 Rhizobium endophyticum S6-260 JQ660209
S000967537 Rhizobium tibeticum CCBAU 85039 EU256404
S000055319 Rhizobium sp WSM749 AF325772
S000364392 Rhizobium sullae type strain DSM 14623 Y10170
S000776010 Rhizobium fabae CCBAU 33202 DQ835306
S000393807 Rhizobium gallicum DASA12020 AF417557
S000635888 Rhizobium mesosinicum CCBAU 41026 DQ310797
S000261327 Rhizobium etli S1 AY509210
S000437446 Rhizobium etli CFN 42 USDA 9032 U28916
S003284111 Rhizobium vallis R3-65 JQ659637
S000265215 Rhizobium pisi DSM 30132 AY509899
S000323103 Rhizobium sp TCK AJ294417
S000806232 Rhizobium soli DS-42 EF363715
Caulobacter/158-602 mirabilis T FWC38 AJ22777
93
91
90
89
87
85
79
79
75
70
Supplementary Figure 11. NJ dendrogram showing the relationships among the 16S rDNA sequences of 25 isolates belonging to the genus Pantoea and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves.
LL9
LL62
LL70
LL69
LL53
LL86
LL92
LL56
LL55
LL46
LL47
LL40
LL61
LL48
LL90
LS100
LL78
LS93
LL41
LS11
LS9
LL54
LL89
LL95
S001187642 Pantoea brenneri LMG 5343 EU216735
LS99
S001187456 Pantoea vagans LMG 24199 EF688012
S001187644 Pantoea conspicua LMG 24534 EU216737
S000016079 Pantoea agglomerans DSM 3493 AJ233423
S001187454 Pantoea anthophila LMG 2558 EF688010
S001187455 Pantoea deleyi LMG 24200 EF688011
S001187453 Pantoea eucalypti LMG 24197 EF688009
S000381168 Pantoea ananatis ATCC 33244 U80196
S000412194 Pantoea allii BD 390 1 AY530795
S000000125 Pantoea cypripedii DSM 3873 AJ233413
S001610452 Pantoea calida 1400/07 GQ367478
S001610453 Pantoea gaviniae A18/07 GQ367483
S001187641 Pantoea septica LMG 5345 EU216734
S000381179 Pantoea stewartii ATCC 8199 U80208
S000691510 Pantoea dispersa LMG2603 DQ504305
S001187643 Pantoea eucrina LMG 2781 EU216736
S001020552 Escherichia coli J01695
100
99
9088
95
100
99
74
72
94
70
Supplementary Figure 12. NJ dendrogram showing the relationships among the 16S rDNA sequences of 30 isolates belonging to the genus Microbacterium and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT = bacteria isolated from the rhizosphere, LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves.
LT6
LT8
LT4
LT7
LT5
LT2
LL5
S000019591 Microbacterium liquefaciens DSM 20638 X77444
S000440800 Microbacterium maritypicum type strain: DSM 12512 AJ853910
S000007793 Microbacterium oxydans DSM 20578 Y17227
S000381732 Microbacterium luteolum IFO 15074 AB004718
S000381733 Microbacterium saperdae IFO 15038 AB004719
S000121408 Microbacterium paraoxydans CF36 AJ491806
LL29
LT85
LL6
LT3
LS87
S000020165 Microbacterium testaceum DSM 20166 X77445
S001417385 Microbacterium pseudoresistens CC005209 FJ86521
S000001703 Microbacterium resistens DMMZ 1710 Y14699
S000650697 Microbacterium thalassium type strain: DSM 12511 AM181507
S000427347 Microbacterium halophilum IFO 16062 AB004714
S000901905 Microbacterium aquimaris type strain: JS542 AM778449
S000892535 Microbacterium profundi Shh49 EF623999
S000965858 Microbacterium binotii CIP 101303 EF567306
S000427348 Microbacterium aurantiacum IFO 15234 AB004726
S000469185 Microbacterium kitamiense kitami C2 AB013907
S000381738 Microbacterium chocolatum IFO 3758 AB004725
S000006251 Microbacterium dextranolyticum DSM 8607 Y17230
S000010831 Microbacterium laevaniformans DSM 20140 Y17234
LL57
S000539539 Microbacterium hydrocarbonoxydans type strain: DSM 16089 BNP48Type AJ698726
LL82
LL81
LL85
LL8
LL67
LT67
LT5
LL59
LL31
LL1
LL84
S000014753 Microbacterium foliorum DSM 12966 P 333/02 AJ249780
S000012860 Microbacterium phyllosphaerae DSM 13468 P 369/06 AJ277840
S000083932 Microbacterium aerolatum V73 AJ309929
S000440798 Microbacterium xylanilyticum type strain: S3E AJ853908
S000967183 Microbacterium insulae DS66 EU239498
S000503539 Microbacterium natoriense TNJL1432 AY566291
S000381731 Microbacterium keratanolyticum IFO 13309 AB004717
S001577352 Microbacterium radiodurans GIMN1.002 GQ329713
S000650694 Microbacterium hominis type strain: DSM 12509 AM181504
S000002734 Microbacterium arborescens DSM 20754 X77443
S000003131 Microbacterium imperiale DSM 20530 X77442
LL2
LL30
LL32
LL100
LL83
S000539538 Microbacterium oleivorans type strain: DSM 16091 BAS69Type AJ698725
LL7
S000381734 Microbacterium terrae IFO 15300 AB004720
S000381737 Microbacterium ketosireducens IFO 14548 AB004724
S000000028 Microbacterium flavescens DSM 20643 Y17232
S000843265 Microbacterium kribbense MSL 04 EF466125
S000021147 Microbacterium trichothecenolyticum DSM 8608 Y17240
S000390332 Microbacterium gubbeenense LMG S19263 NCIMB 30129 AF263563
S000841857 Microbacterium indicum type strain: BBH6 AM158907
S000473677 Microbacterium halotolerans YIM 70130 AY376165
S000022611 Microbacterium barkeri DSM 20145 X77446
S000891240 Microbacterium luticocti type strain: SC087B AM747814
S000001603 Microbacterium arabinogalactanolyticum DSM 8611 Y17228
S000018525 Microbacterium esteraromaticum DSM 8609 Y17231
S000871546 Microbacterium soli DCY17 EF593038
S001417386 Microbacterium humi CC012309 FJ865215
S001155658 Microbacterium lindanitolerans MNA2 EU873539
S001351455 Microbacterium agarici CCSBCK209 FJ807673
S000727788 Microbacterium ginsengisoli Gsoil 259 AB271048
S001577784 Microbacterium mitrae M48 GQ351351
S001187351 Microbacterium invictum type strain: DC200 AM949677
S001014065 Microbacterium hatanonis JCM 14558 AB274908
S000711001 Microbacterium terricola KV448 AB234025
S000964147 Microbacterium fluvii YSL315 AB286028
S000541107 Microbacterium koreense JS532 AY962574
S000964146 Microbacterium awajiense YM13414 AB286027
S000964148 Microbacterium flavum YM18098 AB286029
S000013457 Microbacterium lacticum DSM 20427 X77441
S000009659 Microbacterium schleiferi DSM 20489 Y17237
S000006247 Microbacterium aurum DSM 8600 Y17229
S000964149 Microbacterium lacus A5E52 AB286030
S000381735 Microbacterium terregens IFO 12961 AB004721
S000711011 Microbacterium pygmaeum KV490 AB248875
S000622938 Microbacterium deminutum KV483 AB234026
S000622939 Microbacterium pumilum KV488 AB234027
S000622940 Microbacterium aoyamense KV492 AB234028
S001020552 Escherichia coli J01695
100
100
100
99
99
98
96
95
96
77
81
80
79
75
72
72
Supplementary Figure 13. NJ dendrogram showing the relationships among the 16S rDNA sequences of 47 isolates belonging to the genus Bacillus and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT = bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem.
LT61
LT62
LT20
LT46
LT24
LT86
LT84
LT57
LT14
LT83
LT25
LT11
LT60
LT30
LT58
LT64
LT19
S000006847 Bacillus mojavensis IFO15718 AB021191
S000428475 Bacillus subtilis NRRL B-23049 AF074970
S000003473 Bacillus subtilis DSM10 AJ276351
LT33
S002234727 Bacillus tequilensis 10b HQ223107
S000012241 Bacillus vallismortis DSM11031 AB021198
S000014133 Bacillus atrophaeus JCM9070 AB021181
S000734915 Bacillus amyloliquefaciens NBRC 15535 AB255669
LT18
S001239910 Bacillus methylotrophicus CBMB205 EU194897
LT81
S001576866 Bacillus siamensis PD-A10 GQ281299
LT16
LR39
LR40
LR37
S000390972 Bacillus sonorensis NRRL B-23154 AF302118
S000417319 Bacillus aerius24K AJ831843
S000858658 Bacillus licheniformis ATCC 14580 DSM 13 CP000002
S001098353 Bacillus marmarensis GMBE72 EU621902
S000013858 Bacillus pseudofirmus DSM 8715 X76439
S000429574 Bacillus aquimaris TF-12 AF483625
S000439486 Bacillus vietnamensis 15-1 AB099708
S000429573 Bacillus marisflavi TF-11 AF483624
LS8
LS1
LT40
S000010351 Bacillus halodurans DSM 497T AJ302709
S000083979 Bacillus okuhidensis AB047684
S000366697 Bacillus indicus Sd/3 AJ583158
S000503246 Bacillus cibi JG-30 AY550276
S000644546 Bacillus idriensis SMC 4352-2 AY904033
S001014161 Bacillus stratosphericus41KF2a AJ831841
S001014162 Bacillus aerophilus28K AJ831844
S000417318 Bacillus altitudinis41KF2b AJ831842
LT34
LT71
LT10
LT39
S000481068 Bacillus pumilus ATCC 7061 AY876289
S000458519 Bacillus safensis FO-036b AF234854
LT98
LT26
LT97
LT93
LT27
LT94
LT96
LT31
LT36
S000001559 Bacillus halmapalus DSM 8723 X76447
S000383284 Bacillus horikoshii DSM8719 AB043865
S000008098 Bacillus cohnii DSM 6307 T X76437
S000457154 Bacillus alkalitelluris BA288 AY829448
S000130053 Bacillus luciferensis LMG 18422 AJ419629
S000649848 Bacillus acidiceler CBD 119 DQ374637
S000941821 Bacillus azotoformans NBRC 15712 AB363732
S000331995 Bacillus litoralis SW-211 AY608605
S000598282 Bacillus niabensis 4T19 AY998119
S000129063 Bacillus fastidiosus DSM 91 X60615
S001265319 Bacillus galliciensis BFLP-1 FM162181
S000447571 Bacillus herbersteinensis D-15a AJ781029
LT78
S000979524 Bacillus thuringiensis IAM 12077 D16281
S000376345 Bacillus anthracis ATCC 14578 AB190217
S002291145 Bacillus cereus ATCC 14579 AE016877
S000628319 Bacillus cereus ATCC 14579 AE016877
S000001855 Bacillus mycoides ATCC6462 AB021192
S000016288 Bacillus weihenstephanensis DSM11821 AB021199
S000383283 Bacillus mannanilyticus AM-001 AB043864
S000435906 Bacillus horti K13 D87035
S000768919 Bacillus coahuilensis m4-4 EF014452
S000428419 Bacillus siralis 171544 AF071856
S000373337 Bacillus koreensis BR030 AY667496
LT22
LT23
LT76
S000979521 Bacillus megaterium IAM 13418 D16273
S000012966 Bacillus flexus IFO15715 AB021185
S000469513 Bacillus asahii MA001 AB109209
S000021968 Bacillus psychrosaccharolyticus ATCC23296 AB021195
LR89
LR90
S000446637 Bacillus muralis LMG 20238 AJ316309
S000005711 Bacillus simplex DSM 1321T AJ439078
S000805894 Bacillus butanolivorans K9 EF206294
LT63
S000995279 Bacillus acidiproducens SL213 EF379274
S000727823 Bacillus coagulans NBRC 12583 AB271752
S000001560 Bacillus smithii DSM 4216 Z26935
S000414555 Bacillus thermoamylovorans CNCM I-1378 L27478
S000016369 Bacillus badius ATCC 14574 X77790
S000622315 Bacillus kribbensis BT080 DQ280367
S001098152 Bacillus korlensis ZLC-26 EU603328
S000390853 Bacillus endophyticus 2DT AF295302
S001187364 Bacillus lehensis MLB2 AY793550
S000496869 Bacillus oshimensis K11 AB188090
S000473524 Bacillus patagoniensis PAT 05 AY258614
S000003470 Bacillus clausii DSM 8716 X76440
S000006950 Bacillus gibsonii DSM 8722 X76446/
S000446644 Bacillus murimartini LMG 21005 AJ316316
S000484380 Bacillus plakortidis P203 AJ880003
S000117161 Bacillus algicola KMM 3737 AY228462
S000351293 Bacillus hwajinpoensis SW-72 AF541966
S000362993 Bacillus taeanensis BH030017 AY603978
S000824850 Bacillus alkalinitrilicus ANL-iso4 EF422411
S001744238 Bacillus nanhaiisediminis NH3 GQ292773
S000383270 Bacillus wakoensis N-1 AB043851
S000653122 Bacillus okhensis Kh10-101 DQ026060
S000147238 Bacillus krulwichiae AM31D AB086897
S000383277 Bacillus akibai 1139 AB043858
S000383265 Bacillus hemicellulosilyticus C-11 AB043846
S000501792 Bacillus bogoriensis LBB3 AY376312
S000008091 Bacillus alcalophilus DSM 485 T X76436
S001291460 Bacillus trypoxylicola SU1 AB434284
S000010355 Bacillus pseudalcaliphilus DSM 8725 X76449
S001199925 Bacillus persepolensis HS-136 FM244839
S001152386 Bacillus qingdaonensis CM1 DQ115802
S000373335 Bacillus salarius BH169 AY667494
S001093971 Bacillus halochares MSS4 AM982516
S000711958 Bacillus aidingensis 17-5 DQ504377
S000276014 Bacillus galactosidilyticus LMG 17892 AJ535638
S000276781 Bacillus ruris R-6760 LMG 22866 AJ535639
S000000169 Bacillus lentus NCIMB8773 AB021189
S000485126 Bacillus fortis R-6514 AY443038
S000485127 Bacillus fordii R-7190 AY443039
S001264210 Bacillus chungangensis CAU 348 FJ514932
S000485124 Bacillus farraginis R-6540 AY443036
S000843929 Bacillus infernus TH-23 (SMCC/W 479) U20385
S000108528 Bacillus aeolius 4-1 AJ504797
S000548368 Bacillus alveayuensis TM 1 AY605232
S000278327 Bacillus methanolicus NCIMB 13113T AB112727
S000446621 Bacillus decolorationis LMG 19507 AJ315075
S001577240 Bacillus oceanisediminis H2 GQ292772
S000644545 Bacillus infantis SMC 4352-1 AY904032
S000979519 Bacillus firmus IAM 12464 D16268
S000424697 Bacillus circulans ATCC 4513 NCTC 2610 NCDO1775 AY724690
S000434839 Bacillus circulans AY043084
S001098928 Bacillus nealsonii DSM 15077 EU656111
S000130255 Bacillus benzoevorans NCIMB 12555 X60611
S001416952 Bacillus horneckiae 1P01SC EU861362
S000842524 Bacillus canaveralius KSC SF8b DQ870688
S000389386 Bacillus jeotgali YKJ-10 AF221061
S000543426 Bacillus boroniphilus T-15Z AB198719
S000649704 Bacillus thioparans BMP-1 DQ371431
S000701172 Bacillus selenatarsenatis SF-1 AB262082
S000544167 Bacillus foraminis CV53 AJ717382
S000021836 Bacillus fumarioli LMG 17489 AJ250056
S000627913 Bacillus pocheonensis Gsoil 420 AB245377
S000014510 Bacillus niacini IFO15566 AB021194
S000323275 Bacillus drentensis LMG 21831 AJ542506
S000323277 Bacillus bataviensis LMG 21833 AJ542508
S000323282 Bacillus soli LMG 21838 AJ542513
S000323278 Bacillus vireti LMG 21834 AJ542509
S000323281 Bacillus novalis LMG 21837 AJ542512
S000016025 Bacillus thermocloacae DSM 5250 Z26939
S000383485 Bacillus funiculus NAF001 AB049195
S000627916 Bacillus panaciterrae Gsoil 1517 AB245380
S000366467 Bacillus gelatini LMG 21880 AJ551329
S001156575 Bacillus rigui WPCB074 EU939689
S000408851 Bacillus macauensis ZFHKF-1 AY373018
S000903108 Bacillus solisalsi YC1 EU046268
S000543964 Bacillus arsenicus con a/3 AJ606700
S002034580 Bacillus nanhaiensis JSM 082006 GU477780
S000133610 Bacillus barbaricus VII-B3-A2 AJ422145
S000007628 Bacillus carboniphilus JCM9731 AB021182
S000366852 Bacillus humi LMG 22167 AJ627210
S000842016 Bacillus isabeliae CVS-8 AM503357
S000131291 Bacillus shackletonii LMG 18435 AJ250318
S000627914 Bacillus ginsengihumi Gsoil 114 AB245378
S000102217 Bacillus acidicola 105-2 AF547209
S000373336 Bacillus seohaeanensis BH724 AY667495
S000437736 Bacillus sporothermodurans M215 U49078
S000528024 Bacillus oleronius ATCC 700005 AY988598
S001020552 Escherichia coli J01695
99
99
99
99
99
89
74
99
99
99
99
88
99
99
99
77
99
99
70
99
99
97
89
99
99
99
99
88
80
98
84
98
96
95
95
89
81
74
79
70
71
94
94
93
93
71
89
92
91
88
87
86
86
85
84
82
82
82
80
71
70
Supplementary Figure 14. NJ dendrogram showing the relationships among the 16S rDNA sequences of isolates belonging to the genus Pseudomonas and those of reference type strains. Scale bars represent the Kimura-2 distance. Bootstrap values are indicated at the node. Nodes are collapsed at 70% probability. LT= bacteria isolated from the rhizosphere, LR = bacteria isolated from the roots, LS = bacteria isolated from the stem, LL = bacteria isolated from the leaves.
LS13
LS97
LS38
LL16
LS60
S000000053 Pseudomonas amygdali LMG 2123T Z76654
LR83
LL33
LS24
LS2
LS16
LS72
LS95
LS42
LS21
LS71
LS26
S000013175 Pseudomonas frederiksbergensis JAJ28 AJ249382
LS4
LS10
LL58
LS14
LS34
LL50
LS96
LR100
LL36
LR85
LL20
LS5
LS17
LS35
LL35
LS70
LL73
LS6
LS15
LS32
LL68
LL97
LL60
LL65
LR74
S000366447 Pseudomonas proteolytica CMS 64 AJ537603
S000390413 Pseudomonas brenneri CFML 97-391T AF268968
S000575187 Pseudomonas panacis CG20106 AY787208
S000428465 Pseudomonas migulae CIP 105470 AF074383
LS7
LS29
LS47
LS50
LS63
LS49
S000145155 Pseudomonas cedrina DSM 14938 LMG 21467 P 515/12 AJ492830
S000428332 Pseudomonas cedrina CFML 96-198 AF064461
S000005898 Pseudomonas azotoformans IAM1603 D84009
S000001334 Pseudomonas mucidolens IAM12406 D84017
S000009690 Pseudomonas synxantha IAM12356 D84025
S000428466 Pseudomonas gessardii CIP 105469 AF074384
LS51
LR38
LS90
LS28
LS89
LS64
LS36
LS91
LS18
LS25
LS56
LS61
LS45
S000428195 Pseudomonas libanensis CIP 105460 AF057645
LS46
LS54
LS59
LS98
LS20
LS27
LS19
LS41
S000436974 Pseudomonas flavescens B62 U01916
S000011995 Pseudomonas straminea IAM1598 D84023
S000541019 Pseudomonas argentinensis CH01 AY691188
LL71
S000259962 Pseudomonas vancouverensis DhA-51ATCC 700688 AJ011507
S000858470 Pseudomonas moorei RW10 AM293566
S000395040 Pseudomonas umsongensis Ps 3-10 AF468450
S000858471 Pseudomonas mohnii IpA-2 AM293567
S000358323 Pseudomonas lutea OK2 AY364537
S000398317 Pseudomonas rhizosphaerae IH5 AY152673
LS57
LS23
S000013965 Pseudomonas graminis DSM 11363 Y11150
S000005892 Pseudomonas cichorii LMG 2162T Z76658
S002221855 Pseudomonas chlororaphis JF3835 FJ168539
LL21
LS22
LS30
LS31
LS65
LL72
LL74
LL91
S000146512 Pseudomonas congelans DSM 14939 LMG 21466 P 538/23 AJ492828
S000010260 Pseudomonas ficuserectae JCM 2400T AB021378
S000651000 Pseudomonas syringae NCPPB 281 8511 DQ318866
S000004781 Pseudomonas caricapapayae ATCC33615 D84010
S000004193 Pseudomonas savastanoi ATCC 13522T AB021402
S000146818 Pseudomonas tremae CFBP 6111 AJ492826
LL10
LL12
LL15
LL22
LT54
LL24
LL42
S000428211 Pseudomonas mandelii CIP 105273 AF058286
LL18
LL23
LL11
LL14
S000145522 Pseudomonas cannabina CFBP 2341 AJ492827
LL34
LT90
LL4
S000006483 Pseudomonas plecoglossicida FPC951 AB009457
S000013341 Pseudomonas monteilii CIP 104883 AF064458
S000841838 Pseudomonas mosselii CIP 105259 AF072688
S001095516 Pseudomonas taiwanensis BCRC 17751 EU103629
LT66
LT89
LS33
LS74
LT35
LS66
LT15
LS84
LS44
LT9
LS78
LS92
LR3
LS82
LS81
LS83
LS53
LS79
LS48
LS75
LS68
LS76
LS85
LS55
LS58
LS62
LS77
LT17
S000392851 Pseudomonas mediterranea CFBP 5447 AF386080
LT44
LT41
LS37
LS39
LT69
S001171509 Pseudomonas lini CFBP 5737 AY035996
LR36
LR43
S000355057 Pseudomonas salomonii CFBP 2022 AY091528
LR33
S000010434 Pseudomonas corrugata ATCC29736 D84012
S001095875 Pseudomonas brassicacearum CIP 109457 EU391388
S000108891 Pseudomonas kilonensis 520-20 AJ292426
S000428886 Pseudomonas brassicacearum DBK11 CFBP 11706 AF100321
S000428888 Pseudomonas thivervalensis SBK26 CFBP 11261T AF100323
LS43
LT45
LT65
LT68
LT70
LT29
LT55
LT53
LT59
LT32
LT95
LS52
S000400225 Pseudomonas viridiflava CECT 458 AY180972
LT51
LS67
S000003555 Pseudomonas alcaligenes IAM12411 D84006
LS73
LR1
LR84
S002151284 Pseudomonas arsenicoxydans VC-1 FN645213
S000749691 Pseudomonas simiae OLi AJ936933
S000355056 Pseudomonas palleroniana CFBP 4389 AY091527
S000498899 Pseudomonas tolaasii LMG 2342 T AF255336
S000499371 Pseudomonas costantinii CFBP 5705 HAMBI 2444 AF374472
S000143918 Pseudomonas lurida DSM 15835 P 513/18 AJ581999
LL63
S000428331 Pseudomonas orientalis CFML 96-170 AF064457
S000002018 Pseudomonas fluorescens IAM 12022 D84013
S000366445 Pseudomonas antarctica CMS 35 AJ537601
S000366446 Pseudomonas meridiana CMS 38 AJ537602
S000499514 Pseudomonas extremorientalis KMM 3447 AF405328
S001043991 Pseudomonas extremaustralis CT14-3 AJ583501
S000004663 Pseudomonas veronii CIP 104663 AF064460
S000145154 Pseudomonas poae DSM 14936 LMG 21465 P 527/13 AJ492829
S000145156 Pseudomonas trivialis DSM 14937 LMG 21464 P 513/19 AJ492831
S000390380 Pseudomonas grimontii CFML 97-514T AF268029
S000011992 Pseudomonas marginalis LMG 2210T Z76663
S000013342 Pseudomonas rhodesiae CIP 104664 AF064459
LR91
LL79
LR44
LR82
LR2
LR87
LR88
LR58
LR13
LR73
LR4
S000269325 Pseudomonas chlororaphis DSM 6698 AY509898
S000721984 Pseudomonas chlororaphis NCIB 10068 DQ682655
S000000900 Pseudomonas chlororaphis DSM 50083T Z76673
LR14
S000008929 Pseudomonas taetrolens IAM1653 D84027
S000014863 Pseudomonas lundensis ATCC 49968T AB021395
S000002852 Pseudomonas psychrophila E-3 AB041885
S000428774 Pseudomonas fragi ATCC 4973 AF094733
LR35
LR42
LR94
LR30
LL49
LT47
LT4
S000516032 Pseudomonas moraviensis CCM 7280 AY970952
LT77
S000004324 Pseudomonas oryzihabitans IAM 1568 D84004
S000690384 Pseudomonas japonica IAM 15071 AB126621
S000262316 Pseudomonas parafulva IAM 1541 AB046999
S000383942 Pseudomonas cremoricolorata IAM 1541T AB060137
LT43
S000003153 Pseudomonas putida IAM 1236 D84020
S000516031 Pseudomonas vranovensis CCM 7279 AY970951
LT50
S000015943 Pseudomonas asplenii ATCC 23835T AB021397
S001243670 Pseudomonas fuscovaginae ICMP 5940 FJ483519
LT79
S000022067 Pseudomonas agarici LMG 2112T Z76652
S000260088 Pseudomonas abietaniphila ATCC 700689 AJ011504
S000009281 Pseudomonas pseudoalcaligenes LMG 1225T Z76666
S000016452 Pseudomonas mendocina NCIB 10541 D84016
S000010130 Pseudomonas alcaliphila AL15-21 AB030583
S001350578 Pseudomonas oleovorans RS1 DQ842018
S000543032 Pseudomonas xanthomarina KMM 1447 AB176954
S000395038 Pseudomonas jinjuensis Pss 26 AF468448
S000008928 Pseudomonas oleovorans IAM 1508 D84018
S000416841 Pseudomonas psychrotolerans C36 AJ575816
S000626936 Pseudomonas nitroreducens IAM 1439 AM088473
S000010427 Pseudomonas aeruginosa DSM50071 X06684
S000428789 Pseudomonas stutzeri ATCC 17588 AF094748
S000514601 Pseudomonas otitidis MCC10330 AY953147
S000824948 Pseudomonas panipatensis Esp1 EF424401
S000427988 Pseudomonas knackmussii B13 AF039489
S000006645 Pseudomonas citronellolis DSM 50332T Z76659
S000639965 Pseudomonas delhiensis RLD-1 DQ339153
S000437396 Pseudomonas balearica SP1402 U26418
S000567747 Pseudomonas azotifigens 6H33b AB189452
S000390990 Pseudomonas indica AF302795
LT72
S000007012 Pseudomonas resinovorans LMG 2274T Z76668
S000010364 Pseudomonas luteola IAM 13000 D84002
S000903111 Pseudomonas duriflava HR2 EU046271
S000495962 Pseudomonas pachastrellae KMM 330 AB125366
S000639962 Pseudomonas pohangensis H3-R18 DQ339144
S000942753 Pseudomonas sabulinigri J64 EU143352
S001156249 Pseudomonas pelagia CL-AP6 EU888911
S000968494 Pseudomonas xinjiangensis S3-3 EU286805
S000001098 Pseudomonas pertucinogena IFO 14163T AB021380
S000558609 Pseudomonas xiamenensis C10-2 DQ088664
LT82
S000428381 Pseudomonas jessenii CIP 105274 AF068259
S000263191 Pseudomonas fulva AJ 2129 AB046996
S000395042 Pseudomonas koreensis Ps 9-14 AF468452
S000858469 Pseudomonas reinekei MT1 AM293565
S001098319 Pseudomonas caeni HY-14 EU620679
S000444074 Pseudomonas segetis FR1439 AY770691
S001014073 Pseudomonas marincola KMM 3042 AB301071
S000608925 Pseudomonas peli R-20805 AM114534
S000964788 Pseudomonas guineae LMG 24016 M8 AM491810
S000260543 Pseudomonas anguilliseptica NCIMB 1949 X99540
S000608918 Pseudomonas borbori R-20821 AM114527
S001153684 Pseudomonas cuatrocienegasensis 1N EU791281
S001241637 Pseudomonas taeanensis MS-3 FJ424813
S001020552 Escherichia coli J01695
100
99
99
98
98
92
91
90
88
87
85
84
78
78
78
78
77
73
73
72
71
70
Supplementary Table 1. List of bacterial endophytic strains used in this work as tester in the cross-streak experiments.
Isolate Genus Origin LL1 Microbacterium Leaf LL2 Microbacterium Leaf LL3 Plantibacter Leaf LL4 Pseudomonas Leaf LL6 Microbacterium Leaf LL7 Microbacterium Leaf LL9 Pantoea Leaf LL10 Pseudomonas Leaf LS1 Bacillus Stem LS2 Pseudomonas Stem LS3 Bacillus Stem LS4 Pseudomonas Stem LS5 Pseudomonas Stem LS6 Pseudomonas Stem LR1 Pseudomonas Root LR2 Pseudomonas Root LR3 Pseudomonas Root LR4 Pseudomonas Root LR5 Rizhobium Root
Abbreviations: LL, LS, LR, strains isolated from leaf; stem, and root, respectively.
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Supplementary Table 2. Number of Bcc target strains whose growth is inhibited by lavender bacterial endophytes.
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Endophytic isolate Genus Number of Bcc strains inhibited LL1 Microbacterium 5 LL2 Microbacterium 21 LL3 Plantibacter 28 LL4 Pseudomonas 16 LL6 Microbacterium 23 LL7 Microbacterium 20 LL9 Pantoea 35 LL10 Pseudomonas 15 LS1 Bacillus 21 LS2 Pseudomonas 30 LS3 Bacillus 12 LS4 Pseudomonas 16 LS5 Pseudomonas 29 LS6 Pseudomonas 30 LR1 Pseudomonas 10 LR2 Pseudomonas 21 LR3 Pseudomonas 11 LR4 Pseudomonas 25 LR5 Rhizobium 36 !
Abbreviations: LL, LS, LR: strains isolated from leaf, stem and root, respectively.
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Supplementary Table 3. Sensitivity spectrum exhibited by the 40 Bcc strains in the cross streak experiment vs a panel of lavender endophytic bacterial isolates. N° Species Strain Origin Inhibited by 1 B. cepacia (I) FCF 1 CF All tested endophytes 2 B. cepacia (I) FCF 3 CF All tested endophytes 3 B. multivorans (II) LMG 17588 ENV All tested endophytes except for LL1, LL4, LS1,
LS3, LR1, LR3 4 B. cenocepacia (IIIA) FCF 16 CF All tested endophytes 5 B. cenocepacia (IIIA) J2315 CF All tested endophytes except for LL1, LS3, 6 B. cenocepacia (IIB) FCF 18 CF All tested endophytes except for LL1 7 B. cenocepacia (IIB) FCF 20 CF Partially by LS1, LS2, LS3, LS5, LR1 8 B. cenocepacia (IIB) FCF 23 CF All tested endophytes except for LL1, LS3, LR1 9 B. cenocepacia (IIB) FCF 24 CF All tested endophytes except for LL1, LR1 10 B. cenocepacia (IIB) FCF 27 CF All tested endophytes except for LL1 11 B. cenocepacia (IIB) FCF 29 CF All tested endophytes except for LL1, LR1, LR3 12 B. cenocepacia (IIB) FCF 30 CF All tested endophytes except for LL1, LR1, LR3 13 B. cenocepacia (IIB) LMG 16654 CF LL2, LL3, LL6, LL9, LS2, LS5, LS6, LR2, LR4,
LR5 14 B. cenocepacia (IIB) C5424 CF LL3, LL6, LL7, LL9, LS1, LS2, LS4, LS5, LS6 15 B. cenocepacia (IIB) CEP511 CF LL2, LL3, LL6, LL7, LL9, LS2, LS5, LS6 16 B. cenocepacia (IIB) MVPC 1/16 ENV LL3, LL9, LS4, LS6, LR2, LR4 17 B. cenocepacia (IIB) MVPC 1/73 ENV LL3, LL9, LR5 18 B. cenocepacia (IIIC) LMG 19230 ENV LL9, LR5 19 B. cenocepacia (IIIC) LMG 19240 ENV LL6, LL9, LS2, LS6, LR5 20 B. cenocepacia (IIID) FCF 38 CF All tested endophytes except for LL1 21 B. cenocepacia (IIID) LMG 21462 CF All tested endophytes 22 B. stabilis (IV) FCF 41 CF LL9, LS3, LS6, LR5 23 B. vietnamiensis (V) FCF 42 CF All tested endophytes 24 B. vietnamiensis (V) TVV 75 ENV LL3, LL6, LL7, LL9, LS1, LS2, LS5, LS6, LR2,
LR4, LR5 25 B. dolosa (VI) LMG 18941 CF LL2, LL3, LL9, LS1, LS2, LS5, LS6, LR4, LR5 26 B. dolosa (VI) LMG 18942 CF LL3, LL9, LS5, LS6, LR5 27 B. dolosa (VI) LMG 18943 CF LL3, LL9, LS2, LS5, LS6, LR4, LR5 28 B. ambifaria (VII) MCI 7 ENV LL3, LL9, LS2, LS5, LS6, LR2, LR4, LR5 29 B. ambifaria (VII) LMG 19467 CF LL3, LL7, LL9, LS2, LS5, LS6, LR2, LR4, LR5 30 B. ambifaria (VII) LMG 19182 ENV LL3, LL7, LL9, LS1, LS2, LS4, LS5, LS6, LR2,
LR4, LR5 31 B. anthina (VIII) LMG 16670 ENV LL2, LL3, LL4, LL6, LL9, LS1, LS2, LS5, LS6,
LR2, LR4, LR5 32 B. pyrrocinia (IX) FCF 43 CF LL2, LL3, LL4, LL6, LL7, LL9, LL10, LS1, LS2,
LS5, LS6, LR4, LR5 33 B. lata LSED 4 CF LL2, LL4, LL6, LL9, LS1, LS2, LS5, LS6, LRA,
LR5 34 B. latens LMG 24064 CF LL2, LL6, LL9, LS2, LS5, LR5 35 B. diffusa LMG 24065 CF LL9, LS2, LS5, LR5 36 B. contaminans LMG 23361 AI LL9, LR5 37 B. seminalis LMG 24067 CF LR5 38 B. metallica LMG 24068 CF LR5 39 B. arboris LMG 24066 ENV LR5 40 B. ubonensis LMG 24263 NI LR5 Abbreviations: CF, strains isolated from Cystic Fibrosis patients; AI, strains isolated from Animal Infection; NI, strains isolated from Nosocomial Infection; ENV, environmental strain; LL, LS, LR: strains isolated from leaf, stem, and root, respectively.
Supplementary Table 4. Length of aligned matrices (bp), Variable and conserved characters number, Parsimony-informative characters, Consistency Index (CI), Retention Index (RI) and species used as outgroup of dendrograms obtained with Maximun Parsimony (see Materials and Methods for details).
Dendrogram Aligned matrix
length (bp) Conserved characters
Variable characters
Parsimony informative characters
Retention Index
Consistency Index
Species used as outgroup
Pantoea 545 344 201 161 0.9487 0.6383 E. coli Pseudomonas 610 175 423 210 0.9717 0.4434 E. coli
Bacillus 619 281 327 227 0.9241 0.1904 E. coli Rhizobium 458 296 152 75 0.9593 0.4379 C. mirabilis
Stenotrophomonas 524 314 192 89 0.9707 0.6874 E. coli Microbacterium 566 337 199 111 0.9522 0.3379 E. coli
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