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S. morelense Lc04 T

100. 70. 75. 80. 85. 90. 95. 60. 65. S. morelense Lc04 T. A.vitis IAM 14140 T. A. rhizogenes IAM 13570 T. R. tropici B CIAT 899 T. R. leguminosarum USDA 2370 T. R. yanglingense CCBAU 71623 T. R. etli CFN42 T. CCBAU 05689. A. tumefaciense IAM 13129 T. A. rubi IAM 13569 T.

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S. morelense Lc04 T

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  1. 100 70 75 80 85 90 95 60 65 S. morelense Lc04T A.vitis IAM 14140T A. rhizogenes IAM 13570T R. tropici B CIAT 899T R. leguminosarum USDA 2370T R. yanglingense CCBAU 71623T R. etli CFN42T CCBAU 05689 A. tumefaciense IAM 13129T A. rubi IAM 13569T CCBAU 05672 and other 26 strains S. saheli LMG 7837T S. kostiense HAMBI 1489T S. saheli USDA 4102 S. saheli LMG 8310 S. fredii CCBAU 110 S. fredii USDA 205T CCBAU 05557 and other 93 strains S. sojae CCBAU 05684T and other 12 strains S. mexicanus HAMBI 2910T S. kummerowiae CCBAU 71714T S. medicae USDA 1037T S. meliloti USDA 1002T CCBAU 05600 and other 2 strains M. amorphae ACCC 19665T M. huakuii CCBAU 2609T M. plurifarium LMG 1892T CCBAU 05623 and other 31 strains B. yuanmingense CCBAU 10071T B. japonicum B15 B. japonicum USDA 110 CCBAU 05707 and other 29 strains B. liaoningense USDA 3622T B. japonicum USDA 6T B. elkanii USDA 76T CCBAU 05737 and other 14 strains Supplementary Fig. A. Dendrogram based on the cluster analysis of 16S rDNA-RFLP.

  2. CCBAU 20016 (HM057449) S. fredii CCBAU 110 (AF250354) CCBAU 05560 (HM057446) CCBAU 05698 (HM057458) S.americanum CFNEI 156T (AF506513) S.fredii USDA205T (AY260149) 63 CCBAU 05557 (HM057450) CCBAU 05657 (HM057442) CCBAU 05673 (HM057443) 55 CCBAU 05702 (HM057448) S. saheli LMG 7837T (X68390) CCBAU 05631 (HM057451) CCBAU 05672 (HM057462) 51 CCBAU 05617 (HM057447) S. sojae CCBAU 05684T (GU593061) 83 62 S.kostiense HAMBI 1489T (Z78203) S. mexicanus HAMBI 2910T (DQ411930) 73 S. terangae LMG7837T (X68387) Ensifer garamanticus ORS 1400T (AY500255) S. arboris HAMBI 1552T (Z78204) 56 CCBAU 05600 (HM057444) 99 Ensifer numidicus ORS 1407T (AY500254) 70 S. medicae A321T (I39882) S. kummerowiae CCBAU71714T (AF364067) 53 83 S. meliloti USDA 1002T (X67222) 95 S. morelense Lc04T (AY024335) M. tianshanense USDA 3592T (U71079) M. ciceri USDA 3383T (AJ294395) 100 99 M. loti LMG 6125T (X67229) M. huakuii USDA 4779 T (D13431) 93 M. mediterraneum USDA 3392T (I38825) 53 R. tropici A USDA 9039T (X67234) 99 R. tropici B USDA 9030T (U89832) R. indigoferae CCBAU 71042T (AY034027) 99 84 R. leguminosarum USDA 2370T (U29386) R. fabae CCBAU 33202T ( DQ835306) 99 R. etli CFN 42T (U28916) 91 CCBAU 05689 (HM057445) 93 R. galegae ATCC 43677T (D11343) 100 98 R. huautlensese LMG 18254T (AF025852) R. soilDS-42T (EF363715) R. loessense CCBAU 7190BT (AF364069) 63 R. gallicum R602spT (U86343) 100 R. yanglingense CCBAU 71623T (AF003375) 62 B. elkanii USDA 76T (U35000) B. pachyrhizi PAC48T (AY624135) 97 CCBAU 05737 (HM057457) 100 CCBAU 05727 (HM057461) B. jicamae PAC68T (AY624134) B. iriomotense LMG 24129T (AB300992) 100 B. denitrificans LMG 8443T (X66025) B. betae LMG21987T (AY372184) 51 96 B. japonicum USDA 110 (NC004463) CCBAU 05585 (HM057452) 55 60 CCBAU 05625 (HM057456) 0.01 86 CCBAU 05623 (HM057453) 72 B. yuanmingense CCBAU 10071T (AF193818) CCBAU 05705 (HQ174474) 84 B. japonicum USDA6T (AB231927) CCBAU 05707 (HM057454) CCBAU 05588 (HM057459) B. liaoningense USDA 3622T (AF208513) B. canariense BTA-1T (AJ558025) CCBAU 05716 (HM057455) 53 CCBAU 05724 (HM057460) 77 Supplementary Fig. B. Phylogenetic relationships based on 16S rDNA sequences.

  3. S. fredii CCBAU 110 (AM418745) S. fredii CCBAU 45276 (EU513342) CCBAU 20016 (HM057471) CCBAU 05698 (HM057463) S. fredii USDA 205T (AJ294402) 99 Sinorhizobium sp. CCBAU 83643 (EU152339) Sinorhizobium sp. CCBAU 83666 (EU152342) CCBAU 05560 (HM057468) 61 Sinorhizobium sp. CCBAU 83622 (EU152338) CCBAU 05657 (HM057464) 65 CCBAU 05557 (HM057472) CCBAU 05702 (HM057470) 99 CCBAU 05600 (HM057467) CCBAU 05673 (HM057466) S. fredii CCBAU 03158 (EU513345) 100 S. americanum CFNEI 156T (AM418742) R. fabae CCBAU 33202T (EF579929) 86 R. leguminosarum USDA 2370T (AJ294405) R. etli CFN 42T (CP000133) CCBAU 05689 (HM057482) 82 R. yanglingense SH22623T (AY907373) R. tropici B LMG 9503T (AM418789) E. adhaerens ATCC 33212T (AM418746) S. morelense Lc04T (FJ032259) 93 S. medicae A321T (AJ294401) S. arboris HAMBI 1552T (AM418767) S. terangae LMG 7834T (AM418764) S. mexicanus HAMBI 2910T (GU994045) 84 S. sojae CCBAU 05684T (GU994042) S. kostiense HAMBI 1489T (AM418771) S. saheli LMG 7837T (AM418756) CCBAU 05617 (HM057469) Rhizobium sp. NGR 234 (NC012587) CCBAU 05672 (HM057465) 96 CCBAU 05631 (HM057473) 100 E. garamanticus ORS 1400T (AM946546) E. numidicus ORS 1407T (AM946551) S. meliloti USDA 1002T (AJ294400 ) S. kummeriwiae CCBAU 71714T (GU994044) 100 M. tianshanense USDA 3592T (AJ294392) M. loti LMG 6125T (AM076365) 100 M. huakuii USDA 4779T (AJ294394) 82 B. elkanii USDA 76T (AY386758) 59 CCBAU 05737 (HM057479) 64 B. pachyrhizi PAC48T (FJ428208) B. japonicum CCBAU 05185 (EU513344) 100 CCBAU 05716 (HM057476) 50 CCBAU 05724 (HM057480) 64 B. betae LMG21987T (FM253129) B. japonicum CCBAU 41267 (EU419716) 100 B. japonicum USDA 110 (NC004463) 99 CCBAU 05588 (HM057477) B. liaoningense CCBAU 43298 (EU419709) 58 B. liaoningense USDA 3622T (AY493450) B. denitrificans LMG8443T (FM253153) 0.02 B. jicamae PAC68T (FJ428211) B. iriomotense NBRC 102520T (AB300994) B. canariense BTA-1T (AY386739) B. japonicum USDA 6T (AJ294388) 71 94 B. japonicum X6-9 (AY653765) B. japonicum CCBAU 65068 (EU419715) B. yuanmingense CCBAU 10071T (AY386760) 99 B. yuanmingense CCBAU 83648 (EU152341) CCBAU 05585 (HM057474) B. yuanmingense CCBAU 33109 (EU419711) B. yuanmingense CCBAU 33079 (EU419713) 51 CCBAU 05623 (HM057475) CCBAU 05625 (HM057478) 63 CCBAU 05727 (HM057481) 98 (a) atpD Supplementary Fig. C Phylogenies of housekeeping genes atpD (a), recA (b) and glnII (c).

  4. S. fredii USDA 205T (AJ294379) S. fredii CCBAU110 (DQ411944) CCBAU 05657 (HM057505) 99 S. fredii CCBAU 45276 (EU518365) CCBAU 05557 (HM057513) CCBAU 05560 (HM057509) 90 Sinorhizobium sp CCBAU 83622 (EU152374) CCBAU 05698 (HM057504) 94 Sinorhizobium sp CCBAU 83643 (EU152375) 82 Sinorhizobium sp CCBAU 83666 (EU152378) 71 CCBAU 20016 (HM057512) 89 CCBAU 05673 (HM057507) 61 CCBAU 05702 (HM057511) Rhizobium sp. NGR 234 (NC012587) CCBAU 05617 (HM057510) S. americanum CFNEI 156T (DQ411943) CCBAU 05631 (HM057514) 100 CCBAU 05672 (HM057506) 100 CCBAU 05600 (HM057508) 90 S. sojae CCBAU 05684T (GU994055) S. kostiense HAMBI 1489T (AM182142) S. medicae A321T (AJ294381) 76 S. arboris HAMBI 1552T (AM182130) 71 S. kummerowiae CCBAU 71714T (DQ411945) 62 S. meliloti USDA 1002T (AJ294382) 100 E. garamanticus ORS 1400T (AM946573) S. terangae LMG 7834T (AJ294383) 69 S. mexicanus HAMBI 2910T (DQ411951) 100 S. chiapanecum ITTG S70T ( EF463926) E. adhaerens ATCC 33212T (HM997099) S. morelense Lc04T (AJ505601) 70 E. numidicus ORS 1407T (AM946578) 95 S. saheli LMG 7837T (AM182138) R. tropici A USDA 9039T (AJ294372) 76 R. tropici B USDA 9030T (AJ294373) R. yanglingense SH22623T (AY907359) CCBAU 05689 (HM057524) 99 82 R. etli CFN 42T (CP000133) R. fabae CCBAU 33202T (EF579941) 69 R. leguminosarum USDA 2370T (AJ294376) 94 M. loti LMG 6125T (AM182156) 100 M. tianshanense USDA 3592T (AJ294368) B. denitrificans LMG 8443T (FM253196) B. jicamae PAC68T (HM047133) CCBAU 05727 (HM057523) 77 99 99 B. elkanii CCBAU 65617 (EU419738) 91 B. elkanii USDA 76T (AY591568) 74 CCBAU 05737 (HM057521) 61 B. pachyrhizi LMG 24246T (HM047130) CCBAU 05588 (HM057519) CCBAU 05623 (HM057516) 86 56 B. yuanmingense CCBAU 83648 (EU152377) 57 CCBAU 05585 (HM057515) 65 CCBAU 05625 (HM057520) B. yuanmingense CCBAU 33079 (EU419741) 86 B. yuanmingense CCBAU 10071T (AY591566) B. yuanmingense CCBAU 33109 (EU419735) 53 CCBAU 05716 (HM057518) 100 B. japonicum CCBAU 05185 (EU518367) B. liaoningense USDA 3622T (AY494833) B. iriomotense NBRC 102520T (AB300996 ) B. canariense BTA-1T (AY591553) 0.02 B. betae LMG 21987T (AB353734) 73 B. japonicum CCBAU 41267 (EU419734) 100 B. japonicum USDA 110 (NC004463) 67 B. japonicum USDA 6T (AM168341) 63 B. japonicum X6-9 (AY591557) B. japonicum CCBAU 65068 (EU419739) 100 CCBAU 05724 (HM057522) 52 CCBAU 05707 (HM057517) CCBAU 05705 (HQ174516) (b) recA

  5. CCBAU 05707 (HM057495) CCBAU 05705 (HQ174494) 65 B. japonicum USDA 6T (AF169582) 99 B. japonicum CCBAU 65068 (EU419730) B. japonicum X6-9 (AY599121) B. japonicum USDA 110 (NC004463) 100 Bradyrhizobium sp. CCBAU 41267 (EU419718) CCBAU 05716 (HM057496) CCBAU 05724 (HM057501) 100 B. japonicum CCBAU 05185 (EU513319) B. betae PL7HG1T (AB353733) B. canariense BTA-1T (AY386765) B. iriomotense NBRC 102520T (AB300995) 76 B. liaoningense USDA 3622T (AY494803) 98 CCBAU 05588 (HM057497) 100 Bradyrhizobium sp. CCBAU 53135 (EU419706) CCBAU 05625 (HM057498) 99 B. yuanmingense CCBAU 330799 (EU419728) B. yuanmingense CCBAU 83648 (EU152359) 68 96 CCBAU 05585 (HM057493) 100 CCBAU 05623 (HM057494) 66 B. yuanmingense CCBAU 10071T (AY386780) 53 B. jicamae PAC68T (FJ428204) 79 CCBAU 05737 (HM057499) 100 99 B. pachyrhizi PAC48T (FJ428201) B. elkanii USDA 76T (AY599117) 99 CCBAU 05727 (HM057502) 62 100 B. elkanii CCBAU 65617 (EU419722) 65 B. denitrificans LMG 8443T (HM047121) M. loti LMG 6125T (AF169581) 94 M. tianshanense USDA 3592T (AF169579) 99 R. tropici A USDA 9039T (AF169583) 98 R. tropici B USDA 9030T (AF169584) R. leguminosarum USDA 2370T (EU155089) 94 CCBAU 05689 (HM057503) 90 R. etli USDA 9032T (AF169585) 99 E. adhaerens ATCC 33212T (HM997090) 100 S. morelence Lc04T (HM997095) E. numidicus ORS 1407T (HM997092) S. kummeriwiae CCBAU 71714T (GU994062) 100 54 S. meliloti USDA 1002T (AF169593) 97 S. medicae A321T (AF169592) S. arboris HAMBI 1552T (HM997093) 70 E. garamanticus ORS 1400T (HM997091) 58 88 S. terangae LMG 7834T (AF169590) S. mexicanus HAMBI 2910T (GU994064) CCBAU 05600 (HM057486) S. sojae CCBAU 05684T (GU994060) 81 CCBAU 05672 (HM057484) 77 100 CCBAU 05631 (HM057492) 62 S. americanum CFNEI 156T (GU994065) S. saheli ORS 609T (AF169589) CCBAU 05702 (HM057489) CCBAU 05617 (HQ174489) 100 S. kostiense HAMBI 1489T (GU994063) CCBAU 05673 (HM057485) Rhizobium NGR 234 (NC012587) 72 CCBAU 05657 (HM057483) 99 S. fredii USDA 205T (AF169591) 97 Sinorhizobium sp.CCBAU 83666 (EU152360) 0.02 CCBAU 05557 (HM057491) 81 CCBAU 05560 (HM057487) 68 84 S. fredii CCBAU 45276 (EU513316) 69 S. fredii CCBAU 110 (EU155088) Sinorhizobium sp.CCBAU 83643 (EU152357) 57 CCBAU 20016 (HM057490) 96 CCBAU 05698 (HM057500) 76 (c) glnII

  6. B. liaoningense CCBAU 83789 (EU146031) 64 S. fredii CPAC402 (DQ485716) B. japonicum CPAC 15 (DQ485693) B.japonicum CCBAU 83623 (EU146018) a. nodC B. japonicum SEMIA 566 (DQ485699) B. japonicum USDA 6T (AB354632) 99 B. japonicum CCBAU 05705 (HQ174508) B. elkanii CCBAU 05727 (HM057548) B. japonicum CCBAU 05724 (HM057547) B. liaoningense-related CCBAU 05588 (HM057544) B. japonicum CCBAU 05716 (HM057543) 99 B. japonicum CCBAU 05707 (HM057542) B. japonicum USDA 110 (NC004463) 64 B. yuanmingense CCBAU 10071T (AB354633) B. japonicum CCBAU 35139 (EF394183) B. yuanmingense CCBAU 05585 (HM057540) B. yuanmingense CCBAU 05623 (HM057541) 99 99 B. yuanmingense CCBAU 05625 (HM057545) B. yuanmingense CCBAU45079 (EF153405) 99 B.yuanmingense CCBAU 83648 (EU146022) B. yuanmingense CCBAU 23230 (DQ010033) 79 B. yuanmingense CCBAU 33079 (EF394182) B. pachyrhizi LMG 24246T (HM047128) 99 B. elkaniiCCBAU 05737 (HM057546) 99 B. elkanii USDA 76T (AB354631) B. canariense BTA-1T (AJ560653) B. iriomotense LMG 24129T(AB301000) S. medicae USDA 1037T (EF209422) 84 99 S. melilotiUSDA 1002T (EF428922) 58 S. kummerowiae CCBAU 71714T (GU994071) B. jicamae LMG 24556T (HM047129) B. elkanii CCBAU 05041(EU418394) S. fredii CCBAU 05698 (HM057529) S. fredii CCBAU 05657 (HM057530) S. americanum-relaedCCBAU 05672 (HM057531) 64 S. fredii CCBAU 05673 (HM057532) S. fredii CCBAU 05560 (HM057534) Sinorhizobium sp. ICCBAU 05617 (HM057535) S. fredii CCBAU 20016 (HM057537) 99 S. fredii CCBAU 05557 (HM057538) S. sojae CCBAU 05684T (GU994069) S. fredii USDA 205T (GU994972) S. frediiHH103 (DQ060002) Sinorhizobium sp.CCBAU 83643 (EU146020) 0.05 85 Sinorhizobium sp. CCBAU 83666 (EU146023) 85 S. fredii CCBAU45274 (EU753431) 85 Rhizobium sp.NGR 234 (NC000914) 70 Sinorhizobium sp. IICCBAU 05600 (HM057533) 82 S. fredii CCBAU 05702 (HM057536) 66 S. americanum-relaedCCBAU 05631 (HM057539) Supplementary Fig. D. Phylogenetic relationships based on nodC (a) and nifH (b)

  7. b. nifH B. liaoningense-related CCBAU 05588 (HM057563) B. japonicum CCBAU 83626 (EU146002) B. japonicum CCBAU 05705 (HQ174495) B.liaoningense LMG 18230T (EU818925) B. japonicum USDA 110 (NC004463) S. fredii CPAC 402 (DQ485715) 99 B. japonicum CCBAU 05707 (HM057561) B. japonicum CCBAU 05724 (HM057567) B. japonicum USDA 6T (HM047126) B. japonicum CCBAU 05716 (HM057562) 84 B.japonicum USDA 110 (NC004463) B. liaoningense CCBAU 83789 (EU146014) 99 B. yuanmingense CCBAU 10071T (EU818927) B. yuanmingense SR69 (EU357925) B. yuanmingense CCBAU 05623 (HM057560) 77 B. yuanmingense CCBAU 45079 (EF153397) 88 60 98 B. yuanmingenseCCBAU 05585 (HM057559) B. yuanmingense CCBAU 05625 (HM057564) 95 B. yuanmingense CCBAU23230 (AY934871) B. yuanmingense CCBAU 83648 (EU146005) 65 B. yuanmingense SR66 (EU357924) 50 B. pachyrhizi LMG 24246T (HM047124) B. elkanii USDA 76T (AB094963) 89 B. elkaniiCCBAU 05727 (HM057568) 99 B. elkaniiCCBAU 05737 (HM057565) 94 B. elkanii S127 (DQ485701) B. jicamae LMG 24556T (HM047127) B. canariense BTA-1T (EU818926) B. denitrificans LMG 8443T (HM047125) 99 S. meliloti ATCC 9930T (M55229) S. kummerowiae CCBAU 71714T (DQ411931) 76 S. mexicanus HAMBI 2910T (DQ411936) 99 S. chiapanecum ITTG S70T (EU291982) S. americanum CFNEI 156T (AF506514) 83 64 S. kostiense HAMBI 1489T (DQ411934) S. arboris HAMBI 1552T (Z95214) 95 51 S. terangae ORS1009T (Z95218) S. saheli ORS 609T (Z95221) S. americanum-relaedCCBAU 05631 (HM057558) 90 71 Sinorhizobium sp. IICCBAU 05600 (HM057552) S. fredii CCBAU 05702 (HM057555) 99 S. fredii CCBAU 45276 (EU418416) Sinorhizobium sp. CCBAU 83666 (EU146006) 64 Rhizobium sp.NGR 234 (NC000914) Sinorhizobium sp. CCBAU 83643 (EU146003) 0.02 S. fredii CCBAU 05673 (HM057551) S. fredii CCBAU 20016 (HM057556) 63 S. fredii CCBAU 110 (DQ411933) S. fredii CPAC 402 (DQ485714) S. fredii CCBAU 05560 (HM057553) S. americanum-relaedCCBAU 05672 (HM057550) 66 S. sojae CCBAU 05684T (GU994077) S. fredii CCBAU 05657 (HM057549) Sinorhizobium sp. ICCBAU 05617 (HM057554) S. fredii CCBAU 05557 (HM057557) S. fredii CCBAU 05698 (HM057566)

  8. Supplementary Fig. E. Correlation analysis between sample sites and CACAI group.

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