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根瘤菌主要指与豆类作物根部共生形成根瘤并能固氮的细菌，一般指根瘤菌属和慢生根瘤菌属；两属都属于根瘤菌目。
根瘤菌侵入寄主根内，刺激根部皮层和中柱鞘的某些细胞，引起这些细胞的强烈生长，使根的局部膨大形成根瘤；根瘤菌在根内定居，植物供给根瘤菌以矿物养料和能源，根瘤菌固定大气中游离氮气，为植物提供氮素养料，两者在拮抗寄生关系中处于均衡状态而表现共生现象。
根瘤菌细胞呈杆状，有鞭毛和荚膜，鞭毛为正常的活动器官，无芽孢，革兰氏染色阴性，属需氧型。在根瘤中生活的菌体形式多种多样，有梨形、棍棒型或T、X、Y等型，这种变形的菌体成为类菌体；类菌体在豆科植物体内不生长繁殖，却能与豆科植物共同固氮，对豆科植物有良好作用。
每种根瘤菌只能与一种或几种植物建立共生关系，如下表：
此外，还有些微生物能同非豆类植物共同形成根瘤固氮，主要是一些放线菌（如：小头木麻黄、赤杨、杨梅）、蓝绿菌（如：苏铁、竹柏、满江红）。
根瘤菌属 包括以下物种：
- Rhizobium acaciae Hsouna et al. 2023[2]
- Rhizobium acidisoli Román-Ponce et al. 2016
- 埃及根瘤菌 Rhizobium aegyptiacum Shamseldin et al. 2017
- Rhizobium aethiopicum Aserse et al. 2017
- Rhizobium aggregatum (Hirsch and Müller 1986) Kaur et al. 2011
- Rhizobium alamii Berge et al. 2009
- Rhizobium alkalisoli Lu et al. 2009，为Neorhizobium alkalisoli (Lu et al. 2009) Mousavi et al. 2015的异名
- Rhizobium altiplani Baraúna et al. 2016
- Rhizobium alvei Sheu et al. 2015
- 安徽根瘤菌 Rhizobium anhuiense Zhang et al. 2015
- Rhizobium aquaticum Máthé et al. 2019
- Rhizobium arenae Zhang et al. 2017
- Rhizobium arsenicireducens Mohapatra et al. 2020
- Rhizobium azibense Mnasri et al. 2014
- Rhizobium azooxidifex Behrendt et al. 2016
- Rhizobium bangladeshense Rashid et al. 2015
- Rhizobium beringeri Young et al. 2023[3]
- Rhizobium binae Rashid et al. 2015
- Rhizobium borbori Zhang et al. 2011，为Allorhizobium borbori (Zhang et al. 2011) Mousavi et al. 2016的异名
- Rhizobium brockwellii Young et al. 2023[4]
- Rhizobium calliandrae Rincón-Rosales et al. 2013
- Rhizobium capsici Lin et al. 2015
- Rhizobium cauense Liu et al. 2015
- Rhizobium cellulosilyticum García-Fraile et al. 2007
- Rhizobium chutanense Huo et al. 2019
- Rhizobium ciceri Nour et al. 1994，为Mesorhizobium ciceri (Nour et al. 1994) Jarvis et al. 1997的异名
- Rhizobium croatiense Rajnovic et al. 2023[5]
- 大田根瘤菌 Rhizobium daejeonense Quan et al. 2005[6]
- Rhizobium dioscoreae Ouyabe et al. 2020
- Rhizobium ecuadorense Ribeiro et al. 2015
- Rhizobium endolithicum Parag et al. 2014
- Rhizobium endophyticum López-López et al. 2011
- Rhizobium esperanzae Cordeiro et al. 2017
- Rhizobium etli Segovia et al. 1993
- Rhizobium fabae Tian et al. 2008
- Rhizobium favelukesii Torres Tejerizo et al. 2016
- Rhizobium flavum Gu et al. 2014
- Rhizobium fredii Scholla and Elkan 1984，为Ensifer fredii (Scholla and Elkan 1984) Young 2003的异名
- Rhizobium freirei Dall'Agnol et al. 2013
- Rhizobium galegae Lindström 1989，为Neorhizobium galegae (Lindström 1989) Mousavi et al. 2015的异名
- Rhizobium gallicum Amarger et al. 1997
- 格氏根瘤菌 Rhizobium gei Shi et al. 2016
- Rhizobium giardinii Amarger et al. 1997
- Rhizobium grahamii López-López et al. 2012
- 海南根瘤菌 Rhizobium hainanense Chen et al. 1997
- Rhizobium halophytocola Bibi et al. 2012
- Rhizobium helianthi Wei et al. 2015
- Rhizobium herbae Ren et al. 2011，为Pararhizobium herbae (Ren et al. 2011) Mousavi et al. 2016的异名
- Rhizobium hidalgonense Yan et al. 2020
- 华氏根瘤菌 Rhizobium huakuii Chen et al. 1991，为Mesorhizobium huakuii (Chen et al. 1991) Jarvis et al. 1997的异名
- Rhizobium huautlense Wang et al. 1998，为Neorhizobium huautlense (Wang et al. 1998) Mousavi et al. 2015的异名
- Rhizobium indigoferae Wei et al. 2002
- Rhizobium ipomoeae Sheu et al. 2016
- Rhizobium jaguaris Rincón-Rosales et al. 2013
- 日本根瘤菌 Rhizobium japonicum (Kirchner 1896) Buchanan 1926，为Bradyrhizobium japonicum (Kirchner 1896) Jordan 1982的异名
- Rhizobium johnstonii Young et al. 2023[7]
- Rhizobium laguerreae Saïdi et al. 2014
- Rhizobium larrymoorei (Bouzar and Jones 2001) Young 2004，为Agrobacterium larrymoorei Bouzar and Jones 2001的异名
- 豌豆根瘤菌 Rhizobium leguminosarum (Frank 1879) Frank 1889
- Rhizobium lemnae Kittiwongwattana and Thawai 2014
- Rhizobium lentis Rashid et al. 2015
- Rhizobium leucaenae Ribeiro et al. 2012
- Rhizobium loessense Wei et al. 2003，为Rhizobium mongolense subsp. loessense (Wei et al. 2003) Hördt et al. 2020的异名
- Rhizobium loti Jarvis et al. 1982，为Mesorhizobium loti (Jarvis et al. 1982) Jarvis et al. 1997的异名
- Rhizobium lupini (Schroeter 1886) Eckhardt et al. 1931，基异名：Phytomyxa lupini Schroeter 1886
- Rhizobium lusitanum Valverde et al. 2006
- Rhizobium marinum Liu et al. 2015
- Rhizobium mayense Rincón-Rosales et al. 2013
- 地中海根瘤菌 Rhizobium mediterraneum Nour et al. 1995，为Mesorhizobium mediterraneum (Nour et al. 1995) Jarvis et al. 1997的异名
- Rhizobium meliloti Dangeard 1926，为Ensifer meliloti (Dangeard 1926) Young 2003的异名
- Rhizobium mesoamericanum López-López et al. 2012
- Rhizobium mesosinicum Lin et al. 2009
- Rhizobium metallidurans Grison et al. 2015
- Rhizobium miluonense Gu et al. 2008
- 内蒙根瘤菌 Rhizobium mongolense Van Berkum et al. 1998
- Rhizobium multihospitium Han et al. 2008
- Rhizobium naphthalenivorans Kaiya et al. 2018
- Rhizobium nepotum Puławska et al. 2012，为Agrobacterium nepotum (Puławska et al. 2012) Mousavi et al. 2016的异名
- Rhizobium oryzae Peng et al. 2008，为Allorhizobium oryzae (Peng et al. 2008) Mousavi et al. 2016的异名
- 稻生根瘤菌 Rhizobium oryzicola Zhang et al. 2015
- Rhizobium oryziradicis Zhao et al. 2017，为Allorhizobium oryziradicis (Zhao et al. 2017) Lin et al. 2020的异名
- 巴基斯坦根瘤菌 Rhizobium pakistanense Khalid et al. 2015，也拼作：Rhizobium pakistanensis
- Rhizobium paknamense Kittiwongwattana and Thawai 2013
- Rhizobium paranaense Dall'Agnol et al. 2014
- Rhizobium petrolearium Zhang et al. 2012
- Rhizobium phaseoli Dangeard 1926
- Rhizobium pisi Ramírez-Bahena et al. 2008
- Rhizobium populi Rozahon et al. 2014
- Rhizobium populisoli Shen et al. 2022[8]
- Rhizobium pseudoryzae Zhang et al. 2011，为Allorhizobium pseudoryzae (Zhang et al. 2011) Mousavi et al. 2016的异名
- Rhizobium puerariae Boonsnongcheep et al. 2016
- Rhizobium pusense Panday et al. 2011，为Agrobacterium pusense (Panday et al. 2011) Mousavi et al. 2016的异名
- Rhizobium radiobacter (Beijerinck and van Delden 1902) Young et al. 2001，为Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn, 1942 的异名
- Rhizobium redzepovicii Rajnovic et al. 2023[9]
- Rhizobium rhizogenes (Riker et al. 1930) Young et al. 2001
- Rhizobium rhizophilum Gao et al. 2020
- Rhizobium rhizoryzae Zhang et al. 2014
- Rhizobium rhododendri Kuzmanović et al. 2023[10]
- Rhizobium rosettiformans Kaur et al. 2011
- Rhizobium rubi (Hildebrand 1940) Young et al. 2001，为Agrobacterium rubi (Hildebrand 1940) Starr and Weiss 1943的异名
- Rhizobium ruizarguesonis Jorrin et al. 2020
- Rhizobium selenitireducens Hunter et al. 2008，也拼作：Rhizobium selenireducens
- Rhizobium setariae Kang and Seo 2023
- Rhizobium skierniewicense Puławska et al. 2012
- Rhizobium smilacinae Zhang et al. 2015
- 土壤根瘤菌 Rhizobium soli Yoon et al. 2010
- Rhizobium sophorae Jiao et al. 2015
- Rhizobium sophoriradicis Jiao et al. 2015
- Rhizobium sphaerophysae Xu et al. 2012
- Rhizobium straminoryzae Lin et al. 2014
- Rhizobium subbaraonis Ramana et al. 2013
- Rhizobium sullae Squartini et al. 2002
- 太白山根瘤菌 Rhizobium taibaishanense Yao et al. 2012，为Allorhizobium taibaishanense (Yao et al. 2012) Hördt et al. 2020的异名
- Rhizobium tarimense Turdahon et al. 2013
- 土生根瘤菌 Rhizobium terricola Dahal et al. 2023[11]
- 天山根瘤菌 Rhizobium tianshanense Chen et al. 1995，为Mesorhizobium tianshanense (Chen et al. 1995) Jarvis et al. 1997的异名
- 西藏根瘤菌 Rhizobium tibeticum Hou et al. 2009
- Rhizobium trifolii Dangeard 1926，为Rhizobium leguminosarum (Frank 1879) Frank 1889的异名
- Rhizobium tropici Martínez-Romero et al. 1991
- Rhizobium tubonense Zhang et al. 2011
- Rhizobium tumorigenes Kuzmanović et al. 2019
- Rhizobium undicola (de Lajudie et al. 1998) Young et al. 2001，为Allorhizobium undicola de Lajudie et al. 1998的异名
- Rhizobium vallis Wang et al. 2011
- Rhizobium vignae Ren et al. 2011，为Neorhizobium vignae (Ren et al. 2011) Hördt et al. 2020的异名
- Rhizobium viscosum (Gasdorf et al. 1965) Flores-Félix et al. 2017
- Rhizobium vitis (Ophel and Kerr 1990) Young et al. 2001，为Allorhizobium vitis (Ophel and Kerr 1990) Mousavi et al. 2016的异名
- 文新根瘤菌 Rhizobium wenxiniae Gao et al. 2017，以土壤微生物及细菌分类学家、中国科学院院士陈文新的名字命名
- 梧州根瘤菌 Rhizobium wuzhouense Yuan et al. 2018[12]
- 杨凌根瘤菌 Rhizobium yanglingense Tan et al. 2001
- 盐亭根瘤菌 Rhizobium yantingense Chen et al. 2015
- Rhizobium zeae Celador-Lera et al. 2017
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