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。
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Rhizobium 是一类土壤中常见的一类微生物，它们与豆科植物建立共生关系，对植物具有重要的作用，尤其是在提供氮源方面。以下是 Rhizobium 在根际微生物群落中可能对植物产生的主要作用：
固氮作用：Rhizobium 菌株与豆科植物根系中的根瘤中形成共生结构。在这种关系中，Rhizobium 能够将大气中的氮气转化为可被植物吸收的氨或亚硝酸盐。这有助于提供植物所需的氮源，促进植物的生长和发育。
生长促进：除了固氮作用外，Rhizobium 菌株还可以产生植物生长激素，如吲哚乙酸，有助于促进植物的生长、根系发育和产量。
养分提供：Rhizobium 菌株还能够提供其他重要的养分，如磷和钾，帮助植物吸收这些养分，从而提高植物的养分利用效率。
抗逆性提高：共生关系中的 Rhizobium 能够增强植物的抵抗力，帮助植物对抗逆境条件，如干旱、盐碱土壤和土壤污染。
生物多样性和土壤改善：与 Rhizobium 相互作用的豆科植物通常有助于改善土壤质地，增加土壤有机质和微生物多样性，从而提高土壤的健康和生态系统稳定性。
需要注意的是，Rhizobium 与豆科植物建立共生关系，对其他植物的作用相对较小。其他植物通常与不同的根际微生物建立不同类型的共生关系，以满足它们的养分和生长需求。因此，在研究和应用中，通常需要考虑具体的植物物种、根际微生物群落和土壤条件，以更好地理解 Rhizobium 在不同生态系统中的作用。
3、Rhizobium Soaking Promoted Maize Growth by Altering Rhizosphere Microbiomes and Associated Functional Genes
Rhizobium is a Gram-negative bacterium, which dissolves minerals, produces growth
hormones, promotes root growth, and protects plants from different soil-borne pathogens. In the
present study, roots, stalks, and fresh weight of maize (Zea mays L.) were significantly increased
after soaking in Bradyrhizobium japonicum compared with the control. Subsequently, transcriptome
sequencing results of the whole maize plant soaked in B. japonicum showed that multiple growth
and development-related genes were up-regulated more than 100-fold compared to the control.
Furthermore, the abundance of plant growth promoting bacteria, such as Acidobacteria Subgroup_6
and Chloroflexi KD4-96, were increased significantly. On the contrary, the abundance of multiple
pathogens, such as Curvularia, Fusarium and Mycocentrospora, were significantly decreased. Moreover,
inoculation with B. japonicum could inhibit the infection of the pathogen Fusarium graminearum in
maize. These results suggest that soaking seeds in B. japonicum may affect the expression of maize
growth and development-related genes as the bacteria changes the soil microorganism community
structure. These findings may help to expand the application of B. japonicum in crop production and
provide new opportunities for food security.
根瘤菌是一种革兰氏阴性菌，可以溶解矿物质，产生生长激素，促进根系生长，并保护植物免受不同土壤传播的病原体的侵害。本研究中，与对照相比，慢生根瘤菌浸泡后玉米(Zea mays L.)的根、茎和鲜重均显著提高。随后，整个玉米植株的转录组测序结果显示，与对照相比，多个生长发育相关基因上调了100倍以上。此外，促进植物生长的细菌如酸杆菌亚群_6和Chloroflexi KD4-96的丰度也显著增加。而弯孢菌、镰刀菌和蕈状孢子菌等多种病原菌的丰度则显著降低。此外，接种日本芽孢杆菌可抑制玉米禾谷镰刀菌的侵染。这些结果表明，日本芽孢杆菌浸种可能会改变土壤微生物群落结构，从而影响玉米生长发育相关基因的表达。这些发现有助于扩大日本芽孢杆菌在作物生产中的应用，并为粮食安全提供新的机遇。
4、Transcriptomic Responses of Rhizobium phaseoli to Root Exudates Reflect Its Capacity to Colonize Maize and Common Bean in an Intercropping System
Corn and common bean have been cultivated together in Mesoamerica for thousands
of years in an intercropping system called “milpa,” where the roots are intermingled,
favoring the exchange of their microbiota, including symbionts such as rhizobia. In this
work, we studied the genomic expression of Rhizobium phaseoli Ch24-10 (by RNA-seq)
after a 2-h treatment in the presence of root exudates of maize and bean grown in
monoculture and milpa system under hydroponic conditions. In bean exudates, rhizobial
genes for nodulation and degradation of aromatic compounds were induced; while in
maize, a response of genes for degradation of mucilage and ferulic acid was observed,
as well as those for the transport of sugars, dicarboxylic acids and iron. Ch24-10
transcriptomes in milpa resembled those of beans because they both showed high
expression of nodulation genes; some genes that were expressed in corn exudates
were also induced by the intercropping system, especially those for the degradation of
ferulic acid and pectin. Beans grown in milpa system formed nitrogen-fixing nodules
similar to monocultured beans; therefore, the presence of maize did not interfere with
Rhizobium–bean symbiosis. Genes for the metabolism of sugars and amino acids,
flavonoid and phytoalexin tolerance, and a T3SS were expressed in both monocultures
and milpa system, which reveals the adaptive capacity of rhizobia to colonize both
legumes and cereals. Transcriptional fusions of the putA gene, which participates
in proline metabolism, and of a gene encoding a polygalacturonase were used to
validate their participation in plant–microbe interactions. We determined the enzymatic
activity of carbonic anhydrase whose gene was also overexpressed in response to
root exudates.
玉米和普通豆类在中美洲以一种被称为“milpa”的间作系统共同栽培了数千年，在这种间作系统中，它们的根交织在一起，有利于它们的微生物群的交换，包括像根瘤菌这样的共生体。本研究利用RNA-seq技术研究了玉米根瘤菌(Rhizobium phaseoli) Ch24-10在单作和密尔巴体系(milpa)水培条件下，在玉米和大豆根瘤菌(Rhizobium phaseoli Ch24-10)根系分泌物中处理2 h后的基因组表达。在大豆分泌物中，根瘤菌的结瘤基因和芳香化合物降解基因被诱导;而在玉米中，观察到粘液和阿魏酸降解基因的响应，以及糖、二羧酸和铁的运输基因的响应。米帕的Ch24-10转录组与大豆相似，因为它们都表现出高表达的结瘤基因;间作系统也诱导了一些在玉米分泌物中表达的基因，特别是阿魏酸和果胶降解的基因。在米尔帕体系下生长的豆子形成了类似于单一栽培的固氮根瘤;因此，玉米的存在不会干扰根瘤菌与大豆的共生关系。在单作和milpa系统中，根瘤菌糖和氨基酸代谢、类黄酮和植物抗毒素耐受以及T3SS基因均有表达，揭示了根瘤菌对豆科和谷类植物的适应能力。参与脯氨酸代谢的putA基因和编码多聚半乳糖醛酸酶的基因的转录融合被用来验证它们在植物-微生物相互作用中的参与。我们确定了碳酸酐酶的酶活性，其基因也过表达响应根渗出物。