豆科植物根瘤内生细菌的发现及其研究进展

近年来研究报道显示,某些豆科植物与根瘤菌在形成固氮共生体的同时,其根瘤内还存在多种其他类群的内生细菌,该现象在根瘤菌研究领域越来越引起关注和重视。本文综述了根瘤内生土壤杆菌、非共生根瘤菌、其它细菌的发现、种类及其对共生关系和植物生长的影响等研究进展,同时对该研究方向提出一些初步观点和认识,旨在增加人们对根瘤微生态的了解,拓展根瘤菌研究与应用的视野。     

基于高通量测序分析西藏沙棘根瘤内生菌的多样性

根瘤是微生物侵染植物根部并与之形成的共生结构,这些微生物都可被称为植物内生菌。豆科植物根瘤中的内生菌常常又被称为根瘤菌,而侵染非豆科植物形成根瘤的主要是放线菌弗兰克氏菌,这些非豆科植物又被称为放线菌结瘤植物。西藏沙棘是一种典型的放线菌结瘤植物,由于其分布生境的特殊性,对其根瘤内生菌的研究具有重要的生态意义。对于西藏沙棘根瘤内生菌的研究,培养方法因难以模拟自然条件而不易获得纯培养,高通量测序技术对其多样性的研究提供了便利。因此,本研究以生长在甘肃省天祝县金强河河滩地的西藏沙棘根瘤为材料,采用16S rRNA基因扩增子高通量测序方法,结合OTU分析,对西藏沙棘根瘤内生菌的多样性进行探讨。实验结果表明,西藏沙棘根瘤内生菌具有丰富的多样性,根瘤内的优势属为共生固氮的弗兰克氏菌属（Frankia）,其相对丰度为47.63%,共检测到7个弗兰克氏菌属的OTUs;根瘤内除弗兰克氏菌外,还存在大量的非弗兰克氏菌,共检测到1523个OTUs,隶属于22个门、33个纲、69个目、113个科和202个属,相对丰度排名前9的属中有25个非弗兰克氏菌属的OTUs。该研究也表明,西藏沙棘根瘤内生菌具有丰富的多样性,西藏沙棘根瘤中不仅存在着可共生固氮的弗兰克氏菌,并且还分布着非弗兰克氏菌;在同一根瘤样品中,弗兰克氏菌属还具有不同的物种。本研究不仅拓展了西藏沙棘根瘤内生菌多样性的研究方法,还为同一寄主植物中弗兰克氏菌多样性的研究提供了分析思路。     

根瘤内生细菌

在研究根瘤菌与豆科植物共生关系的过程中,人们发现根瘤中同时定居着许多与根瘤菌不同的内生菌,这些非共生细菌生活在根瘤中,但不引起植物产生明显的病害,为根瘤内生细菌.根瘤内生细菌不仅将植物作为其栖息场所,而且对宿主植物有促生、防病、内生联合固氮等广泛的生物学作用.     

豆科植物SHR-SCR模块——根瘤“奠基细胞”的命运推手

豆科植物-根瘤菌共生固氮是可持续性农业氮肥的最重要来源。根瘤作为豆科植物共生固氮的一种特化植物侧生器官, 提供了根瘤菌生物固氮必需的微环境, 是根瘤菌的安身之本, 因此, 根瘤的正常发育是实现豆科植物-根瘤菌共生固氮的结构基础。根瘤器官的从头发生主要起始于根瘤菌诱导的根皮层细胞分裂。通常认为豆科植物的根皮层具备有别于非豆科植物根皮层的某种特异属性, 从而响应根瘤菌并与之建立固氮共生, 但长期以来该属性决定的分子机制一直不明确。近日, 中国科学院分子植物科学卓越创新中心王二涛团队以蒺藜苜蓿(Medicago truncatula)等豆科植物和拟南芥(Arabidopsis thaliana)等非豆科植物为研究对象, 发现豆科植物中保守的SHR-SCR干细胞模块决定了其皮层细胞分裂潜能从而赋予根瘤器官发生的命运。该研究揭示了豆科植物根瘤发育的全新机制, 提供了研究和理解植物-根瘤菌固氮共生进化的重要线索, 对提高豆科作物固氮效率和非豆科作物固氮工程具有重要意义。     

The Legume SHR-SCR Module Predetermines Nodule Founder Cell Identity

豆科植物-根瘤菌共生固氮是可持续性农业氮肥的最重要来源。根瘤作为豆科植物共生固氮的一种特化植物侧生器官, 提供了根瘤菌生物固氮必需的微环境, 是根瘤菌的安身之本, 因此, 根瘤的正常发育是实现豆科植物-根瘤菌共生固氮的结构基础。根瘤器官的从头发生主要起始于根瘤菌诱导的根皮层细胞分裂。通常认为豆科植物的根皮层具备有别于非豆科植物根皮层的某种特异属性, 从而响应根瘤菌并与之建立固氮共生, 但长期以来该属性决定的分子机制一直不明确。近日, 中国科学院分子植物科学卓越创新中心王二涛团队以蒺藜苜蓿(Medicago truncatula)等豆科植物和拟南芥(Arabidopsis thaliana)等非豆科植物为研究对象, 发现豆科植物中保守的SHR-SCR干细胞模块决定了其皮层细胞分裂潜能从而赋予根瘤器官发生的命运。该研究揭示了豆科植物根瘤发育的全新机制, 提供了研究和理解植物-根瘤菌固氮共生进化的重要线索, 对提高豆科作物固氮效率和非豆科作物固氮工程具有重要意义。     

沙棘属植物弗兰克氏菌研究进展

弗兰克氏菌(Frankia spp.)能够与沙棘等非豆科植物形成根瘤进行共生固氮,其固氮效率远远高于豆科植物根瘤菌,与沙棘共生的弗兰克氏菌还能够促进沙棘对旱寒等各种不同生境的适应性,是自然界一类具有开发潜力的放线菌资源。为了更好地开发利用弗兰克氏菌资源,推进弗兰克氏菌分类鉴定工作,加强弗兰克氏菌与寄主植物共生结瘤固氮的机制研究,促使弗兰克氏菌在农业生产中得到尽快应用,本文简要介绍沙棘属(Hippophae L.)物种多样性、结瘤状况与分布特点、沙棘根瘤形态结构与功能、弗兰克氏菌物种多样性与分布特征,讨论弗兰克氏菌的结瘤机制、生理生态效应与作用机制以及影响沙棘属植物与弗兰克氏菌共生的主要因子,以期为进一步开展沙棘属植物弗兰克氏菌的系统研究提供有价值的参考。     

一株分离自裸子植物罗汉松根瘤的根瘤菌

根瘤菌与豆科植物共生结瘤固氮被认为是地球上最重要的生物固氮体系. 裸子植物罗汉松与根瘤菌共生结瘤至今未见报道. 采用常规根瘤菌分离技术从罗汉松及其变种小叶罗汉松根瘤中分离获得11株内生细菌, 将它们回接宿主可导致结瘤, 乙炔还原法测出微弱的固氮酶活性. 传统的生理生化鉴定方法和16S rDNA全序列分析证明该内生细菌代表菌株GXLO 02隶属于根瘤菌.     

甘南高寒地区不同海拔西藏沙棘根瘤内生菌多样性

为了研究甘南高寒地区3个不同海拔西藏沙棘根瘤中内生菌的多样性,采用Illumina MiSeq高通量测序技术对3种不同海拔的西藏沙棘根瘤内生菌的菌群组成和多样性进行了分析。实验结果表明,3个不同海拔西藏沙棘根瘤中的内生菌主要包括6大门,分别为蓝藻门(Cyanobacteria),放线菌门(Actinobacteria),变形菌门(Proteobacteria),拟杆菌门(Bacteroidetes),梭杆菌门(Fusobacteria)和厚壁菌门(Firmicutes)。其中占主导地位的微生物是蓝藻门和放线菌门,蓝藻门在3个海拔的西藏沙棘根瘤中的丰度分别为68.1%,64.7%和66.0%,放线菌门在3个海拔的西藏沙棘根瘤中的丰度分别为28.6%,30.2%和29.5%。放线菌门弗兰克氏菌属(Frankia)为共同的优势菌属之一,在3个海拔的丰度分别为28.2%,29.8%和29.1%。3个不同海拔西藏沙棘根瘤中的内生菌除了能与沙棘共生固氮的弗兰克氏菌外,还存在其他的微生物群落,可能存在一些潜在的有价值的内生菌种资源。     

西藏沙棘5种不同组织内生细菌多样性

西藏沙棘(Hippophae tibetana)是分布于高寒高海拔地区的一类特殊的放线菌结瘤植物, 弗兰克氏菌能够侵染其根部形成根瘤, 因共生固氮等作用而增强其生态适应性。在西藏沙棘的根瘤中, 除了弗兰克氏菌之外还有其他内生菌, 而弗兰克氏菌又不仅仅在根瘤中有分布。为了探究弗兰克氏菌在西藏沙棘不同组织中的定殖及可能的迁移规律, 分析不同组织中内生细菌的群落结构及多样性, 本研究以生长在甘肃省天祝藏族自治县抓喜秀龙金强河河滩地的西藏沙棘为材料, 应用16S rRNA扩增子高通量测序技术, 对西藏沙棘根瘤、茎、枝、叶和种子等不同组织的内生细菌多样性进行了分析。研究结果表明, 西藏沙棘根瘤内生细菌群落丰富度及多样性最高, 种子内生细菌群落丰富度最低, 茎内生细菌群落多样性最低。西藏沙棘5种不同组织中的弗兰克氏菌和其他内生细菌多样性都具有一定差异, 变形菌门均为优势门, 弗兰克氏菌属(Frankia)为根瘤内生细菌群落的优势属, 弗莱德门菌属(Friedmanniella)为茎内生细菌群落的优势属, 寡养单胞菌属(Stenotrophomonas)为枝、叶和种子内生细菌群落的优势属。研究结果还表明, 弗兰克氏菌属不仅仅存在于西藏沙棘的根瘤, 还能够分布于其他组织, 且在同一种组织中存在弗兰克氏菌属的不同“种”; 而在西藏沙棘不同组织中, 也分布有弗兰克氏菌属的相同“种”。此外, 对西藏沙棘5种不同组织内生细菌中的功能菌株的分析表明, 不同组织中均存在着具有固氮、促生和抑菌功能的内生细菌, 但具有固氮作用的内生细菌主要分布于根瘤, 具有促生作用以及抑菌功能的内生细菌主要分布于枝和叶。综上, 西藏沙棘5种不同组织内生细菌具有丰富的多样性, 但各组织内生细菌的群落结构和优势种群有所不同, 且不同组织也能够定殖具有多种功能的内生细菌。     

豆科植物早期共生信号转导的研究进展

豆科植物与根瘤菌建立特异的共生关系,在寄主根部产生固氮根瘤。此过程包含了共生信号识别与传递、根瘤菌侵染、根瘤形成以及固氮功能实现等生物学事件。研究人员已经从2种豆科模式植物蒺藜苜蓿（Medicago truncatula）和百脉根（Lotus japonicus）的共生固氮体系中,筛选到许多与根瘤菌共生相关的突变体及其相对应的功能基因,建立起包含结瘤因子识别、共生信号传递和转录响应在内的早期共生信号途径。该文对豆科植物早期共生信号途径的新进展进行了综述。     

Diversity of endophytic bacteria within nodules of the Sphaerophysa salsula in different regions of Loess Plateau in China

A total of 115 endophytic bacteria were isolated from root nodules of the wild legume Sphaerophysa salsula grown in two ecological regions of Loess Plateau in China. The genetic diversity and phylogeny of the strains were revealed by restriction fragment length polymorphism and sequencing of 16S rRNA gene and enterobacterial repetitive intergenic consensus-PCR. Their symbiotic capacity was checked by nodulation tests and analysis of nifH gene sequence. This is the first systematic study on endophytic bacteria associated with S. salsula root nodules. Fifty of the strains found were symbiotic bacteria belonging to eight putative species in the genera Mesorhizobium, Rhizobium and Sinorhizobium, harboring similar nifH genes; Mesorhizobium gobiense was the main group and 65 strains were nonsymbiotic bacteria related to 17 species in the genera Paracoccus, Sphingomonas, Inquilinus, Pseudomonas, Serratia, Mycobacterium, Nocardia, Streptomyces, Paenibacillus, Brevibacillus, Staphylococcus, Lysinibacillus and Bacillus, which were universally coexistent with symbiotic bacteria in the nodules. Differing from other similar studies, the present study is the first time that symbiotic and nonsymbiotic bacteria have been simultaneously isolated from the same root nodules, offering the possibility to accurately reveal the correlation between these two kinds of bacteria. These results provide valuable information about the interactions among the symbiotic bacteria, nonsymbiotic bacteria and their habitats.     

Manipulation of Auxin Transport in Plant Roots during Rhizobium Symbiosis and Nematode Parasitism

The plant rhizosphere harbors many different microorganisms, ranging from plant growth–promoting bacteria to devastating plant parasites. Some of these microbes are able to induce de novo organ formation in infected roots. Certain soil bacteria, collectively called rhizobia, form a symbiotic interaction with legumes, leading to the formation of nitrogen-fixing root nodules. Sedentary endoparasitic nematodes, on the other hand, induce highly specialized feeding sites in infected plant roots from which they withdraw nutrients. In order to establish these new root structures, it is thought that these organisms use and manipulate the endogenous molecular and physiological pathways of their hosts. Over the years, evidence has accumulated reliably demonstrating the involvement of the plant hormone auxin. Moreover, the auxin responses during microbe-induced de novo organ formation seem to be dynamic, suggesting that plant-associated microbes can actively modify their host''s auxin transport. In this review, we focus on recent findings in auxin transport mechanisms during plant development and on how plant symbionts and parasites have evolved to manipulate these mechanisms for their own purposes.     

Lifestyle alternatives for rhizobia: mutualism, parasitism, and forgoing symbiosis

Strains of rhizobia within a single species can have three different genetically determined strategies. Mutualistic rhizobia provide their legume hosts with nitrogen. Parasitic rhizobia infect legumes, but fix little or no nitrogen. Nonsymbiotic strains are unable to infect legumes at all. Why have rhizobium strains with one of these three strategies not displaced the others? A symbiotic (mutualistic or parasitic) rhizobium that succeeds in founding a nodule may produce many millions of descendants. The chances of success can be so low, however, that nonsymbiotic rhizobia can have greater reproductive success. Legume sanctions against nodules that fix little or no nitrogen favor more mutualistic strains, but parasitic strains that use plant resources only for their own reproduction may do well when they share nodules with mutualistic strains.     

The sulfate transporter SST1 is crucial for symbiotic nitrogen fixation in Lotus japonicus root nodules

Symbiotic nitrogen fixation (SNF) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. Little is known at the molecular level about plant transporters that mediate such exchanges. Several mutants of the model legume Lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. Map-based cloning of defective genes in two such mutants, sst1-1 and sst1-2 (for symbiotic sulfate transporter), revealed two alleles of the same gene. The gene is expressed in a nodule-specific manner and encodes a protein homologous with eukaryotic sulfate transporters. Full-length cDNA of the gene complemented a yeast mutant defective in sulfate transport. Hence, the gene was named Sst1. The sst1-1 and sst1-2 mutants exhibited normal growth and development under nonsymbiotic growth conditions, a result consistent with the nodule-specific expression of Sst1. Data from a previous proteomic study indicate that SST1 is located on the symbiosome membrane in Lotus nodules. Together, these results suggest that SST1 transports sulfate from the plant cell cytoplasm to the intracellular rhizobia, where the nutrient is essential for protein and cofactor synthesis, including nitrogenase biosynthesis. This work shows the importance of plant sulfate transport in SNF and the specialization of a eukaryotic transporter gene for this purpose.     

Binding of Isolated Plant Lectin by Rhizobia during Episodes of Reduced Gravity Obtained by Parabolic Flight

Development of a legume root nodule is a complex process culminating in a plant/bacterial symbiosis possessing the capacity for biological dinitrogen fixation. Formation of root nodules is initiated by the binding and stabilization of rhizobia to plant root hairs, mediated in part by a receptor/ligand recognition system composed of lectins on the plant root surface and lectin-binding sites on the rhizobial cell surface. The dinitrogen fixation activity of these root nodules may be an important feature of enclosed, space-based life support systems, and may provide an ecological method to recycle nitrogen for amino acid production. However, the effects on nodule development of varied gravitational fields, or of root nutrient delivery hardware, remain unknown. We have investigated the effects of microgravity on root nodule formation, with preliminary experiments focused upon the receptor/ligand component. Microgravity, obtained during parabolic flight aboard NASA 930, has no apparent effect on the binding of purified lectin to rhizobia, a result that will facilitate forthcoming experiments using intact root tissues.     

Manipulation of Ethylene Synthesis in Roots Through Bacterial ACC Deaminase for Improving Nodulation in Legumes

Symbiotic association between rhizobia and legumes results in the development of unique structures on roots, called nodules. Nodulation is a very complex process involving a variety of genes that control NOD factors (bacterial signaling molecules), which are essential for the establishment, maintenance and regulation of this process and development of root nodules. Ethylene is an established potent plant hormone that is also known for its negative role in nodulation. Ethylene is produced endogenously in all plant tissues, particularly in response to both biotic and abiotic stresses. Exogenous application of ethylene and ethylene-releasing compounds are known to inhibit the formation and functioning of nodules. While inhibitors of ethylene synthesis or its physiological action enhance nodulation in legumes, some rhizobial strains also nodulate the host plant intensively, most likely by lowering endogenous ethylene levels in roots through their 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Co-inoculation with ACC deaminase containing plant growth promoting rhizobacteria plus rhizobia has been shown to further promote nodulation compared to rhizobia alone. Transgenic rhizobia or legume plants with expression of bacterial ACC deaminase could be another viable option to alleviate the negative effects of ethylene on nodulation. Several studies have well documented the role of ethylene and bacterial ACC deaminase in development of nodules on legume roots and will be the primary focus of this critical review.     

Chemotaxis,induced gene expression and competitiveness in the rhizosphere

Rhizobia are soil bacteria which symbiotically infect legume roots and generate nodules in which they fix atmospheric nitrogen for the plant in exchange for photosynthetically fixed carbon. A crucial aspect of signal exchange between these symbionts is the secretion of phenolic compounds by the host root which induce nodulation gene expression in the bacteria. Stimulation of nod gene expression by host phenolics is required for nodule formation, is biochemically specific at 10^-6 M, and is mediated by nodD. We and others have shown that rhizobia display chemotaxis to 10^-9 M of the same phenolic compounds. Chemotaxis to inducer phenolics is selectively reduced or abolished by mutations in certain nod genes governing nodulation efficiency or host specificity. Conversely, mutations in rhizobia that affect general motility or chemotaxis have substantial effects on nodulation efficiency and competitiveness. These findings suggest that microbes entering the rhizosphere environment may utilize minor, non-nutrient components in root exudates as signals to guide their movement towards the root surface and elicit changes in gene expression appropriate to this environment.     

Rhizobia can induce nodules in white clover by "hijacking" mature cortical cells activated during lateral root development

We examined a range of responses of root cortical cells to Rhizobium sp. inoculation to investigate why rhizobia preferentially nodulate legume roots in the zone of emerging root hairs, but generally fail to nodulate the mature root. We tested whether the inability to form nodules in the mature root is due to a lack of plant flavonoids to induce the bacterial genes required for nodulation or a failure of mature cortical cells to respond to Rhizobium spp. When rhizobia were inoculated in the zone of emerging root hairs, changes in beta-glucuronidase (GUS) expression from an auxin-responsive promoter (GH3), expression from three chalcone synthase promoters, and the accumulation of specific flavonoid compounds occurred in cortical cells prior to nodule formation. Rhizobia failed to induce these responses when inoculated in the mature root, even when co-inoculated with nod gene-inducing flavonoids. However, mature root hairs remained responsive to rhizobia and could support infection thread formation. This suggests that a deficiency in signal transduction is the reason for nodulation failure in the mature root. However, nodules could be initiated in the mature root at sites of lateral root emergence. A comparison between lateral root and nodule formation showed that similar patterns of GH3:gusA expression, chalcone synthase gene expression, and accumulation of a particular flavonoid compound occurred in the cortical cells involved in both processes. The results suggest that rhizobia can "hijack" cortical cells next to lateral root emergence sites because some of the early responses required for nodule formation have already been activated by the plant in those cells.     

Control of nodule number by the phytohormone abscisic Acid in the roots of two leguminous species

The effects of the phytohormone abscisic acid (ABA) on plant growth and root nodule formation were analyzed in Trifolium repense (white clover) and Lotus japonicus, which form indeterminate and determinate nodules, respectively. In T. repense, although the number of nodules formed after inoculation with Rhizobium leguminosarum bv. trifolii strain 4S (wild type) was slightly affected by exogenous ABA, those formed by strain H1(pC4S8), which forms ineffective nodules, were dramatically reduced 28 days after inoculation (DAI). At 14 and 21 DAI, the number of nodules formed with the wild-type strain was decreased by exogenous ABA. In L. japonicus, the number of nodules was also reduced by ABA treatment. Thus, exogenous ABA inhibits root nodule formation after inoculation with rhizobia. Observation of root hair deformation revealed that ABA blocked the step between root hair swelling and curling. When the ABA concentration in plants was decreased by using abamine, a specific inhibitor of 9-cis-epoxycarotenoid dioxygenase, the number of nodules on lateral roots of abamine-treated L. japonicus increased dramatically, indicating that lower-than-normal concentrations of endogenous ABA enhance nodule formation. We hypothesize that the ABA concentration controls the number of root nodules.     

沙冬青根瘤菌的电子显微镜研究

用透射电镜研究沙冬青根瘤中的根瘤菌。这种根瘤菌的精细结构不仅与生态环境有关,而且还随寄主细胞发育程度不同而异。在早期侵染细胞中,根瘤菌很少,一般呈圆形或椭圆形,电子密度很高,位于细胞壁附近。在成熟侵染细胞中,根瘤菌很多,布满了整个细胞,形态出现多样化。在衰老侵染细胞中,根瘤菌形状不规则,细胞质收缩,电子密度增高,内部结构模糊不清,有的甚至变成一团膜泡状结构