Insights into the history of the legume‐betaproteobacterial symbiosis

The interaction between legumes and rhizobia has been well studied in the context of a mutualistic, nitrogen‐fixing symbiosis. The fitness of legumes, including important agricultural crops, is enhanced by the plants’ ability to develop symbiotic associations with certain soil bacteria that fix atmospheric nitrogen into a utilizable form, namely, ammonia, via a chemical reaction that only bacteria and archaea can perform. Of the bacteria, members of the alpha subclass of the protebacteria are the best‐known nitrogen‐fixing symbionts of legumes. Recently, members of the beta subclass of the proteobacteria that induce nitrogen‐fixing nodules on legume roots in a species‐specific manner have been identified. In this issue, Bontemps et al. reveal that not only are these newly identified rhizobia novel in shifting the paradigm of our understanding of legume symbiosis, but also, based on symbiotic gene phylogenies, have a history that is both ancient and stable. Expanding our understanding of novel plant growth promoting rhizobia will be a valuable resource for incorporating alternative strategies of nitrogen fixation for enhancing plant growth.     

Nitrogen fixation and carbon metabolism in legume nodules

A large amount of energy is utilized by legume nodules for the fixation of nitrogen and assimilation of fixed nitrogen (ammonia) into organic compounds. The source of energy is provided in the form of photosynthates by the host plant. Phosphoenol pyruvate carboxylase (PEPC) enzyme, which is responsible for carbon dioxide fixation in C4 and crassulacean acid metabolism plants, has also been found to play an important role in carbon metabolism in legume root nodule. PEPC-mediated CO2 fixation in nodules results in the synthesis of C4 dicarboxylic acids, viz. aspartate, malate, fumarate etc. which can be transported into bacteroids with the intervention of dicarboxylate transporter (DCT) protein. PEPC has been purified from the root nodules of few legume species. Information on the relationship between nitrogen fixation and carbon metabolism through PEPC in leguminous plants is scanty and incoherent. This review summarizes the various aspects of carbon and nitrogen metabolism in legume root nodules.     

Arbuscular mycorrhizal fungi colonize nonfixing root nodules of several legume species

Many legumes form tripartite symbiotic associations with rhizobia and arbuscular mycorrhizal fungi (AMF). Rhizobia are located in root nodules and provide the plant with fixed atmospheric nitrogen, while AMF colonize plant roots and deliver several essential nutrients to the plant. Recent studies showed that AMF are also associated with root nodules. This might point to interactions between AMF and rhizobia inside root nodules. Here, we test whether AMF colonize root nodules in various plant-AMF combinations. We also test whether nodules that are colonized by AMF fix nitrogen. Using microscopy, we observed that AMF colonized the root nodules of three different legume species. The AMF colonization of the nodules ranged from 5% to 74% and depended on plant species, AMF identity and nutrient availability. However, AMF-colonized nodules were not active, that is, they did not fix nitrogen. The results suggest that AMF colonize old senescent nodules after nitrogen fixation has stopped, although it is also possible that AMF colonization of nodules inhibits nitrogen fixation.     

MtMOT1.2 is responsible for molybdate supply to Medicago truncatula nodules

Symbiotic nitrogen fixation in legume root nodules requires a steady supply of molybdenum for synthesis of the iron‐molybdenum cofactor of nitrogenase. This nutrient has to be provided by the host plant from the soil, crossing several symplastically disconnected compartments through molybdate transporters, including members of the MOT1 family. Medicago truncatula Molybdate Transporter (MtMOT) 1.2 is a Medicago truncatula MOT1 family member located in the endodermal cells in roots and nodules. Immunolocalization of a tagged MtMOT1.2 indicates that it is associated to the plasma membrane and to intracellular membrane systems, where it would be transporting molybdate towards the cytosol, as indicated in yeast transport assays. Loss‐of‐function mot1.2‐1 mutant showed reduced growth compared with wild‐type plants when nitrogen fixation was required but not when nitrogen was provided as nitrate. While no effect on molybdenum‐dependent nitrate reductase activity was observed, nitrogenase activity was severely affected, explaining the observed difference of growth depending on nitrogen source. This phenotype was the result of molybdate not reaching the nitrogen‐fixing nodules, since genetic complementation with a wild‐type MtMOT1.2 gene or molybdate‐fortification of the nutrient solution, both restored wild‐type levels of growth and nitrogenase activity. These results support a model in which MtMOT1.2 would mediate molybdate delivery by the vasculature into the nodules.     

Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).     

The role of legumes as a component of biodiversity in a cross-European study of grassland biomass nitrogen

To investigate how plant diversity loss affects nitrogen accumulation in above‐ground plant biomass and how consistent patterns are across sites of different climatic and soil conditions, we varied the number of plant species and functional groups (grasses, herbs and legumes) in experimental grassland communities across seven European experimental sites (Switzerland, Germany, Ireland, United Kingdom (Silwood Park), Portugal, Sweden and Greece). Nitrogen pools were significantly affected by both plant diversity and community composition. Two years after sowing, nitrogen pools in Germany and Switzerland strongly increased in the presence of legumes. Legume effects on nitrogen pools were less pronounced at the Swedish, Irish and Portuguese site. In Greece and UK there were no legume effects. Nitrogen concentration in total above‐ground biomass was quite invariable at 1.66±0.03% across all sites and diversity treatments. Thus, the presence of legumes had a positive effect on nitrogen pools by significantly increasing above‐ground biomass, i.e. by increases in vegetation quantity rather than quality. At the German site with the strongest legume effect on nitrogen pools and biomass, nitrogen that was fixed symbiotically by legumes was transferred to the other plant functional groups (grasses and herbs) but varied depending on the particular legume species fixing N and the non‐legume species taking it up. Nitrogen‐fixation by legumes therefore appeared to be one of the major functional traits of species that influenced nitrogen accumulation and biomass production, although effects varied among sites and legume species. This study demonstrates that the consequences of species loss on the nitrogen budget of plant communities may be more severe if legume species are lost. However, our data indicate that legume species differ in their N₂ fixation. Therefore, loss of an efficient N₂‐fixer (Trifolium in our study) may have a greater influence on the ecosystem function than loss of a less efficient species (Lotus in our study). Furthermore, there is indication that P availability in the soil facilitates the legume effect on biomass production and biomass nitrogen accumulation.     

Nonlegumes, Legumes, and Root Nodules Harbor Different Arbuscular Mycorrhizal Fungal Communities

Legumes are an important plant functional group since they can form a tripartite symbiosis with nitrogen-fixing Rhizobium bacteria and phosphorus-acquiring arbuscular mycorrhizal fungi (AMF). However, not much is known about AMF community composition in legumes and their root nodules. In this study, we analyzed the AMF community composition in the roots of three nonlegumes and in the roots and root nodules of three legumes growing in a natural dune grassland. We amplified a portion of the small-subunit ribosomal DNA and analyzed it by using restriction fragment length polymorphism and direct sequencing. We found differences in AMF communities between legumes and nonlegumes and between legume roots and root nodules. Different plant species also contained different AMF communities, with different AMF diversity. One AMF sequence type was much more abundant in legumes than in nonlegumes (39 and 13%, respectively). Root nodules contained characteristic AMF communities that were different from those in legume roots, even though the communities were similar in nodules from different legume species. One AMF sequence type was found almost exclusively in root nodules. Legumes and root nodules have relatively high nitrogen concentrations and high phosphorus demands. Accordingly, the presence of legume- and nodule-related AMF can be explained by the specific nutritional requirements of legumes or by host-specific interactions among legumes, root nodules, and AMF. In summary, we found that AMF communities vary between plant functional groups (legumes and nonlegumes), between plant species, and between parts of a root system (roots and root nodules).     

About the Existence of Circadian Activity in Cave Crayfish

Evidence of a circadian clock mechanism was found in the cave crayfish Procambarus cavernicola. Analysis of motor activity recorded in this species during 12 consecutive days in either free running (constant darkness, DD or constant light, LL) or entrainment conditions (12 h of light alternated with 12 h of darkness, 12 : 12 LD) showed a well recognized circadian rhythm. In this rhythm however, the absence of synchronization by periodical external signals was notorious. The comparison between the motor circadian rhythm in cave crayfish and epigeous crayfish Procambarus clarkii (these last studied during juvenile and adult stages), evidenced strong similitude between the motor circadian rhythm of cave crayfish and juvenile epigeous crayfish.     

Regulation of legume nodulation by acidic growth conditions

Legumes represent some of the most important crop species worldwide. They are able to form novel root organs known as nodules, within which biological nitrogen fixation is facilitated through a symbiotic interaction with soil-dwelling bacteria called rhizobia. This provides legumes with a distinct advantage over other plant species, as nitrogen is a key factor for growth and development. Nodule formation is tightly regulated by the plant and can be inhibited by a number of external factors, such as soil pH. This is of significant agricultural and economic importance as much of global legume crops are grown on low pH soils. Despite this, the precise mechanism by which low pH conditions inhibits nodule development remains poorly characterized.     

Legume nodulation: The host controls the party

Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic relationship that legume plants establish with nitrogen‐fixing rhizobia bacteria is central to their advantage. This plant–microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.     

氮肥添加对青藏高原高寒草甸6个群落优势种生态化学计量学特征的影响

以青藏高原高寒草甸为研究对象, 通过人工氮肥添加试验, 研究6个群落优势种在不同施氮(N)水平下叶片碳(C)、N、磷(P)元素含量的变化以及生态化学计量学特征。结果表明: 自然条件下, 6个物种叶片N、P质量浓度存在显著的差异, 表现为: 黄花棘豆(Oxytropis ochrocephala)最高, 为24.5和2.51 g·kg^-1, 其叶片N含量低于而P含量高于我国其他草地的豆科植物; 其余5个物种叶片N、P质量浓度分别为11.5-18.1和1.49-1.72 g·kg^-1, 嵩草(Kobresia myosuroides)叶片N含量最低, 垂穗披碱草(Elymus nutans)叶片P含量最低, 与我国其他区域的研究结果相比, 其叶片N和P含量均低于我国其他草地非豆科植物。随氮素添加量的增大, 6种群落优势种叶片的C和P含量保持不变; 其他5种植物叶片N含量显著增加, 黄花棘豆叶片N含量保持不变。未添加氮肥时, 6种植物叶片N:P为7.3-11.2, 说明该区植物生长更多地受N限制。随N添加量的增加, 除黄花棘豆外, 其他5种植物叶片N:P大于16, 表现为植物生长受P限制。综合研究表明, 青藏草原高寒草甸植物叶片N含量较低, 植物受N影响显著, 但不同物种对N的添加反应不同, 豆科植物黄花棘豆叶片对N添加不敏感, 其他5个物种叶片全N含量随着N添加量的升高而增加, 该研究结果可为高寒草甸科学施肥提供理论依据。     

A molecular link between autophagy and circadian rhythm in plants

Extremely high or low autophagy levels disrupt plant survival under nutrient starvation. Recently, autophagy has been reported to display rhythms in animals. However, the mechanism of circadian regulation of autophagy is still unclear. Here, we observed that autophagy has a robust rhythm and that various autophagy-related genes (ATGs) are rhythmically expressed in Arabidopsis. Chromatin immunoprecipitation (ChIP) and dual-luciferase (LUC) analyses showed that the core oscillator gene TIMING OF CAB EXPRESSION 1 (TOC1) directly binds to the promoters of ATG (ATG1a, ATG2, and ATG8d) and negatively regulates autophagy activities under nutritional stress. Furthermore, autophagy defects might affect endogenous rhythms by reducing the rhythm amplitude of TOC1 and shortening the rhythm period of CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). Autophagy is essential for the circadian clock pattern in seedling development and plant sensitivity to nutritional deficiencies. Taken together, our studies reveal a plant strategy in which the TOC1-ATG axis involved in autophagy-rhythm crosstalk to fine-tune the intensity of autophagy.     

The LATD gene of Medicago truncatula is required for both nodule and root development

The evolutionary origins of legume root nodules are largely unknown. We have identified a gene, LATD, of the model legume Medicago truncatula, that is required for both nodule and root development, suggesting that these two developmental processes may share a common evolutionary origin. The latd mutant plants initiate nodule formation but do not complete it, resulting in immature, non-nitrogen-fixing nodules. Similarly, lateral roots initiate, but remain short stumps. The primary root, which initially appears to be wild type, gradually ceases growth and forms an abnormal tip that resembles that of the mutant lateral roots. Infection by the rhizobial partner, Sinorhizobium meliloti, can occur, although infection is rarely completed. Once inside latd mutant nodules, S. meliloti fails to express rhizobial genes associated with the developmental transition from free-living bacterium to endosymbiont, such as bacA and nex38. The infecting rhizobia also fail to express nifH and fix nitrogen. Thus, both plant and bacterial development are blocked in latd mutant roots. Based on the latd mutant phenotype, we propose that the wild-type function of the LATD gene is to maintain root meristems. The strong requirement of both nodules and lateral roots for wild-type LATD gene function supports lateral roots as a possible evolutionary origin for legume nodules.     

How does a legume nodule work?

Nitrogen fixation in legume root nodules requires biochemical cooperation between the plant and Rhizobium cells. Bacteroids contribute the N₂-fixing system and haem for leghaemoglobin, but apart from the production of the globin moiety of leghaemoglobin and the assimilation and export of the NH₃ produced, little is known about the contributions of the plant. It now appears that the plant cell may regulate the type and/or quantity of carbon compounds supplied to the Rhizobium bacteroids.     

The diversity of actinorhizal symbiosis

Filamentous aerobic soil actinobacteria of the genus Frankia can induce the formation of nitrogen-fixing nodules on the roots of a diverse group of plants from eight dicotyledonous families, collectively called actinorhizal plants. Within nodules, Frankia can fix nitrogen while being hosted inside plant cells. Like in legume/rhizobia symbioses, bacteria can enter the plant root either intracellularly through an infection thread formed in a curled root hair, or intercellularly without root hair involvement, and the entry mechanism is determined by the host plant species. Nodule primordium formation is induced in the root pericycle as for lateral root primordia. Mature actinorhizal nodules are coralloid structures consisting of multiple lobes, each of which represents a modified lateral root without a root cap, a superficial periderm and with infected cells in the expanded cortex. In this review, an overview of nodule induction mechanisms and nodule structure is presented including comparisons with the corresponding mechanisms in legume symbioses.