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Legumes and rhizobia establish symbiosis in root nodules. To balance the gains and costs associated with the symbiosis, plants have developed two strategies for adapting to nitrogen availability in the soil: plants can regulate nodule number and/or stop the development or function of nodules. Although the former is accounted for by autoregulation of nodulation, a form of systemic long-range signaling, the latter strategy remains largely enigmatic. Here, we show that the Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) gene encoding a NIN-LIKE PROTEIN transcription factor acts as a key regulator in the nitrate-induced pleiotropic control of root nodule symbiosis. NRSYM1 accumulates in the nucleus in response to nitrate and directly regulates the production of CLE-RS2, a root-derived mobile peptide that acts as a negative regulator of nodule number. Our data provide the genetic basis for how plants respond to the nitrogen environment and control symbiosis to achieve proper plant growth.

Legumes control root nodule symbiosis (RNS) in response to environmental nitrogen availability. Despite the recent understanding of the molecular basis of external nitrate-mediated control of RNS, it remains mostly elusive how plants regulate physiological processes depending on internal nitrogen status. In addition, iron (Fe) acts as an essential element that enables symbiotic nitrogen fixation; however, the mechanism of Fe accumulation in nodules is poorly understood. Here, we focus on the transcriptome in response to internal nitrogen status during RNS in Lotus japonicus and identify that IRON MAN (IMA) peptide genes are expressed during symbiotic nitrogen fixation. We show that LjIMA1 and LjIMA2 expressed in the shoot and root play systemic and local roles in concentrating internal Fe to the nodule. Furthermore, IMA peptides have conserved roles in regulating nitrogen homeostasis by adjusting nitrogen-Fe balance in L. japonicus and Arabidopsis thaliana . These findings indicate that IMA-mediated Fe provision plays an essential role in regulating nitrogen-related physiological processes. The authors show IRON MAN peptides have an essential role in symbiotic nitrogen fixation during legume-rhizobium symbiosis. The peptides additionally function to regulate nitrogen homeostasis by controlling nitrogen-iron balance.

Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells. In model legumes such as Lotus japonicus and Medicago truncatula, rhizobia enter into roots through an intracellular invasion system that depends on the formation of a root-hair infection thread (IT). While IT-mediated intracellular rhizobia invasion is thought to be the most evolutionarily derived invasion system, some studies have indicated that a basal intercellular invasion system can replace it when some nodulation-related factors are genetically modified. In addition, intracellular rhizobia accommodation is suggested to have a similar mechanism as AMF accommodation. Nevertheless, our understanding of the underlying genetic mechanisms is incomplete. Here we identify a L. japonicus nodulation-deficient mutant, with a mutation in the LACK OF SYMBIONT ACCOMMODATION (LAN) gene, in which root-hair IT formation is strongly reduced, but intercellular rhizobial invasion eventually results in functional nodule formation. LjLAN encodes a protein that is homologous to Arabidopsis MEDIATOR 2/29/32 possibly acting as a subunit of a Mediator complex, a multiprotein complex required for gene transcription. We also show that LjLAN acts in parallel with a signaling pathway including LjCYCLOPS. In addition, the lan mutation drastically reduces the colonization levels of AMF. Taken together, our data provide a new factor that has a common role in symbiont accommodation process during root nodule and AM symbiosis.

Cell-to-cell communication, principally mediated by short- or long-range mobile signals, is involved in many plant developmental processes. In root nodule symbiosis, a mutual relationship between leguminous plants and nitrogen-fixing rhizobia, the mechanism for the autoregulation of nodulation (AON) plays a key role in preventing the production of an excess number of nodules. AON is based on long-distance cell-to-cell communication between roots and shoots. In Lotus japonicus , two CLAVATA3/ESR-related (CLE) peptides, encoded by CLE - ROOT SIGNAL 1 ( CLE - RS1 ) and - RS2 , act as putative root-derived signals that transmit signals inhibiting further nodule development through interaction with a shoot-acting receptor-like kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1). Here, an in silico search and subsequent expression analyses enabled us to identify two new L. japonicus CLE genes that are potentially involved in nodulation, designated as CLE - RS3 and LjCLE40 . Time-course expression patterns showed that CLE - RS1 / 2 / 3 and LjCLE40 expression is induced during nodulation with different activation patterns. Furthermore, constitutive expression of CLE - RS3 significantly suppressed nodule formation in a HAR1 -dependent manner. TOO MUCH LOVE, a root-acting regulator of AON, is also required for the CLE-RS3 action. These results suggest that CLE-RS3 is a new component of AON in L. japonicus that may act as a potential root-derived signal through interaction with HAR1. Because CLE - RS2 , CLE - RS3 and LjCLE40 are located in tandem in the genome and their expression is induced not only by rhizobial infection but also by nitrate, these genes may have duplicated from a common gene.

Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant–microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant–microbe interactions in the soil.

Legumes can survive in nitrogen-deficient environments by forming root-nodule symbioses with rhizobial bacteria; however, forming nodules consumes energy, and nodule numbers must thus be strictly controlled. Previous studies identified major negative regulators of nodulation in Lotus japonicus, including the small peptides CLAVATA3/ESR (CLE)-RELATED-ROOT SIGNAL1 (CLE-RS1), CLE-RS2, and CLE-RS3, and their putative major receptor HYPERNODULATION AND ABERRANT ROOT FORMATION1 (HAR1). CLE-RS2 is known to be expressed in rhizobia-inoculated roots, and is predicted to be post-translationally arabinosylated, a modification essential for its activity. Moreover, all three CLE-RSs suppress nodulation in a HAR1-dependent manner. Here, we identified PLENTY as a gene responsible for the previously isolated hypernodulation mutant plenty. PLENTY encoded a hydroxyproline O-arabinosyltransferase orthologous to ROOT DETERMINED NODULATION1 in Medicago truncatula. PLENTY was localized to the Golgi, and an in vitro analysis of the recombinant protein demonstrated its arabinosylation activity, indicating that CLE-RS1/2/3 may be substrates for PLENTY. The constitutive expression experiments showed that CLE-RS3 was the major candidate substrate for PLENTY, suggesting the substrate preference of PLENTY for individual CLE-RS peptides. Furthermore, a genetic analysis of the plenty har1 double mutant indicated the existence of another PLENTY-dependent and HAR1-independent pathway negatively regulating nodulation.

Soybeans fix atmospheric N 2 through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N 2 O)-reducing (N 2 OR) activities, can be leveraged to reduce N 2 O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N 2 OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N 2 OR activity predominantly infect. Our optimize symbiotic system substantially reduces N 2 O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices. During plant cultivation, denitrification process can release greenhouse gas nitrous oxide (N 2 O) to atmosphere. Here, the authors develop a soybean–bradyrhizobial symbiosis system with enhanced capacity to reduce N 2 O emissions using the incompatibility between two soybean R genes and their effector present in bradyrhizobia.

[This corrects the article DOI: 10.1371/journal.pgen.1007865.].

Soybeans fix atmospheric N through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N O)-reducing (N OR) activities, can be leveraged to reduce N O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N OR activity predominantly infect. Our optimize symbiotic system substantially reduces N O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices.

Many adult tissues are composed of differentiated cells and stem cells, each working in a coordinated manner to maintain tissue homeostasis during physiological cell turnover. Old differentiated cells are believed to typically die by apoptosis. Here, we discovered a previously uncharacterized, new phenomenon, which we name erebosis based on the ancient Greek word erebos (“complete darkness”), in the gut enterocytes of adult Drosophila . Cells that undergo erebosis lose cytoskeleton, cell adhesion, organelles and fluorescent proteins, but accumulate Angiotensin-converting enzyme (Ance). Their nuclei become flat and occasionally difficult to detect. Erebotic cells do not have characteristic features of apoptosis, necrosis, or autophagic cell death. Inhibition of apoptosis prevents neither the gut cell turnover nor erebosis. We hypothesize that erebosis is a cell death mechanism for the enterocyte flux to mediate tissue homeostasis in the gut.