Stable symbiotic nitrogen fixation under water-deficit field conditions by a stress-tolerant alfalfa microsymbiont and its complete genome sequence (original) (raw)
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Proceedings of the National Academy of Sciences, 2008
The nitrogen-fixing symbiosis between rhizobia and legume plants is a model of coevolved nutritional complementation. The plants reduce atmospheric CO 2 by photosynthesis and provide carbon compounds to symbiotically associated bacteria; the rhizobia use these compounds to reduce (fix) atmospheric N 2 to ammonia, a form of nitrogen the plants can use. A key feature of symbiotic N 2 fixation is that N2 fixation is uncoupled from bacterial nitrogen stress metabolism so that the rhizobia generate ''excess'' ammonia and release this ammonia to the plant. In the symbiosis between Sinorhizobium meliloti and alfalfa, mutations in GlnD, the major bacterial nitrogen stress response sensor protein, led to a symbiosis in which nitrogen was fixed (Fix ؉ ) but was not effective (Eff ؊ ) in substantially increasing plant growth. Fixed 15 N2 was transported to the shoots, but most fixed 15 N was not present in the plant after 24 h. Analysis of free-living S. meliloti strains with mutations in genes related to nitrogen stress response regulation (glnD, glnB, ntrC, and ntrA) showed that catabolism of various nitrogen-containing compounds depended on the NtrC and GlnD components of the nitrogen stress response cascade. However, only mutants of GlnD with an amino terminal deletion had the unusual Fix ؉ Eff ؊ symbiotic phenotype, and the data suggest that these glnD mutants export fixed nitrogen in a form that the plants cannot use. These results indicate that bacterial nitrogen stress regulation is important to symbiotic productivity and suggest that GlnD may act in a novel way to influence symbiotic behavior.
mSystems, 2020
Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii . Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial fo...
Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation
Nature, 2009
nitrogenase, where nitrogen fixation occurs 1,2 . NifV, which encodes homocitrate synthase (HCS) 3 , has been identified from various diazotrophs, but is not present in most of rhizobium species that exert efficient nitrogen fixation only in symbiotic association with legumes. Here we show that the FEN1 gene of a model legume, Lotus japonicus, overcomes the lack of NifV in rhizobia for symbiotic nitrogen fixation. A Fixplant mutant, fen1, forms morphologically normal but ineffective nodules 4,5 . The causal gene, FEN1, was shown to encode HCS by its ability to
Molecular Plant-Microbe Interactions, 2012
To contribute nitrogen for plant growth and establish an effective symbiosis with alfalfa, Sinorhizobium meliloti Rm1021 needs normal operation of the GlnD protein, a bifunctional uridylyltransferase/uridylyl-cleavage enzyme that measures cellular nitrogen status and initiates a nitrogen stress response (NSR). However, the only two known targets of GlnD modification in Rm1021, the PII proteins GlnB and GlnK, are not necessary for effectiveness. We introduced a Tyr→Phe variant of GlnB, which cannot be uridylylated, into a glnBglnK background to approximate the expected state in a glnD-sm2 mutant, and this strain was effective. These results suggested that unmodified PII does not inhibit effectiveness. We also generated a glnBglnK-glnD triple mutant and used this and other mutants to dissect the role of these proteins in regulating the free-living NSR and nitrogen metabolism in symbiosis. The glnD-sm2 mutation was dominant to the glnBglnK mutations in symbiosis but recessive in some f...
Genomes of the Symbiotic Nitrogen-Fixing Bacteria of Legumes
PLANT PHYSIOLOGY, 2007
Over the last several decades, there have been a large number of studies done on the genetics, biochemistry, physiology, ecology, and agronomics of the bacteria forming nitrogen-fixing symbioses with legumes. These bacteria, collectively referred to as the rhizobia, are taxonomically and physiologically diverse members of the a and b subclasses of the Proteobacteria, and mostly comprise members of the genera Rhizobium, Bradyrhizobium, Mesorhizobium, Sinorhizobium, and Azorhizobium (Fig. 1). Most studies have focused on mutational and biochemical analyses to define bacterial genes involved in root-nodule formation, symbiotic specificity, nitrogen fixation, and plant-microbe signal exchange. More recently, however, several genomic approaches have been used to define and understand the involvement of whole bacterial genomes in the symbiotic process. Genomic analyses of the model symbiotic bacterial species Sinorhizobium meliloti, Rhizobium leguminosarum, and Bradyrhizobium japonicum have revealed a few surprises concerning genome evolution and structure, how plant and microbes communicate, and physiological diversity among the microsymbionts of legumes. In this review we discuss what is currently known about the genomes of several rhizobia and how genome-enabled studies have provided insights into the symbiotic interaction of the rhizobia and their respective host legumes.
2018
Understanding the concept of symbiosis in a more localized natural selective way and optimizing for the yielding advantages of confined geography is the prime objective of the study. Precisely the aim is to isolate and identify crop specific Rhizobium strains for Glycine max using physical, biochemical and in silico techniques from Bhadrachalam forest lands. Randomly collected soil samples from 45 different locations across Bhadrachalam forest were sown with soybean in triplets. The basic parameters like Nitrogen, Phosphorous, Potassium (NPK) and levels of micronutrients for all the soil samples were identified to be similar. Out of 45 samples in triplets, top five growth supporting soils were taken for further investigation. Organisms from the root nodules of these five plants were screened and pure cultures were maintained. Log phase cultures in broth form were inoculated on the seeds sown in sterile soils with respective controls. Tremendous improvement in the growth parameters were observed in results when compared with controls. The polyphasic analysis discovered that the contributing organisms were Bradyrhizobium japonicum, Bradyrhizobium paxllaeri, Bradyrhizobium canariense, Sinorhizobium xinjiangense, Bradyrhizobium betae sp. Pure forms of these Rhizobial species have shown elevated rate of plant growth in in vitro fallowed by field experiments in low vegetative agriculture soils of the same geography. Out of these five species the Bradyrhizobium japonicum, which was the best plant growth supporting for Glycine max has been studies further to explore the Nif genes responsible for plant growth and Nitrogen fixation. The in-silico analysis of Nif A protein revealed the underlying precursors of indole acetic acid (IAA) production and nitrogenase activity. This novel method of soil selection may be adopted for easy identification of Rhizobial species, specific for not only for Glycine max but also for various other legume crops from respective geographies.
Molecular Plant-Microbe Interactions, 2005
To study the role of the decarboxylating leg of the bacterial TCA cycle in symbiotic nitrogen fixation, we used DNA shuffling and localized random polymerase chain reaction mutagenesis to construct a series of temperature-sensitive and impaired-function mutants in the Sinorhizobium meliloti Rm104A14 citrate synthase (gltA) gene. Reducing citrate synthase (CS) activity by mutation led to a corresponding decrease in the free-living growth rate; however, alfalfa plants formed fully effective nodules when infected with mutants having CS activities as low as 7% of the wild-type strain. Mutants with approximately 3% of normal CS activity formed nodules with lower nitrogenase activity and a mutant with less than 0.5% of normal CS activity formed Fix- nodules. Two temperature-sensitive (ts) mutants grew at a permissive temperature (25°C) with 3% of wild-type CS activities but were unable to grow on minimal medium at 30°C. Alfalfa plants that were inoculated with the ts mutants and grown wit...
A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii
Molecular plant-microbe interactions : MPMI, 2017
Rhizobia colonize legumes and reduce N2 to NH3 in root nodules. The current model is that symbiotic rhizobia bacteroids avoid assimilating this NH3. Instead, host legume cells form glutamine from NH3, and the nitrogen is returned to the bacteroid as dicarboxylates, peptides, and amino acids. In soybean cells surrounding bacteroids, glutamine also is converted to ureides. One problem for soybean cultivation is inefficiency in symbiotic N2 fixation, the biochemical basis of which is unknown. Here, the proteomes of bacteroids of Bradyrhizobium elkanii USDA76 isolated from N2 fixation-efficient Peking and inefficient Williams 82 soybean nodules were analyzed by mass spectrometry. Nearly half of the encoded bacterial proteins were quantified. Efficient bacteroids produced greater amounts of enzymes to form Nod factors and had increased amounts of signaling proteins, transporters, and enzymes needed to generate ATP to power nitrogenase and to acquire resources. Parallel investigation of n...
Current Progress in Nitrogen Fixing Plants and Microbiome Research
Plants
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to ...