Proteomics reveals differential expression of proteins related to a variety of metabolic pathways by genistein-induced Bradyrhizobium japonicum strains

The rhizobia-legume symbiosis requires a coordinated molecular interaction between the symbionts, initiated by seed and root exudation of several compounds, mainly flavonoids, that trigger the expression of nodulation genes in the bacteria. Since the role of flavonoids seems to be broader than the induction of nodulation genes, we aimed at characterizing genistein-induced proteins of Bradyrhizobium japonicum CPAC 15 (= SEMIA 5079), used in commercial soybean inoculants in Brazil, and of two genetically related strains grown in vitro. Whole-cell proteins were extracted both from induced (1 μM genistein) and from non-induced cultures of the three strains, and separated by two-dimensional electrophoresis. Spot profiles were compared between the two conditions and selected spots were excised and identified by mass spectrometry. Forty-seven proteins were significantly induced by genistein, including several hypothetical proteins, the cytoplasmic flagellar component FliG, periplasmic ABC transporters, a protein related to biosynthesis of exopolysaccharides (ExoN), and proteins involved in redox-state maintenance. Noteworthy was the induction of the PhyR-σ^EcfG regulon, recently demonstrated to be involved in the symbiotic efficiency of, and general stress response in B. japonicum. Our results confirm that the role of flavonoids, such as genistein, can go far beyond the expression of nodulation-related proteins in B. japonicum.     

Strain-Specific Inhibition of nod Gene Induction in Bradyrhizobium japonicum by Flavonoid Compounds

A broad-host-range plasmid, pEA2-21, containing a Bradyrhizobium japonicum nodABC'-'lacZ translational fusion was used to identify strain-specific inhibitors of the genes required for soybean nodulation, the common nod genes. The responses of type strains of B. japonicum serogroups USDA 110, USDA 123, USDA 127, USDA 129, USDA 122, and USDA 138 to nod gene inhibitors were compared. Few compounds inhibited nod gene expression in B. japonicum USDA 110. In contrast, nod gene expression in strains belonging to several other serogroups was inhibited by most of the flavonoids tested. However, the application of two of these strain-specific compounds, chrysin and naringenin, had little effect on the pattern of competition between indigenous and inoculum strains of B. japonicum in greenhouse and field trials. Preliminary studies with radiolabeled chrysin and naringenin suggest that the different responses to nod gene inhibitors may be partly due to the degree to which plant flavonoids can be metabolized by each strain.     

Pre-incubation of Bradyrhizobium japonicum with jasmonates accelerates nodulation and nitrogen fixation in soybean (Glycine max) at optimal and suboptimal root zone temperatures

Jasmonic acid (JA) and methyl jasmonate, collectively known as jasmonates, are naturally occurring in plants; they are important signal molecules involved in induced disease resistance and mediate many physiological activities in plants. We studied the effect of JA and its methyl ester, methyl jasmonate (MeJA), on the induction of nod genes in Bradyrhizobium japonicum GG4 (USDA3) carrying a plasmid with a translational fusion between B. japonicum nodY and lacZ of Escherichia coli, and the expression activity was measured by β-galactosidase activity. Both JA and MeJA strongly induced the expression of nod genes. They have little or no deleterious effects on the growth of B. japonicum cells, while genistein (Gen) showed inhibitory effects. We further studied the effect of JA- and MeJA-induced B. japonicum on soybean nodulation and nitrogen fixation under optimal (25°C) and suboptimal (17°C) root zone temperature (RZT) conditions. B. japonicum cells were grown in liquid yeast extract mannitol media and induced with a range of Gen, JA, and MeJA concentrations, including a treatment control with no inducer added. Soybean seedlings were grown at 25 or 17°C RZT with a constant air temperature (25°C) and inoculated, at the vegetative cotyledonary stage, with various B. japonicum induction treatments. Addition of Gen or jasmonates to B. japonicum, prior to inoculation, enhanced nodulation, nitrogen fixation, and plant growth at suboptimal RZT conditions. A higher concentration of Gen was inhibitory at 25°C, while this same concentration was stimulatory at 17°C. Interestingly, pre-incubation of B. japonicum with JA and MeJA enhanced soybean nodulation and nitrogen fixation under both optimal and suboptimal RZTs. We show that jasmonates are thus a new class of signaling molecules in the B. japonicum-soybean symbiosis and that pre-induction of B. japonicum with jasmonates can be used to enhance soybean nodulation, nitrogen fixation, and early plant growth.     

Regulation of nod gene expression in Bradyrhizobium japonicum

Summary The best inducers of nod:: lacZ translational fusions in Bradyrhizobium japonicum are isoflavones, primarily genistein and daidzein. Upstream of the nodABC genes in B. japonicum is a novel gene, nodY, which is coregulated with nodABC. Measurements of the activity of lacZ fusions to the nodD gene of B. japonicum show that this gene is inducible by soybean seed extract and selected flavonoid chemicals. The induction of the nodY ABC and nodD operons appears to require a functional nodD gene, indicating that the nodD gene product controls its own synthesis as well as other nod genes.     

Variability in yield and yield component responses to genistein pre-incubated Bradyrhizobium japonicum by soybean [Glycine max (L.) Merr] cultivars

The sub-tropical legume, soybean [Glycine max (L.) Merr.], has lower grain yields at low temperatures, mainly due to reduced nitrogen fixation. The isoflavone genistein has been identified as one of the major compounds in soybean seed and root extracts responsible for inducing the expression of the B. japonicum nod genes. A 2-year field study was conducted in 1997 and 1998 with 11 soybean cultivars recommended for Québec, and representing a range of yield potentials and maturity groups. The objective of this study was to assess the variability among soybean cultivar maturity groups in terms of response to genistein application under Canadian short season and cool-spring conditions. The experiments were organized in a randomized complete block design with three replications. The two genistein treatments included B. japonicum inoculant pre-incubated with 20 m genistein and B. japonicum inoculant only. The inoculants were applied into the furrow at the time of planting. The results of this study showed that genistein pre-incubated B. japonicum increased soybean grain yield and protein content over two years. In 1998, pod number per plant^–1 and seed number plant^–1 were also clearly increased. When 20 m genistein was applied in 1998, cultivars in the late maturity group had 28 and 70% more shoot and total protein content, respectively, than the early maturity groups with or without genistein, or the late maturity without genistein, in 1998. There was no interaction between genistein application and soybean cultivar in this study, indicating that both early and late maturing cultivars responded similarly to genistein pretreated inocula. Pre-incubation of B. japonicum with genistein can increase N₂ fixation potential in short season areas. Key words: Soybean, cultivars, genistein, yield, and yield components     

Root Isoflavonoid Response to Grafting between Wild-Type and Nodulation-Mutant Soybean Plants

It was previously reported that the hypernodulating soybean (Glycine max [L.] Merr.) mutants, derived from the cultivar Williams, had higher root concentration of isoflavonoid compounds (daidzein, genistein, and coumestrol) than did Williams at 9 to 12 days after inoculation with Bradyrhizobium japonicum. These compounds are known inducers of nod genes in B. japonicum and may be involved in subsequent nodule development. The current study involving reciprocal grafts between NOD1-3 (hypernodulating mutant) and Williams showed that root isoflavonoid concentration and content was more than twofold greater when the shoot genotype was NOD1-3. When grafted, NOD1-3 shoots also induced hypernodulation on roots of both Williams and NOD1-3, while Williams shoots induced normal nodulation on both root genotypes. This shoot control of hypernodulation may be causally related to differential root isoflavonoid levels, which are also controlled by the shoot. In contrast, the nonnodulating characteristic of the NN5 mutant was strictly root controlled, based on reciprocal grafts. Delayed inoculation (7 days after planting) resulted in greater nodule numbers on both NOD1-3 and Williams, compared with a seed inoculation treatment. The nodulation pattern of grafted plants was independent of whether the shoot portion was derived from inoculated seed or uninoculated seed, when grafted at day 7 onto seedling roots derived from inoculated seed. This observation, coupled with the fact that no difference existed in nodule number of NOD1-3 and Williams until after 9 days from seed inoculation, indicated that if isoflavonoids play a role in differential nodulation of the hypernodulating mutant and the wild type, the effect is on advanced stages of nodule ontogeny, possibly related to autoregulation, rather than on initial infection stages.     

Preincubation of B. japonicum cells with genistein reduces the inhibitory effects of mineral nitrogen on soybean nodulation and nitrogen fixation under field conditions

Genistein is the major root produced isoflavonoid inducer of nod genes in the symbiosis between B. japonicum and soybean plants. Reduction in the isoflavonoid content of the host plants has recently been suggested as a possible explanation for the inhibition of mineral nitrogen (N) on the establishment of the symbiosis. In order to determine whether genistein addition could overcome this inhibition, we incubated B. japonicum cells (strain 532C) with genistein. Mineral N (in the form of NH₄NO₃) was applied at 0, 20 and 100 kg ha^-1. The experiments were conducted on both a sandy-loam soil and a clay-loam soil. Preincubation of B. japonicum cells with genistein increased soybean nodule number and nodule weight, especially in the low-N-containing sandy-loam soil and the low N fertilizer treatment. Plant growth and yield were less affected by genistein preincubation treatments than nitrogen assimilation. Total plant nitrogen content was increased by the two genistein preincubation treatments at the early flowering stage. At maturity, shoot and total plant nitrogen contents were increased by the 40 μM genistein preincubation treatment at the sandy-loam soil site. Total nitrogen contents were increased by the 20 μM genistein preincubation treatment only at the 0 and 20 kg ha^-1 nitrate levels in clay-loam soil. Forty μM genistein preincubation treatment increased soybean yield on the sandy-loam soil. There was no difference among treatments for 100-seed weight. The results suggest that preincubation of B. japonicum cells with genistein could improve soybean nodulation and nitrogen fixation, and at least partially overcome the inhibition of mineral nitrogen on soybean nodulation and nitrogen fixation. This revised version was published online in June 2006 with corrections to the Cover Date.     

Effect of legume seed exudates on the formation of Rhizobium-legume symbiosis

The effect of exudates from germinating lupine and soybean seeds on the development of legumerhizobia symbiosis in the same plants was studied. Treatment with the exudates increased the nodulation activity of Bradyrhizobium sp. (Lupinus) and slowed down the formation of nodules by Bradyrhizobium japonicum 634b. The number of nodules produced by B. japonicum 631 on soybean roots increased when the strain was treated with soybean exudate at a lower concentration. The exudates differently affected nodulation on the primary and secondary roots of the host plant. The formation of symbiosis by B. japonicum 631 incubated with legume seed exudates increased the weight of the green parts of plants at the bud stage.     

Inoculation of soybean (Glycine max. (L.) Merr.) with genistein-preincubated Bradyrhizobium japonicum or genistein directly applied into soil increases soybean protein and dry matter yield under short season conditions

In short-season soybean production areas, low soil temperature is the major factor limiting plant growth and yield. The decreases in soybean yield at low temperatures are mainly due to nitrogen limitation. Genistein, the most effective plant-to-bacterium signal in the soybean (Glycine max (L.) Merr.) nitrogen fixation symbiosis, was used to pretreat Bradyrhizobium japonicum. We have previously reported that this increased soybean nodulation and nitrogen fixation in growth chamber studies. Two field experiments were conducted on two adjacent sites in 1994 to determine whether the incubation of B. japonicum with genistein, prior to application as an inoculant, or genistein, without B. japonicum, applied onto seeds in the furrow at the time of planting, increased soybean grain yield and protein yield in short season areas. The results of these experiments indicated that genistein-preincubated bradyrhizobia increased the grain yield and protein yield of AC Bravor, the later maturing of the two cultivars tested. Genistein without B. japonicum, applied onto seeds in the furrow at the time of planting also increased both grain and protein yield by stimulation of native soil B. japonicum. Interactions existed between genistein application and soybean cultivars, and indicated that the cultivar with the greatest yield potential responded more to genistein addition.     

Conservation of a Symbiotic DNA Region in Soybean Root Nodule Bacteria

Bradyrhizobium japonicum USDA 3I1b110 contains a DNA region in which symbiotic genes and many repeated sequences are closely linked. Hybridization analysis revealed that this region was highly conserved in some B. japonicum strains (USDA 24, USDA 122, USDA 123, ATCC 10324, 61A24) but not in others (USDA 76, 61A76, 61A101). The genomic presence of multiple copies of one of the repeated sequences (RSα) appeared to be specifically characteristic for soybean root nodule bacteria, including the fast-growing Rhizobium fredii, which carries most of these RSα copies on the symbiotic plasmid.     

Improving Soybean (Glycine max L.) N2 Fixation under Stress

Soybean is a major leguminous plant that has the ability to establish a symbiotic association with the N-fixing bacteria, Bradyrhizobium japonicum. Soils are usually subjected to stress including salinity, drought, acidity, and suboptimal root zone temperature, adversely affecting the symbiotic process between soybean and the bacteria. One of the important processes affecting the performance of soybean under stress is the inhibited exchange of symbiosis-related signaling molecules, specifically genistein, between the host legume and B. japonicum during the initiation of symbiosis. Interestingly, inoculation of B. japonicum with the signal molecule genistein can partially or completely alleviate the stress. Understanding the techniques and the precise molecular pathways, which may be influenced by the signaling molecules during the stress, can be useful to determine parameters that enhance the plant’s ability to cope with stress. For example, the use of proteomic techniques to identify proteins expressed under stress can help characterize those proteins and their involvement in stress. Biotechnological-genetic techniques, either breeding or transformation, are also among the effective methods of improving soybean’s ability to fix N₂ under stress. This can be achieved by identifying the genes, which may be expressed under stress in tolerant bacterial and plant species, and inserting them into the non-tolerant species. This article highlights some important advances in soybean N₂ fixation under different stress conditions, and reviews some of the techniques used to improve the ability of plants and bacteria to efficiently fix N₂ under stress.     

Release of Flavonoids by the Soybean Cultivars McCall and Peking and Their Perception as Signals by the Nitrogen-Fixing Symbiont Sinorhizobium fredii

Sinorhizobium fredii strain USDA191 forms N-fixing nodules on the soybean (Glycine max L. Merr.) cultivars (cvs) McCall and Peking, but S. fredii strain USDA257 nodulates only cv Peking. We wondered whether specificity in this system is conditioned by the release of unique flavonoid signals from one of the cultivars or by differential perception of signals by the strains. We isolated flavonoids and used nodC and nolX, which are nod-box-dependent and -independent nod genes, respectively, to determine how signals activate genes in the microsymbionts. Seeds of cv McCall and cv Peking contain the isoflavones daidzein, genistein, and glycitein, as well as their glucosyl and malonylglucosyl glycosides. Roots exude picomolar concentrations of daidzein, genistein, glycitein, and coumestrol. Amounts are generally higher in cv Peking than in cv McCall, and the presence of rhizobia markedly influences the level of specific signals. Nanomolar concentrations of daidzein, genistein, and coumestrol induce expression of nodC and nolX in strain USDA257, but the relative nolX-inducing activities of these signals differ in strain USDA191. Glycitein and the conjugates are inactive. Strain USDA257 deglycosylates daidzin and genistin into daidzein and genistein, respectively, thereby converting inactive precursors into active inducers. Although neither soybean cultivar contains unique nod-gene-inducing flavonoids, strain- and cultivar-specific interactions are characterized by distinct patterns of signal release and response.     

Bradyrhizobium elkanii Induces Outer Cortical Root Swelling in Soybean

When soybean roots were inoculated with Bradyrhizobium elkaniiUSDA76, USDA94 or USDA31, a localized swelling of the root outercortical cells was observed within 10 days after inoculation.This phenotype was designated outer cortical swelling (OCS).OCS was not observed in roots inoculated with B.japonicum USDA110or USDA122. Therefore, the OCS response appears to be specificfor B. elkanii. To determine the involvement of the nodulationgenes in OCS formation, we constructed a nod^- mutant, strainUSDA94     

Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential

An assessment was made of the evolutionary relationships of soybean nodulating bacteria associated with legumes native to eastern Canada to identify potential new sources of soybean inoculant strains.Short season soybeans were used to selectively trap bacteria from root zone soils of four native legume species. Screening of more than 800 bacterial isolates from soybean root nodules by analysis of recA gene sequences followed by analyses of selected genotypes using six core and two symbiosis (nodC and nifH) gene sequences permitted identification of diverse taxa that included eight novel and four named Bradyrhizobium species as well as lineages attributed to the genera Afipia and Tardiphaga.Plant tests showed that symbionts related to four named species as well as a novel Bradyrhizobium lineage were highly efficient with regard to nitrogen fixation on soybeans relative to an inoculant strain.A new symbiovar (sv. septentrionalis) is proposed based on a group of four novel Bradyrhizobium spp. that possess distinctive nodC and nifH gene sequences and symbiotic characteristics.Evidence is provided for horizontal transfer of sv. septentrionalis symbiosis genes between novel Bradyrhizobium spp., a process that rendered recipient bacteria ineffective on soybeans.Diverse lineages of non-symbiotic and symbiotic Bradyrhizobium spp. co-occured within monophyletic clusters in a phylogenetic tree of concatenated core genes, suggesting that loss and/or gain of symbiosis genes has occurred in the evolutionary history of the bacterial genus.Our data suggest that symbiont populations associated with legumes native to eastern Canada harbour elite strains of Bradyrhizobium for soybean inoculation.     

Soybean lectin as a component of a composite biopreparation involving Bradyrhizobium japonicum 634b

The effects of the composite biopreparation Bralec (involving the soybean-specific root nodule bacterium Bradyrhizobium japonicum strain 634b and soybean lectin at concentrations of 500, 50, and 5 μg/ml as major components) on the development and functional activity of soybean-rhizobium symbiosis (development phases of one leaf, four true leaves, and budding) was studied. It was demonstrated that pretreatment of seed with this preparation stimulated the development of both the macro-and microsymbionts. The experimental plants displayed an active accumulation of biomass (4–42% higher compared with the variant with inoculation), development of root nodules (the number increased by 11–110% and the weight by 27–157%), and elevated nitrogen-fixing activity (by 45–204%). The soybean yield increased by 8–10% upon treatment with Bralec 500 and Bralec 5 as compared with the traditional seed bacterization with root nodule bacteria.     

Morphological and physiological response of soybean treated with the microsymbiont Bradyrhizobium japonicum pre-incubated with genistein

Genistein, a major root-secreted isoflavone of soybean (Glycine max (L.) Merr), is critical for the legume-Bradyrhizobium symbiosis as it induces several bacterial nod-gene systems. An experiment with soybean grown under salt stress was conducted to evaluate the effect of exogenous genistein addition to the Bradyrhizobium culture medium on subsequent nodulation, nitrogen fixation and selected plant physiological attributes. Five day-old plants (in pots) were inoculated with a liquid B. japonicum broth culture and irrigated with B&D solution containing either 0, 25, 50 and 100 mM NaCl. Four weeks after inoculation, maximum photochemical efficiency of PSII (Fv/Fm), photosynthetic rate, stomatal conductance, and transpiration rate were measured. Number of nodules per plant and apparent nitrogen fixation (as acetylene reduction activity) were determined. Salt stress decreased nodule number/plant and nitrogenase activity/plant and induced large changes of both photosynthetic parameters and antioxidant enzyme activity, compared to the control, genistein reversed the effect in each level of salinity tested. Moreover, pre-treatment of the microsymbiont with genistein enhanced maximum photochemical efficiency, photosynthetic rate, stomatal conductance and transpiration rate, while the enzymatic activities of catalase, superoxide dismutase and peroxidase in leaves and roots were not affected. It can be concluded that preincubation of the B. japonicum inoculant with genistein probably contributed towards growth in soybean via enhancement of nodulation and nitrogen fixation under both normal and salt stress conditions.     

Relationships of Bradyrhizobium strains nodulating three Algerian Genista species

The Mediterranean world is the cradle for the diversification of a large number of plant species, including legumes belonging to the Tribe Genisteae. Nodule bacteria from three species of Genista legumes indigenous to northwestern Africa (G. ferox, G. numidica, G. tricuspidata) were sampled across a 150 km region of Algeria in order to investigate symbiotic relationships. Partial 23S rRNA sequences from 107 isolates indicated that Bradyrhizobium was the predominant symbiont genus (96% of isolates), with the remainder belonging to Rhizobium or Mesorhizobium. A multilocus sequence analysis on 46 Bradyrhizobium strains using seven housekeeping (HK) genes showed that strains were differentiated into multiple clades with affinities to seven species: B. canariense (17 isolates), B. japonicum (2), B. ottawaense (2), B. cytisi/B. rifense (9), ‘B. valentinum’ (5), and B. algeriense (11). Extensive discordance between the HK gene phylogeny and a tree for four loci in the symbiosis island (SI) region implied that horizontal transfer of SI loci has been common. Cases of close symbiont relationship across pairs of legumes hosts were evident, with 33% of isolates having as their closest relative a strain sampled from a different Genista species. Nevertheless, tree permutation tests also showed that there was substantial host-related phylogenetic clustering. Thus, each of the three Genista hosts utilized a measurably different array of bacterial lineages.     

Diverse rhizobia associated with soybean grown in the subtropical and tropical regions of China

Aiming at investigating the species composition and the association between ribosomal/housekeeping genes and symbiotic genes of rhizobia nodulating with soybean grown in the subtropical and tropic regions of China, a total of 252 rhizobial strains isolated from five eco-regions was characterized. Four genomic groups, Bradyrhizobium japonicum complex (including B. liaoningense, B. japonicum and a B. japonicum related genomic species) and B. elkanii as the major groups, B. yuanmingense and Sinorhizobium fredii as the minor groups, were identified by the ribosomal/housekeeping gene analyses. The symbiotic gene phylogenies were coherent with those of the housekeeping genes in these four genomic groups, indicating that the symbiotic genes were mainly maintained by vertical transfer in the soybean rhizobia. In correspondence analysis, the Bradyrhizobium species were not significantly related to the eco-regions, possibly due to the similar climate and soil conditions in these regions.