Enhanced competitiveness of a Bradyrhizobium japonicum mutant strain improved for nodulation and nitrogen fixation

Bradyrhizobium japonicum strain TA-11NOD⁺, with altered indole biosynthesis, exhibited enhanced nodulation and nitrogen fixation on soybean in previous greenhouse studies. In this study, field experiments were conducted at Upper Marlboro, Maryland, in the summers of 1988 and 1993. In 1988, the site used was essentially free of soybean-nodulating bacteria and seed yield in plots inoculated with either I-110ARS or TA-11NOD⁺ was significantly higher by 12 or 20%, respectively, than that of the uninoculated controls. The 1993 site had an indigenous soil population (about 10⁴ cells g^-1) of symbiotically ineffective soybean-nodulating bacteria. Nevertheless, six-week-old Morgan soybean plants inoculated with strain TA-11NOD⁺ had 44% more nodules and exhibited 50% more nitrogen fixation by acetylene reduction when compared with plants that received the parental strain I-110ARS. Nodule occupancy, as determined using genetic markers for rifampicin and streptomycin resistance, was significantly higher for strain TA-11NOD⁺ than for strain I-110ARS. Overall, for the two years and the two soybean genotypes, the yield obtained with TA-11NOD⁺ was 6% higher than that obtained with I-110ARS. Competition experiments were conducted in the greenhouse and strain TA-11NOD⁺ was significantly more competitive than strain I-110ARS in competition with strains USDA 6 or USDA 438.     

Genetic allelism and linkage tests of a soybean gene,Rfg1, controlling nodulation with Rhizobium fredii strain USDA 205

A soybean gene, Rfg1, controlling nodulation with strain USDA 205, the type strain for the fast-growing species Rhizobium fredii, was tested for allelism with the Rj4 gene. The Rj4 gene conditions ineffective nodulation primarily with certain strains of the slow-growing soybean microsymbiont, Bradyrhizobium elkanii. The F2 seeds of the cross of the cultivars Peking, carrying the alleles rfg1, Rj4, i (controlling inhibition of seed coat color) and W1 (controlling flower color), and Kent, carrying the alleles Rfg1, rj4, i-i and w1, were evaluated for nodulation response with strain USDA 205 by planting surface disinfested seeds in sterilized vermiculite in growth trays and inoculating with a stationary phase broth culture of strain USDA 205 at planting. Plants were classified for nodulation response visually after four weeks growth and transplanted to the field for F3 seed production. Flower color, purple (W1) vs white (w1), was determined in the field. The allele present at the i locus was determined by classification of F3 seed coat color. The F3 seeds were planted in growth trays and inoculated with strain USDA 61 of Bradyrhizobium elkanii to determine the genotype for the Rj4 locus. The Rfg1 and Rj4 genes were determined to be located at separate loci. Chi-square analysis for linkage indicated that Rfg1 segregated independently of the Rj4, I and W1 loci.     

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.     

Effects of inoculation with plant growth promoting rhizobacteria (PGPRs) andSinorhizobium fredii on biological nitrogen fixation, nodulation and growth ofGlycine max cv. Osumi

We investigated the effects of three plant growth promoting rhizobacteria (PGPR), on Biological Nitrogen Fixation (BNF), nodulation and growth promotion by soybean (Glycine max) var. Osumi plants. The strains, Aur 6, Aur 9 and Cell 4, belong toPsedomonas fluorescens, Chryseobacterium balustinum andSerratia fonticola, respectively. Inoculation modes for the PGPRs andSinorhizobium fredii (carried out through irrigation), were examined. In the first mode, PGPRs andS. fredii were co-inoculated. In the second mode, we first inoculatedS. fredii and after the PGPRs, which were added 5 or 10 days later (each inoculation being an independent treatment). In the third mode, the PGPRs were inoculated first, and theS. fredii was inoculated 5 days later. We also included treatments inoculated with only the PGPRs (one PGPR per treatment) and only withS. fredii. Plants were maintained in a greenhouse under controlled environmental conditions, and were sampled 3 months after sowing. The results obtained showed the effects of the inoculation sequence. The most significant effects on growth parameters (stem plus leaf weight and fresh root weight) were found when inoculations with PGPR andS. fredii were at different times or when we inoculated only with PGPR and the plants were watered with nitrogen. Co-inoculation had no positive effects on any parameter, probably due to competition between the PGPR andS. fredii. Our results indicate that the inoculation modes with PGPR and rhizobia play a very important role in the effects produced. Thus, although plant growth promoting rhizobacteria may interact synergistically with root-nodulating rhizobia, plant growth promoting rhizobacteria selected for one crop should be assessed for potentially hazardous effects on other crops before being used as inoculants.     

Competitiveness of a nif− Bradyrhizobium japonicum mutant against the wild-type strain

Abstract By mixed inoculation experiments, the competitive ability of a nifD ::Tn 5 mutant of Bradyrhizobium japonicum was compared to its effective, isogenic parent strain. When the strains were inoculated in a 1:1 ratio at high concentration, the mutant was found to colonize almost as many nodules as the wild type. Thus, lack of expression of a functional nitrogenase system does not severely reduce competitiveness. In such experiments the majority of the nodules (> 60%) were infected by both wild-type and mutant strains. From statistical analysis it was concluded that a mean number of 2–4 bacteria have successfully elicited one nodule under the described conditions. Visual and microscopic observations of sections from mixed infected nodules revealed separated sectors containing effective or ineffective bacteroids.     

Effect of osmotically induced leaf moisture stress on nodulation and nitrogenase activity ofGlycine max

Summary The effect of 2-day cycles of osmotically induced leaf moisture stress followed by partial recovery on the nodulation and nitrogenase activity of 2 soya cultivars was studied. Fourteen days after plant inoculation (mid-growth stage) the total leaf electrochemical water potential (w^leaf) of control plants ranged from –0.8 to –1.9 bars, whereas the concentrations of osmoticum (polyethylene glycol 4000) induced w^leaf values ranging from –1.4 (recovery value) to –3.1 bars (low stress), –1.8 to –4.4 bars (mild stress), and –2.2 to –6.2 bars (medium stress). The low stress treatment reduced nodule numbers and their specific activity in both cultivars, without affecting nodule size or the time required for nodule initiation. Nodule initiation was delayed in both cultivars by the mild and medium stress treatments, the former treatment reducing the number and size of the nodules and such nodules exhibited very low specific activity. The medium stress treatment prevented the further development of nodule initials, which remained inactive throughout the experiment. Such results imply an effect of water stress on the infection process and on nodule morphogenesis. The reduction in nodule numbers observed in water stressed plants was not associated with a reduced number of rhizobia in the rhizoplane nor due to an effect on root growth or root hair formation.At a stage prior to the formation of macroscopic nodule initials, the roots of plants under medium stress (w^leaf=–5.5 bar)s) had a higher content of abscisic acid (ABA) (4-fold increase) and a lower content of gibberellin (GA)-like substances (21.4% reduction) as compared to control plants (w^leaf=–1.0 bar). Although the medium stress treatment slightly increased the stomatal resistance of leaves, photosynthetic and transpiration rates were unaffected. Similar alterations of the hormononal balance occurred in the nodulated roots of plants subjected to naturally induced leaf moisture stress.Since the foliar application of ABA (1.92×10^–5 M) to unstressed plants inhibited nodulation (45% reduction in nodule numbers), the increased endogenous content of thishormone in the roots of plants under leaf moisture stress may provide some physiological insight into the inhibitory effect of water stress on the nodulation process.     

Mutants of Rhizobium japonicum defective in nodulation

Several mutants defective in nodulation were isolated from Rhizobium japonicum strains 3I1b110 and 61A 76. Mutants of class I do not form nodules after incubation with soybean [Glycine max (L.) Merrill] for 17 days, but will do so by 28 days. When host plants other than G. max are infected with several of these strains, there is no detectable difference in the time of nodulation or size of nodules as compared to the wild type. Two mutants of class I (i. e., SM1 and SM2) have been shown previously to be altered in the lipopolysaccharide portion of their cell wall. Mutants of class II are not slow to nodulate but form fewer nodules than the wild type on all the host plants tested. Mutants of class III are unable to form nodules. Some bacteriophage-resistant mutants, altered in cell surface structure, fall into this class. Two mutants of class III do not bind to soybean roots.     

Relationship between autoregulation and nitrate inhibition of nodulation in soybeans

Ten of 11 supernodulating mutants of soybean [ Glycine max (L.) Merr.] cv. Bragg, in which nodulation was far in excess of that in the wild type, showed pronounced tolerance of nodulation to applied nitrate. Mutant nts (nitrate-tolerant symbiosis) 1116 had an intermediate nodulation response and also showed some inhibition by nitrate. Mutant 1029, a revertant of nts382 (an extreme supernodulator), showed a wild-type nodulation pattern and was equally sensitive to nitrate as cv. Bragg. Grafting experiments with cv. Bragg and nts382 indicated that both supernodulation and tolerance of nodulation to nitrate were dependent on shoot factors. Total leaf nitrate reductase (EC 1.6.6.1 and EC 1.6.6.2) activity of the supernodulating mutants was similar to that in cv. Bragg. We conclude from these results that the inhibitory effect of nitrate on nodule initiation and development in soybean depends on an interaction between nitrate and the autoregulation singal. In the supernodulating mutants, the autoregulation signal is either altered or absent and cosequently nodulation in these mutants is not sensitive to nitrate.     

Effect of Rhizobium sp. BARIRGm901 inoculation on nodulation,nitrogen fixation and yield of soybean (Glycine max) genotypes in gray terrace soil

Soybean plants require high amounts of nitrogen, which are mainly obtained from biological nitrogen fixation. A field experiment was conducted by soybean (Glycine max) genotypes, growing two varieties (Shohag and BARI Soybean6) and two advanced lines (MTD10 and BGM02026) of soybean with or without Rhizobium sp. BARIRGm901 inoculation. Soybean plants of all genotypes inoculated with Rhizobium sp. BARIRGm901 produced greater nodule numbers, nodule weight, shoot and root biomass, and plant height than non-inoculated plants. Similarly, inoculated plants showed enhanced activity of nitrogenase (NA) enzyme, contributing to higher nitrogen fixation and assimilation, compared to non-inoculated soybean plants in both years. Plants inoculated with Rhizobium sp. BARIRGm901 also showed higher pod, stover, and seed yield than non-inoculated plants. Therefore, Rhizobium sp. BARIRGm901 established an effective symbiotic relationship with a range of soybean genotypes and thus increased the nodulation, growth, and yield of soybean grown in gray terrace soils in Bangladesh.     

Influence of soil moisture on the nodulation of post fire seedlings of Ceanothus spp. growing in the Santa Monica Mountains of Southern California

During the dry season (early May through September of 1994), following a fall 1993 wildfire, a survey of seedling nodulation was conducted at several sites in the Santa Monica Mountains of Southern California. Seedlings of Ceanothus spinosus, C. megacarpus, C. oliganthus , and C. cuneatus were manually excavated. During this period, only 12 of the 182 seedlings excavated were nodulated, and all of the nodulated seedlings were found in the relatively moist clay soils of a stream bank. No nodules were observed on the 170 seedlings excavated from the drier sites. An irrigation experiment was established in midsummer to assess whether water stress inhibits nodulation of post-fire Ceanothus seedlings. Four plots with numerous seedlings of C. cuneatus and C. spinosus were irrigated with distilled water and monitored over a 9-week period. There was a significant increase in nodulation frequency, water potential, stomatal conductance, transpiration, shoot elongation, and photosynthetic rate of irrigated seedlings compared with adjacent controls. Although these data support the hypothesis that water stress inhibits nodulation. it is unclear whether this is because of an effect of soil moisture on the nodulation capacity of the soils (i.e. on the size and physiological state of the soil Frankia population) or to a host plant response to drought which might prevent actinorhizal root infection and/or nodule development.     

Root hairs and phosphorus acquisition of wheat and barley cultivars

Several genes that restrict nodulation with specific Bradyrhizobiumstrains are known in Glycine max (soybean), and a similar system of nodulation restriction has recently been discovered in the related North American legume Amphicarpaea bracteata. We analyzed how nodulation-restrictive genotypes of each plant interacted with Bradyrhizobium strains sampled from the other host species. Ten bacterial isolates from A. bracteata that nodulated differentially with genotypes of their homologous host legume showed uniform responses to two soybean isogenic lines that differed at the Rj4 locus controlling nodulation restriction: all isolates formed nodules of normal size and morphology on both isolines. However, little or no nitrogen fixation occurred in any of these symbioses. A. bracteata genotypes that displayed broad vs. restricted symbiotic phenotypes toward naturally-associated bradyrhizobia were also tested with two bacterial isolates from soybean (USDA 76 and USDA 123). Both isolates formed nodules and fixed nitrogen in association with both A. bracteata genotypes. However, symbiotic effectiveness (as measured by acetylene reduction assays) was normal only for the combination of USDA 76 with the restrictive A. bracteata genotype. Overall, these results indicate that plant genes that restrict nodulation by certain naturally-associated bradyrhizobia do not confer comparable specificity when plants interact with bacteria from another related legume species.     

Characterization of the Bradyrhizobium japonicum galE gene: its impact on lipopolysaccharide profile and nodulation of soybean

The galE gene from Bradyrhizobium japonicum 61A101C, a soybean endosymbiont, was cloned and characterized. Its deduced amino-acid sequence showed a high similarity with that of other rhizobia. Functional identification of the galE gene was achieved by complementation of a galE mutant strain, PL2, with a series of pKM subclones. Disruption of the B. japonicum galE gene affects the lipopolysaccharide profile compared with that of the wild type, suggesting that galE is responsible for alteration of lipopolysaccharide structure. Examination of nodule formation by the wild-type and galE mutant revealed that the former displayed normal nodule development on soybean roots, whereas the latter showed no nodule formation at all time points examined except for 20 days after inoculation when <10% of soybean formed pseudo-nodules.     

<Emphasis Type="Italic">In vitro</Emphasis> plant regeneration of <Emphasis Type="Italic">Alnus acuminata</Emphasis> H.B.K. ssp. <Emphasis Type="Italic">acuminata</Emphasis> and its root nodulation by <Emphasis Type="Italic">Frankia</Emphasis>

A procedure for in vitro plant regeneration of Alnus acuminata from epicotyls with cotyledonary buds was developed using different media formulations with different growth regulators and carbon sources. The development of multiple buds on explants at the initiation step was obtained with MS at 1/2 strength with either 1 or 2M of BAP but not without it. Multiplication gave up to 15 elongating shoots by explant, the best medium being MS supplemented with vitamins from B5 medium, 1M of BAP and 87mM sucrose. Rooting of about 88% occurred in the medium MS with 83 mM sucrose and 1M IBA. Alnus acuminata did not developed well on WPM. Roots of in vitro propagated plants were nodulated by Alnus-infective Frankia. The root nodules show a typical alder root nodule anatomy and differentiation pattern and effectively fixed nitrogen. Rhamnaceae-infective Frankia did not nodulate in vitro cultivated Alnus acuminata suggesting that symbiotic recognition was not altered by in vitro regeneration of the plant.     

Crystal structures of NodS N-methyltransferase from Bradyrhizobium japonicum in ligand-free form and as SAH complex

NodS is an S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule that is recognized by the legume host, where it initiates symbiotic processes leading to atmospheric nitrogen fixation. We report the crystal structure of recombinant NodS protein from Bradyrhizobium japonicum, which infects lupine and serradella legumes. Two crystal forms—ligand-free NodS and NodS in complex with S-adenosyl-l-homocysteine, which is a by-product of the methylation reaction—were obtained, and their structures were refined to resolutions of 2.43 Å and 1.85 Å, respectively. Although the overall fold (consisting of a seven-stranded β-sheet flanked by layers of helices) is similar to those of other SAM-dependent methyltransferases, NodS has specific features reflecting the unique character of its oligosaccharide substrate. In particular, the N-terminal helix and its connecting loop get ordered upon SAM binding, thereby closing the methyl donor cavity and shaping a long surface canyon that is clearly the binding site for the acceptor molecule. Comparison of the two structural forms of NodS suggests that there are also other conformational changes taking place upon the binding of the donor substrate. As an enzyme that methylates a COS substrate, NodS is the first example among all SAM-dependent methyltransferases to have its three-dimensional structure elucidated. Gaining insight about how NodS binds its donor and acceptor substrates helps to better understand the mechanism of NodS activity and the basis of its functional difference in various rhizobia.     

Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.

The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by G?ttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.     

Concentration-dependent influence of quercetin on nodulation process and the main characteristics of soybean inoculated with Bradyrhizobium japonicum

Soybean plants cv. Corsoy were grown in greenhouse conditions on sterilized quartz sand. They were inoculated with Bradyrhizobium japonicum, strain 542. The plants were treated with different concentrations of quercetin (ranging from 10 nM to 1M) at regular intervals during the experiment. The experiment was terminated at flower development. The following parameters, important for symbiosis efficiency were determined: shoot, root and nodule weights, nodule number, total leghemoglobin in the nodules,total nitrogen and soluble protein concentrations in shoots and roots, as well as chlorophyll concentration in the leaves.The results obtained partly confirmed the earlier findings that quercetin inhibits nodulation since increasing quercetin concentration decreased the number of nodules. However, at very low concentrations, quercetin stimulated the number of nodules. Quercetin also exerted a stimulating influence on other characteristics of the plant and nodules which did not correlate with nodule number and quantity of N fixed. These are: nodule weight, leghemoglobin concentration, total soluble protein content in shoots and roots as well as shoot and root weight.     

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.     

Insertion and deletion mutations within the nif region of Rhizobium japonicum

Insertion and deletion mutants were used to characterize a genomic region of Rhizobium japonicum where the nitrogenase structural genes are located on two separate operons nifDK and nifH. In addition to previously described nifD:: Tn5 and nifK:: Tn5 mutations we have now generated, by localized mutagenesis, further Tn5 insertion mutations in the vicinity of nifDK as well as within and adjacent to nifH. The nifD:: Tn5, nifK:: Tn5, and nifH:: Tn5 mutant strains were of the Nod⁺ Fix^- phenotype whereas all other mutants were symbiotically fully effective (Nod⁺ Fix⁺). The nifH:: Tn5 mutation was helpful in the identification of the nifH gene product (the dinitrogenase reductase) by two-dimensional gel electrophoresis: due to its polar effect this insertion specifically abolished the synthesis of that protein under microaerobic culture conditions. The ultrastructure of soybean root nodules infected with either the nif ⁺ wild-type or with the nif ^- (but otherwise isogenic) mutant strains was analyzed by electron microscopy. All contained fully developed bacteroids, but the nitrogen non-fixing mutants showed massive accumulation of PHB.Of Tn5-containing strains, kanamycin sensitive derivatives were obtained which contained deletions. Several classes of deletion mutants were found which, as judged by their physical DNA structure and their phenotypes, allowed the following most important conclusions: (i) deletions lacking both the nifDK and nifH regions indicate linkage between the two operons whereby at least 15 kb of DNA separate them; (ii) one deletion ending upstream from nifH, and lacking only nifDK, indicates that the nifDK operon is located on the 5-flanking side of the nifH operon; (iii) all deletion mutants are Nod⁺ indicating that there are no essential nodulation gnes located between and adjacent to nifDK and nifH.