Cysteine protease and cystatin expression and activity during soybean nodule development and senescence

BACKGROUND

Nodules play an important role in fixing atmospheric nitrogen for soybean growth. Premature senescence of nodules can negatively impact on nitrogen availability for plant growth and, as such, we need a better understanding of nodule development and senescence. Cysteine proteases are known to play a role in nodule senescence, but knowledge is still fragmented regarding the function their inhibitors (cystatins) during the development and senescence of soybean nodules. This study provides the first data with regard to cystatin expression during nodule development combined with biochemical characterization of their inhibition strength.

RESULTS

Seventy nine non-redundant cysteine protease gene sequences with homology to papain, belonging to different subfamilies, and several legumain-like cysteine proteases (vacuole processing enzymes) were identified from the soybean genome assembly with eighteen of these cysteine proteases actively transcribed during nodule development and senescence. In addition, nineteen non-redundant cystatins similar to oryzacystatin-I and belonging to cystatin subgroups A and C were identified from the soybean genome assembly with seven actively transcribed in nodules. Most cystatins had preferential affinity to cathepsin L-like cysteine proteases. Transcription of cystatins Glyma05g28250, Glyma15g12211, Glyma15g36180 particularly increased during onset of senescence, possibly regulating proteolysis when nodules senesce and undergo programmed cell death. Both actively transcribed and non-actively transcribed nodule cystatins inhibited cathepsin-L- and B-like activities in different age nodules and they also inhibited papain and cathepsin-L activity when expressed and purified from bacterial cells.

CONCLUSIONS

Overlap in activities and specificities of actively and non-actively transcribed cystatins raises the question if non-transcribed cystatins provide a reservoir for response to particular environments. This data might be applicable to the development of strategies to extend the active life span of nodules or prevent environmentally induced senescence.

Transcriptional and physiological changes in relation to Fe uptake under conditions of Fe-deficiency and Cd-toxicity in roots of Vigna radiata L

We investigated transcriptional and physiological changes in relation to Fe transport and uptake under various conditions of iron (Fe)-deficiency and cadmium (Cd) toxicity. Responses to four such Fe/Cd conditions were evaluated, revealing that oxidative stress was generated in the presence of Cd, followed by a decrease in Fe and an increase in Cd concentrations in green gram (Vigna radiata) material, whereas supplementation with Fe had a protective effect against Cd toxicity. The involvement of enzymes in Fe-uptake for the formation of root-nodules was largely reduced in the presence of Cd toxicity, a condition recovered by Fe-supplementation. Insufficient ferric chelate reducing activity in Fe-deprived roots in the presence of Cd was also largely improved by Fe supplementation. The expression of Fe(2+) transporters (IRT1, IRT2, and IRT3), Fe(III) chelate reductase (FRO1-FRO8) and phytochelatin synthase (PCS1, PCS2 and PCS3) genes was up regulated for the first 5 days and decreased after 10 days in roots in the presence of Cd toxicity, but was sustained with Fe-supplementation. Additionally, root biomass was fully recovered in plants in the presence of Fe during Cd toxicity. Our results suggest that Fe-status plays a significant role in ameliorating the damage in Fe transport for chelation and its uptake caused by Cd toxicity. This supports the hypothesis that leguminous plants, particularly those that are sensitive to Fe such as green gram, can cope to some extent with Cd toxicity by improving the uptake and transport of Fe.

RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N₂ fixation before emerging P deficiency reaches the nodules

Legume nodules are plant tissues with an exceptionally high concentration of phosphorus (P), which, when there is scarcity of P, is preferentially maintained there rather than being allocated to other plant organs. The hypothesis of this study was that nodules are affected before the P concentration in the organ declines during whole-plant P depletion. Nitrogen (N₂) fixation and P concentration in various organs were monitored during a whole-plant P-depletion process in Medicago truncatula. Nodule gene expression was profiled through RNA-seq at day 5 of P depletion. Until that point in time P concentration in leaves reached a lower threshold but was maintained in nodules. N₂-fixation activity per plant diverged from that of fully nourished plants beginning at day 5 of the P-depletion process, primarily because fewer nodules were being formed, while the activity of the existing nodules was maintained for as long as two weeks into P depletion. RNA-seq revealed nodule acclimation on a molecular level with a total of 1140 differentially expressed genes. Numerous genes for P remobilization from organic structures were increasingly expressed. Various genes involved in nodule malate formation were upregulated, while genes involved in fermentation were downregulated. The fact that nodule formation was strongly repressed with the onset of P deficiency is reflected in the differential expression of various genes involved in nodulation. It is concluded that plants follow a strategy to maintain N₂ fixation and viable leaf tissue as long as possible during whole-plant P depletion to maintain their ability to react to emerging new P sources (e.g. through active P acquisition by roots).

Roles of rhizobial symbionts in selenium hyperaccumulation in Astragalus (Fabaceae)

PREMISE OF THE STUDY

Are there dimensions of symbiotic root interactions that are overlooked because plant mineral nutrition is the foundation and, perhaps too often, the sole explanation through which we view these relationships? In this paper we investigate how the root nodule symbiosis in selenium (Se) hyperaccumulator and nonaccumulator Astragalus species influences plant selenium (Se) accumulation.

METHODS

In greenhouse studies, Se was added to nodulated and nonnodulated hyperaccumulator and nonaccumulator Astragalus plants, followed by investigation of nitrogen (N)-Se relationships. Selenium speciation was also investigated, using x-ray microprobe analysis and liquid chromatography-mass spectrometry (LC-MS).

KEY RESULTS

Nodulation enhanced biomass production and Se to S ratio in both hyperaccumulator and nonaccumulator plants. The hyperaccumulator contained more Se when nodulated, while the nonaccumulator contained less S when nodulated. Shoot [Se] was positively correlated with shoot N in Se-hyperaccumulator species, but not in nonhyperaccumulator species. The x-ray microprobe analysis showed that hyperaccumulators contain significantly higher amounts of organic Se than nonhyperaccumulators. LC-MS of A. bisulcatus leaves revealed that nodulated plants contained more γ-glutamyl-methylselenocysteine (γ-Glu-MeSeCys) than nonnodulated plants, while MeSeCys levels were similar.

CONCLUSIONS

Root nodule mutualism positively affects Se hyperaccumulation in Astragalus. The microbial N supply particularly appears to contribute glutamate for the formation of γ-Glu-MeSeCys. Our results provide insight into the significance of symbiotic interactions in plant adaptation to edaphic conditions. Specifically, our findings illustrate that the importance of these relationships are not limited to alleviating macronutrient deficiencies.

Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria

Some beneficial plant-interacting bacteria can biologically fix N2 to plant-available ammonium. Biological nitrogen fixation (BNF) is an important source of nitrogen (N) input in agriculture and represents a promising substitute for chemical N fertilizers. Diazotrophic bacteria have the ability to develop different types of root associations with different plant species. Among the highest rates of BNF are those measured in legumes nodulated by endosymbionts, an already very well documented model of plant-diazotrophic bacterial association. However, it has also been shown that economically important crops, especially monocots, can obtain a substantial part of their N needs from BNF by interacting with associative and endophytic diazotrophic bacteria, that either live near the root surface or endophytically colonize intercellular spaces and vascular tissues of host plants. One of the best reported outcomes of this association is the promotion of plant growth by direct and indirect mechanisms. Besides fixing N, these bacteria can also produce plant growth hormones, and some species are reported to improve nutrient uptake and increase plant tolerance against biotic and abiotic stresses. Thus, this particular type of plant-bacteria association consists of a natural beneficial system to be explored; however, the regulatory mechanisms involved are still not clear. Plant N status might act as a key signal, regulating and integrating various metabolic processes that occur during association with diazotrophic bacteria. This review will focus on the recent progress in understanding plant association with associative and endophytic diazotrophic bacteria, particularly on the knowledge of the N networks involved in BNF and in the promotion of plant growth.

Burkholderia sp. induces functional nodules on the South African invasive legume Dipogon lignosus (Phaseoleae) in New Zealand soils

The South African invasive legume Dipogon lignosus (Phaseoleae) produces nodules with both determinate and indeterminate characteristics in New Zealand (NZ) soils. Ten bacterial isolates produced functional nodules on D. lignosus. The 16S ribosomal RNA (rRNA) gene sequences identified one isolate as Bradyrhizobium sp., one isolate as Rhizobium sp. and eight isolates as Burkholderia sp. The Bradyrhizobium sp. and Rhizobium sp. 16S rRNA sequences were identical to those of strains previously isolated from crop plants and may have originated from inocula used on crops. Both 16S rRNA and DNA recombinase A (recA) gene sequences placed the eight Burkholderia isolates separate from previously described Burkholderia rhizobial species. However, the isolates showed a very close relationship to Burkholderia rhizobial strains isolated from South African plants with respect to their nitrogenase iron protein (nifH), N-acyltransferase nodulation protein A (nodA) and N-acetylglucosaminyl transferase nodulation protein C (nodC) gene sequences. Gene sequences and enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive element palindromic PCR (rep-PCR) banding patterns indicated that the eight Burkholderia isolates separated into five clones of one strain and three of another. One strain was tested and shown to produce functional nodules on a range of South African plants previously reported to be nodulated by Burkholderia tuberum STM678(T) which was isolated from the Cape Region. Thus, evidence is strong that the Burkholderia strains isolated here originated in South Africa and were somehow transported with the plants from their native habitat to NZ. It is possible that the strains are of a new species capable of nodulating legumes.

Mechanistic action of gibberellins in legume nodulation

Legume plants are capable of entering into a symbiotic relationship with rhizobia bacteria. This results in the formation of novel organs on their roots, called nodules, in which the bacteria capture atmospheric nitrogen and provide it as ammonium to the host plant. Complex molecular and physiological changes are involved in the formation and establishment of such nodules. Several phytohormones are known to play key roles in this process. Gibberellins (gibberellic acids; GAs), a class of phytohormones known to be involved in a wide range of biological processes (i.e., cell elongation, germination) are reported to be involved in the formation and maturation of legume nodules, highlighted by recent transcriptional analyses of early soybean symbiotic steps. Here, we summarize what is currently known about GAs in legume nodulation and propose a model of GA action during nodule development. Results from a wide range of studies, including GA application, mutant phenotyping, and gene expression studies, indicate that GAs are required at different stages, with an optimum, tightly regulated level being key to achieve successful nodulation. Gibberellic acids appear to be required at two distinct stages of nodulation: (i) early stages of rhizobia infection and nodule primordium establishment; and (ii) later stages of nodule maturation.

The soybean (Glycine max) nodulation-suppressive CLE peptide, GmRIC1, functions interspecifically in common white bean (Phaseolus vulgaris), but not in a supernodulating line mutated in the receptor PvNARK

Legume plants regulate the number of nitrogen-fixing root nodules they form via a process called the Autoregulation of Nodulation (AON). Despite being one of the most economically important and abundantly consumed legumes, little is known about the AON pathway of common bean (Phaseolus vulgaris). We used comparative- and functional-genomic approaches to identify central components in the AON pathway of common bean. This includes identifying PvNARK, which encodes a LRR receptor kinase that acts to regulate root nodule numbers. A novel, truncated version of the gene was identified directly upstream of PvNARK, similar to Medicago truncatula, but not seen in Lotus japonicus or soybean. Two mutant alleles of PvNARK were identified that cause a classic shoot-controlled and nitrate-tolerant supernodulation phenotype. Homeologous over-expression of the nodulation-suppressive CLE peptide-encoding soybean gene, GmRIC1, abolished nodulation in wild-type bean, but had no discernible effect on PvNARK-mutant plants. This demonstrates that soybean GmRIC1 can function interspecifically in bean, acting in a PvNARK-dependent manner. Identification of bean PvRIC1, PvRIC2 and PvNIC1, orthologues of the soybean nodulation-suppressive CLE peptides, revealed a high degree of conservation, particularly in the CLE domain. Overall, our work identified four new components of bean nodulation control and a truncated copy of PvNARK, discovered the mutation responsible for two supernodulating bean mutants and demonstrated that soybean GmRIC1 can function in the AON pathway of bean.

A thaumatin-like protein, Rj4, controls nodule symbiotic specificity in soybean

Soybeans exhibit a nitrogen-fixing symbiosis with soil bacteria of the genera Bradyrhizobium and Ensifer/Sinorhizobium in a unique organ, the root nodule. It is well known that nodulation of soybean is controlled by several host genes referred to as Rj (rj) genes. Among these genes, a dominant allele, Rj4, restricts nodulation with specific bacterial strains such as B. elkanii USDA61 and B. japonicum Is-34. These incompatible strains fail to invade the host epidermal cells as revealed by observations using DsRed-labeled bacteria. Here, we describe the molecular identification of the Rj4 gene by using map-based cloning with several mapping populations. The Rj4 gene encoded a thaumatin-like protein (TLP) that belongs to pathogenesis-related (PR) protein family 5. In rj4/rj4 genotype soybeans and wild soybeans, we found six missense mutations and two consecutive amino acid deletions in the rj4 gene as compared with the Rj4 allele. We also found, using hairy root transformation, that the rj4/rj4 genotype soybeans were fully complemented by the expression of the Rj4 gene. Whereas the expression of many TLPs and other PR proteins is induced by biotic/abiotic stress, Rj4 gene expression appears to be constitutive in roots including root nodules.

Abundance and diversity of soybean-nodulating rhizobia in black soil are impacted by land use and crop management

To investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) were distributed widely in all treatments, while Bradyrhizobium sp. II was found only in GL treatment. Cultivation with soybeans increased the rhizobial abundance and diversity, except for the soybean monoculture (S-S) treatment. In monoculture systems, soybeans favored Bradyrhizobium sp. I, while maize and wheat favored Bradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes but did not change the species composition. The organic carbon (OC) and available phosphorus (AP) contents and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I and II and Bradyrhizobium japonicum and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land uses and crop management could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and legume or nonlegume plants, which offered novel information about the biogeography of rhizobia.

Shaping bacterial symbiosis with legumes by experimental evolution

Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.

Endophytic Bradyrhizobium spp. isolates from sugarcane obtained through different culture strategies

Brazilian sugarcane has been shown to obtain part of its nitrogen via biological nitrogen fixation (BNF). Recent reports, based on the culture independent sequencing of bacterial nifH complementary DNA (cDNA) from sugarcane tissues, have suggested that members of the Bradyrhizobium genus could play a role in sugarcane-associated BNF. Here we report on the isolation of Bradyrhizobium spp. isolates and a few other species from roots of sugarcane cultivar RB867515 by two cultivation strategies: direct isolation on culture media and capture of Bradyrhizobium spp. using the promiscuous legume Vigna unguiculata as trap-plant. Both strategies permitted the isolation of genetically diverse Bradyrhizobium spp. isolates, as concluded from enterobacterial repetitive intergenic consensus polymerase chain reaction (PCR) fingerprinting and 16S ribosomal RNA, nifH and nodC sequence analyses. Several isolates presented nifH phylotypes highly similar to nifH cDNA phylotypes detected in field-grown sugarcane by a culture-independent approach. Four isolates obtained by direct plate cultivation were unable to nodulate V. unguiculata and, based on PCR analysis, lacked a nodC gene homologue. Acetylene reduction assay showed in vitro nitrogenase activity for some Bradyrhizobium spp. isolates, suggesting that these bacteria do not require a nodule environment for BNF. Therefore, this study brings further evidence that Bradyrhizobium spp. may play a role in sugarcane-associated BNF under field conditions.

Actinorhizal root nodule symbioses: what is signalling telling on the origins of nodulation?

Two groups of bacteria are able to induce the formation of nitrogen-fixing nodules: proteobacteria called rhizobia, which associate with Legumes or Parasponia and actinobateria from the genus Frankia which are able to interact with ∼220 species belonging to eight families called actinorhizal plants. Legumes and different lineages of actinorhizal plants differ in bacterial partners, nodule organogenesis and infection patterns and have independent evolutionary origins. However, recent technical achievements are revealing a variety of conserved signalling molecules and gene networks. Actinorhizal interactions display several primitive features and thus provide the ideal opportunity to determine the minimal molecular toolkit needed to build a nodule and to understand the evolution of root nodule symbioses.

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins

In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots.

Implications of non-specific strigolactone signaling in the rhizosphere

Strigolactones produced by various plant species are involved in the development of different plant parts. They are also exuded by plant roots to the rhizosphere, where they are involved in the induction of seed germination of the parasitic plants Striga and Orobanche, hyphal branching of the symbiotic arbuscular mycorrhizal fungi (AMF), and the symbiotic interaction with Rhizobium. In the present discussion paper, the essentialness of strigolactones as communication signals in these plant interactions is discussed in view of the existence of other plant-derived substances that are able to promote these plant interactions. In addition, the importance of strigolactones for determination of interaction specificity is discussed based on current knowledge on strigolactone composition, perception and delivery. The different activities of strigolactones in plant development and in the rhizosphere suggest their possible use in agriculture. However, despite efforts made in this direction, there is no current, practical implementation. Possible reasons for the encountered difficulties and suggested solutions to promote strigolactone use in agriculture are discussed.

MiR171h restricts root symbioses and shows like its target NSP2 a complex transcriptional regulation in Medicago truncatula

BACKGROUND

Legumes have the unique capability to undergo root nodule and arbuscular mycorrhizal symbiosis. Both types of root endosymbiosis are regulated by NSP2, which is a target of microRNA171h (miR171h). Although, recent data implies that miR171h specifically restricts arbuscular mycorrhizal symbiosis in the root elongation zone of Medicago truncatula roots, there is limited knowledge available about the spatio-temporal regulation of miR171h expression at different physiological and symbiotic conditions.

RESULTS

We show that miR171h is functionally expressed from an unusual long primary transcript, previously predicted to encode two identical miR171h strands. Both miR171h and NSP2 transcripts display a complex regulation pattern, which involves the symbiotic status and the fertilization regime of the plant. Quantitative Real-time PCR revealed that miR171h and NSP2 transcript levels show a clear anti-correlation in all tested conditions except in mycorrhizal roots, where NSP2 transcript levels were induced despite of an increased miR171h expression. This was also supported by a clear correlation of transcript levels of NSP2 and MtPt4, a phosphate transporter specifically expressed in a functional AM symbiosis. MiR171h is strongly induced in plants growing in sufficient phosphate conditions, which we demonstrate to be independent of the CRE1 signaling pathway and which is also not required for transcriptional induction of NSP2 in mycorrhizal roots. In situ hybridization and promoter activity analysis of both genes confirmed the complex regulation involving the symbiotic status, P and N nutrition, where both genes show a mainly mutual exclusive expression pattern. Overexpression of miR171h in M. truncatula roots led to a reduction in mycorrhizal colonization and to a reduced nodulation by Sinorhizobium meliloti.

CONCLUSION

The spatio-temporal expression of miR171h and NSP2 is tightly linked to the nutritional status of the plant and, together with the results from the overexpression analysis, points to an important function of miR171h to integrate the nutrient homeostasis in order to safeguard the expression domain of NSP2 during both, arbuscular mycorrhizal and root nodule symbiosis.

A new PGPR co-inoculated with Bradyrhizobium japonicum enhances soybean nodulation

A new PGPR (plant growth promoting rhizobacteria) strain was isolated from soybean seeds and the bacterial mechanisms related to plant growth promotion were evaluated and characterized. Isolates were genotypically compared and identified by amplification of partial sequences of 16S DNAr as Bacillus amyloliquefaciens strain LL2012. Isolates were grown until exponential growth phase to evaluate the atmospheric nitrogen fixation, enzymatic activities, phosphate solubilization, siderophores and phytohormones production. LL2012 strain was able to grow and to produce high levels of auxin, gibberellins and salicylic acid in chemically defined medium. Co-inoculation of soybean plants with LL2012 strain and the natural symbiont (Bradyrhizobium japonicum) altered plant growth parameters and significantly improved nodulation. Our results show that the association of LL2012 with B. japonicum, enhanced the capacity of the latter to colonize plant roots and increase the number of nodules, which make the co-inoculation technique attractive for use in commercial inoculant formulations following proper field evaluation.

Rhizobium tibeticum activated with a mixture of flavonoids alleviates nickel toxicity in symbiosis with fenugreek (Trigonella foenum graecum L.)

The objective of this study is to explore the response of an activated Rhizobium tibeticum inoculum with a mixture of hesperetin (H) and apigenin (A) to improve the growth, nodulation, and nitrogen fixation of fenugreek (Trigonella foenum graecum L.) grown under nickel (Ni) stress. Three different sets of fenugreek seed treatments were conducted, in order to investigate the activated R. tibeticum pre-incubation effects on nodulation, nitrogen fixation and growth of fenugreek under Ni stress. Group (I): uninoculated seeds with R. tibeticum, group (II): inoculated seeds with uninduced R. tibeticum group (III): inoculated seeds with induced R. tibeticum. The present study revealed that Ni induced deleterious effects on rhizobial growth, nod gene expression, nodulation, phenylalanine ammonia-lyase (PAL) and glutamine synthetase activities, total flavonoids content and nitrogen fixation, while the inoculation with an activated R. tibeticum significantly improved these values compared with plants inoculated with uninduced R. tibeticum. PAL activity of roots plants inoculated with induced R. tibeticum and grown hydroponically at 75 and 100 mg L(-1) Ni and was significantly increased compared with plants receiving uninduced R. tibeticum. The total number and fresh mass of nodules, nitrogenase activity of plants inoculated with induced cells grown in soil treated up to 200 mg kg(-1) Ni were significantly increased compared with plants inoculated with uninduced cells. Plants inoculated with induced R. tibeticum dispalyed a significant increase in the dry mass compared with those treated with uninduced R. tibeticum. Activation of R. tibeticum inoculum with a mixture of hesperetin and apigenin has been proven to be practically important in enhancing nodule formation, nitrogen fixation and growth of fenugreek grown in Ni contaminated soils.

Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island

The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.

[Sinorhizobium meliloti strains screening for efficient bactarization of Melilotus albus Medik]

The data presents about analytical selection of root nodule bacteria of Melilotus to obtain bacterial fertilizer under sweet clover, presowing inoculation of it seeds and form a legume-rhizobial effective symbiosis. From natural melilot population a number of new strains had been allocated, inoculation of them was contributed to an increase of height. biomass Melilotus albus Medik., and nitrogenase activity in comparison to the influence of the existing production strains. The identification of most effective strains Sinorhizobium meliloti had been determined.

A soybean acyl carrier protein, GmACP, is important for root nodule symbiosis

Legumes (members of family Fabaceae) establish a symbiotic relationship with nitrogen-fixing soil bacteria (rhizobia) to overcome nitrogen source limitation. Single root hair epidermal cells serve as the entry point for bacteria to infect the host root, leading to development of a new organ, the nodule, which the bacteria colonize. In the present study, the putative role of a soybean acyl carrier protein (ACP), GmACP (Glyma18g47950), was examined in nodulation. ACP represent an essential cofactor protein in fatty acid biosynthesis. Phylogenetic analysis of plant ACP protein sequences showed that GmACP was classified in a legume-specific clade. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that GmACP was expressed in all soybean tissues but showed higher transcript accumulation in nodule tissue. RNA interference-mediated gene silencing of GmACP resulted in a significant reduction in nodule numbers on soybean transgenic roots. Fluorescent protein-labeled GmACP was localized to plastids in planta, the site of de novo fatty acid biosynthesis in plants. Analysis of the fatty acid content of root tissue silenced for GmACP expression, as determined by gas chromatography-mass spectrometry, showed an approximately 22% reduction, specifically in palmitic and stearic acid. Taken together, our data provide evidence that GmACP plays an important role in nodulation.

Sinorhizobium meliloti flavin secretion and bacteria-host interaction: role of the bifunctional RibBA protein

Sinorhizobium meliloti, the nitrogen-fixing bacterial symbiont of Medicago spp. and other legumes, secretes a considerable amount of riboflavin. This precursor of the cofactors flavin mononucleotide and flavin adenine dinucleotide is a bioactive molecule that has a beneficial effect on plant growth. The ribBA gene of S. meliloti codes for a putative bifunctional enzyme with dihydroxybutanone phosphate synthase and guanosine triphosphate (GTP) cyclohydrolase II activities, catalyzing the initial steps of the riboflavin biosynthesis pathway. We show here that an in-frame deletion of ribBA does not cause riboflavin auxotrophy or affect the ability of S. meliloti to establish an effective symbiosis with the host plant but does affect the ability of the bacteria to secrete flavins, colonize host-plant roots, and compete for nodulation. A strain missing the RibBA protein retains considerable GTP cyclohydrolase II activity. Based on these results, we hypothesize that S. meliloti has two partly interchangeable modules for biosynthesis of riboflavin, one fulfilling the internal need for flavins in bacterial metabolism and the other producing riboflavin for secretion. Our data also indicate that bacteria-derived flavins play a role in communication between rhizobia and the legume host and that the RibBA protein is important in this communication process even though it is not essential for riboflavin biosynthesis and symbiosis.

Soybean ureases, but not that of Bradyrhizobium japonicum, are involved in the process of soybean root nodulation

Ureases are abundant in plants, bacteria, and in the soil, but their role in signaling between soybean and soil microorganisms has not been investigated. The bacterium Bradyrhizobium japonicum forms nitrogen-fixing nodules on soybean roots. Here, we evaluated the role(s) of ureases in the process of soybean nodulation. Chemotaxis assays demonstrated that soybean and jack bean ureases were more chemotactic toward bacterial cells than the corresponding plant lectins. The eu1-a,eu4 soybean, deficient in urease isoforms, formed fewer but larger nodules than the wild-type, regardless of the bacterial urease phenotype. Leghemoglobin production in wild-type plants was higher and peaked earlier than in urease-deficient plants. Inhibition of urease activity in wild-type plants did not result in the alterations seen in mutated plants. We conclude that soybean urease(s) play(s) a role in the soybean-B. japonicum symbiosis, which is independent of its ureolytic activity. Bacterial urease does not play a role in nodulation.

Nodulation study of natural forage legume in semiarid region, Turkey

In this study, we investigated the natural nodulation of legume forage crops were widely grown in the natural pastures in Sanliurfa, Turkey. This legume forage crops are Vicia sativa L. subsp. sativa L., Vicia narbonensis L. var. narbonensis L., Vicia palaestina Boiss., Vicia hybrida L., Vicia lutea L. var. lutea Boiss. ET Ball., Pisum sativum L. subsp. sativum L. var. sativum L, Cicer echinospermum P.H. Davis, Trifolium tomentosum L., Trifolium retusum L., Trifolium campestre SCHREB., Medicago truncatula GAERTN. var. truncatula Schultz Bip., Trigonella mesopotamica Hub.-Mor., Lens culinaris Medik., Onobrychis crista-galli, Lathyrus cassius Boiss., Melilotus officinalis (L.) DESR., Coronilla scorpioides (L.) W.D.J. Koch. Nodulation, nodule colors and shapes were examined at the blooming period of forage legumes. In this study, the colour of the interior of nodules are pink-red colour and may be related to high rates of nitrogen fixation in legume crops.

Localization of the Bacillus subtilis beta-propeller phytase transcripts in nodulated roots of Phaseolus vulgaris supplied with phytate

Soil organic phosphorus (Po) such as phytate, which comprises up to 80 % of total Po, must be hydrolyzed by specific enzymes called phytases to be used by plants. In contrast to plants, bacteria, such as Bacillus subtilis, have the ability to use phytate as the sole source of P due to the excretion of a beta-propeller phytase (BPP). In order to assess whether the B. subtilis BPP could make P available from phytate for the benefit of a nodulated legume, the P-sensitive recombinant inbred line RIL147 of Phaseolus vulgaris was grown under hydroaeroponic conditions with either 12.5 μM phytate (C₆H₁₈O₂₄P₆) or 75 μmol Pi (K₂HPO₄), and inoculated with Rhizobium tropici CIAT899 alone, or co-inoculated with both B. subtilis DSM 10 and CIAT899. The in situ RT-PCR of BPP genes displayed the most intense fluorescent BPP signal on root tips. Some BPP signal was found inside the root cortex and the endorhizosphere of the root tip, suggesting endophytic bacteria expressing BPP. However, the co-inoculation with B. subtilis was associated with a decrease in plant P content, nodulation and the subsequent plant growth. Such a competitive effect of B. subtilis on P acquisition from phytate in symbiotic nitrogen fixation might be circumvented if the rate of inoculation were reasoned in order to avoid the inhibition of nodulation by excess B. subtilis proliferation. It is concluded that B. subtilis BPP gene is expressed in P. vulgaris rhizosphere.