The genetic analysis of Rhizobium in relation to symbiotic nitrogen fixation

Analysis of the Interaction between Pisum sativum L. and Rhizobium laguerreae Strains Nodulating This Legume in Northwest Spain

Pisum sativum L. (pea) is one of the most cultivated grain legumes in European countries due to the high protein content of its seeds. Nevertheless, the rhizobial microsymbionts of this legume have been scarcely studied in these countries. In this work, we analyzed the rhizobial strains nodulating the pea in a region from Northwestern Spain, where this legume is widely cultivated. The isolated strains were genetically diverse, and the phylogenetic analysis of core and symbiotic genes showed that these strains belong to different clusters related to R. laguerreae sv. viciae. Representative strains of these clusters were able to produce cellulose and cellulases, which are two key molecules in the legume infection process. They formed biofilms and produced acyl-homoserine lactones (AHLs), which are involved in the quorum sensing regulation process. They also exhibited several plant growth promotion mechanisms, including phosphate solubilization, siderophore, and indole acetic acid production and symbiotic atmospheric nitrogen fixation. All strains showed high symbiotic efficiency on pea plants, indicating that strains of R. laguerreae sv. viciae are promising candidates for the biofertilization of this legume worldwide.

Calcium-dependent regulation of genes for plant nodulation in Rhizobium leguminosarum detected by iTRAQ quantitative proteomic analysis

Rhizobia, the nitrogen-fixing bacterial symbionts of legumes, represent an agricultural application of primary relevance and a model of plant-microbe molecular dialogues. We recently described rhizobium proteome alterations induced by plant flavonoids using iTRAQ. Herein, we further extend that experimentation, proving that the transient elevation in cytosolic calcium is a key signaling event necessary for the expression of the nodulation (nod) genes. Ca(2+) involvement in nodulation is a novel issue that we recently flagged with genetic and physiological approaches and that hereby we demonstrate also by proteomics. Exploiting the multiple combinations of 4-plex iTRAQ, we analyzed Rhizobium leguminosarum cultures grown with or without the nod gene-inducing plant flavonoid naringenin and in the presence or absence of the extracellular Ca(2+) chelator EGTA. We quantified over a thousand proteins, 189 of which significantly altered upon naringenin and/or EGTA stimulation. The expression of NodA, highly induced by naringenin, is strongly reduced when calcium availability is limited by EGTA. This confirms, from a proteomic perspective, that a Ca(2+) influx is a necessary early step in flavonoid-mediated legume nodulation by rhizobia. We also observed other proteins affected by the different treatments, whose identities and roles in nodulation and rhizobium physiology are likewise discussed.

Early symbiotic responses induced by Sinorhizobium meliloti iIvC mutants in alfalfa

A mutation in the ilvC gene of Sinorhizobium meliloti 1021 determines a symbiotically defective phenotype. ilvC mutants obtained from different S. meliloti wild-type strains are able to induce root hair deformation on alfalfa roots and show variable activation of the common nodulation genes nodABC. All of these mutants are noninfective. The presence of extra copies of nodD3-syrM in an IlvC- background does not promote nod expression but allows the detection of low levels of Nod factor production. The sulphation of the Nod factor metabolites, however, is not affected. Furthermore, IlvC- strains induce a specific pattern of starch accumulation on alfalfa roots as well as of early nodulin expression. Hence, the pleiotropic action of the ilvC gene in S. meliloti may reveal novel complexities involved in the symbiotic interaction.

Population genetics of rhizobia: construction and analysis of an "Infection and Release" model

A mathematical model is created to assess the inputs of sym gene transfer of in planta multiplication and of interstrain competition into dynamics of the rhizobia populations. Their microevolution is presented as a series of the "infection and release" cycles; each cycle includes transfer of sym genes from virulent initial symbionts to avirulent local bacteria yielding the virulent novel symbionts; competition between initial symbionts and novel symbionts for the host nodulation; multiplication of initial symbionts and novel symbionts in planta and their release into soil; competition between the released novel symbionts and resident local bacteria for ex planta survival. A recurrent equation is created to determine the number of novel symbionts at each cycle of evolution of the closed bacteria-plant system. Its analysis demonstrates that under certain, really allowable values of the introduced parameters two major effects may occur: (a) rapid multiplication of novel symbionts arisen from sym gene transfer; and (b) increase of frequency of rare local bacteria genotypes after acquisition of virulence. Multiplication of very rare strains (p<10(-19)) in the plant-associated bacteria population is possible at certain parameters of the system. Variation of the sizes of bacteria populations and of the parameters for interstrain competition may influence the evolutionary rate of the bacteria population. The "infection and release" model represents a selective mechanism which may be responsible for a high taxonomic diversity of rhizobia and for a panmictic structure of their populations.

Molecular analysis of theRhizobiumgenes involved in the induction of nitrogen-fixing nodules on legumes

Recent developments in the molecular genetics ofRhizobium spp. are presented, and the use of mutant bacterial strains to determine which properties are required for symbiotic nitrogen fixation and nodulation of legumes is described. Both the lipopolysaccharide and the exopolysaccharide ofRhizobium spp. are implicated in infection. Recent studies have identified several genes involved in the early steps of this process and in the determination of host-range specificity. Analysis of their products has given some indications of their functions. The expression of most of these nodulation (nod) genes is controlled by the regulatory genenodD, which is itself expressed constitutively, whereas other nod genes are transcribed only when the cells are exposed to compounds present in the rhizosphere of legumes. These compounds were identified as various flavones and flavanones. Other plant-specified aromatic molecules, such as isoflavonoids, antagonize this induction.

The genetic and biochemical basis for nodulation of legumes by rhizobia

Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.

A novel response-regulator is able to suppress the nodulation defect of a Bradyrhizobium japonicum nodW mutant

The two-component regulatory system Nod-VW of Bradyrhizobium japonicum is essential for the nodulation of the legume host plants Vigna radiata, V. unguiculata and Macroptilium atropurpureum. The NodV protein shares homology with the sensor-kinases, whereas the NodW protein is a member of the response-regulator class. We report here the identification of a new B. japonicum DNA region that is able to suppress the phenotypic defect of a nodW mutant, provided that this region is expressed from a foreign promoter. The minimal complementing region, which itself is not essential for nodulation in a nodW+ background, consists of one gene designated nwsB (nodW-suppressor). The deduced amino acid sequence of the nwsB gene product shows a high degree of homology to NodW. The nws B gene is preceded by a long open reading frame, nwsA, whose putative product appears to be a sensor-kinase. Downstream of nwsB, an open reading frame encoding a second putative response-regulator was identified. Interspecies hybridization revealed the presence of nwsAB-like DNA also in other Bradyrhizobium strains. Using nwsB'-'lacZ fusions, the nwsB gene was found to be expressed rather weakly in B. japonicum. This low level of expression is obviously not sufficient to compensate for a nodW- defect, whereas strong overexpression of nwsB is a condition that leads to suppression of the nodW- mutation.

Asymbiotic Acetylene Reduction by a Fast-Growing Cowpea Rhizobium Strain with Nitrogenase Structural Genes Located on a Symbiotic Plasmid

A procedure was designed which enabled the detection of ex planta nitrogenase activity in the fast-growing cowpea Rhizobium strain IHP100. Nitrogenase activity in agar culture under air occurred at a rate similar to that found for Bradyrhizobium strain CB756 but lower than that for Rhizobium strain ORS571. Hybridization studies showed that both nod and nif genes were located on a 410-kilobase Sym plasmid in strain IHP100.

Nodule initiation elicited by noninfective mutants of Rhizobium phaseoli

Rhizobium phaseoli CE106, CE110, and CE115, originally derived by transposon mutagenesis (Noel et al., J. Bacteriol. 158:149-155, 1984), induced the formation of uninfected root nodule-like swellings on bean (Phaseolus vulgaris). Bacteria densely colonized the root surface, and root hair curling and initiation of root cortical-cell divisions occurred normally in mutant-inoculated seedlings, although no infection threads formed. The nodules were ineffective, lacked leghemoglobin, and were anatomically distinct from normal nodules. Ultrastructural specialization for ureide synthesis, characteristic of legumes that form determinate nodules, was absent. Colony morphology of the mutant strains on agar plates was less mucoid than that of the wild type, and under some cultural conditions, the mutants did not react with Cellufluor, a fluorescent stain for beta-linked polysaccharide. These observations suggest that the genetic lesions in these mutants may be related to extracellular polysaccharide synthesis.

Bacteriocin small of fast-growing rhizobia is chloroform soluble and is not required for effective nodulation

Small bacteriocin is a low-molecular-weight bacteriocin which is common in fast-growing rhizobia. As its activity could not be detected in chloroform-sterilized culture supernatants (P.R. Hirsch, J. Gen. Microbiol. 113:219-228, 1979), the bacteriocin could not be purified in order to study its mechanism of action. We report here that small is soluble in chloroform, an observation which led to effective and simple (partial) purification. Other properties of small are its low molecular weight, which is estimated to be between 700 and 1,500, its resistance to proteolytic enzymes, pectinase, and lysozyme, and its heat stability at pH 5.5 but not at pH 7.0. Its bactericidal action on exponentially growing sensitive cells was not detected until 11 h after its addition. The bactericidal action was preceded by inhibition of cell division. To determine whether small activity is required for nodulation or nitrogen fixation, a transposon Tn5-induced small-negative mutant was isolated. The observation that this strain formed normal, acetylene-reducing root nodules showed that small production is not a prerequisite for the formation of effective nodules.

Conserved Nodulation Genes in Rhizobium meliloti and Rhizobium trifolii

Plasmids which contained wild-type or mutated Rhizobium meliloti nodulation ( nod ) genes were introduced into Nod − R. trifolii mutants ANU453 and ANU851 and tested for their ability to nodulate clover. Cloned wild-type and mutated R. meliloti nod gene segments restored ANU851 to Nod + , with the exception of nodD mutants. Similarly, wild-type and mutant R. meliloti nod genes complemented ANU453 to Nod + , except for nodCII mutants. Thus, ANU851 identifies the equivalent of the R. meliloti nodD genes, and ANU453 specifies the equivalent of the R. meliloti nodCII genes. In addition, cloned wild-type R. trifolii nod genes were introduced into seven R. meliloti Nod − mutants. All seven mutants were restored to Nod + on alfalfa. Our results indicate that these genes represent common nodulation functions and argue for an allelic relationship between nod genes in R. meliloti and R. trifolii .

Physical and genetic map of a Rhizobium meliloti nodulation gene region and nucleotide sequence of nodC

Infection of alfalfa by the soil bacterium Rhizobium meliloti proceeds by deformation of root hairs and bacterial invasion of host tissue by way of an infection thread. We studied an 8.7-kilobase (kb) segment of the R. meliloti megaplasmid, which contains genes required for infection. Site-directed Tn5 mutagenesis was used to examine this fragment for nodulation genes. A total of 81 R. meliloti strains with mapped Tn5 insertions in the 8.7-kb fragment were evaluated for nodulation phenotype on alfalfa plants; 39 of the insertions defined a 3.5-kb segment containing nodulation functions. Of these 39 mutants, 37 were completely nodulation deficient (Nod-), and 2 at the extreme nif-distal end were leaky Nod-. Complementation analysis was performed by inoculating plants with strains carrying a genomic Tn5 at one location and a plasmid-borne Tn5 at another location in the 3.5-kb nodulation segment. Mutations near the right border of the fragment behaved as two distinct complementation groups. The segment in which these mutations are located was analyzed by DNA sequencing. Several open reading frames were found in this region, but the one most likely to function is 1,206 bases long, reading from left to right (nif distal to proximal) and spanning both mutation groups. The genetic behavior of this segment may be due either to the gene product having two functional domains or to a recombinational hot spot between the apparent complementation groups.

Generalized transduction in Rhizobium meliloti

Generalized transduction of Rhizobium meliloti 1021 was carried out by bacteriophage N3. Genetic markers on the chromosome and the pSym megaplasmid were transduced, along with markers on several IncP plasmids. Cotransduction between transposon Tn5 insertions and integrated recombinant plasmid markers permitted correlation of cotransductional frequencies and known physical distances. Bacteriophage N3 was capable of infecting several commonly used strains of R. meliloti.

Identification of a rhizosphere protein encoded by the symbiotic plasmid of Rhizobium leguminosarum

A protein was identified which was made by wild-type strains of Rhizobium leguminosarum but not by nodulation-deficient derivatives which had deletions of their symbiotic plasmids. The protein, which had a subunit molecular weight of ca. 24,000 ( 24K ), was found to be present in large amounts within bacteria that had been reisolated from the surface of inoculated pea roots but was not detected in bacteroids isolated from nodules. The protein could also be induced during growth of R. leguminosarum on nutrient medium and was purified from the cytoplasmic fraction of broken cells. Antiserum raised against the purified protein was used to screen transposon-induced mutants of R. leguminosarum, and four independent mutants were isolated which lacked the protein. The sites of the Tn5 insertions were found to map between the nitrogenase and nodulation genes on symbiotic plasmid pRL1JI , ca. 5 kilobases from the nitrogenase genes and 13 kilobases from the nodulation genes. Genetic determinants for the 24K protein were found to be closely linked to plasmid-borne nodulation genes for all strains of R. leguminosarum tested. However, the mutants which lacked the 24K protein still formed normal nitrogen-fixing nodules on peas, and the function of the protein is unknown.

Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions

Rhizobium phaseoli CFN42 DNA was mutated by random insertion of Tn5 from suicide plasmid pJB4JI to obtain independently arising strains that were defective in symbiosis with Phaseolus vulgaris but grew normally outside the plant. When these mutants were incubated with the plant, one did not initiate visible nodule tissue (Nod-), seven led to slow nodule development (Ndv), and two led to superficially normal early nodule development but lacked symbiotic nitrogenase activity (Sna-). The Nod- mutant lacked the large transmissible indigenous plasmid pCFN42d that has homology to Klebsiella pneumoniae nitrogenase (nif) genes. The other mutants had normal plasmid content. In the two Sna- mutants and one Ndv mutant, Tn5 had inserted into plasmid pCFN42d outside the region of nif homology. The insertions of the other Ndv mutants were apparently in the chromosome. They were not in plasmids detected on agarose gels, and, in contrast to insertions on indigenous plasmids, they were transmitted in crosses to wild-type strain CFN42 at the same frequency as auxotrophic markers and with the same enhancement of transmission by conjugation plasmid R68.45. In these Ndv mutants the Tn5 insertions were the same as or very closely linked to mutations causing the Ndv phenotype. However, in two mutants with Tn5 insertions on plasmid pCFN42d, an additional mutation on the same plasmid, rather than Tn5, was responsible for the Sna- or Ndv phenotype. When plasmid pJB4JI was transferred to two other R. phaseoli strains, analysis of symbiotic mutants was complicated by Tn5-containing deleted forms of pJB4JI that were stably maintained.

Tn5 carries a streptomycin resistance determinant downstream from the kanamycin resistance gene

In Rhizobium meliloti, Tn5 conferred resistance not only to kanamycin but to streptomycin, as well, in Escherichia coli, however only to kanamycin. Using in vitro recombinant DNA techniques, it was shown that the streptomycin resistance determinant was located downstream from the kanamycin resistance gene in the unique central region of Tn5. Expression of various cloned fragments of Tn5 suggested that both kanamycin and streptomycin resistance genes were transcribed from the same promoter. E. coli mutants allowing the expression of streptomycin resistance from Tn5 were isolated. The differential expression of the streptomycin resistance gene provides a simple selection/counterselection criterion, using only streptomycin in transfer experiments of Tn5 between E. coli and R. meliloti.

Cyanobacteria-eukaryotic plant symbioses

N2-fixing heterocystous cyanobacteria develop in symbiotic association with a small number of eukaryotic plant species belonging to the algae, fungi, liverworts, ferns, gymnosperms and angiosperm. When the free-living cyanobacteria develop in symbiosis, they become modified morphologically, physiologically and biochemically. The symbiosis are relatively specific, and among the changes which occur in the endophytic cyanobacteria are increases in the size of the vegetative cells, changes in the ultrastructure of the vegetative cells, a tendency for a reduction in the filamentous habit, an increased heterocyst frequency when another photosynthetic partner is present, reduced activities of glutamine synthetase and glutamate synthase, and NH4+ release by; the endophytic cyanobacteria. These and other aspects are considered, emphasizing, in particular, work carried out in the authors' laboratory.

Localization of symbiotic mutations in Rhizobium meliloti

A total of 5 Nod- and 57 Fix- symbiotic mutants of Rhizobium meliloti strain 41 have been isolated after either nitrosoguanidine or Tn5 transposition mutagenesis. Chromosomal locations of mutations in 1 Nod- and 11 Fix- derivatives were ascertained by transferring the chromosome (mobilized by plasmid R68.45), in eight fragments, into symbiotically effective recipients and testing the recombinants for symbiotic phenotype. Alternatively, the kanamycin resistance marker of Tn5 was mapped. In five mutants the fix alleles were localized on different chromosomal regions, but six other fix mutations and one nod mutation tested did not map onto the chromosome. It was shown that the chromosome-mobilizing ability (Cma+) of R68.45 was not involved in the mobilization of genes located extrachromosomally. Moreover, Cma- derivatives of R68.45 could mobilize regions of the indigenous plasmid pRme41b but not chromosomal genes. Thus, mobilization of a marker by Cma- R68.45 indicates its extrachromosomal location. With a 32P-labeled DNA fragment carrying Tn5 as a hybridization probe, it was shown that in five extrachromosomally located Tn5-induced fix mutants and one nod mutant Tn5 was localized on plasmid pRme41b. This is in agreement with the genetic mapping data.

Identification and mobilization by cointegrate formation of a nodulation plasmid in Rhizobium trifolii

A nodulation plasmid, pRtr-514a, of molecular size 180 megadaltons (Mdal) was identified in Rhizobium trifolii strain NZP514. This plasmid was absent in both spontaneous and heat-cured Nod- derivatives of NZP514, and these strains were unable to induce root hair curling. The ability to nodulate clover was transferred from the wild-type strain to a Nod- derivatives, PN104, with the broad-host-range plasmid R68.45 (39 megadaltons) at a cotransfer frequency of about 4 X 10(-3). Most of the Nod+ transconjugants were resistant to kanamycin, tetracycline, and carbenicillin and had received a plasmid approximately 36 or 70 Mdal larger than pRtr514a but did not contain a plasmid of the size of R68.45, indicating that pRtr-514a was mobilized as a cointegrate plasmid containing either one or possibly two copies of R68.45. Use of these cointegrate-containing strains as donors in further crosses with the Nod- derivative strain PN118 resulted in high-frequency transfer of Nod+ (10(-3) to 10(-4), with cotransfer frequencies with kanamycin of up to 100%. Introduction of R68.45 into a derivative of NZP514 containing the broad-host-range plasmid pJP4 (52 Mdal) resulted in a high frequency of transconjugants carrying a cointegrate plasmid composed of pRtr-514a and pJP4. When used as donors to Nod- derivatives, such strains cotransferred Nod+ with kanamycin plus mercury at a frequency of 67%. The identification of stable cointegrates between pRtr-514a and the broad-host-range plasmids R68.45 and pJP4 should enable several genetic manipulations to be carried out with this nodulation plasmid, including the transfer of the plasmid to most gram-negative bacterial genera.

Molecular mechanism for loss of nodulation properties of Rhizobium trifolii

Of 18 Rhizobium trifolii strains tested, 12 showed a high frequency of loss of nodulation ability after incubation in cultures at elevated temperatures. A correlation between loss of nodulation ability and loss of a large plasmid was demonstrated for R. trifolii. In some nonnodulating (Nod-) mutants, deletions occurred instead of total elimination of the plasmid molecule. The maximum curing effect was observed in bacteria incubated at 35 degrees C. After 4 or more days of incubation at this temperature, the viability of bacteria decreased markedly, and the number of nonnodulating mutants increased significantly. At the elevated temperature DNA synthesis was stopped completely after 2 h, whereas protein synthesis proceeded for a few days. Microscopic observations showed that during the first 3 days of incubation at the elevated temperature, the bacterial cells increased markedly in size. These large irregular cells then divided and produced Nod- clones. Nonnodulating clones did not result from the selection of temperature-resistant mutants. The presence of P-group plasmids in Rhizobium strains strongly inhibited the loss of nodulation ability during incubation at 35 degrees C. The observed phenomenon did not result from integrative suppression. It is possible that a product(s) of the genes of R-plasmids acts as a stabilizing agent on the replication process of the indigenous Rhizobium plasmids.

Location of nodulation and nitrogen fixation genes on a high molecular weight plasmid of R. meliloti

R. meliloti strain 41 (Rm41) was shown to harbour two indigenous plasmids with molecular weights of 140 Mdal (pRme41a) and more than 300 Mdal (pRme41b), respectively. Using a heat-treatment procedure, derivatives of Rm41 defective in nodulation (Nod-) or nitrogen fixation (Fix-) have been readily obtained. In some Nod- mutants the deletion of a segment of plasmid pRme41b was found. Based on the demonstrated homology between the nitrogen fixation (nif) genes of Klebsiella pneumoniae and of R. meliloti the Rhizobium nif region has been cloned into the cosmid vector pHC79, then recloned into pBR322 and the restriction map of the nif region has been determined. 32P-labelled nick-translated probe prepared from the cloned nif DNA fragment hybridized to pRme41b of Rm41 but for most Nod- mutants this hybridization was not detected. Hybridization of a cosmid containing Rm41 DNA to total DNA digest from the wild-type bacterium and from a series of Nod- mutants revealed that at least a 2 kb DNA fragment including the nif structural genes was missing from most of the Nod- mutants. These results, together with the genetic analyses of these symbiotic mutations suggest that some nod and fix genes are located on pRme41b.