Genotypic and phenotypic characterization of rhizobia that nodulate snap bean (Phaseolus vulgaris L.) in Egyptian soils

Snap bean fields in 12 of the 25 governorates of Egypt were surveyed to determine the distribution and taxonomy of snap bean-nodulating rhizobia. Nodulation rates in the field were very low, indicating that Egyptian soils do not have sufficient numbers of snap bean-compatible Rhizobium spp. A total of 87 rhizobial isolates were assayed on the most commonly grown cultivars in order to identify the most effective strains. The five most effective isolates (R11, R13, R28, R49 and R52) were fast-growing and utilized a wide range of carbon and nitrogen sources. A phylogenetic assignment of these strains by analysis of the 16S ribosomal RNA gene suggested that all fell within the Rhizobium etli–Rhizobium leguminosarum group. Strains R11, R49 and R52 all clustered with other identified R. etli strains, while strains R13 and R28 were more distinct. The distinctness of R13 and R28 was supported by physiological characteristics, such as their ability to utilize citrate, erythritol, dulcitol and lactate. Strains R13 and R28 also yielded the highest plant nitrogen content of all isolates.The highly effective strains isolated in this study, in particular strains R13 and R28, are promising candidates for improving crop yields. The data also suggested that these two strains represented a novel sub-group within the R. etli–R. leguminosarum group. As snap bean is a crop of great economic value to Egypt, the identification of highly effective rhizobial strains adapted to Egyptian soils, such as strains R13 and R28, is of great interest.     

Rhizobium phaseoli: A molecular genetics view

We have used molecular genetics techniques to analyze the structural and functional organization of genetic information ofRhizobium phaseoli, the symbiont of the common bean plantPhaseolus vulgaris. As in otherRhizobium species, the genome consists of the chromosome and plasmids of high molecular weight. Symbiotic determinants, nitrogen fixation genes as well as nodulation genes, are localized on a single replicon, the symbiotic (sym) plasmid. Thesym plasmid of differentR. phaseoli strains was transferred to anAgrobacterium tumefaciens strain cured of its native plasmids. In all cases, Agrobacterium transconjugants able to nodulate bean plants were obtained. Some of the transconjugants had the capacity to elicit an effective symbiosis. The genome ofR. phaseoli is complex, containing a large amount of reiterated DNA sequences. In mostR. pahseoli strains one of such reiterated DNA families corresponds to the nitrogenase structural genes (nif genes). A functional analysis of these genes suggested that the presence of reiteratednif genesis is related to the capacity of fixing atmospheric nitrogen in the symbiotic state. The presence of several repeated sequences in the genome might provide sites for recombination, resulting in genomic rearrangements. By analyzing direct descendants of a single cell in the laboratory, evidence of frequent genomic rearrangements inR. phaseoli was found. We propose that genomic rearrangements constitute the molecular basis of the frequent variability and loss of symbiotic properties in different Rhizobium strains.     

Utilization of carbon and nitrogen sources and acid/alkali production by cowpea rhizobia

Summary Sixteen slow-growing strains of rhizobia (15 cowpea rhizobia and oneR. japonicum) were examined to determine the effects of carbon and nitrogen sources on acid/alkali production in culture media. We found that the pH changes of the medium were more influenced by nitrogen sources than carbon sources (with the exception of ribose). When ammonium sulphate was used as a nitrogen source, all the cowpea rhizobia strains produced acid. When yeast-extract was used as a nitrogen source, however, a heterogenous pattern for acid/alkali production was found. The majority of the strains produced alkali from nitrate, glutamate and urea irrespective of carbon sources and acid from ribose irrespective of nitrogen sources.     

Site specific transposition of Tn7 into a Rhizobium meliloti megaplasmid

Summary Transposon Tn7 was shown to insert specifically into the megaplasmid of different Rhizobium meliloti strains. Tn7 transposition could not be detected in other Rhizobium strains such as R. trifolii, R. leguminosarum, R. phaseoli and R. japonicum. In R. meliloti strains, two unique sites in the megaplasmid were observed into which Tn7 can transpose at different frequencies. Only one copy of Tn7 could be detected in the megaplasmid and the insertion sites for Tn7 are outside the nif and nod region. Tn7 transposition in R. meliloti showed a marked preference for sites on plasmid RP4 compared to the megaplasmid sites. Attempts to cure Tn7 from the megaplasmid were unsuccessful. This site specific transposition of Tn7 in R. meliloti provides an additional genetic tool to further manipulate this important plasmid in symbiotic nitrogen fixation.     

The effect of Rhizobium inoculation and nitrogen fertiliser on nitrogen fixation and seed yield of dry beans (Phaseolus vulgaris)

The potential benefit to be derived from seed inoculation of Phaseolus vulgaris beans with effective strains of Rhizobium phaseoli, was investigated in field experiments over three years on a site low in soil nitrogen and lacking indigenous effective strains of R. phaseoli. Inoculation with R. phaseoli (strain RCR 3644) produced significant increases in nodulation, nitrogenase activity and plant growth in all experiments. In trials in 1978 and 1979, with cv. Seafarer, inoculation, in the absence of nitrogen fertiliser doubled seed yields. In 1978, the seed yields from inoculated beans without nitrogen fertiliser (1–6 t/ha) were not significantly different from those obtained with uninoculated beans receiving the optimum nitrogen fertiliser treatment of 120 kg N/ha (1–75 t/ha). In 1979, with lower rainfall favouring more efficient utilisation of nitrogen fertiliser, inoculation gave seed yields (1–88 t/ha) equivalent to those obtained with 60 kg N/ha (1–70 t/ha) but significantly less than with 120 kg N/ha (2–88 t/ha). More precise estimates from nitrogen response curves showed that inoculation supplied the fertiliser equivalent of 105 and 70 kg N/ha in 1978 and 1979 respectively. In both years, significant benefits were also obtained by the combination of inoculation and nitrogen fertiliser. In a separate experiment in 1979, with four R. phaseoli strains inoculated onto eight bean cultivars, three were highly effective nitrogen fixers on all cultivars. Two strains (RCR 3644 and NVRS 963A) each increased mean yields, in the absence of nitrogen fertiliser, from 1–39 t/ha uninoculated to c. 2–5 t/ha inoculated whilst strain RCR 3622 was outstanding with a mean yield of 3-0 t/ha. An analysis of the nitrogen content of seed showed that gains from nitrogen fixation were 37–57 kg N/ha/growing cycle for the combination RCR 3644 with cv. Seafarer. However, 106 kg N/ha/growing cycle was recorded for the combination RCR 3622 and cv. Aurora.     

STUDIES ON INDUCED VARIATION IN THE RHIZOBIA. III. HOST RANGE MODIFICATION OF RHIZOBIUM TRIFOLII BY SPONTANEOUS AND RADIATION-INDUCED MUTATION

Schwinghamer , E. A. (Brookhaven Natl. Lab., Upton, New York.) Studies on induced variation in the rhizobia. III. Host range modification of Rhizobium trifolii by spontaneous and radiation-induced mutation. Amer. Jour. Bot. 49(3): 269–277. Illus. 1962.—Mutant strains capable of nodulating pea seedings ineffectively (incapable of nitrogen fixation) have been obtained from 2 antibiotic-resistant marked strains of Rhizobium trifolii which normally do not form nodules on this host. Such variant forms apparently occur spontaneously in these strains at a low frequency which can be significantly increased by irradiation with ultraviolet light, X rays, and fast neutrons. Nodulation of vetch, sweet peas and several varieties of peas by the mutant strains suggests a close parallelism of the extended host range with the range of R. leguminosarum, although nitrogen fixation by the mutants on the new hosts is negligible or absent. The mutant nodules on these hosts also differ from those of the pea strains in slightly smaller size, spherical form, and lighter pink color. Nodule morphology on the homologous host, clover. appears unaltered but a slight loss of effectiveness was noted on red clover. This loss may be attributed partly to a reduction in infective ability since the average number of nodules formed per plant of clover or pea is appreciably lower than for comparable inoculation by strains of nonmutant R. trifolii or R. leguminosarum, respectively. Cultural characteristics of mutant strains resemble those of the nonmutant R. trifolii strains.     

Experiments on nitrogen fixation by nodulated lucerne

Summary Field experiments at five sites (two on clay loam, two on a sandy soil and one on chalky loam) compared dry-matter yields and nitrogen contents of lucerne and ryegrass. These tested Rhizobium inoculation and fertilizer treatments in an experimental design proposed by Vincent and Nutman (IBP 69(66), amended 57/68). The crop and inoculation treatments (using large inocula of effective or ineffective strains) were set out in strips across each site to minimise contamination, and the fertilizer treatments (nitrogen, limeetc.) distributed at random within strips. This proved satisfactory and allowed valid statistical analysis. The massive inoculation with the ineffective strain suppressed the few naturally occurring effectiveR. meliloti at some of the sites, and provided a basis of comparison for assessing the amounts of nitrogen fixed by the native strains and by the introduced effective strains. However, it did so only during the first year because the introduced ineffective strains were overgrown by effective strains in the second year. Hence, ryegrass without nitrogen fertilizer was a better measure of the amounts of nitrogen obtainable from the soil. Estimates of fixation ranged from 0 to more than 300 kg N ha⁻¹ at the different sites, treatment comparisons indicating the main factors limiting fixation. Parallel experiments were done using a soil core technique described by Vincent. These gave very similar results to the field trials in their first years. Studies of the changes in the populations ofR. meliloti in the field trial plots and soil cores gave information on the effects of crop and fertilizers on numbers and effectiveness of isolates and was useful in interpreting the results.     

Derivatives of Rhizobium meliloti strains carrying a plasmid of Rhizobium leguminosarum specifying hydrogen uptake and pea-specific symbiotic functions

pIJ1008, a Rhizobium leguminosarum plasmid which determines hydrogen uptake ability and symbiotic functions in pea was transferable to three of seven natural isolates of R. meliloti tested. In these three strains, pIJ1008 was maintained stably with the respective sym megaplasmid indigenous to each R. meliloti strain. These strains carrying both plasmids nodulated alfalfa but not pea. By reisolation and examination of the strains from alfalfa nodule tissue, it was shown that pIJ1008 continued to be maintained but that pea-nodulation ability was suppressed.In one strain of R. meliloti which carries a 200 kb cryptic plasmid (in addition to a megaplasmid), the transfer and selection for pIJ1008 resulted in the loss of the cryptic plasmid.In three separate plant growth experiments, alfalfa nodules induced by each of the R. meliloti strain carrying both sym plasmids were assayed for hydrogen uptake activity. The average activity was 40-, 3.5-and 2-fold higher than with the respective pIJ1008-free strains. However, this higher activity was not accompanied by an increase in plant biomass or nitrogen content of shoots.C.B.R.I. Contribution Number: 1478     

Plasmid pSym1-32 of Rhizobium leguminosarumbv. viceae Controlling Nitrogen Fixation Activity,Effectiveness of Symbiosis,Competitiveness, and Acid Tolerance

The symbiotic plasmid (pSym1-32) of the highly effective Rhizobium leguminosarumbv. viceae1-32 strain was identified after the conjugal transfer of replicons carrying Tn5-mobinto the plasmidless Agrobacterium tumefaciensGm1-9023 strain. Plasmid pSym1-32 was transferred intoR. leguminosarumbv. viceaestrains Y14 (showing low effectiveness of symbiosis with Vicia villosa) and Y57 (unable to fix nitrogen). Transconjugants formed Fix⁺nodules on roots of V. villosaand had a highly enhanced nitrogen fixing ability, increased plant weight, and increased nitrogen accumulation compared to the recipient strains. Variation of transconjugants in symbiotic properties (accompanied by alterations in plasmid composition in some of the conjugants) was detected. Moreover, the donor strain R. leguminosarumbv. viceae1-32 was shown to be more efficient in the competitiveness and acid tolerance than the recipient Y14 strain. Both these properties were transmitted upon transfer of pSym1-32 into the recipient. Thus, plasmid pSym1-32 was shown to carry genes involved in the control of the nitrogen fixing ability, symbiotic effectiveness, competitiveness, and acid tolerance in R. leguminosarumbv. viceae.     

Host range,RFLP, and antigenic relationships betweenRhizobium fredii strains andRhizobium sp. NGR234

Rhizobium fredii is a nitrogen-fixing symbiont from China that combines broad host range for nodulation of legume species with cultivar specificity for nodulation of soybean. We have compared 10R. fredii strains withRhizobium sp. NGR234, a well known broad host range strain from Papua New Guinea. NGR234 nodulated 16 of 18 tested lugume species, and nodules on 14 of the 16 fixed nitrogen. TheR. fredii strains were not distinguishable from one another. They nodulated 13 of the legumes, and in only nine cases were nodules effective. All legumes nodulated byR. fredii were included within the host range of NGR234. Restriction fragment length polymorphisms (RFLPs) were detected with four DNA hybridization probes: the regulatory and commonnod genes,nodDABC; the soybean cultivar specificity gene,nolC; the nitrogenase structural genes, nifKDH; and RFRS1, a repetitive sequence fromR. fredii USDA257. A fifth locus, corresponding to a second set of soybean cultivar specificity genes,nolBTUVWX, was monomorphic. Using antisera against whole cells of threeR. fredii strains and NGR234, we separated the 11 strains into four serogroups. The anti-NGR234 sera reacted with a singleR. fredii strain, USDA191. Only one serogroup, which included USDA192, USDA201, USDA217, and USDA257, lacked cross reactivity with any of the others. Although genetic and phenotypic differences amongR. fredii strains were as great as those between NGR234 andR. fredii, our results confirm that NGR234 has a distinctly wider host range thanR. fredii.     

Rhodopseudomonas sphaeroides forma sp. denitrificans,a denitrifying strain as a subspecies of Rhodopseudomonas sphaeroides

From polluted water of a lagoon pond a new type of denitrifying photosynthetic purple bacteria was isolated. With respect to morphology, fine structure, photopigments, requirement for growth factors, the range of utilization of organic substrates for phototrophic growth and DNA base ratio, the denitrifying strains show the closest resemblance to Rhodopseudomonas sphaeroides and were therefore described as a subspecies named R. sphaeroides forma sp. denitrificans. The new isolates grow well with nitrate anaerobically in the dark accompanying the evolution of nitrogen gas. They cannot assimilate nitrate as the nitrogen source for growth.     

Characteristics of Plasmids in Rhizobium huakuii

Rhizobium huakuii nodulates Astragalus sinicus, an important green manuring crop in Southern China, which can be used as forage. The plasmid profiles of 154 R. huakuii strains were examined with the Eckhardt procedure. The plasmid number of the strains varied from one to five, and their molecular weights were estimated from 42 to 600 mDa or more. The plasmids were hybridized with probes nodABC and nifHDK. The results showed that there was one plasmid carrying the nod and nif genes in the strains that harbor two or more plasmids, and the molecular weights of the symbiotic plasmids varied from 117 to 251 mDa. Homology was not observed on plasmids in the strains having only one plasmid; presumably the symbiotic genes are on the chromosome. Plasmid curing was carried out with the Bacillus subtilus sacB to generate derivatives of Rhizobium huakuii strain CH203, which harbors three plasmids, pRHa(97MD), pRHb(168MD), and pRHc(251MD). The largest plasmid (pRHc) carried both nodulation and nitrogen fixation genes. When pRHc was cured, the strain lost its symbiotic ability. The other two plasmids were also related to symbiosis. The derivative cured of pRHb did not nodulate on the host plant, had an altered lipopolysaccharide, and grew much more slowly than the parent strain. Curing of the smallest plasmid (pRHa) resulted in delaying the strain nodulation and made it lose nitrogen fixation ability. Curing of each plasmid in strain CH203 reduced its acid tolerance. Complementation of plasmid-cured strains with appropriate plasmids restored their original phenotypes. Received: 18 December 1996 / Accepted: 28 March 1997     

Nitrogen fixation by Beijerinckia in relation to slime formation

Summary Results of studies of nitrogen fixation and slime formation in Derx's medium by sixteen strains of Beijerinckia indica showed that the amounts of nitrogen fixed at different periods were related positively and significantly with the amount of slime formed. From the rates of increase in nitrogen fixation with increase in slime formation the strains could be divided into two groups corresponding to (1) Beijerinckia indica with an average rate of increase of 0.066±0.003 and to (2) Beijerinckia indica var. alba with an average rate of increase of 0.132±0.010.     

高氨氮利用酵母菌的筛选及相关酶活性

【背景】蛋白饲料的缺乏,促进了蛋白含量高、安全性能好的酵母类单细胞蛋白的研究与应用。【目的】筛选氨氮利用能力强的菌株,为单细胞蛋白的发酵提供优良菌株。【方法】从土壤、奶制品、水果采集样品分离酵母菌,根据形态学和分子生物学鉴定菌株,然后以硫酸铵为唯一氮源培养基,测定菌落大小、菌体干重、蛋白质含量,复筛氨氮利用率高的酵母菌,并对复筛菌株氨同化相关酶活性进行测定。【结果】经过形态学、分子生物学鉴定和氨氮利用能力评价,获得3株高氨氮利用的酵母菌,分别是胶红酵母(Rhodotorula mucilaginosa)、酿酒酵母(Saccharomyces cerevisiae)和戴尔有孢圆酵母(Torulaspora delbrueckii)。通过比较3株酵母菌的谷氨酸脱氢酶、谷氨酸合成酶、谷氨酰胺合成酶活性,酿酒酵母的3种酶活性最高,其次是胶红酵母。【结论】从奶酪和西瓜中分离的胶红酵母N5和酿酒酵母J1具有较强的氨氮利用能力以及酶活性,可为单细胞蛋白发酵提供优良菌株。     

Ability of selected accessions of Phaseolus vulgaris L. to restrict nodulation by particular rhizobia

Plant genotypes that limit nodulation by indigenous rhizobia while nodulating normally with inoculant-strain nodule occupancy in Phaseolus vulgaris. In this study, eight of nine Rhizobium tropici strains and six of 15 Rhizobium etli strains examined, showed limited ability to nodulate and fix nitrogen with the two wild P. vulgaris genotypes G21117 and G10002, but were effective in symbiosis with the cultivated bean genotypes Jamapa and Amarillo Gigante. Five of the R. etli strains restricted in nodulation by G21117 and G10002 produced an alkaline reaction in yeast mannitol medium. In a competition experiment in which restricted strains were tested in 1:1 mixtures with the highly effective R. etli strain CIAT632, the restricted strains produced a low percentage of the nodules formed on G2117, but produced over 40% of the nodules formed on Jamapa. The interaction of the four Rhizobium strains with the two bean genotypes, based on the percentage of nodules formed, was highly significant (P<0.001).     

Characterization of frankial strains isolated from <Emphasis Type="Italic">Hippophae salicifolia</Emphasis> D. Don,based on physiological,SDS–PAGE of whole cell proteins and RAPD PCR analyses

Different Frankia strains (HsIi2, HsIi4, HsIi5, HsIi8, HsIi9, HsIi10, HsIi11, HsIi12, HsIi13, HsIi14) nodulating Hippophae salicifolia D. Don, were characterized on the basis of physiological, biochemical and molecular attributes. Results suggest that the physiological approaches i.e., nitrogenase activity, glutamine synthetase (GS) activity and ammonia excretion are strain specific. The highest rate of nitrogen fixation and maximum production of ammonia with low GS makes the strain HsIi11, a suitable biofertilizer as compared to other strains. Analysis of total protein pattern (SDS–PAGE) revealed that the most closely related strains HsIi10 and HsIi4 were found to be most distantly related to the most similar strains HsIi14, HsIi5, HsIi13, HsIi11 and HsIi12. RAPD PCR analyses with an arbitrary primer 1253 produced distinct, unique and specific DNA fingerprints for each of the Frankia strain and 100% polymorphism was observed which uncovers the genetic diversity. These approaches might be helpful in rapid identification, in designing the marker for the specific strains as well as in improving nitrogen fixation in agroforestry.     

Characterization of recA genes and recA mutants of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae

Summary DNA fragments carrying the recA genes of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae were isolated by complementing a UV-sensitive recA ^– Escherichia coli strain. Sequence analysis revealed that the coding region of the R. meliloti recA gene consists of 1044 by coding for 348 amino acids whereas the coding region of the R. leguminosarum bv. viciae recA gene has 1053 bp specifying 351 amino acids. The R. meliloti and R. leguminosarum bv. viciae recA genes show 84.8% homology at the DNA sequence level and of 90.1% at the amino acid sequence level. recA ^– mutant strains of both Rhizobium species were constructed by inserting a gentamicin resistance cassette into the respective recA gene. The resulting recA mutants exhibited an increased sensitivity to UV irradiation, were impaired in their ability to perform homologous recombination and showed a slightly reduced growth rate when compared with the respective wild-type strains. The Rhizobium recA strains did not have altered symbiotic nitrogen fixation capacity. Therefore, they represent ideal candidates for release experiments with impaired strains.The accession numbers: X59956 R. LEGUMINOSARUM REC A ALAS-DNA; X59957 R. MELITOTI REC A ALAS-DNA     

New taxonomic markers for identification of <Emphasis Type="Italic">Rhizobium leguminosarum</Emphasis> and discrimination between closely related species

Rhizobia, producing species-specific exopolysaccharides (EPSs), comprise a very diverse group of soil bacteria that are able to establish nitrogen-fixing symbioses with legumes. Based on the sequences of R. leguminosarum EPS synthesis genes, a sensitive and reliable PCR-based method for identification and subsequent discrimination between Rhizobium species has been developed and tested. For identification of R. leguminosarum, primer sets I–III complementary to sequences of rosR, pssA and pssY genes were proposed. Further sets of primers (IV–VII) were designed for discrimination between R. leguminosarum biovars. The usefulness of the method was examined using a wide range of R. leguminosarum strains isolated from different host plants nodules originating from different regions of Poland. We demonstrate a high discriminating power of primer sets I–III that allow distinguishing R. leguminosarum and two closely related species, R. etli and R. gallicum. This new approach is applicable to identification of R. leguminosarum strains, originating from nodules or soil, where many other closely related bacteria are expected to be present. Based on the nucleotide sequence of rosR and pssA genes, phylogenetic relationships of selected R. leguminosarum isolates were determined. Our results indicate that both rosR and pssA might be useful markers to differentiate and define relationships within a group of R. leguminosarum strains.     

Nodulation ofTrifolium subterraneum byRhizobium leguminosarum

Summary Four cultivars ofTrifolium subterraneum were nodulated by five strains ofRhizobium leguminosarum; all combinations except one gave 100% nodulation. Rates of nodule formation and total nodule numbers were similar to those with an effectiveR. trifolii strain. The nodules were more commonly associated with lateral roots and were ineffective in nitrogen fixation.     

酸性旱地红壤无机氮同化菌株筛选及其全基因组分析

微生物执行的无机氮同化作用可固定施入土壤后未被作物直接吸收的化学氮肥,有效减少化学氮肥损失、降低环境氮素污染风险。土壤无机氮同化作用不是由大量冗余微生物共同执行的,而是由一小部分功能微生物优先执行。【目的】对酸性旱地红壤中的优势无机氮同化细菌进行富集、菌株分离鉴定及全基因组测序,并明确菌株在土壤中的氮同化能力,为酸性土壤化学氮肥应用及其转化过程研究提供菌株资源和理论依据。【方法】在酸性旱地红壤中添加KNO3或(NH4)2SO4作为无机氮源,以葡萄糖作为碳源,在好氧条件下进行富集预培养,采用稀释分离法筛选出优势无机氮同化细菌菌株;将菌株回接至土壤中从而验证其无机氮同化能力,并通过全基因组测序分析菌株的氮素代谢途径及相关功能基因。【结果】酸性旱地红壤经富集预培养一周后,优势无机氮同化微生物的16SrRNA基因相对丰度从0.20%–0.94%增长至20.2%–30.2%;分离筛选后得到的3株优势无机氮同化细菌菌株,鉴定为伯克霍尔德氏菌(Burkholderia sp.) M6-3、索状芽孢杆菌(Bacillus funiculus) M2-4和节杆菌(Arthrobacter sp.) M7...