Alleviation of water stress effects in cowpea by Bradyrhizobium spp. inoculation

Experiments were carried out to investigate the effects of different degrees of water stress on cowpea in the presence and absence of Bradyrhizobium spp. inoculation and to evaluate physiological responses to stress. The soil used was Yellow Latosol, pH 6.3 and the crop used was cowpea (Vigna unguiculata (L.) Walp.) cv. ‘IPA 204’. Stress was applied continuously by the control of matric potential (ψ _m ) through a porous cup. The lowered soil ψ _m had a direct effect on the N2 fixation, but the strains Bradyrhizobium introduced by inoculation in the cowpea plants were superior to the indigenous strain demonstrating the importance of inoculation in the stressed plants. At the more negative ψ _m plants inoculated with the strains EI 6 formed associations of greater symbiotic efficiency which helped the cowpea plants to withstand drought stress better than the strain BR 2001 and the uninoculated control. The leghaemoglobin concentration was not inhibited in the drought-stressed plants at ψ _m -70 kPa when inoculated with the strain EI 6, which confered a differential degree of drought resistance in plants. The ψ _w declined in the stressed plants reaching values of -1.0 MPa which was sufficient to cause disturbance in nodulation and biomass production. This revised version was published online in June 2006 with corrections to the Cover Date.     

Detection of genic interactions by analyzing the F2 generation of diallel crosses

Summary The ability of the Hayman and Jinks method of analysis of diallel crosses to detect genic interactions was studied in peanuts. Six traits, measured in the F₂ generation of a diallel cross of four cultivars, were analyzed. In F₂ analyses of the diallel, least squares estimates of variance components D, H₁ , H₂, F, E, were used as an additional criteria for the adequacy of the diallel model. They were found to be in substantial agreement with the tests based on W_r and V_r values, and probably more reliable. The regression of W_r on V_r was shown to be unsuitable to detect duplicate gene type of interactions; it was detected, however, by the ratio of the mean within-F₂ — family variance and the variance among the parents. Using the different criteria, duplicate genes type of interactions was detected for two traits, complementary genes type was detected for one trait and three traits were found to fit the additive-dominance model without any genic interactions.     

Regulation of nitrogenase activity in Bradyrhizobium japonicum/soybean symbiosis by plant N status as determined by shoot C:N ratio

Regulation of nitrogenase is not sufficiently understood to engineer symbioses that achieve a high N₂ fixation rate under high levels of soil N. In the present hydroponic growth chamber study we evaluated the hypothesis that nitrogenase activity and the extent of its inhibition by NO₃⁻ may be related to both N and carbohydrate levels in plant tissues. A wide range of C:N ratios in various plant tissues (8.5 to 41.0, 1.9 to 3.7, and 0.8 to 1.8, respectively, in shoots, roots, and nodules) was generated through a combination of light and CO₂ levels, using two soybean genotypes differing in C and N acquisition rates. For both genotypes, N concentration in shoots was negatively correlated to nitrogenase activity and positively correlated to the extent of nitrogenase inhibition by NO₃⁻. Furthermore, nitrogenase activity was positively correlated to total nonstructural carbohydrates (TNC) and C:N ratio in shoot and nodules for both genotypes. Nitrogenase inhibition by NO₃⁻ was negatively correlated to TNC and C:N ratio in shoots, but not in nodules for both genotypes. At the onset of nitrogenase inhibition by NO₃⁻, C:N ratio declined in shoots but not in nodules. These results indicate that both C and N levels in plant tissues are involved in regulation of nitrogenase activity. We suggest that the level of nitrogenase activity may be determined by (1) N needs (as determined by shoot C:N) and (2) availability of carbohydrates in nodules. Modulation of the nitrogenase activity may occur through sensing changes in plant N, i.e. changes in shoot C:N ratio, possibly through some phloem translocatable compound(s).     

Quantification of Campylobacter spp. in pig feces by direct real-time PCR with an internal control of extraction and amplification

The rapid and direct quantification of Campylobacter spp. in complex substrates like feces or environmental samples is crucial to facilitate epidemiological studies on Campylobacter in pig production systems. We developed a real-time PCR assay for detecting and quantifying Campylobacter spp. directly in pig feces with the use of an internal control. Campylobacter spp. and Yersinia ruckeri primers-probes sets were designed and checked for specificity with diverse Campylobacter, related organisms, and other bacterial pathogens before being used in field samples. The quantification of Campylobacter spp. by the real-time PCR then was realized on 531 fecal samples obtained from experimentally and naturally infected pigs; the numeration of Campylobacter on Karmali plate was done in parallel. Yersinia ruckeri, used as bacterial internal control, was added to the samples before DNA extraction to control DNA-extraction and PCR-amplification. The sensitivity of the PCR assay was 10 genome copies. The established Campylobacter real-time PCR assay showed a 7-log-wide linear dynamic range of quantification (R² = 0.99) with a detection limit of 200 Colony Forming Units of Campylobacter per gram of feces. A high correlation was found between the results obtained by real-time PCR and those by culture at both qualitative and quantitative levels. Moreover, DNA extraction followed by real-time PCR reduced the time needed for analysis to a few hours (within a working day). In conclusion, the real-time PCR developed in this study provides new tools for further epidemiological surveys to investigate the carriage and excretion of Campylobacter by pigs.     

Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction.

In order to develop a rapid and specific detection test for bacteria in soil, we improved a method based on the polymerase chain reaction (PCR). Each step of the protocol, including direct lysis of cells, DNA purification, and PCR amplification, was optimized. To increase the efficiency of lysis, a step particularly critical for some microorganisms which resist classical techniques, we used small soil samples (100 mg) and various lytic treatments, including sonication, microwave heating, and thermal shocks. Purification of nucleic acids was achieved by passage through up to three Elutip d columns. Finally, PCR amplifications were optimized via biphasic protocols using booster conditions, lower denaturation temperatures, and addition of formamide. Two microorganisms were used as models: Agrobacterium tumefaciens, which is naturally absent from the soil used and was inoculated to calibrate the validity of the protocol, and Frankia spp., an actinomycete indigenous to the soil used. Specific primers were characterized either in the plasmid-borne vir genes for A. tumefaciens or in the variable regions of the 16S ribosomal gene for Frankia spp. Specific detection of the inoculated A. tumefaciens strain was routinely obtained when inocula ranged from 10(7) to 10(3) cells. Moreover, the strong correlation we observed between the size of the inocula and the results of the PCR reactions permitted assessment of the validity of the protocol in enumerating the number of microbial cells present in a soil sample. This allowed us to estimate the indigenous population of Frankia spp. at 0.2 x 10(5) genomes (i.e., amplifiable target sequences) per g of soil.     

Detection of bacteria in environmental samples by direct PCR without DNA extraction

Cultured cells and environmental samples were used directly in PCRs without the isolation of DNA. Serial dilution was used to eliminate the inhibitory effect of materials in natural samples. Primers specific for pmoA, which encodes a subunit of the particulate methane monooxygenase, were used to detect and quantify methanotrophic bacteria by direct most probable number PCR. Phototrophic bacteria were detected in environmental samples by direct PCR with primers specific for pufM, and members of the bacterial domain were detected with primers for 16S rDNA. Direct PCR provides a rapid, simple, and sensitive methodfor detecting and quantifying bacteria in environmental samples. Detection of methanotrophic bacteria can be applied to monitoring bioremediation.     

Isolation and characterization of the DNA region encoding nodulation functions in Bradyrhizobium japonicum.

The DNA region encoding early nodulation functions of Bradyrhizobium japonicum 3I1b110 (I110) was isolated by its homology to the functionally similar region from Rhizobium meliloti. Isolation of a number of overlapping recombinant clones from this region allowed the construction of a restriction map of the region. The identified nodulation region of B. japonicum shows homology exclusively to those regions of R. meliloti and Rhizobium leguminosarum DNA known to encode early nodulation functions. The region of homology with these two fast-growing Rhizobium species was narrowed to an 11.7-kilobase segment. A nodulation-defective mutant of Rhizobium fredii USDA 201, strain A05B-2, was isolated and found to be defective in the ability to curl soybean root hairs. Some of the isolated recombinant DNA clones of B. japonicum were found to restore wild-type nodulation function to this mutant. Analysis of the complementation results allows the identification of a 1.8-kilobase region as essential for restoration of Hac function.     

Detection of Helicobacter pylori in water by direct PCR

AIMS: This paper demonstrates a rapid, simple method for the detection of Helicobacter pylori in water that eliminates the need for recovery of cells or DNA extraction prior to PCR. METHODS AND RESULTS: Direct polymerase chain reaction (DPCR) with primers specific for H. pylori ureA (urease, subunit A) were used to detect H. pylori added to groundwater. DPCR also detected H. pylori in a naturally contaminated water sample. CONCLUSIONS: DPCR should provide an improved method to assess contamination of water by H. pylori. SIGNIFICANCE AND IMPACT OF THE STUDY: This simple, rapid method for detection of H. pylori in water will provide an improved means to investigate the possible role of water as a disease vector.     

Detection of Polymorphic DNA and Taxonomic Relationships Among 10 Wild Perennial Soybean Species Using Specific and Arbitrary Nucleotide Primers

Polymorphic DNA in complex genomes of agronomic crops can be detected using specific nucleotide and arbitrary primers and the polymerase chain reaction (PCR). Nineteen accessions representing 10 species of the wild perennial soybean were evaluated using 4 sets of specific primers and 3 sets of random amplified polymorphic DNAs (RAPD) primers. The potential of the RAPD assays was further increased by combining two primers in a single PCR. The fragments generated by the two assays discriminated 10 wild species by banding profiles. The size of the amplified DNA fragments ranged from 100 to 2100 base pairs. The resolved PCR products yielded highly characteristic and homogeneous DNA fingerprints. The fingerprints were useful not only for investigating genetic variability but also for further characterizing the wild soybean species by detecting inter- and intra-specific polymorphisms, constructing dendrograms defining the phylogenetic relationships among these species, and identifying molecular markers for the construction of genetic linkage maps. Furthermore, unique markers distinguishing particular species were also identified. Thus, it is expected that PCR will have great relevance for taxonomic studies. This revised version was published online in July 2006 with corrections to the Cover Date.     

Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction.

It was the aim of this study to specifically detect the DNA sequences for the bphC gene, the meta-cleavage enzyme of the aerobic catabolic pathway for biphenyl and polychlorinated biphenyl degradation, in aquatic sediments without prior cultivation of microorganisms by using extraction of total DNA, PCR amplification of bphC sequences, and detection with specific gene probes. The direct DNA extraction protocol used was modified to enhance lysis efficiency. Crude extracts of DNA were further purified by gel filtration, which yielded DNA that could be used for the PCR. PCR primers were designed for conserved regions of the bphC gene from a sequence alignment of five known sequences. The specificity of PCR amplification was verified by using digoxigenin-labeled DNA probes which were located internal to the amplified gene sequence. The detection limit for the bphC gene of Pseudomonas paucimobilis Q1 and Pseudomonas sp. strain LB400 was 100 cells per g (wet weight) or approximately five copies of the target sequence per PCR reaction mixture. In total-DNA extracts of aerobic top layers of sediment samples obtained from three different sampling sites along the Elbe River, which has a long history of anthropogenic pollution, Pseudomonas sp. strain LB 400-like sequences for the bphC gene were detected, but P. paucimobilis Q1 sequences were not detected. No bphC sequences were detected in an unpolluted lake sediment. A restriction analysis did not reveal any heterogeneity in the PCR product, and the possibility that sequences highly related to the bphC gene (namely, nahC and todE) were present was excluded.(ABSTRACT TRUNCATED AT 250 WORDS)     

Changes in CO2 Exchange Rate,Stomatal Conductance,Activities of Photosystems 1 and 2, and Chloroplast Polypeptide Profile Induced by Simulated Acidic Rain

In seedlings of Vigna radiata (L.) R. Wilczek cultivars ADT-1 and CO-5 exposed to acidic showers (H2SO4 : HNO3 : HCl, 4 : 2 : 1, v/v) of different pH (7.0, 5.5, 4.0, and 2.5) for 10 d, net CO2 uptake and stomatal conductance were reduced. The chlorophyll (Chl) a and b contents were reduced but the carotenoid (Car) content increased. In vivo Chl a fluorescence patterns of both the cultivars were altered. No significant change in photosystem (PS) 1 activity was observed except at pH 2.5 where an inhibition was evident. By contrast, PS2 activities declined rapidly with increasing acidity. The room temperature absorption spectra of isolated chloroplasts showed very little changes. SDS-PAGE analysis revealed depletion of 23, 33, and 55 kDa polypeptides. Cultivar CO-5 was more sensitive to acidic rain than cv. ADT-1.     

Effects of ultraviolet-B radiation on plants during mild water stress. III. Effects on photosynthetic recovery and growth in soybean

Soybean { Glycine max (L.) Merr. ev. Essex} was grown from seed in a greenhouse under ultraviolet-B (UV-B, 280–320 nm) radiation supplied by filtered FS-40 sunlamps. On a weighted, total daily dose basis these plants received either 0 (control) or 2875 effective J m⁻² day⁻¹ UV-B_BE. When weighted with the generalized plant action spectrum (Caldwell 1971), this simulated the solar ultraviolet-B irradiance expected to occur at College Park, Maryland, USA (39°N) in the event the global stratospheric ozone column is reduced by 23%. The effects of ultraviolet radiation on the photosynthetic recovery from water stress were measured with an infrared gas analyzer. These effects were examined in plants which were either well-watered or previously preconditioned to water stress, during two distinct phenological stages of development. During the early stages of soybean growth, enhanced levels of UV-B reduced net photosynthesis by 25%, and water stress also reduced photosynthesis to nearly the same extent (by 20%). The combination of these two stresses resulted in smaller biomass than that produced by plants exposed to either stress independently. Photosynthesis in older, larger plants was much more sensitive to water stress and was reduced by as much as 50–60% in non-preconditioned plants. Although non-irradiated, non-preconditioned (control) plants recovered to only within 60% of their prestressed value, preconditioned plants recovered to within 70–80% during the 3 day recovery period. Both water stress and UV-B radiation affected non-stomatal conductance, while stomatal conductance was primarily affected by water stress.     

Detection of Sphingomonas spp in soil by PCR and sphingolipid biomarker analysis

Sphingomonas spp possess unique abilities to degrade refractory contaminants and are found ubiquitously in the environment. We developed Sphingomonas genus-specific PCR primers (SPf-190 and SPr1-852) which showed specific amplification of a 627-bp 16S rDNA fragment from Sphingomonas spp. A PCR assay using these Sphingomonas specific primers was developed to detect Sphingomonas aromaticivorans B0695R in three texturally distinct soil types, showing detection limits between 1.3–2.2 × 10³ CFU g⁻¹ dry soil. A sphingolipid extraction protocol was also developed to monitor Sphingomonas populations in soil quantitatively. The detection limit of the assay was 20 pmol g⁻¹ dry soil, equivalent to about 3 × 10⁵ cells g⁻¹ dry soil. Survival of S. aromaticivorans B0695R was monitored in the three different soils by antibiotic selective plate counting, PCR and sphingolipid analysis. All three approaches showed that the B0695R cells persisted in the low biomass Sequatchie sub-soil at about 3–5 × 10⁷cells g⁻¹ dry soil. In comparison to the plate counting assay, both the PCR and sphingolipid analysis detected a significantly higher level of B0695R cells in the clay soil and Sequatchie top-soil, indicating the possibility of the presence of viable but non-culturable B0695R cells in the soils. The combination of PCR and sphingolipid analysis may provide a more realistic estimation of Sphingomonas population in the environment. Received 17 March 1999/ Accepted in revised form 07 April 1999     

Changes in the mineral composition of soybean xylem sap during monocarpic senescence and alterations by depodding

Evidence from earlier studies with explants (stem cutting with a leaf and a pod) indicates that a decline in the supply of mineral nutrients from the roots may prepare the leaves for induction of monocarpic senescence in soybean [ Glycine max (L.) Merrill cv. Anoka). In order to assess the changes in mineral flux from the root system, xylem sap was collected from a decapitated plant under 100 kPa pressure over 50 min. The sap volume yield declines after flowering starts, but increases during pod extension and then decreases again during podfill. The concentrations of K, Ca, Mg, P, S, Zn, Fe, Mn, Cu, Mo and Si rise and then fall during reproductive development, but the exact timing differs among the elements. In contrast, B, Al and Na concentrations show a slow rise initially with a large increase in late pod development. Depodding, which prevents the early death of the plant, inhibits the changes of some elements (K, Mg) but not others (Ca. Mg, P, S, Zn. Fe. Mn, B, Cu, Al), and it does not prevent the decrease in sap volume delivered. Inasmuch as the mineral concentration of xylem sap quantitatively reflects upward mineral flux, the supply of most minerals to the shoot declines, and this decrease seems to be an important factor in the preparatory phase of monocarpic senescence. The different minerals show different patterns of change, which indicate differences in the transport mechanisms and their regulation.     

Detection of genetic variation in Bradyrhizobium japonicum USDA 110 variants using DNA fingerprints generated with GC rich arbitrary PCR primers

Bradyrhizobium japonicum USDA 110 has been shown to contain several genetically similar naturally occurring colony morphology variants. These variants differ in symbiotic nitrogen fixation ability and in the utilization of various carbon substrates. They have been shown to share extensive DNA homology and appear to be derived from a common ancestor. Despite these similarities certain B. japonicum USDA 110 variants have been shown to be devoid of symbiotic nitrogen fixation. One of these variants (L2-110), however, was recently shown to possess significant levels of explanta nitrogen fixation and to synthesize functional dinitrogenase enzyme within bacteroids. In an effort to identify genetic markers which could explain differences in symbiotic nitrogen fixation between B. japonicum variants, DNA fingerprints were generated by PCR using arbitrary primers. Two of these primers with GC rich sequences were able to differentiate between B. japonicum USDA 110 variants I-110, L2-110, and MN-110. Unique markers have now been identified which could be examined further to determine if they explain the differences in symbiotic nitrogen fixation between USDA 110 variants.