Comparison of molecular and antibiotic resistance profile methods for the population analysis of Bradyrhizobium spp. (TGx) isolates that nodulate the new TGx soybean cultivars in Africa.

AIMS: Comparison of molecular and antibiotic resistance profile methods to identify an easy method that can differentiate between strains of introduced Bradyrhizobium japonicum and the indigenous Bradyrhizobium spp. (TGx) isolates which nodulate the newly developed TGx soybean cultivars in Africa. METHODS AND RESULTS: Restriction fragment length polymorphism (RFLP) of 16S rDNA generated by five restriction enzymes, banding patterns in Southern hybridization using nod and nif genes as probes, and resistance patterns of the isolates to nine antibiotics, were used to group 26 Bradyrhizobium spp. (TGx) isolates and four other Bradyrhizobium strains. The clusters of isolates obtained from the four grouping methods were all different, although all methods revealed large genetic diversity among the isolates. CONCLUSIONS: Results indicate that the antibiotic resistance profile method is as good as the three molecular methods used in this study for phylogenetic grouping of the Bradyrhizobium spp. (TGx) isolates, which may serve as a basis for further characterization of selected isolates from each group. SIGNIFICANCE AND IMPACT OF THE STUDY: The antibiotic resistance profile method can be used as a simple means of assessing genetic variability and grouping of a large number of Bradyrhizobium spp. (TGx) isolates. Representative isolates from each group can then be selected for further characterization.

Bradyrhizobium spp. (TGx) isolates nodulating the new soybean cultivars in Africa are diverse and distinct from bradyrhizobia that nodulate North American soybeans.

The newly developed cultivars of soybean in Africa, known as Tropical Glycine cross (TGx), are nodulated by bradyrhizobia indigenous to African soils, here designated Bradyrhizobium spp. (TGx). Isolates of Bradyrhizobium spp. (TGx) obtained from nodules of TGx soybeans that were inoculated with soils from 65 locations in six African countries were characterized and grouped into 11 phylogenetic clusters on the basis of RFLP of the 16S rRNA gene. Five restriction enzymes (RsaI, HinfI, MspI, CfoI and HaeIII) established RFLP groups within these Bradyrhizobium spp. (TGx) isolates, which were used to construct a phylogenetic tree showing their genetic relationship with other Bradyrhizobium species. RFLP analysis indicated that Bradyrhizobium spp. (TGx) is a heterogeneous group with some isolates related to Bradyrhizobium japonicum and Bradyrhizobium elkanii strains and some to Bradyrhizobium spp. (misc.) reference strains isolated from a variety of tropical legumes. The heterogeneity within the large phylogenetic clusters was further examined through analysis of randomly amplified polymorphic DNA (RAPD) using GC-rich PCR primers. The RAPD analysis showed additional heterogeneity in the Bradyrhizobium spp. (TGx) phylogenetic clusters, which was not revealed by separations based on RFLP analysis. The Bradyrhizobium spp. (TGx) isolates were classified into effective and ineffective types based on their symbiotic performance on TGx soybean. The isolates were randomly distributed throughout the phylogenetic clusters regardless of their symbiotic effectiveness on TGx soybean.

Variability among Rhizobium Strains Originating from Nodules of Vicia faba.

Rhizobium strains from nodules of Vicia faba were diverse in plasmid content and serology. Results of multilocus gel electrophoresis and restriction fragment length polymorphism indicated several deep chromosomal lineages among the strains. Linkage disequilibrium among the chromosomal types was detected and may have reflected variation of Rhizobium strains in the different geographical locations from which the strains originated. An investigation of pea strains with antibodies prepared against fava bean strains and restriction fragment length polymorphism analyses, targeting DNA regions coding for rRNA and nodulation, indicated that Rhizobium strains from V. faba nodules were distinguishable from those from Pisum sativum, V. villosa, and Trifolium spp.

The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans.

Several soybean genotypes have been identified which specifically exclude nodulation by members of Bradyrhizobium japonicum serocluster 123. We have identified and sequenced a DNA region from B. japonicum strain USDA 110 which is involved in genotype-specific nodulation of soybeans. This 2.3-kilobase region, cloned in pMJS12, allows B. japonicum serocluster 123 isolates to form nodules on plants of serogroup 123-restricting genotypes. The nodules, however, were ineffective for symbiotic nitrogen fixation. The nodulation-complementing region is located approximately 590 base pairs transcriptionally downstream from nodD2. The 5' end of pMJS12 contains a putative open reading frame (ORF) of 710 base pairs, termed nolA. Transposon Tn3-HoHo mutations only within the ORF abolished nodulation complementation. The N terminus of the predicted nolA gene product has strong similarity with the N terminus of MerR, the regulator of mercury resistance genes. Translational lacZ fusion experiments indicated that nolA was moderately induced by soybean seed extract and the isoflavone genistein. Restriction fragments that hybridize to pMJS12 were detected in genomic DNAs from both nodulation-restricted and -unrestricted strains.

DNA Hybridization Probe for Use in Determining Restricted Nodulation among Bradyrhizobium japonicum Serocluster 123 Field Isolates.

Several soybean plant introduction (PI) genotypes have recently been described which restrict nodulation of Bradyrhizobium japonicum serocluster 123 in an apparently serogroup-specific manner. While PI 371607 restricts nodulation of strains in serogroup 123 and some in serogroup 127, those in serogroup 129 are not restricted. When DNA regions within and around the B. japonicum I-110 common nodulation genes were used as probes to genomic DNA from the serogroup strains USDA 123, USDA 127, and USDA 129, several of the probes differentially hybridized to the nodulation-restricted and -unrestricted strains. One of the gene regions, cloned in plasmid pMJS12, was subsequently shown to hybridize to 4.6-kilobase EcoRI fragments from DNAs from nodulation-restricted strains and to larger fragments in nodulation-unrestricted strains. To determine if the different hybridization patterns could be used to predict nodulation restriction, we hybridized pMJS12 to EcoRI-digested genomic DNAs from uncharacterized serocluster 123 field isolates. Of the 36 strains examined, 15 were found to have single, major, 4.6-kilobase hybridizing EcoRI fragments. When tested for nodulation, 80% (12 of 15) of the strains were correctly predicted to be restricted for nodulation of the PI genotypes. In addition, hybridization patterns obtained with pMJS12 and nodulation phenotypes on PI 371607 indicated that there are at least three types of serogroup 127 strains. Our results suggest that the pMJS12 gene probe may be useful in selecting compatible host-strain combinations and in determining the suitability of field sites for the placement of soybean genotypes containing restrictive nodulation alleles.

Host Plant Effects on Nodulation and Competitiveness of the Bradyrhizobium japonicum Serotype Strains Constituting Serocluster 123.

Strains in Bradyrhizobium japonicum serocluster 123 are the major indigenous competitors for nodulation in a large portion of the soybean production area of the United States. Serocluster 123 is defined by the serotype strains USDA 123, USDA 127, and USDA 129. The objective of the work reported here was to evaluate the ability of two soybean genotypes, PI 377578 and PI 417566, to restrict the nodulation and reduce the competitiveness of serotype strains USDA 123, USDA 127, and USDA 129 in favor of the highly effective strain CB1809 and to determine how these soybean genotypes alter the competitive relationships among the three serotype strains in the serocluster. The soybean genotypes PI 377578 and PI 417566 along with the commonly grown cultivar Williams were planted in soil essentially free of soybean rhizobia and inoculated with single-strain treatments of USDA 123, USDA 127, USDA 129, or CB1809 and six dual-strain competition treatments of USDA 123, USDA 127, or USDA 129 versus CB1809, USDA 123 versus USDA 127, USDA 123 versus USDA 129, and USDA 127 versus USDA 129. PI 377578 severely reduced the nodulation and competitiveness of USDA 123 and USDA 127, while PI 417566 similarly affected the nodulation and competitiveness of USDA 129. Thus, the two soybean genotypes can reduce the nodulation and competitiveness of each of the three serocluster 123 serotype strains. Our results indicate that host control of restricted nodulation and reduced competitiveness is quite specific and effectively discriminates between B. japonicum strains which are serologically related.

Nodulation and Nitrogen Fixation Efficacy of Rhizobium fredii with Phaseolus vulgaris Genotypes.

Phaseolus plant introduction (PI) genotypes (consisting of 684 P. vulgaris, 26 P. acutifolius, 39 P. lunatus, and 5 P. coccineus accessions) were evaluated for their ability to form effective symbioses with strains of six slow-growing (Bradyrhizobium) and four fast-growing (Rhizobium fredii) soybean rhizobia. Of the 684 P. vulgaris genotypes examined, three PIs were found to form effective nitrogen-fixing symbioses with the R. fredii strains. While none of the Bradyrhizobium strains nodulated any of the genotypes tested, some produced large numbers of undifferentiated root proliferations (hypertrophies). A symbiotic plasmid-cured R. fredii strain failed to nodulate the P. vulgaris PIs and cultivars, suggesting that P. vulgaris host range genes are Sym plasmid borne in the fast-growing soybean rhizobia.

Influence of Glycine spp. on Competitiveness of Bradyrhizobium japonicum and Rhizobium fredii.

The displacement of indigenous Bradyrhizobium japonicum in soybean nodules with more effective strains offers the possibility of enhanced N(2) fixation in soybean (Glycine max (L.) Merr.). Our objective was to determine whether the wild soybean (G. soja Sieb. & Zucc.) genotype PI 468397 would cause reduced competitiveness of important indigenous B. japonicum strains USDA 31, 76, and 123 and thereby permit nodulation by Rhizobium fredii, the fast-growing microsymbiont of soybean. In an initial experiment, PI 468397 nodulated and fixed moderate amounts of N(2) with USDA 31 and 76 but, despite the formation of nodules, fixed essentially no N(2) with USDA 123. In contrast, PI 468397 formed a highly effective symbiosis with R. fredii strain USDA 193. In two subsequent experiments, Williams soybean and PI 468397 were grown in a pasteurized soil mixture or in soybean rhizobium-free soil and inoculated with both USDA 123 and USDA 193. In each experiment, more than 90% of the nodules of Williams contained USDA 123, while only a maximum of 2% were occupied with USDA 193. In contrast, in the two experiments, 16 and 11%, respectively, of the nodules produced on PI 468397 were occupied by USDA 123, while in both experiments 87% contained USDA 193. Thus, in relation to the cultivar Williams, which is commonly grown and used as a parent in soybean breeding programs in the United States, PI 468397 substantially reduced the competitive ability of B. japonicum strain USDA 123 in relation to R. fredii strain USDA 193.

Genetic Diversity in Bradyrhizobium japonicum Serogroup 123 and Its Relation to Genotype-Specific Nodulation of Soybean.

The genetic diversity among 20 field isolates of Bradyrhizobium japonicum serogroup 123 was examined by using restriction endonuclease digestions, one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cell proteins, Southern hybridization analysis of nif and nod genes, and intrinsic antibiotic resistance profiles. All of the isolates were previously separated into three broad nodulation classes (low, medium, and high) based on their ability to form symbioses with specific soybean genotypes. Results of our studies indicate that there is a relationship between these three genotype-specific nodulation classes and groupings that have been made based on genomic DNA digestion patterns, sodium dodecyl sulfate-protein profiles, and Southern hybridizations to a nifHD gene probe. Intrinsic antibiotic resistance profiles and nodAB gene hybridizations were not useful in determining interrelationships between isolates and nodulation classes. Southern hybridizations revealed that two of the isolates had reiterated nod genes; however, there was no correlation between the presence of extra nodAB genes and the nodulation classes or symbiotic performance on permissive soybean genotypes. Hybridizations with the nif gene probe indicated that there is a relationship among serogroup, nodulation class, and the physical organization of the genome.

Nodulation and Competition for Nodulation of Selected Soybean Genotypes among Bradyrhizobium japonicum Serogroup 123 Isolates.

Twenty recently obtained field isolates of Bradyrhizobium japonicum serogroup 123 were tested for their nodule mass production on the standard commercial soybean (Glycine max (L.) Merr. cv. Williams) and on two soybean plant introduction (PI) genotypes previously determined to restrict nodulation by strain USDA 123. Four of the field isolates showed similar restricted nodulation on the two genotypes, while all 20 isolates produced a normal amount of nodules on G. max cv. Williams. Serological analyses with adsorbed fluorescent antibodies showed that members of the 123 serotype ranked low in nodulation of the two PIs, in contrast to members of serotypes 127 and 129. Competition studies on the PIs indicated that isolates which were restricted were not competitive for nodule occupancy against strain USDA 110. However, unrestricted isolates of serogroup 123 were very competitive against USDA 110. On G. max cv. Williams, all serogroup 123 isolates tested were very competitive against USDA 110.

Serological Relatedness of Rhizobium fredii to Other Rhizobia and to the Bradyrhizobia.

Several isolates of Rhizobium fredii were examined for their serological relatedness to each other, to Bradyrhizobium japonicum, and to other fast- and slow-growing rhizobia. Immunofluorescence, agglutination, and immunodiffusion analyses indicated that R. fredii contains at least three separate somatic serogroups, USDA 192, USDA 194, and USDA 205. There was no cross-reaction between any of the R. fredii isolates and 13 of the 14 B. japonicum somatic serogroups tested. Cross-reactions were obtained with antisera from R. fredii and serogroup 122 of B. japonicum, Rhizobium meliloti, and several fast-growing Rhizobium spp. for Leucaena, Sesbania, and Lablab species. The serological relationship between R. fredii and R. meliloti was examined in more detail, and of 23 R. meliloti strains examined, 8 shared somatic antigens with the type strains from all three R. fredii serogroups. The serological relatedness of R. fredii to B. japonicum and R. meliloti appears to be unique since the strains are known to be biochemically and genetically diverse.

Long-Term Effects of Metal-Rich Sewage Sludge Application on Soil Populations of Bradyrhizobium japonicum.

The application of sewage sludge to land may increase the concentration of heavy metals in soil. Of considerable concern is the effect of heavy metals on soil microorganisms, especially those involved in the biocycling of elements important to soil productivity. Bradyrhizobium japonicum is a soil bacterium involved in symbiotic nitrogen fixation with Glycine max, the common soybean. To examine the effect of metal-rich sludge application on B. japonicum, the MICs for Pb, Cu, Al, Fe, Ni, Zn, Cd, and Hg were determined in minimal media by using laboratory reference strains representing 11 common serogroups of B. japonicum. Marked differences were found among the B. japonicum strains for sensitivity to Cu, Cd, Zn, and Ni. Strain USDA 123 was most sensitive to these metals, whereas strain USDA 122 was most resistant. In field studies, a silt loam soil amended 11 years ago with 0, 56, or 112 Mg of digested sludge per ha was examined for total numbers of B. japonicum by using the most probable number method. Nodule isolates from soybean nodules grown on this soil were serologically typed, and their metal sensitivity was determined. The number of soybean rhizobia in the sludge-amended soils was found to increase with increasing rates of sludge. Soybean rhizobia strains from 11 serogroups were identified in the soils; however, no differences in serogroup distribution or proportion of resistant strains were found between the soils. Thus, the application of heavy metal-containing sewage sludge did not have a long-term detrimental effect on soil rhizobial numbers, nor did it result in a shift in nodule serogroup distribution.

Anaerobic Growth and Denitrification among Different Serogroups of Soybean Rhizobia.

We screened soybean rhizobia originating from three germplasm collections for the ability to grow anaerobically in the presence of NO(3) and for differences in final product formation from anaerobic NO(3) metabolism. Denitrification abilities of selected strains as free-living bacteria and as bacteroids were compared. Anaerobic growth in the presence of NO(3) was observed in 270 of 321 strains of soybean rhizobia. All strains belonging to the 135 serogroup did not grow anaerobically in the presence of NO(3). An investigation with several strains indicated that bacteria not growing anaerobically in the presence of NO(3) also did not utilize NO(3) as the sole N source aerobically. An exception was strain USDA 33, which grew on NO(3) but failed to denitrify. Dissimilation of NO(3) by the free-living cultures proceeded without the significant release of intermediate products. Nitrous oxide reductase was inhibited by C(2)H(2), but preceding steps of denitrification were not affected. Final products of denitrification were NO(2), N(2)O, or N(2); serogroups 31, 46, 76, and 94 predominantly liberated NO(2), whereas evolution of N(2) was prevalent in serogroups 110 and 122, and all three were formed as final products by strains belonging to serogroups 6 and 123. Anaerobic metabolism of NO(3) by bacteroid preparations of Bradyrhizobium japonicum proceeded without delay and was evident by NO(2) accumulation irrespective of which final product was formed by the strain as free-living bacteria. Anaerobic C(2)H(2) reduction in the presence of NO(3) was observed in bacteroid preparations capable of NO(3) respiration but was absent in bacteria that were determined to be deficient in dissimilatory nitrate reductase.

Relationship between Ureide N and N(2) Fixation, Aboveground N Accumulation, Acetylene Reduction, and Nodule Mass in Greenhouse and Field Studies with Glycine max L. (Merr).

The relationship between ureide N and N(2) fixation was evaluated in greenhouse-grown soybean (Glycine max L. Merr.) and lima bean (Phaseolus lunatus L.) and in field studies with soybean. In the greenhouse, plant N accumulation from N(2) fixation in soybean and lima bean correlated with ureide N. In soybean, N(2) fixation, ureide N, acetylene reduction, and nodule mass were correlated when N(2) fixation was inhibited by applying KNO(3) solutions to the plants. The ureide-N concentrations of different plant tissues and of total plant ureide N varied according to the effectiveness of the strain of Bradyrhizobium japonicum used to inoculate plants. The ureide-N concentrations in the different plant tissues correlated with N(2) fixation. Ureide N determinations in field studies with soybean correlated with N(2) fixation, aboveground N accumulation, nodule weight, and acetylene reduction. N(2) fixation was estimated by (15)N isotope dilution with nine and ten soybean genotypes in 1979 and 1980, respectively, at the V9, R2, and R5 growth stages. In 1981, we investigated the relationship between ureide N, aboveground N accumulation, acetylene reduction, and nodule mass using four soybean genotypes harvested at the V4, V6, R2, R4, R5, and R6 growth stages. Ureide N concentrations of young stem tissues or plants or aboveground ureide N content of the four soybean genotypes varied throughout growth correlating with acetylene reduction, nodule mass, and aboveground N accumulation. The ureide-N concentrations of young stem tissues or plants or aboveground ureide-N content in three soybean genotypes varied across inoculation treatments of 14 and 13 strains of Bradyrhizobium japonicum in 1981 and 1982, respectively, and correlated with nodule mass and acetylene reduction. In the greenhouse, results correlating nodule mass with N(2) fixation and ureide N across strains were variable. Acetylene reduction in soybean across host-strain combinations did not correlate with N(2) fixation and ureide N. N(2) fixation, ureide N, acetylene reduction, and nodule mass correlated across inoculation treatments with strains of Bradyrhizobium spp. varying in effectiveness on lima beans. Our data indicate that ureide-N determinations may be used as an additional method to acetylene reduction in studies of the physiology of N(2) fixation in soybean. Ureide-N measurements also may be useful to rank strains of B. japonicum for effectiveness of N(2) fixation.

Rhizobium japonicum Serogroup and Hydrogenase Phenotype Distribution in 12 States.

A survey was conducted in 1980 on 972 isolates of Rhizobium japonicum obtained from 65 soybean field locations in 12 states. Isolates were examined for the hydrogenase (Hup) phenotype and somatic serogroup identity. Only 20% of the isolates were Hup, with a majority of Hup isolates occurring in 10 of the 12 states. The most predominant serogroup was 31 (21.5%), followed by 123 (13.6%). Although most serogroups contained a majority of Hup isolates, marked differences occurred. None of the isolates in serogroup 135 were Hup, but 93% of the isolates in serogroup 122 were Hup. The serogroups with relatively high frequencies of Hup isolates (122 and 110) constitute only a small part (<5% each) of the R. japonicum field population in the 12 states.

A Comparative Study of the Physiology of Symbioses Formed by Rhizobium japonicum with Glycine max, Vigna unguiculata, and Macroptilium atropurpurem.

Although Rhizobium japonicum nodulates Vigna unguiculata and Macroptilium atropurpurem, little is known about the physiology of these symbioses. In this study, strains of R. japonicum of varying effectiveness on soybean were examined. The nonhomologous hosts were nodulated by all the strains tested, but effectiveness was not related to that of the homologous host. On siratro, compared to soybean, many strains reversed their relative effectiveness ranking. Both siratro and cowpea produced more dry matter with standard cowpea rhizobia CB756 and 176A22 than with the strains of R. japonicum. Strains USDA33 and USDA74 were more effective with siratro and cowpea than with soybean. The strain USDA122 expressed high rates of hydrogenase activity in symbiosis with the cowpea as well as the soybean host. The strains USDA61 and USDA74 expressed low levels of hydrogenase activity in symbiosis with cowpea, but no activity was found with soybean. Our results indicate host influence for the expression of hydrogenase activity, and suggest the possibility of host influence of nitrogenase for the allocation of electrons to N(2) and H(+).

Fast-growing rhizobia isolated from root nodules of soybean.

Fast-growing rhizobia have been isolated from soybean root nodules collected in China. These new isolates are physiologically distinct from slow-growing soybean rhizobia. They formed effective nitrogen-fixing associations with wild soybean and an unbred soybean cultivar from China, but were largely ineffective as nitrogen-fixing symbionts with common commercial cultivars of soybeans.

Basal body temperature recordings in spontaneous abortion.

PIP: Basal body temperature (BBT) charts taken during the cycle of conception in cases that resulted in spontaneous abortion appear to provide the best available information concerning events associated with time of fertilization in doomed gestations. This study is based on a series of 227 patients who had early spontaneous abortion occurring between January 1967 and December 1974. A diagnosis of pregnancy initiated regular assays of urinary estrogen and pregnanediol excretion. Patients were instructed to report any bleeding episode which might occur, and to preserve all tissues that might be expelled. A total of 11 basal body temperature charts were obtained from patients who had subsequent early spontaneous abortion. Chromosome studies and histologic investigations were conducted. Another group of 11 consecutive BBT records were obtained from patients who had normal deliveries. The study shows that women with normal cycles experience a midcycle temperature rise requiring 1 to 3 days. In subsequent patients, this time limit was exceeded in 7 out of 11 cases of early abortion, and in 4 of 11 fertilization that resulted in an apparently normal gestation and infant. As temperature rise resulted from vigorous progesterone secretion by the corpus luteum, subnormal levels indicate inadequate steroidogenesis in the early luteal phase, and falling estrogen and progesterone levels predicted fetal demise in all cases. These findings are useful in the management of early pregnancy that follows repeated spontaneous first trimester abortions or a prolonged period of infertility. They also confirm experimental and clinical evidence regarding the role of ovulation defects in the occurrence of various types of reproductive wastage, including early abortion, anatomic and chromosome defects of the embryo and others. Prospective studies of cycles of conception through BBT recordings/hormone assays may shed light in the understanding of defects of human reproduction.^ieng

Basal body temperature recordings in ectopic pregnancy.

Basal body temperature charts taken during the cycle of conception of tubal pregnancies suggested the presence of luteal phase defect in the background of ectopic implantation and the recurrence of an apparent menstruation at the expected time of the next period. The temperature changes were compatible with the occurrence of a "superovulation" shortly before the occurrence of tubal abortion.

PIP: This paper presents basal body temperature recordings to support the hypothesis that defects of ovulation and corpus luteum function are important factors in the pathogenesis of ectopic gestations. Temperature charts taken from a woman with an ectopic pregnancy during the cycle of conception indicated the presence of a luteal phase defect and the recurrence of an apparent menstruation at the expected time of the next period. The temperature changes were compatible with the occurrence of a superovulation shortly before the tubal abortion. The diagnosis of a luteal phase defect is based on the presence of delayed ovulation, shortened luteal phase, unsustained temperature in the secretory phase, low pregnandiol secretion levels after ovulation, inadequate and often repeated luteinizing hormone surges, or inadequate endometrial development for the day of the cycle. Basal body temperature charts can usually identify the 1st 3 of these criteria. Animal studies suggest that unsuppressed cycling explains the occurrence of tubal implantation on 1 side and corpus luteum on the other.