Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 μm in diameter were sampled with spatial coordinates in 1 cm³ of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10³ agrobacteria g⁻¹), a high genetic diversity was maintained. In two independent microsamples (500 μm in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.     

Fast, efficient and reproducible genetic transformation of Phaseolus spp. by Agrobacterium rhizogenes

This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants in high-humidity conditions. Callogenesis always precedes hairy-root formation, and after 15 days, when roots develop at wounded sites, the stem with the normal root is cleaved below the hairy root zone. Transgenic roots and nodules co-transformed with a binary vector can be easily identified using a reporter gene. This procedure, in addition to inducing robust transgenic hairy roots that are susceptible to being nodulated by rhizobia and to fixing nitrogen efficiently, sets the foundation for a high-throughput functional genomics approach on the study of root biology and root-microbe interactions. This protocol can be completed within 30 days.     

Relationship between heterozygosity and genetic distance in the three major races of man

In pairwise comparisons of gene frequency data from the three major races of man, the single locus measures of the heterozygosity within and the genetic distance between races are shown to be strongly correlated across the loci coding for red cell proteins and enzymes. The intercept of the regression line of genetic distance on heterozygosity in protein enzyme loci is statistically insignificant. These findings suggest that the genetic variability at the enzyme and protein loci in man is probably maintained by a balance of mutation and random genetic drift. At the blood group loci, however, the observed relationship between genetic distance and heterozygosity does not follow the expectation of the neutral mutation hypothesis. These observations are discussed in terms of the changes in probability of identical monomorphism in two populations during the process of gene differentiation.     

Reiterated DNA sequences in Rhizobium and Agrobacterium spp.

Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more than 10 elements. Rhizobium and Agrobacterium spp. contain large plasmids in addition to the chromosomes. Analysis of the two Rhizobium strains indicated that DNA reiteration is not confined to the chromosome or to some plasmids but is a property of the whole genome.     

Cytokinin production by Agrobacterium and Pseudomonas spp.

The production of cytokinins by plant-associated bacteria was examined by radioimmunoassay. Strains producing trans-zeatin were identified in the genera Agrobacterium and Pseudomonas. Agrobacterium tumefaciens strains containing nopaline tumor-inducing plasmids, A. tumefaciens Lippia isolates, and Agrobacterium rhizogenes strains produced trans-zeatin in culture at 0.5 to 44 micrograms/liter. Pseudomonas solanacearum and Pseudomonas syringae pv. savastanoi produced trans-zeatin at levels of up to 1 mg/liter. In vitro cytokinin biosynthetic activity was measured for representative strains and was found to correlate with trans-zeatin production. The genetic locus for trans-zeatin secretion (tzs) was cloned from four strains: A. tumefaciens T37, A. rhizogenes A4, P. solanacearum K60, and P. syringae pv. savastanoi 1006. Southern blot analysis showed substantial homology of the Agrobacterium tzs genes to each other but not to the two Pseudomonas genes.     

Competition between Phytophthora cinnamomi and Trichoderma spp. in autoclaved soil.

Results from analyses of beta-glucosidase (EC 3.2.1.21) and phosphatase (EC 3.1.3.1;EC 3.1.3.2) activities indicated that presence of a Trichoderma isolate reduced development of Phytophthora cinnamomi. It was also observed that P. cinnamomi was more competitive in coinoculated cultures than in cultures where Trichoderma was added on day 3. Analysis of trehalase (EC 3.2.1.28) activity indicated that Trichoderma either utilized portions of the P. cinnamomi mycelium as substrate or the action of P. cinnamomi released additional nutrients not normally available to Trichoderma. Ther stronger Trichoderma isolate was T. harzianum.     

Transformation of Stylosanthes spp. using Agrobacterium tumefaciens

Tumours were incited on leaf sections of Stylosanthes humilis, S. hamata, S. guianensis and S. scalra following infection by Agrobacterium tumefaciens. The suitability of 2 binary vectors (pGA472, BIN6) for gene transfer in S. humilis was tested and kanamycin-resistant tumour tissue was obtained from infected leaf pieces. The presence and expression of the neomycin phosphotransferase (NPT II) gene in the plant cells was demonstrated by hybridization of the coding region of the NPT II gene of the transposon Tn5 to DNA and RNA of kanamycin resistant tumours and by detection of significant NPT II activity in tissue extracts. Tumours also produced teratomatous shoots expressing the NPT II gene, but these could not be rooted.     

根癌农杆菌介导的木霉遗传转化及应用进展

木霉作为土传植物病原菌的生防真菌,研究其功能基因具有重要的意义。根癌农杆菌介导的遗传转化(ATMT)为木霉功能基因的研究提供了一个强有力的工具。对根癌农杆菌介导木霉遗传转化的机理、特点、方法及其在木霉中的应用进行了综述。     

The ecology and genetics of fitness in Chlamydomonas. X. The relationship between genetic correlation and genetic distance

Abstract.— A necessary condition for the maintenance of genetic variation in heterogenous environments is that the relative fitnesses of a collection of genotypes vary as conditions of growth change. This can be detected by estimating the amount of gene-by-environment interaction (G X E) when a range of types are tested across a range of conditions. However it is the sign and magnitude of the genetic correlation, which is a component of G X E, that governs the ultimate fate of variation. Whether genetic variation will be preserved, then, depends on how the genetic correlation changes as a function of the ecological differences among environments and the genetic differences among genotypes. To evaluate this, we assayed the performance of 15 chlorophyte species of known genetic relation in 20 environments. We found that the quantity of G X E increased as both the environmental variance across environments and the genetic distance increased. Moreover the genetic correlation declined as the environmental variance between pairs of environments and the genetic distance between pairs of genotypes increased. These results suggest that divergent selection will be more likely to maintain genetic variation when environments are strongly contrasted and genotypes widely divergent.     

Relationship between species richness and spatial and temporal distance from seed source in semi‐natural grassland

Question: How do traditional management practices of field margins maintain the biodiversity of native grassland species? Location: Semi‐natural grassland on the field margins of traditional and consolidated agricultural fields on Awaji Island, central Japan. Methods: The distance to the nearest traditional field margin to the study sites was determined because the traditional field was considered as a seed source of native vegetation to the semi‐natural grasslands under study. We selected field margins in consolidated fields of different ages and distances from seed sources. Indicator species for both field types were sought. Regression analysis and detrended correspondence analysis (DCA) were used to determine the effect of spatial and temporal distances on the species composition of native vegetation. Results: Species richness differed significantly between the margin of traditional and consolidated fields. We identified significant indicator species of traditional fields, but not of consolidated fields. In consolidated fields, species richness increased significantly with age and decreased significantly with increasing distance to the source. At younger sites, species richness decreased faster with distance to the source because of strong negative correlation, but not at older sites. DCA ordination plots similarly indicated that similarities of vegetation composition in consolidated and traditional fields decreased with distance, and the effect of distance decreased with age. Conclusions: The species composition of the grassland margins of consolidated field was more similar to the margins of traditional fields if the consolidated fields were older, and/or closer to traditional fields. This pattern suggests that dispersal may play a role in the establishment of species on field margins.     

Anthropometric and genetic distance between Gonds of Central India

A morphological and genetic study was undertaken on five Gondi-speaking populations of Central India (Andhra Pradesh and Maharashtra States). There has been no systematic biological study on this large Dravidian-speaking tribal group, 4 million in number, amounting to 13% of the total tribal population of India. Data was collected on 16 anthropometric measurements and seven genetic markers (blood groups, hemoglobin, G6PD and plasma protein polymorphisms) on the Raj Gonds, Kolams, Manne, Koyas and Plains Maria Gonds. Various genetic distance measures such as Mahalanobis's D2 and Nei's and Sanghvi's measures and cluster analysis techniques were used to determine the relationship between these groups based on anthropometrics and genetic variables. The statistical analysis revealed the Gonds to be a heterogenous group in both morphology and genetic characteristics. The morphological and genetic distances between these five groups when projected graphically revealed that the spatial distribution of these Gonds generally corresponds to their present geographical distribution. However, the actual relationships among each of the Gond populations show differences when based on these two biological variables, the possible reasons for this being discussed in the paper. The emphasis of this study is on the importance of geographical proximity in producing morphological and genetic similarity between populations, brought about by a short distance as well as similar geographical factors (such as soil, terrain, flora, etc.) drawing these populations together under a common ecocultural umbrella.     

In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative Sphingomonas spp. and soil pH

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field.     

土壤抑真菌作用与细菌群落结构的关系

自然清洁土壤所具有的抑真菌作用,是健康土壤的一种自然属性,也是土壤质量的重要指标之一,对控制农作物土传病原真菌的爆发具有积极的生态学意义.本试验以中国科学院沈阳生态实验站近10年未受农药和肥料影响的撂荒地土壤作为自然清洁土壤样品,通过高温（对照、100 ℃、110 ℃、121 ℃）处理得到具有不同抑真菌作用的土壤模型,采用PCR DGGE(变性梯度凝胶电泳)方法对上述土壤样品的细菌群落结构进行分析.结果表明：土壤抑真菌作用与土壤细菌群落结构紧密相关;对照清洁土壤抑真菌作用最强,处理后土壤细菌群落结构偏离自然清洁土壤愈远,土壤抑真菌能力愈差;DGGE特异性条带切胶测序结果表明,Sphingomonas asaccharolytica、Nitrospira sp.、Hyphomicrobiaceae sp.、Bacillus megaterium和Micrococcus sp.可能与土壤抑真菌作用密切相关.     

Relationship between Nif plasmids of fast-growing Rhizobium species and Ti plasmids of Agrobacterium tumefaciens.

By use of the Southern blot hybridization technique the extent of DNA homology was determined between the Nif plasmid of a number of fast-growing Rhizobium species and Ti plasmids of the octopine (pTiAch5) and nopaline (pTiC58) type. DNA sequences common to these plasmids were located on functional maps of the Ti plasmids. No homology between Nif plasmids and the T region of Ti plasmids was detected.     

Expression of the Agrobacterium tumefaciens chvB virulence region in Azospirillum spp.

Inner membranes of Azospirillum brasilense incubated with UDP-glucose were unable to synthesize beta-(1-2) glucan and lacked the 235-kilodalton intermediate protein known to be involved in the synthesis of beta-(1-2) glucan in Agrobacterium tumefaciens and Rhizobium meliloti. Inner membranes of A. brasilense strains carrying a cosmid containing the chromosomal virulence genes chvA and chvB of Agrobacterium tumefaciens formed beta-(1-2) glucan in vitro and synthesized the 235-kilodalton intermediate protein. No DNA homology to the chvB region was found in different wild-type strains of A. brasilense, but the introduction of a cosmid containing the Agrobacterium tumefaciens chvA and chvB regions yielded strains in which DNA hybridization with the chvB region was detected, provided that the strains were grown under an antibiotic selective pressure.