S. S. Gnanamanickam

Plant-associated bacteria

Preface. Acknowledgements. 1. Plant-associated bacteria: survey, molecular biology genomics and recent advances G.A. Beattie. Beneficial Bacteria. 2. Rhizobium-legume symbioses: molecular signals elaborated by rhizobia that are important for nudulation H.B. Krishnan, J.O. Bennett. 3. Nitorgen fixing bacteria in nonlegumes D.A. Dalton, S. Kramer. 4. Epiphytic bacteria, their ecology and functions S.S. Gnanamanickam, J.E. Immanuel. 5. Bacterial endophytes: The endophytic niche, its occupants and its utility C.W. Bacon, D.M. Hinton. Rhizosphere Bacteria. 6. Plant growth-promoting rhizobacteria (PGPR) A.R. Podile, G.K. Kishore. 7. Contribution of studies on suppressive soils to the identification of bacterial biocontrol agents and to the knowledge of their modes of action P. Lemanceau et al. 8. Root-associated bacteria including systemic resistance L.C. van Loon, P.A.H.M. Bakker. 9. Rhizosphere competence and role of root colonization in biocontrol S. de Weert, G. Bloemberg. 10. Deleterious rhizobacteria R.J. Kremer. Plant Pathogenic Bacteria. 11. Agrobacterium biology and crown gall disease A. Anand, K. Mysore. 12. Clavibacter michiganensis, a group of gram-positive phytopathogenic bacteria R. Eichenlaub et al. 13. The soft rot Erwinia A.O. Charkowsky. 14. Plant pathogenic Pseudomonas species M. Hofte, P. de Vos. 15. Virulence functions of xanthomonads S. Subramoni et al. 16. Plant pathogenic Ralstonia species T. Denny. 17. Burkholderia R. Gitaitis, K. Nischwitz. 18. Plant pathogenic members of the genera Acidovorax and Herbaspirillum M. Fegan. Index.

Rhizosphere Bacteria for Biocontrol of Bacterial Blight and Growth Promotion of Rice

Several bacterial strains were isolated from different rhizospheres. Among these, strain PDY7 exhibited strong antibacterial activity against the rice bacterial blight (BB) pathogen Xanthomonas oryzae pv. oryzae (Xoo) by the laboratory dual plate assays. The antibacterial property of the strain PDY7 was further investigated for the production of 2,4-diacetylphloroglucinol (DAPG), which amplified a characteristic of 629-bp DNA fragment by PCR-based screening method using phlD primers. The application of phlD positive strains was carefully evaluated for disease control and growth promotion of rice plants under field conditions. The selected strain PDY7 suppressed the rice BB by 58.83% and 51.88% under glass house and field conditions, respectively. In addition, the strain PDY7 showed significant two-fold increase in root length (18.08 cm), shoot length (29.81 cm), and grain yield (96.07 g). Strain PDY7 promoted the growth of rice plants by production of indole-3-acetic acid (IAA), which was determined by high performance liquid chromatography (HPLC) analysis. Our findings suggest that PDY7 belongs to the P. fluorescens group and can serve as potential biocontrol of BB as well as biofertilizer agent for growth promotion of rice.

The Effect of Bacterial Secondary Metabolites on Bacterial and Fungal Pathogens of Rice

Certain antagonistic bacteria are considered ideal biological control agents owing to their rapid growth, easy handling and aggressive colonization of the rhizosphere. These bacteria may mediate biocontrol by one or more of the several mechanisms of disease suppression (Weller 1988). A primary mechanism of pathogen inhibition is by the production of secondary metabolites and other factors such as siderophore production and microbial cyanide, and lytic enzymes may also play a role (Fravel 1988; Keel et al. 1992; O’Sullivan and O’Gara 1992). These bacteria are involved in the biological control of bacterial, fungal, and viral diseases of plants. The antagonistic fluorescent pseudomonads produce one or more metabolites, such as phenazine-1-carboxylicacid (PCA), 2,4-diacetylphloroglucinol (DAPG), pyoluteorin , pyrrolnitrin , and oomycin A . Among these, DAPG is an antibiotic produced by fluorescent Pseudomonas spp. of diverse geographic origin (Dowling and O’Gara 1994; Keel et al. 1996; Thomashow and Weller 1995; Raaijmakers et al. 1997). It has been implicated as the mechanism involved in the biological control of some of the most important crop diseases, such as the root rot of wheat caused by Fusarium oxysporum f. sp. graminis (Garagulya et al. 1974), black root rot of tobacco caused by Thielaviopsis basicola (Defago et al. 1990; Keel et al. 1992), damping-off of sugarbeet caused by Pythium ultimum and Rhizoctonia solani (Nowak-Thompson et al. 1994), and the “take-all” of wheat caused by Gaeumannomyces graminis tritici (Defago et al. 1990; Keel et al. 1992). Strains of Pseudomonas fluorescens that produce DAPG also have had a key role in the natural biological control of “take-all” known as “take-all decline” (Raaijmakers et al. 1997). DAPG is a bacterial and plant metabolite (Bangera and Thomashow 1996, 1999; Keel et al. 1992), phenolic in nature, probably of polyketide origin with a broad spectrum of antifungal, antibacterial, antiviral, and antihelminthic properties (Garagulya

Improvement of Bacterial Blight Resistance in Rice Cultivars Jyothi and IR50 via Marker-Assisted Backcross Breeding

Abstract In pathogen population analysis of 208 Xanthomonas oryzae pv. oryzae(Xoo) strains that were assembled from different parts of India, 21 pathotypes were identified on the basis of disease reactions on near-isogenic lines (NILs) and 13 pathotypes, on rice differentials. Rice cultivars, Jyothi and IR50, which are high yielding but highly prone to bacterial blight (BB) caused by pathogen populations of Xanthomonas oryzae pv. oryzae in India, were chosen. To improve the BB resistance of these two varieties, a pyramid line, NH56, containing four R-genes, Xa4, xa5, xa13, and Xa21, was selected as the R-donor based on resistance to existing pathogen population. The four R-genes were successfully transferred to cultivars through a traditional backcross method and their presence was documented with marker-aided selection (MAS). Thirty BC4F2 plants derived from JxNH56 (cv. Jyothi) and 45 BC4F2 plants derived from IR50xNH56 (cv. IR50) had all four resistance genes (Xa4, xa5, xa13, and Xa21), which should be useful resistance donors for breeding other BB-resistant elite indica varieties.

Lineage-Exclusion Resistance Breeding: Pyramiding of Blast Resistance Genes for Management of Rice Blast in India

By MGR-DNA fingerprinting analyses, we identified 29 lineages of Magnaporthe grisea among rice blast pathogen population in Southern India. The population structure of M. grisea in different states of India was also characterized by a Pot2-based rep-PCR method. The latter method identified 1 to 22 bands in the fingerprints of rice-infecting and less than 10 bands in the fingerprints of non rice-infecting strains of M. grisea which were in the size range of 0.4 to 23 kb. Lineage-exclusion assays showed that a combination of Pi-1 and Pi-2 genes for blast-resistance can exclude all the lineages identified. This virulence characteristic of M grisea remained stable while its lineage-composition showed drastic changes over the period 1993–97 in rice-growing areas of Kerala where annual blast epidemics is common. Therefore, gene pyramids of Pi-1/Pi-1b+Pi-2 were constructed in the CO39 (blast-susceptible) genomic background and such pyramids were resistant to blast in hot-spot locations. The CO39 pyramid now serves as the R-donor for introgressing the Pi-1+Pi-2 genes for blast resistance into cultivars such as Jyothi and IR50 which are high-yielding but blast-prone to make them durably resistant.

Genetic Diversity of Biocontrol Strains of Pseudomonas fluorescens Producing 2, 4-diacetylphloroglucinol from Southern India

Production of the antibiotic 2,4-diacetylphloroglucinol (DAPG) contributes to biological control activity of many beneficial strains of the bacterium Pseudomonas fluorescens. The DAPG is toxic to many organisms, and crop yield increases have been reported after application of DAPG-producing Pseudomonas fluorescens. Here the genotypic diversity of the efficient biocontrol strains of Pseudomonas fluorescens was investigated. Amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA analysis (RAPD), and whole cell BOX PCR analysis were carried out to determine the genetic variability among DAPG-producing strains of Pseudomonas fluorescens assembled from rice (Oryza sativa) rhizosphere in Southern India. As the outcome of these studies, phlD restriction pattern can be used as a marker for ecological studies or when selecting phl+ Pseudomonas strains for specific biocontrol application.