Plant and Soil

, Volume 259, Issue 1–2, pp 19–27 | Cite as

Identifying microorganisms which fill a niche similar to that of the pathogen: a new investigative approach for discovering biological control organisms

  • Bei Yin
  • Alexandra J Scupham
  • John A. Menge
  • James Borneman


Understanding the mechanisms of suppressive soils should lead to the development of new strategies to manage pests and diseases. For suppressive soils that have a biological nature, one of the first steps in understanding them is to identify the organisms contributing to this phenomenon. Here we present a new approach for identifying microorganisms involved in soil suppressiveness. This strategy identifies microorganisms that fill a niche similar to that of the pathogen by utilizing substrate utilization assays in soil. To demonstrate this approach, we examined an avocado grove where a Phytophthora cinnamomi epidemic created soils in which the pathogen could not be detected with baiting techniques, a characteristic common to many soils with suppressiveness against P. cinnamomi. Substrate utilization assays were used to identify rRNA genes (rDNA) from bacteria that rapidly grew in response to amino acids known to attract P. cinnamomi zoospores. Six bacterial rDNA intergenic sequences were prevalent in the epidemic soils but uncommon in the non-epidemic soils. These sequences belonged to bacteria related to Bacillus mycoides, Renibacterium salmoninarum, and Streptococcus pneumoniae. We hypothesize that bacteria such as these, which respond to the same environmental cues that trigger root infection by the pathogen, will occupy a niche similar to that of the pathogen and contribute to suppressiveness through mechanisms such as nutrient competition and antibiosis.

avocado root rot BrdU molecular microbial ecology RISA 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Alexander M 1965 Most probable number method for microbial populations. In Methods of Soil Analysis, Part 2, Ed. C A Black. American Society of Agronomy, Madison.Google Scholar
  2. Amann R, Ludwig W and Schleifer K H 1995 Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169.Google Scholar
  3. Aveling T A S and Rijkenberg F H J 1989 Behavior of Phytophthora cinnamomi zoospores on roots of four avocado cultivars. J. Phytopathol. (Berl) 125, 157–164.Google Scholar
  4. Baker K F and Cook R J 1974 Biological control of plant pathogens. Freeman, San Francisco.Google Scholar
  5. Borneman J 1999 Culture-independent identification of microorganisms that respond to specified stimuli. Appl. Environ. Microbiol. 65, 3398–3400.Google Scholar
  6. Borneman J, Skroch P W, O'Sullivan K M, Palus J A, Rumjanek N G, Jansen J L, Nienhuis J and Triplett E W 1996 Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62, 1935–1943.Google Scholar
  7. Borneman J and Triplett E W 1997 Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63, 2647–2653.Google Scholar
  8. Botha T and Kotze J M 1989 Exudates of avacado rootstocks and their possible role in resistance to Phytophthora cinnamomi. SA Avocado Growers' Association Yrb 12, 64–65.Google Scholar
  9. Botha T, Wehner F C and Kotze J M 1990 Evaluation of new and existing techniques for in vitro screening of tolerance to Phytophthora cinnamomi in avocado rootstocks. Phytophylactica 22, 335–338.Google Scholar
  10. Broadbent P and Baker K F 1971 Bacteria and actinomycetes antagonistic to fungal root pathogens in Australian soils. Aust. J. Agric. 24, 925–944.Google Scholar
  11. Broadbent P and Baker K F 1974 Behaviour of Phytophthora cinnamomi in soils suppressive and conducive to root rot. Aust. J. Agric. 25, 121–137.Google Scholar
  12. Broadbent P and Baker K F 1975 Soils suppressive to phytophthora root rot in eastern Australia. In Biology and Control of Soil-Borne Plant Pathogens. Ed. G W Bruehl. pp. 151–157. The American Phytopathological Society, Minneapolis.Google Scholar
  13. Cook R J 1990 Twenty-five years of progress towards biological control. In Biological Control of Soil-Borne Plant Pathogens, Ed. D Hornby. CAB International, Wallinford.Google Scholar
  14. Cooksey D A and Moore L W 1982 Biological control of crown gall with an agrocin mutant of Agrobacterium radiobacter. Phytopathology 72, 919–921.Google Scholar
  15. Dang C and Jayasena S D 1996 Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. J. Mol. Biol. 264, 268–278.Google Scholar
  16. Deacon J W 1991 Significance of ecology in the development of biocontrol agents against soil-borne plant pathogens. Biocontrol Sci. Technol. 1, 5–20.Google Scholar
  17. Emmert E A B and Handelsman J 1999 Biocontrol of plant disease: A (Gram-) positive perspective. FEMS Microbiol. Lett. 171, 1–9.Google Scholar
  18. Erwin D C and Ribeiro O K 1996 Phytophthora diseases worldwide. APS Press, St. Paul.Google Scholar
  19. Halsall D M 1978 Examination of a forest soil suppressive to Phytophthora cinnamomi. Microb. Ecol., 360–363.Google Scholar
  20. Ho H H and Zentmyer G A 1977 Infection of avocado and other species of Persea by Phytophthora cinnamomi. Phytopathology 67, 1085–1089.Google Scholar
  21. Kellam M K and Coffey M D 1985 Quantitative comparison of the resistance to phytophthora root rot in 3 avocado Persea americana var. Drymifolia rootstocks. Phytopathology 75, 230–234.Google Scholar
  22. Malajczuk N 1979 Biological suppression of Phytophthora cinnamomi in eucalypts and avocados in Australia. In Soil-Borne Plant Pathogens. Eds. B Schippers and W Gams. pp. 635–652. Academic Press, London.Google Scholar
  23. Malajczuk N and McComb A J 1977 Root exudates from Eucalyptus calophylla R.Br. and Eucalyptus marginata Donn ex Sm. seedlings and their effects on Phytophthora cinnamomi Rands. Aust. J. Bot. 25, 501–514.Google Scholar
  24. Marais P G and Hattingh M J 1985 Exudates from roots of grapevine rootstocks tolerant and susceptible to Phytophthora cinnamomi. Phytophylactica 17, 205–208.Google Scholar
  25. Menge J A, Guillemet S, Campbell E, Johnson E and Pond E 1992 The performance of rootstocks tolerant to root rot caused by Phytophthora cinnamomi under field conditions in southern California. In Proceedings of the Second World Avocado Congress: The shape of things to come, 1992, pp. 53–59.Google Scholar
  26. Milner J, Silo-Suh L, Goodman R M and Handelsman J 1997 Antibiosis and beyond: Genetic diversity, microbial communities, and biological control. In Ecological Interactions and Biological Control. Eds. D A Andow, D W Ragsdale and R F Nyvall. pp. 107–127. Westview Press, Oxford.Google Scholar
  27. Mircetich S M, Zentmyer G A and Kendrick J B 1968 Physiology of germination of chlamydospores of Phytophthora cinnamomi. Phytopathology 58, 666–671.Google Scholar
  28. Pegg K G 1977 Biological control of Phytophthora cinnamomi root rot of avocado and pineapple in queensland. In Annual Conference of the Australian Nurserymen's Association Ltd., Hobart, Australia, 1977, pp. 7–12.Google Scholar
  29. Schisler D A and Slininger P J 1997 Microbial selection strategies that enhance the likelihood of developing commercial biological control products. J. Ind. Microbiol. Biotechnol. 19, 172–179.Google Scholar
  30. Tippett J T, Holland A A, Marks G C and O'Brien T P 1976 Penetration of Phytophthora cinnamomi into disease tolerant and susceptible eucalypts. Arch. Microbiol. 108, 231–242.Google Scholar
  31. Weller D M, Raaijmakers J M, McSpadden-Gardener B B and Thomashow L S 2002 Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 40, 309–348.Google Scholar
  32. Yin B, Crowley D, Sparovek G, De Melo W J and Borneman J 2000 Bacterial functional redundancy along a soil reclamation gradient. Appl. Environ. Microbiol. 66, 4361–4365.Google Scholar
  33. Zentmyer G A 1961 Chemotaxis of zoospores for root exudates. Science 52, 1595–1596.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Bei Yin
    • 1
  • Alexandra J Scupham
    • 1
  • John A. Menge
    • 1
  • James Borneman
    • 1
  1. 1.Department of Plant PathologyUniversity of CaliforniaRiversideUSA

Personalised recommendations