Monitoring rhizosphere microbial communities of tomato

Deery, Sarah Jane (2012) Monitoring rhizosphere microbial communities of tomato. PhD thesis, University of Nottingham.

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Abstract

Tomato is an economically important crop that can be devastated by many root infecting pathogens. The development of alternative and sustainable crop cultivation techniques and disease control methods is a must for the tomato industry, due to more strict government regulations and concerns over the sustainability of conventional chemical-intensive agriculture (Dixon and Margerison, 2009).

In this thesis, the molecular fingerprinting method Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and next generation sequencing method (pyrosequencing) were used, targeting ITS1, ITS2 and 23S ribosomal DNA to characterize and examine microbial community assemblages in the rhizosphere of tomato. These molecular techniques were employed alongside traditional cultivation, microscopy and plant health assessment techniques to determine the effects of growth media, plant age and disease control methods on rhizosphere microbial populations and tomato root health.

Plant age and media were found to significantly affect microbial community assemblages; conversely, microbial populations were not altered by soil amendments or rootstock disease control measures used. These findings suggest that the factors influencing rhizosphere community structure can be ranked by importance. Furthermore, if the most influential factors are kept consistent then rhizosphere microbial structures are robust and difficult to perturb with changes in a factor contributing less control over microbial community composition.

No direct link between crop health assessments and rhizosphere microbial community diversity or presence of root pathogens could be established. Furthermore, high abundance of potential pathogens and poor crop health assessments during the growing season did not always result in poor health or disease symptoms at the end of cropping assessment in our trials. These results imply that many factors control the rhizosphere competence and ecological role of different species, ultimately affecting the outcome of disease. As no known methods are capable of efficiently assessing the fate of total microorganisms in the rhizosphere over time and space, this study could be considered as part the ‘descriptive phase’ in this field (Kent and Triplett, 2002).

Pyrosequencing increased the resolution and confidence of rDNA analysis compared to T-RFLP, identifying organism within samples to a genus and often species level. Advances in next generation sequencing and analytical tools and pipelines associated with this analysis are likely to develop as these methods become common practice. With this in mind, next generation sequencing represents the future approach for resolving complex microbial communities in environmental samples.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: Dickinson, M.J.
Subjects: S Agriculture > SB Plant culture
Faculties/Schools: UK Campuses > Faculty of Science > School of Biosciences
Item ID: 12759
Depositing User: EP, Services
Date Deposited: 10 Apr 2013 10:05
Last Modified: 14 Sep 2016 23:43
URI: http://eprints.nottingham.ac.uk/id/eprint/12759

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