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Doctoral thesis, 2013

Root-associated microbial communities of different strawberry cultivars as influenced by soil type, Verticillium dahliae Kleb. and biofumigation

Nallanchakravarthula, Srivathsa

Abstract

Rhizosphere microorganisms and their interactions with plant roots play pivotal roles in controlling plant nutrition and health. Extremely high levels of soil microbial diversity, coupled with low levels of cultivability, complicate the study of these organisms but better mechanistic understanding of their interactions with each other and with plant roots is a prerequisite for development of sustainable management strategies to improve nutrient acquisition and control pathogens. This thesis describes different experiments designed to investigate how the community structure of fungi associated with rhizosphere soils and roots of strawberry plants are influenced by different soil types, different plant cultivars, the presence or absence of the soil-borne fungal pathogen Verticillium dahliae and biofumigation using plant residues of oilseed radish Raphanus sativus oleifera. In an outdoor pot experiment, using cloning and Sanger sequencing, the community composition and overall levels of colonization by arbuscular mycorrhizal fungi appeared to be more strongly influenced by soil type than by different strawberry cultivars. In a similar experiment the effects of inoculation with Verticillium dahliae on the total fungal community structure were analyzed using high throughput 454-pyrosequencing. The inoculation with V. dahliae resulted in significant reduction in the numbers of operational taxonomic units (OTUs) associated with rhizosphere soil of four cultivars grown in a conventionally managed soil, but in an organically managed soil, no significant effects in two cultivars, and a large increase in numbers of OTUs in Florence, a tolerant cultivar. Non-metric multidimensional scaling (NMDS) analysis of rhizosphere communities in a less diverse peat-based soil revealed distinct clusters associated with Verticillium and non-Verticillium treatments but this effect was not visible in two more diverse field soils. A third study of fungal communities associated with biofumigation treatments in a field soil, using 454 pyrosequencing, indicated significantly increased numbers of OTUs associated with biofumigation and Verticillium-inoculation in the absence of strawberry plants, suggesting a green-manuring effect of oilseed radish incorporation. Biofumigation did not affect total OTUs in the presence of strawberry plants but NMDS analysis showed a clear effect of all treatments on community structure. Complementary analyses of changes in bacterial community structure in the same experiments are in progress and will hopefully shed more light on possible functional interactions underlying treatment effects and enable construction of hypotheses that can be tested in further experiments.

Keywords

biofumigation; strawberry cultivars; Verticillium dahliae; arbuscular mycorrhiza; pyrosequencing; microbial communities

Published in

Acta Universitatis Agriculturae Sueciae
2013, number: 2013:48
ISBN: 978-91-576-7834-8, eISBN: 978-91-576-7835-5
Publisher: Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences

Authors' information

Nallanchakravarthula, Srivathsa
Swedish University of Agricultural Sciences, Department of Forest Mycology and Pathology

UKÄ Subject classification

Agricultural Science

URI (permanent link to this page)

https://res.slu.se/id/publ/42309