The eco-evolutionary consequences of biofumigation in the rhizosphere bacterial communities


Carrie Alderley

Biofumigation is an agricultural technique involving the mulching of Brassica plants into soils causing the release of a bactericidal chemical, isothiocyanate (ITC) into the soil. ITCs have been shown to suppress pathogens in lab environments, yet there has been little investigation into its effects in complex microbial communities in the soil. This project will focus on the Ralstonia solanacearum bacterial pathogen, which causes the devastating bacterial wilt, or brown rot disease in potatoes in the UK, as well as many other important crops. The pathogen is currently undergoing host range expansion and is able to infect secondary hosts to enable its survival between potato growing seasons. Traditionally crop protection against R. solanacearum involved the application of environmentally harsh chemicals like methyl bromide which have since been banned. Crucially, there is no effective way to control the pathogen outbreaks at the moment.
The proposed research will explore the potential of an environmentally sustainable biofumigation approach in combination with naturally occurring plant growth promoting (PGPB) Pseudomonas bacteria to control R. solanacearum outbreaks in an ecologically relevant agricultural context.
Specifically, I want to study:

  1. The biofumigant effects on pathogen and PGPBs in mono and co-cultures; Does biofumigation have suppressive effects on beneficial bacteria? Are these effects relatively more severe for the pathogen or the PGPBs?
  2. The biofumigant effects on pathogen and PGPBs in diverse bacterial rhizosphere communities; Is the effect dependent on bacterial diversity? Will biofumigation have negative effects on natural bacterial diversity (potential consequences for ecosystem functioning)?
  3. Pathogen and PGPBs potential to evolve tolerance/resistance to biofumigation; Is biofumigation effective as a long-term crop protection technique? How can tolerance evolution be slowed or prevented?
  4. Biofumigation efficiency in combination with PGPBs for potato crop protection; Do in vitro lab results hold true in the potato rhizosphere?
    The project will use an experimental evolution approach to initially test the effects of biofumigation in controlled liquid and soil compost microcosms. These results will then be verified in greenhouse pot experiments to bridge the gap between laboratory and natural environments. The research will aim to understand the direct and indirect effects of pathogen suppression via direct chemical interactions and indirect microbe-microbe interactions at ecological and evolutionary timescales. This work is not only important for securing ecosystem services in the agricultural context via pest control, but also for understanding the dynamics and benefits of biodiversity and rapid microbial adaptation in response to anthropogenic environmental change.

Twitter @carriealderley

Education

MBiolSci, 1st class Hons, University of Sheffield, 2013-2017

Skills and relevant qualifications

Li-cor portable photosynthesis system, X-ray fluorescence spectrometry, scanning electron microscopy, qPCR, spectrophotometry

Work experience

June 2016-June 2017: Research Assistant at the University of Sheffield. Assisting in the set-up of a large-scale plant experiment based on comparing the growth patterns and investment in roots and shoots of C3 and C4 tropical grasses to understand the molecular and anatomical basis underlying the rapid growth and greater productivity of C4 individuals.
July-September 2016: N8 Agrifood Placement at the University of York. Carrying out an original piece of experimental science to evaluate the potential to prime plant Silicon defences against herbivory via application of the ‘wound’ hormone, Jasmonic Acid.
July-September 2015: Research Assistant at the Centre for Agricultural Bioscience International (CABI), Switzerland. Investigating the potential of biocontrol agents as a way of controlling invasive weeds; involving both laboratory-based work such as dissections under a microscope, and field-work collecting plant samples with insect galls from sites in Germany, Poland and the Czech Republic.
June 2015: Tropical Rainforest Field Trip, Danum Valley Field Centre, Borneo. Experimental design and data collection in small groups in the Bornean rainforest to evaluate the impacts of road-induced forest fragmentation on ecosystem interactions.