Resilience of Microbial Communities to Extreme Weather

The rhizosphere microbiome has major influences on plant growth, but its response to extreme weather events is largely unknown. You will discover how the diversity and functioning of the rhizosphere microbiome is affected by extreme weather.The project will provide training in a wide range of modern molecular ecological analyses. The student must be in place by the end of March 2018.
Plant roots live in close association with diverse communities of microbes, including prokaryotes such as bacteria, and eukaryotes such as fungi, which together constitute the root ‘microbiome’. These microbes are selectively recruited from the diverse communities which inhabit soil as a result of their growth on carbon exuded from roots. Root associated microbes interact with the plant in a myriad of ways; some act as symbionts which promote plant growth, while others are parasites which can have deleterious impacts on growth and development. As a result, understanding and harnessing interactions in the root zone (termed the ‘rhizosphere’) has enormous importance for ensuring food and energy security.
Research at Warwick and the Centre for Ecology and Hydrology has demonstrated that a variety of factors control the composition of microbial communities which inhabit the root zone, including plant identity and developmental stage, local environment and geographical distance. Furthermore these communities change over time; some of these changes reflect seasonal preferences of microbial taxa, which may be associated with environmental variables and plant physiology, while others are less predictable and reflect ecological drift. During the course of long term monitoring of rhizosphere microbial communities in bioenergy willow plantations we have found that extreme weather events have major impacts on rhizosphere microbial communities. Prolonged extreme rainfall during the summer of 2012 had a sudden, massive impact on the diversity and composition of the rhizosphere biota, reducing the diversity of beneficial mycorrhizal fungi and promoting growth of pathogens and endophytes which live within the root. These effects dwarfed the normal seasonal patterns of microbial community dynamics which occurred in previous years.
With extreme weather likely to increase in frequency and intensity as climate change proceeds, there is a need to understand how extreme weather impacts ecosystem functions, and the factors which control the severity of these effects and their recovery. You will investigate the impact of extreme weather on rhizosphere communities, and determine the significance of these events for microbial functioning, including interactions with plants.
You will use a variety of molecular approaches to characterise microbial and plant responses to extreme weather. This will include DNA and RNA extraction and purification, PCR, sequencing using next generation platforms and bioinformatic analysis. In particular there will be scope to use ‘metatranscriptome’ approaches, in which mRNA is extracted, sequenced, and used to profile the responses of plant and microbial gene expression to extreme weather.These approaches will will be used in experiments in which soil moisture regimes are manipulated under controlled conditions. A range of land uses will be compared, including forest, grassland and arable systems. Experiments will compare the impact of the regimes on the resistance (ie degree of change) and resilience (ie recovery) of soil and rhizosphere biota. Particular attention will be paid to understanding responses of contrasting biota (eg bacterial, protist and fungal groups) and functional groups (eg symbionts and pathogens) to the extreme weather.
Key experimental skills involved:
CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes. This project will utilise a range of molecular microbiological approaches including PCR, qPCR and next generation sequencing