Microbial transitions in soil ecosystems under land use and climate change

Background: The soil microbiome, which encompasses a vast diversity of microbial life, plays a crucial role in regulating biogeochemical cycles and plant growth. Yet, our understanding of the factors that regulate the dynamics and functioning of the soil microbiome, and its capacity to resist and recover from perturbations, such as those associated with intensive land use and climate change, remains poor2. Added to this, remarkably little is also known about the vulnerability of the soil microbiome to transitions to alternative states, with potentially deleterious consequences for soil functioning and plant growth. Abrupt transitions to alternative states have been widely documented in other ecosystems in response to perturbations, including the human gut; but studies of transitions to alternative stable states, and the factors that trigger them, are lacking in soil microbial communities. This represents an important gap in knowledge given that soil microbial communities are increasingly challenged by multiple co-occurring perturbations associated with land use and climate change, and emerging evidence that: (a) discrete perturbations, such as severe drought, can trigger abrupt transitions to alternative microbial states with consequences for soil functioning; and (b) land use history can modify the response of soil microbial communities to drought, being more vulnerable to transitions to alternative states in soils previously under intensive agriculture. This studentship will tackle these gaps in knowledge and deliver an integrated understanding of the capacity of repeated drought to trigger transitions in the taxonomic and functional state of soil microbiomes and how thresholds for these transitions are modified by land use history. The studentship will focus on drought because the risk of drought is globally pervasive, with increases in drought frequency and intensity expected in most parts of the world, and on grassland soils, given our past BBSRC funded work showing that their microbial communities are highly sensitive to land use change4.

Objectives: This studentship seeks to understand what makes soil microbiomes vulnerable to transitions to alternative states and determine consequences for soil functioning and plant growth. Specifically, the student will test the hypotheses that: (a) repeated drought triggers shifts in soil microbiomes to alternative states with negative consequences for soil nutrient cycling and plant performance; and (b) soil microbiomes shaped intensive land use are more vulnerable to transitions to alternative states than those with a history of sustainable management. By testing these hypotheses, this studentship will not advance understanding of the factors that make the soil microbiome vulnerable to transitions to alternative taxonomic and functional states, but also it will inform on how this vulnerability is modified by land use history, which is key to sustainable management.

Methods and approach: The student will test these hypotheses using a series of highly integrated controlled-environment and field-based experiments and will use state-of-the-art genomic and biogeochemical technologies to interrogate taxonomic and functional attributes of the soil microbiome and quantify nutrient transfers through the soil system in response to perturbations. Specifically, this will include integrated use of amplicon and metagenomics sequencing, in combination with novel experimental manipulation of drought intensity and frequency, to test the vulnerability of microbial communities to transitions to alternative states and to identify critical thresholds for these transitions, and how they are modified by land use history. Experiments will be done using soils taken from well characterized, long-term grassland experiments with treatments reflecting different land use histories, as used in past BBSRC funded research.