Diversity, stability and functioning of the soil microbiome

Project Information

SoilResist

Grant agreement ID: 883621

DOI

10.3030/883621

EC signature date 30 April 2020

Start date 1 June 2021

End date 31 May 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 608,75

EU contribution

€ 2 499 608,75

Coordinated by

UNIVERSITY OF LANCASTER
United Kingdom

Periodic Reporting for period 2 - SoilResist (Diversity, stability and functioning of the soil microbiome)

Reporting period: 2022-12-01 to 2024-05-31

Summary of the context and overall objectives of the project

A vast diversity of microbial life is found in soil, forming one of the most complex ecological communities on Earth. But major questions remain about the functional role of these highly complex soil microbial communities and the ecological consequences of changes in their diversity and structure resulting from perturbations associated with human-induced global change. This is important because soils and their microbial communities are being increasingly challenged by a range of perturbations associated with global change, including climate extremes which are predicted to increase in frequency and intensity with ongoing climate change. SoilResist is addressing this challenge by investigating the mechanisms that enable soil microbial communities and their functions to resist and recover from anthropogenic perturbations, and by identifying critical thresholds for abrupt transitions of microbial communities to alternative states with consequences for soil functioning. The overarching hypothesis of SoilResist is that the stability of microbial functions, in terms of their capacity to resist and recover from abrupt and intense ‘pulse’ perturbations caused by climate extremes, is determined by microbial functional diversity, or the range and relative abundance of microbial traits. A related hypothesis is that shifts in microbial functional diversity caused by sustained ‘press’ perturbations (i.e. those that occur over prolonged time periods) erode the capacity of soil microbial communities to buffer ‘pulse’ perturbations, rendering them vulnerable to transitions to alternative microbial states with potential negative consequences for soil functioning. These hypotheses are being tested in grasslands with a focus on two globally pervasive ‘pulse’ and ‘press’ perturbations, namely drought and nitrogen enrichment respectively, and through complimentary experiments at a global, regional, and local scale, in association with the use of advanced omics and biogeochemical technologies, and within a framework of trait-based microbial ecology for interrogating functional attributes of soil communities. Through its multifaceted approach SoilResist will deliver new understanding of how and why soil microbial communities and their functions respond to anthropogenic perturbations and yield new mechanistic knowledge of factors that can trigger abrupt transitions of soil microbial communities to alternative states with potentially dramatic ecological consequences.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During this reporting period, our focus has been on setting up and conducting experimental work to test our hypotheses.

1. We completed a global-scale sampling campaign, based on NutNet, involving soil sampling from globally distributed grasslands to test microbial resistance and resilience to drought. Soils have been sampled from 32 sites, each with fertilised and unfertilised plots, and spanning 14 countries, 5 continents, and desert grassland to arctic tundra. A laboratory test of microbial resistance and resilience has been completed, yielding >1000 soil samples for microbial community analyses. This work will identify across global environmental gradients the dominant factors determining soil microbial resistance and resilience to drought, and how nutrient enrichment moderates microbial community resistance and resilience.

2. We have characterised a precipitation gradient in Navarra, Spain, spanning desert grassland to mesic grassland (400-2100 mm year). Soils have been sampled for microbial community analysis, and we will test in situ microbial community resistance and resilience using rain shelters, followed by laboratory testing of the vulnerability of microbiomes to shifts to alternative states. This will enable us to test whether increasing frequency and intensity of drought increases the vulnerability of soil microbial communities to state transitions, and whether thresholds for transitions are moderated by extrinsic attributes, especially climate history.

3. A mesocosm experiment has been set up in Manchester with contrasting plant communities and a nutrient enrichment treatment, to be exposed to a gradient of drought to detect thresholds in soil microbiome responses and shifts to alternative microbial states. This work is ongoing and will enable us to test our hypothesis that press perturbations (i.e. nutrient enrichment) weaken the resistance and resilience of soil microbial communities to drought and that response are moderated by vegetation.

4. We demonstrated experimentally that intense and frequent pulses of drought can induce an abrupt shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. This work, involving collaborators in Sweden and in part supported by SoilResist, provides the first quantitative evidence that high intensity drought can induce an abrupt shift to an alternative microbial state with deleterious consequences for soil functioning, a key goal of SoilResist.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

By the end of the project, SoilResist has potential to deliver a step change in understanding of the mechanisms that underpin the stability of soil microbial communities in response to climate-related pulse perturbations and transitions to alternative stable states. SoilResist also offers potential to define and measure microbial traits that can be used to gain an improved understanding of relationships between microbial functional diversity and ecosystem functioning under global change. An important outcome of SoilResist will be the delivery of a highly trained early career researchers with training in multi-disciplinary approaches to the study of the soil microbiome, including cutting edge genomic tools and links to biogeochemical cycles. Our research outcomes will also be of potential interest to land managers and policy makers with interests in the resilience of grassland ecosystems to climate extremes, which are expected to increase in their intensity and frequency with climate change.