Un-stable microbiomes - Stability to drought of soil microbiomes shaped by land use and plant species

Lead Research Organisation: University of Manchester
Department Name: Earth Atmospheric and Env Sciences


Soils are inhabited by a myriad of different microorganisms, including fungi and bacteria. These complex microbial communities are responsible for many ecosystem services such as organic matter decomposition, nutrient cycling, and carbon and nutrient storage. But these services are threatened by climate change. Current climate projections predict an increasing frequency of severe droughts, which are known to strongly affect soil microbial communities and their function. Additionally, there is a second factor that threatens these communities: land use intensification. Soil microbes populating grassland soils have suffered from increasingly intensive management over the last century. Due to the ever-increasing demand for food production, grasslands have been subjected to significant land use intensification through fertilisation, at the expense of biodiversity (both of plants and soil microbes) and the ecosystem services it supports. How these two major threats will interact with one another to impact upon our future lives is still poorly understood.

In this project, I will answer the question of how extreme and frequent drought affects the soil microbial communities, and how that is influenced by different plant species and land management. I will focus on the microbial community stability, in other words, the capacity of soil microbes to resist drought without changing or their capacity to recover after drought to the original state. To do that, I will carry out a series of controlled environment and lab experiments. I will collect soils from paired grasslands that have been subjected to different long-term land use intensity (extensive traditional management and intensive management) and I will grow on them two widespread grass species, which are typically abundant in intensively and extensively managed grasslands, and have markedly contrasting growth strategies (fast-growing vs slow-growing). The effects of drought, land use and plant species on soil microbial structure and function will be evaluated using state-of-the-art techniques.

The results of this project will not only produce new insights into the mechanisms by which the soil microbial communities answer to climate extremes, which represents an important research challenge, but also it will generate new knowledge that is of relevance to BBSRC's strategic research priority of "food security and sustainable management".

Technical Summary

Soil microbial communities are highly complex and provide many ecosystem services. Therefore, changes on them have significant implications for soil functioning, which will affect food security and climate mitigation. Current climate predictions forecast a change in precipitation regimes and increased probability of extreme droughts. There is evidence that soil microbial community structure and function is significantly altered by drought. However, it remains unclear how drought frequency and intensity influence soil microbiomes. There is also growing evidence that plant species and land use strongly modify soil microbial communities and their function. Plant species are known to select for specific rhizospheric microbiomes, which can impact plant performance and health. It is also known that grassland intensification strongly affects soil biodiversity and functioning. However, it remains unknown how plant species and land use together influence the capacity of microbes to resist and recover from droughts of varying intensity and frequency. This is a major knowledge gap that I will tackle in this fellowship.
To address this I will carry out a series of controlled environment and lab experiments. I will collect soils from paired grasslands under different long term land use intensity and I will grow on them two widespread grass species with contrasting growth strategies. The effects of drought, land use and plant species on soil microbial structure and function will be evaluated using state-of-the-art genomic and isotope tracer approaches, such as metabarcoding, soil enzymatic activities, 13C labelling or radio-isotope incorporation. The results of this project will not only yield new insights into the mechanisms by which the soil microbiome copes with climate extremes, which represents an important research challenge, but also it will generate new knowledge that is of relevance to BBSRC's strategic research priority of "food security and sustainable management".

Planned Impact

Who will benefit from my research?
Given that soil microbial community stability underpins grassland systems' stability and provision of services (including food security), and considering that grasslands cover a large proportion of the UK's landscape, my research will benefit key stakeholders, including landowners, farmers' groups, conservation bodies and local and national government departments (Defra), agencies (e.g., Natural England; Scottish Natural Heritage, Countryside Council for Wales) and charities (Plant Life, The Grasslands Trust, National Trust, Wildlife Trusts).The findings of my research will provide fundamental knowledge on the impacts of grassland management on long-term soil function stability, which can inform future policy developments. Specifically, they will benefit from greater understanding of how future frequent extreme droughts predicted by climate change will affect soil biodiversity and functionality, and how land use and plant species selection can modify the outcomes. My project will also benefit the general public with interests on the effects of climate change on grassland function and services. The grassland sites that I use in my project are in an area of high conservation and amenity interest (Yorkshire Dales National Park), and public awareness of my research will be central to my impact plan. Additionally, as new discoveries and applications will be developed in this project, beneficiaries will include the ecology, agriculture, bioscience and the wider scientific research community interested in unravelling the complexities of the soil microbiomes in grassland ecosystems and how they can resist climate change.

How will these benefits be realised?
1: Engage with stakeholders and promote knowledge exchange
I will participate in an Agricultural Show in Yorkshire Dales with a stand, where I can interact with farmers, local land owners and other key stakeholders. I will explain in an easy and engaging way the outcomes of the project and the reasons why this is important for them.
2: Increase public awareness on the importance of my research
I will organise and participate in outreach activities such as science festivals or public exhibitions, where I could explain the key messages to the public. The activities will consist on easy to understand and visual models of the outcomes of my project, with some hands-on activities to really engage the most interested ones. I will also spread the word through the media. I will disseminate the outcomes and key messages of my research through different and more accessible ways to the general public and interested stakeholders. I will publish my research as open access. I will write a press release and a lay summary of every scientific article published. I will also spread the word through the social media with a project specific Twitter account. Finally a promotional video will be shared with the main outcomes of the research and uploaded in YouTube.
3: Dissemination of research findings to international scientific audience
I will contribute with results from my own research to national and international conferences and I will publish my research in leading international journals.
Description Intensive land use changes the soil chemistry, plant species growing on them and soil microbial communities. Soil microbial communities are sensitive to repeated and extreme droughts and not resilient. The effects of land use in their stability to drought intensity and frequency are still under evaluation.
Exploitation Route The results from this project could inform land owners and farmers on the effects of common land use practices on the stability of soils and pastures to drought. This is highly important and timely as drought events are increasing in frequency and intensity. In this scenario, the stability of grasslands and other farming lands is paramount to ensure food security.
Sectors Agriculture, Food and Drink

URL https://twitter.com/SoilEcolUoM/status/1338772275454160899
Description The knowledge of the activity of soil microorganisms from different soil types was used to design a hands-on experiment for children and families that was carried out at a public engagement event. After participating in the activity, visitors realised that soil was alive and that we should take care of it if we want to keep it healthy. This knowledge, which is constantly expanding, will continue to help me shape the different public engagement activities which I will continue to participate on once social interaction is possible again.
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Societal

Description Biodiversity in urban soils - effects of tree litter management 
Organisation University of Reading
Department Soil Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration to evaluate soil biodiversity in urban soils. A PhD student from the University of Reading was trained in our lab, under my supervision and another researcher in the group, to evaluate soil microorganisms and soil fauna.
Collaborator Contribution At the University of Reading, this PhD student evaluates the best land management practices that improve the role of urban trees to mitigate the effects of climate change and urbanization. She particularly focus on soil health and water regulation. She also studies the benefits of citizen science on gathering soil data in urban parks.
Impact Conference presentation to be made in July 2021, in TREESCAPES conference (abstract accepted). "Impact of litter management of urban trees on soil health and water regulation services" N. Ferrando, I. Cordero, M. Chomel, V. Struthers, M. Cardenas, S. Loiselle, T van Noordwijk, H Geoghegan, J Clark Manuscript in preparation
Start Year 2019
Description Biogeochemical coupling in terrestrial ecosystems under global change 
Organisation University of Cadiz
Country Spain 
Sector Academic/University 
PI Contribution Sharing data of nutrient contents and microbial communities in soils collected in fields under different land management
Collaborator Contribution The partner is in charge of a meta-analysis and synthesis study to evaluate how global change drivers affect ecosystem/biogeochemical coupling and the ecosystem/biogeochemical coupling-ecosystem functioning relationship
Impact Manuscript in preparation
Start Year 2020
Description Root-associated microbiomes in wheat cultivars to improve crop production under abiotic stress 
Organisation University of Salford
Country United Kingdom 
Sector Academic/University 
PI Contribution I shared my expertise on soil extracellular enzymes, sharing and explaining protocols. I also helped analysing and interpreting the results. But this collaboration is a starting point of a longer-term collaboration, where we can share ideas and expertise in microbiomes.
Collaborator Contribution They set up and performed the project, including all the lab measurements and the data analysis.
Impact Manuscript in preparation.
Start Year 2019
Description Public engament activity Eureka 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Stand at the Eureka museum during the British Science Week, with different activities regarding soil biodiversity and plant-soil relationships. Intended to reach the general public, it was a success. Many families visited the stand and engaged in convestations with us (kids and parents). Approximately 200 kids participated in the activities.
Year(s) Of Engagement Activity 2019
URL https://twitter.com/SoilEcolUoM/status/1105104998101323777