Periodic Reporting for period 1 - MICOCO (How do biotic and environmental variation affect soil microbial community composition and functioning across spatial scales?)
Reporting period: 2021-10-01 to 2023-09-30
Soil microbial communities hold sway over numerous processes upon which we depend, driving the cycling of elements which sustain life, but also compromising food security and human health. Understanding the mechanisms driving existing soil microbial community diversity and function across disparate climates and ecological communities is key in order to determine future ecosystem responses to global change. Although studies aiming to characterise soil microbes are increasing in their scope, they will only capture the multifaceted interaction between diverse microbial communities if they measure the effects of above ground plant communities and the abiotic environment, when measured at appropriate scales across landscapes.
The proposed MICOCO project will address these shortfalls to achieve the following objectives:
[1] Determine the relative contribution of above ground plant community and soil abiotic conditions to SMC diversity and composition;
[2] Determine how climate influences microbial community turnover at varying spatial scales;
[3] Reveal the relative effects of microclimate, microbe-microbe associations, and microbe-plant associations on microbial function.
The proposed MICOCO project will address these shortfalls to achieve the following objectives:
[1] Determine the relative contribution of above ground plant community and soil abiotic conditions to SMC diversity and composition;
[2] Determine how climate influences microbial community turnover at varying spatial scales;
[3] Reveal the relative effects of microclimate, microbe-microbe associations, and microbe-plant associations on microbial function.
Since starting the project I have been able to:
- Attend a weeklong Joint Species Distribution Modelling (JSDM) workshop to understand how to use this approach to conduct species distribution modelling
- Sequence Fungal, Bacterial and Eukaryote eDNA sequences from Eden Project soil samples. This data was then processed via bioinformatic pipelines
-Undertake the first phase of microclimate data collection to calibrate microclimate model. The next phase begins next week and will be complete in December. Training in the use of NicheMapR demonstrated that this was not an appropriate tool at small landscape scale used for this initial component of research.
- Explored the data produced by the NEON consortium, and undertook training to use bioinformatic pipelines to process associated microbial data.
-Attended BES Aboveground-Belowground Workshop in Marseille and the EGU General Assembly in Vienna to present work on soil microbial communities and learn latest modelling approaches
-Have written, submitted and am currently undertaking revisions of a manuscript submitted to Restoration Ecology on the use of eDNA collected at the Eden Project to assess plant diversity
-Initiated collaboration and secured funding to work with Still/Moving Art collective to produce an art instillation piece on studying belowground communities
- Attend a weeklong Joint Species Distribution Modelling (JSDM) workshop to understand how to use this approach to conduct species distribution modelling
- Sequence Fungal, Bacterial and Eukaryote eDNA sequences from Eden Project soil samples. This data was then processed via bioinformatic pipelines
-Undertake the first phase of microclimate data collection to calibrate microclimate model. The next phase begins next week and will be complete in December. Training in the use of NicheMapR demonstrated that this was not an appropriate tool at small landscape scale used for this initial component of research.
- Explored the data produced by the NEON consortium, and undertook training to use bioinformatic pipelines to process associated microbial data.
-Attended BES Aboveground-Belowground Workshop in Marseille and the EGU General Assembly in Vienna to present work on soil microbial communities and learn latest modelling approaches
-Have written, submitted and am currently undertaking revisions of a manuscript submitted to Restoration Ecology on the use of eDNA collected at the Eden Project to assess plant diversity
-Initiated collaboration and secured funding to work with Still/Moving Art collective to produce an art instillation piece on studying belowground communities
The two key outputs to date have been to show that:
[1] soil eDNA can be used to characterise above ground plant diversity, and that it is useful in reflecting shifts in plant community composition. This means that eDNA metabarcoding of soils can be used to accurately reflect changes in plants during biomonitoring campaigns. The paper which demonstrates this is under revisions with Restoration Ecology.
[2] Differences in the composition of soil microbial communities at local scales can be characterised through a combination of changes in above ground plant communities, soil chemistry as previously observed, but also in combination with experienced soil temperature and moisture.
The socio-economic impact of these finding are:
[1] Performing continual biomonitoring of plant communities with this approach can aid effots to restore degraded ecosystems, and thus reduce the negative impacts of a loss of biodiversity on society.
[2] An improved understanding of how soil microbial communities are structured can help us understand the potential consequences on soil functioning and thus on the services that soil provides at local scales, from supply of nutrients to crops through to suppression of human pathogens.
[1] soil eDNA can be used to characterise above ground plant diversity, and that it is useful in reflecting shifts in plant community composition. This means that eDNA metabarcoding of soils can be used to accurately reflect changes in plants during biomonitoring campaigns. The paper which demonstrates this is under revisions with Restoration Ecology.
[2] Differences in the composition of soil microbial communities at local scales can be characterised through a combination of changes in above ground plant communities, soil chemistry as previously observed, but also in combination with experienced soil temperature and moisture.
The socio-economic impact of these finding are:
[1] Performing continual biomonitoring of plant communities with this approach can aid effots to restore degraded ecosystems, and thus reduce the negative impacts of a loss of biodiversity on society.
[2] An improved understanding of how soil microbial communities are structured can help us understand the potential consequences on soil functioning and thus on the services that soil provides at local scales, from supply of nutrients to crops through to suppression of human pathogens.