The Soil Microbial Black Box - Does What’s Inside Matter?

A single gram of soil can harbor in the order of 1010 bacteria and up to 52 000 individual species. However, the role of this diversity in regulating soil functions (e.g. nutrient cycling and greenhouse gas fluxes) is still remarkably poorly understood (the so-called microbial ‘black box’). Until recently, efforts to understand the role of microbial community composition were hampered by the difficulty and cost of characterizing diversity, but recent developments in next generation sequencing (NGS) have, if coupled with robust characterization of function, largely resolved this issue, shifting the scientific uncertainty to the role of microbial diversity in soil functioning. Physico-chemical conditions imposed in soils can have a dominating effect on microbial community composition and activity, but direct evidence that this controls the potential of these communities to drive soil processes is limited. This has led to the suggestion that microbial diversity per se is not a dominating control on soil functions, and that the huge diversity (and associated functional redundancy) facilitates resilient soil functioning, independent of community composition. However, soil is not a uniform environment and soil process rates are often dominated by hotspots of activity. A specific example is the soil around roots (rhizosphere), where it is now established that plant identity (species and genotype) is a key determinant of microbial communities (control on plant-associated microbiome). Evidence generated by the supervisor team, coupling isotopic and molecular approaches, suggests that this selection of plant-associated microbiomes can function to promote beneficial feedbacks between soil processes and plant productivity. This interaction has strong implications for development of sustainable production systems, but also provides an ideal system within which to test microbial diversity/ function relationships and the relative strength of soil- and plant-mediated controls of them.
Aim; To identify the relative contributions of plant driven selection of microorganism and soil environmental conditions (e.g. pH, moisture) on the rates and products of C and N cycling and to identify if this relationship holds true for different soil processes (e.g. dentification versus nitrification).
Approach; This project will utilize an experimental platform at the James Hutton Institute which consists of replicated plots planted with different grass species known to promote different levels of CO2 emissions from soils. This platform offers a unique opportunity to investigate the role of plant microbiomes on soil function by providing soils adapted to individual grass species. Initially this study will use soil from these plots and deploy NGS to determine whether functional communities differ between different grass species, use 13C and 15N stable isotope techniques to determine the fate of C and N in these soils and use multivariate statistics to partition the contributions of environmental factors and the microbial community to function. The importance of plant microbe interactions in determining process rates will then be assessed using controlled environment experiments utilizing soil and grass species from the grass platform. By using soil adapted to one grass species and using it to grow another it will be possible to determine whether microbiome composition can play a role in determining process rates or whether environmental controls exerted through rhizodeposition, e.g. C addition to soil are more important drivers of nutrient cycling and if this is consistent between processes (e.g. nitrification and denitrification). Results from the initial field work and controlled environment experiment will allow the student scope to determine which mechanisms to focus upon. These could include soil microbial legacy effects on microbial recruitment and thus the applicability of findings across soil types, the role of microbial diversity on function or the role of increasing above and below ground diversity on process rates. Work within this study has synergy to ongoing Scottish government funded work in RESAS RD 1.1.1 and will deliver added value. During this PhD the student will have access to resources and expertise in molecular ecology, including the quantification of N cycling communities and the use of NGS to characterize community structure; access to resources and expertise in biogeochemistry, including the use of stable isotopes to determine process rates, the quantification of GHGs and measurement of C flow from plants.