Katherine Shek
Soil microbial assembly and function across scales of space, time and land use gradients
Microbial trait-environment interactions at the continental scale
Earth’s largest terrestrial C pool is in soils, where diverse consortia of microorganisms control the turnover and stability of organic C through micro scale differences in metabolic activity, directly influencing Earth’s climate. Despite microbial controls on soil organic C distribution and stability, large-scale models aiming to predict soil C under global change do not adequately represent these fine scale processes. I use a ‘big data’ approach with publicly available metagenomic data to investigate microbial metabolic and genomic trait-environment interactions across diverse environmental gradients. Using machine learning-based algorithms, I work towards identifying generalizable traits and properties of soil microbial genomes that represent complex metabolisms and biogeochemical mechanisms to aid in large-scale prediction of ecosystem outcomes.
Agricultural soil microbiomes
Soil microbes are key to the functioning of terrestrial ecosystems through their roles in nutrient cycling, carbon sequestration, and interactions with plants along a mutualistic to parasitic continuum. Agricultural management practices can influence soil microbial assembly patterns with impacts on functional outcomes of agroecosystem productivity and stability under global change. My research aims to unveil generalizable patterns in soil microbial assembly and function in agricultural soils under different management regimes, varying in disturbance intensity and environmental context. I examine bacterial, archaeal and fungal communities in soils managed for production of wine grapes (Vitis vinifera) coffee (Coffea arabica) and pasture grasses in temperate and tropical regions.
Generating reproducible bioinformatics pipelines to increase accessibility of microbial information
A whole-ecosystem approach requires collaboration and expertise across disciplines of ecology and environmental research. Increasing accessibility of information regarding microbial contributions to ecosystem processes may address the ‘black box’ often limiting predictions in other large-scale geochemical research. I aim to produce digestible and interpretable microbial functional data for integration into studies outside of microbial ecology to address our current climate crisis.
I have several other research projects investigating environmental microbiomes and upwards scalability of ecological patterns and processes across land use gradients.
Please reach out if you are interested in collaborating!
