The 3.8 billion year old palimpsest inked by natural selection onto the landscape of earth is slowly being revealed by the determination and ingenuity of interdisciplinary scientists with the help of DNA sequencing technologies. We are now able to explore the idiosyncrasies of evolution and examine the incredible adaptability and diversity of life on planet Earth. The knowledge we gain will help us develop technology for a changing world and tackle wickedly complex problems such as climate change, food and energy security, conservation and inequality.
I study nature's smallest creatures and how they build fertile soils and bolster plant growth. Bacteria and fungi live astonishingly complex lives in soil and their activity changes the quality of the soil habitat for all living things. I am interested in exploring the dynamics of the soil food web, answering questions like "who eats what from whom?" or "who eats whom?" and "when?" It is now possible to study the many facets of soil microbial communities all at once using methods like stable isotope probing and metagenomics or with metabolomics to see what kinds of biological processes shape the soil environment.
Understanding the lifestyles of soil dwellers may seem a bit esoteric, but their activity has a profound impact on the balance of carbon pulled from the atmosphere and buried in soil. The more we know about the ecology and physiology of decomposers, the better we can implement strategies to keep carbon in soils where it improves fertility (a win-win).
I gladly welcome any opportunity to collaborate, discuss ideas and help answer any questions that you may have about microbiology, soil management and, broadly-speaking, the awe-inspiring natural history of planet Earth.
I study the ecological and physiological traits of soil-forming / soil-conditioning microorganisms, specifically those involved in decomposition, mineral surface adhesion and soil aggregation, and how these traits relate to soil health. Fueled by examples like soil aggregating fungi (glomalin), and changes in soil moisture retention due to biofilms, the ecophysiology of soil-forming microorganisms is ripe for exploration. Many members of the ubiquitous soil bacterial group, Alphaproteobacteria, produce incredibly sticky substances, such as holdfast or unipolar polysaccharides. My research has shown that the surface-attachment of these, and other, common soil organisms is important in soil aggregation and plant matter decomposition. Soil microorganisms are also impacted by how we manage soils in agriculture and forestry, meaning that one must consider how disturbances, like harvesting or tilling, effect the process of soil formation and the resiliency of soil communities.
1. Quantifying the role of surface-attachment in carbon sequestration, soil aggregation and organic matter sorption using hyper-adhering or adhering-deficient mutants of Caulobacter, Agrobacterium, Rhodopseudomonas, Bacillus and Pseudomonas.
2. Determining microbial community predictors of common measures of soil health with machine learning on large datasets derived from a collaboration with the Cornell Soil Health Lab.
3. Identifying traits of lignocellulose-degrading microorganisms based on phylogenetic and functional gene markers using stable isotope probing.
4. Describing non-nitrogen-fixing members of the family Bradyrhizobaceae who represent one of the most cosmopolitan and abundant groups of soil bacteria, particularly in temperate forest soils.
5. Contrasting the long-term effects of different soil management strategies on soil microbial community in agriculture and forestry (see Long-term Soil Productivity Study).
• Profiling microbial communities using phylogenetic or functional genes
• Combining metagenomic, metatranscriptomic, metaproteomic and/or metabolomic data in stable isotope experiments.
• Building bioinformatics tools and workflows to accelerate and deepening the analysis of large microbial communities data (section on "Data, Code and Other Paraphernalia").
Visit my Google Scholar Profile for a Complete List of Publications
Public Science, Shared Code and Other Trappings
Science for the classroom and home
• Try this easy experiment to extract DNA from fruit
• What is a 'microbiome'? Here's an answer that includes some ways to cultivate your own microbiome.
My GitHub Repository containing code for :
• An R script to import and analyze community data for profiling differential abundances
• An R script to process phosopholipid fatty acids data
• A python wrapper for simplified, consistent and thorough metagenome QC and assembly (incl. options to perform digital normalization or partitioning and a choice of 3 assemblers: MetaVelvet, RAY-meta and IDBA-UD)
• A python script to map metagenomic reads to draft genomes to create a gene x genome count matrix
• A python script to run an HMM model for CAZymes and tabulate the output
Links to favourite podcasts:
• The Current - Listen to experts discuss current events from a Canadian perspective
• TWIM - Listen to senior professors in microbiology candidly discuss recent publications - fun & informative
• Quirks and Quarks - Listen to radio host Bob MacDonald interview researchers about their work
• RadioLab - Entertaining and always fascinating science or public interest stories told with innovative composition
• The Life Scientific - Interviews with senior scientists regarding their careers with physicist Jim Al-Khalili
• Q - Canadian Arts and Culture revue
Raw data for following studies:
• Datasets Pickles et al. 2017 (doi 10.1111/nph.14325)
Video, Slides and Social Media
Workplace and Contact Information
July. 14th, 2018