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 a new generation of interdisciplinary biologists, biochemists, statisticians and computer scientists using modern sequencing technology. We are now able to delve into the idiosyncrasies of evolution and examine the incredible adaptability and diversity of life on planet Earth. The knowledge we gain will help us develop suitable technology for a changing world and tackle wickedly complex problems such as climate change, food and energy security, conservation and inequality.
As a post-doc in the Buckley Lab, I study microbial communities that break-down plant matter in forest and agricultural soils. I work to better understand how the raw materials from plants (carbon, nitrogen ... etc) are used by members of the microbial community and track where most of it eventually ends up. To achieve this, I focus on identifying which organisms are involved; what tools they use (i.e. enzymes); and 'forensically' track who ate what... or whom.
This knowledge is valuable for our basic understanding of soil ecology and for modeling the fate of carbon pulled from the atmosphere by plants and deposited or leached into soil. This knowledge is also valuable for designing and implementing strategies to optimize carbon sequestration in managed systems. By studying decomposers, my research also contributes to improving the conversion of plant biomass into renewable sources of biofuels and other raw materials, such resin and plastic. Read more in the “Research” section.
I am specialized in soil microbial ecology and have a background in chemistry, biology and environmental science. I have experience with the challenges of extracting information about microbial community structure and function from the marvelously complicated soil environment. I have expertise in balancing multifaceted wet-lab experiments with statistical and computational analyses and how best to apply massive sequencing data to ecological questions.
I am highly appreciative of the opportunity my work affords to engage in collaboration and idea sharing. Feel free to contact me with questions or grand hypotheses.
Areas of Interest
My general focus is the ecology and functional diversity of microbial communities involved in decomposition, soil formation, nutrient cycling and adaptation to disturbance in temperate forest ecosystems. I have been involved in studying cellulose and lignin degrading organisms; ectomycorrhizal networks; evolution and speciation in bacteria; interactions of bacteria and fungi (antibiotics and probiotics) and the long-term impacts of timber-harvesting on carbon cycling.
1. One of the most abundant groups of organisms in coniferous forest soil across North America are from the family Bradyrhizobaceae. These slow-growing and functionally diverse bacteria present an interesting case study in successful adaptation to the soil environment and, due to their abundance, are likely important in geochemical cycling. We study the genetic diversity and metabolic capabilities of this group through comparative genomics and characterization of isolates.
2. The colonization of plant matter during the long process of decomposition involves complex spatial and temporal interactions between fungi and bacteria. Many of our therapeutic antibiotics originate from soil microbes engaged in competition for resources or in defense, yet there is much to learn about other strategies for competing or collaborating. We study in vivo fungal-bacterial interactions during competition for cellulosic substrates.
3. The diversity and ecology of cellulose and lignin decomposing bacteria is not well known, since, historically, most research has relied on culture-based methods. Using stable-isotope probing methods, we are cataloging diversity and prospecting for novel features of cellulose and lignin-degrading bacteria from forest soil.
4. Forestry is one of Canada's oldest industries, yet because of the slow regeneration time of trees (i.e. crop cycle) very little is known about changes in soil fertility over time. In collaboration with the Long-term Soil Productivity Experiment, we study changes in the microbial community decades after harvesting and compare different forms of harvesting.
• Profiling microbial communities using phylogenetic and functional genes, analysis of metagenomic, metatranscriptomic, metaproteomic and metabolomic data, single-cell sorting and culturing-based methods.
• Using radionuclide and stable isotopes to trace the activity and genetic composition of specific functions within a microbial consortium. These methods can be effectively performed under more realistic environmental conditions (microcosm / field studies).
• Plate-based competition assays and functional screens.
• Building bioinformatics tools and analysis pipielines for comparative genomics, metagenomics and networking analyses to identify key features of microbial communities (see section on "Data, Code and Other Paraphernalia").
Visit my Google Scholar Profile for a Complete List of Publications
Data, Code and Other Paraphernalia
Data from the following projects:
• RAW Data for Pickles et al. 2016 (doi 10.1111/nph.14325)
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
Video, Slides and Social Media [Best Viewed By Internet Explorer... sadly...]
Current Video: Watch Me Discussion Evolutionary Pressures on Genome Size
[Prepared for Highschoolers for 'DNA Day', April 21st, 2015]
Workplace and Contact Information
Last updated Jan. 26, 2017