Exploring Microbial Biodiversity
The Palmer lab is situated at the University of Manitoba in Winnipeg, MB, Canada. Our research uses meta-omics approaches to explore biological novelty from underexplored environments and to address fundamental research questions on prokaryotic evolution. This entails discovering and documenting novel microbes and their genes from environmental sources, and population genomics for an improved understanding of microbial evolution.
Research Focus
The broad long-term aims of our research are to discover, understand, and utilize underexplored archaeal and bacterial diversity in environments existing under physical and chemical extremes.
Despite representing most cellular life on Earth, > 99% of archaea and bacteria in existence today have likely never been cultivated or studied and are thus poorly understood. However, with the massive recent technological advancements in large-scale sequencing, cultivation can be bypassed to i) identify who makes up the community in a particular environment, ii) generate hypotheses on what they may be doing within that environment, and iii) investigate their evolution at the hand of environmental pressures experienced in that environment. This is particularly relevant in understudied ecosystems, where new microorganisms with interesting physiologies, representing major lineages of life, are frequently found. Among these understudied environments are those found in physical and chemical extremes; often understudied because we lacked the ability to effectively interrogate them in the past. In the Palmer lab, we use modern molecular tools and bioinformatics to uncover the underexplored diversity in these settings.
Systematics and Ecology
Despite the importance of effectively communicating our science through the use of stable names, in prokaryote biology a disconnect has historically existed between taxonomy and ecology. Often, taxonomic decisions are based on limited molecular or ecological information, and designated groups are not reflective of natural taxon boundaries.
Our lab specializes in taxonomic classification based on genome data, which also allows for meaningful taxon circumscription and generation of hypotheses regarding the ecology of microorganisms.
Bioprospecting
With the massive amounts of biological data generated daily, environmental data contain a treasure trove of yet-to-be-discovered and -characterized genes that may code for enzymes with interesting and useful functions.
Our lab is committed to making the most with the data we generate. For this reason, we mine meta-omics data to identify novel genes with potentially interesting biochemical functions. The evolution of these genes can then be interrogated and functionally verified through heterologous expression and biochemical characterization.
Population genomics
Using composite population genomes (a.k.a. metagenome-assembled genomes), we can now obtain a glimpse into the diversity encompassed by different populations of the same organisms. This data can be used to interrogate how populations adapt, and the level of genetic heterogeneity required to maintain adaptability.
As a key focus in our lab, we investigate the impact of environmental and temporal changes on microbial communities and populations. With this work, we aim to improve our understanding of the underlying mechanisms of evolution, and what internal genetic restrictions may influence the ultimate evolutionary trajectories of different populations.