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Why study microbial communities?

In the environment, microbes live in diverse communities, often with hundreds or thousands of different species. These organisms develop complex networks of interactions, including metabolic hand-off points within nutrient cycles, production and scavenging of co-factors, syntrophy, predation, and competition. The vast majority of environmental microorganisms have proven difficult or impossible to culture, in part because these interactions and networks are not maintained during isolation attempts. Environmental surveys and community-based approaches are currently the best way to characterize the diversity of microbial life on earth, and to identify novel metabolisms impacting global geochemical cycles or contaminants’ fates.

How to study microbial communities?

The Hug lab uses two main approaches to examine microbial communities. We sequence total community DNA (metagenomics), RNA (metatranscriptomics), and proteins (metaproteomics) from environmental samples. The DNA sequencing provides a blueprint of the microbial community, identifying the organisms present and allowing us to model the community’s metabolic potential. We take this one step further with genome-resolved metagenomics, where we can connect a given organism with specific predicted functions, through curation of draft genomes from metagenomes. The RNA and protein data allow us to identify what organisms are active in the environment and which processes are most abundant.

The second approach we use to study microbial communities is in the lab, with enrichment cultures and microcosms. These culture techniques aim to maintain a mixed population of bacteria and archaea. These methods reduce the total complexity of the community but maintain activities of interest, creating a system that is tractable for experiments.

Why contaminated environments?

An organism that evolved to respire, metabolize, or transform a contaminant in an impacted environment is often the most effective and efficient option for developing a bioremediation system. Contaminated sites are often under-studied environments harboring previously unknown microbial lineages and metabolisms.

Region of Waterloo landfill, aerial view.

Our current contaminated system: municipal landfills. Pictured: southern Ontario landfill, aerial view.

We are working with an active landfill in Southern Ontario to identify and characterize the microbial population in terms of the phylogenetic diversity, predicted roles in geochemical cycles, and potential for in situ contaminant attenuation. Sampling liquid leachate from the landfill as well as pristine and impacted groundwater from the surrounding aquifer, we are examining the microbial community’s heterogeneity across the site, the native abilities for contaminant transformations (e.g., vinyl chloride, 1,4-dioxane, ammonia), and the potential for discovery of new remediation systems.