Hallam Lab

Photosynthetic microorganisms (cyanobacteria, microalgae, and phytoplankton) are nature's sustainable powerhouses, using sunlight, water, and COΓéé to produce energy-rich biomass through photosynthesis, all while reducing greenhouse gas emissions. In bio-circular production, they play a vital role by converting environmentally harmful waste streams like agro-industrial residues, wastewater, and industrial emissions into valuable, eco-friendly resources such as biofuels, biodegradable plastics, organic fertilizers, and high-value compounds. Advances in biochemistry enable the optimization of metabolic pathways to enhance productivity, while bioinformatics empowers synthetic biology by providing tools to design, model, and engineer strains with tailored traits for improved performance. Cutting-edge high-throughput lighting system screening accelerates the identification of optimal light conditions for growth and product yield, maximizing energy efficiency and reducing resource consumption in cultivation systems like photobioreactors and open ponds. Biotechnology further drives innovation by integrating these advancements into industrial processes, ensuring minimal environmental impact and large-scale sustainability. By leveraging these interdisciplinary approaches, photosynthetic microorganisms not only reduce reliance on fossil fuels and synthetic chemicals but also promote biodiversity and ecosystem health, paving the way for a greener, more sustainable future.

Microorganisms have spent 3.5 billion years evolving at individual, population, and community levels of biological organizations, innovating diverse solutions to nutrient and energy conversion processes that have withstood the test of time and generated a deep repository of genomic power. Microbial life harnessed energy and materials transforming Earth's surface chemistry, creating vast genomic diversity. Today, approximately nonillion prokaryotes inhabit Earth, and with their coalesced genomic reservoir, they form a metabolic network likely encoding over 15 decillion genes. This potential contains numerous enzyme variants and metabolic pathways that are controlled by multiple regulatory systems to adapt to transforming environmental conditions. Volatile organic compounds (VOCs) are a class of small-molecule chemicals that can be difficult to monitor in chassis organisms despite their important interplay in microbial metabolism, cell-to-cell signaling, adaptation, and response. We describe a multiomics approach to charter the metabolomics, lipidomics, proteomics and volatilomics characteristics of large insert fosmid libraries in EPI300 chassis organisms using the most current mass spectrometry instrumentation. In addition to isolate or enrichment profiling, the multiomics machinery will support functional metagenomic screening of the libraries sourced from different levels of biological organizations to identify genes and gene cassettes in microbes mediating the metabolome, lipidome, proteome and volatilome cycles in various natural and engineered environments. The resulting multiomics profiles will highlight the potential of functional screening to identify biosynthetic routes for heterologously expressed metabolites, such as VOCs, providing valuable insight for process development, and a baseline for developing new screening paradigms for biocatalyst discovery and engineering microbial cell factories for sustainable energy and materials production.

Large insert (fosmid) environmental DNA library production, clone recovery and characterization, sequencing, storage, and information management.

Bacterial and archaeal prokaryotes drive fundamental biochemical processes which shape and support life and ecosystems around the world. Despite their great importance, many prokaryotes remain uncultivated in lab and clinical settings and are underrepresented in public databases, which are dominated by cultured isolates. This underrepresentation reduces the precision of taxonomic classification and metabolic pathway reconstruction from metagenomes that depend on accurate labeling for more quantitative insight. Recent advances in single-cell amplified genomic (SAG) sequencing and metagenome assembled genome (MAG) analysis provide an opportunity to improve precision of taxonomic labelling of environmental genes and genomes needed for consilient metabolic pathway reconstruction. I leverage Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP), a software application supporting gene-centric analysis of phylogenetic and functional marker genes based on reference packages consisting of a multiple sequence alignment, profile hidden Markov model, phylogenetic tree, and taxonomy table. I focus on genes encoding each step in the denitrification pathway (NapA, NxrA/NarG, NirK, NirS, NorB, and NosZ) as a use case. After updating these reference packages with SAGs and MAGs, we assess the diversity of each denitrification gene in Saanich Inlet, a seasonally anoxic fjord in the Strait of Georgia, as well as the Northeastern Subarctic Pacific Ocean.

Anaerobic digestion (AD) is a microbial-driven process that enables resource recovery from organic waste streams, generating renewable natural gas (RNG) and other valuable byproducts. In the AD research group at the Hallam Lab, we leverage next-generation sequencing, isotope-based approaches, and multi-omics to unravel the microbial ecophysiology within AD systems. Our goal is to optimize bioprocess design, enhancing methane production and sustainable waste management.

Mycelium is the filamentous network of mushrooms. The mycelium biofabrication working group in the Hallam Lab is actively pursuing the development of mycelium-derived materials and mycelium biocomposites for applications such as food packaging, medical devices, architectural installations, and product design. In this working group, we collaborate to advance the understanding fundamental mycelium behaviour in various environments, explore the use of mycelium in new applications, and design and deploy mycelium-derived products for sustainable living.