Climate, Microbes, and Medicine: Discovering Antimicrobials in Warming Forest Soils

We are seeking students inspired by the Bio 153 Phage Discovery Lab!

Our lab studies soils from long-term warming experiments at Harvard Forest and National Ecological Observatory Network (NEON) sites, including the Quabbin Reservoir Watershed. These soils harbor an astonishing diversity of bacteria and viruses—some never seen before. In fact, we discovered the world’s second-largest virus genome (2.1 MB) and 15 other novel giant DNA viruses using fluorescence-activated cell sorting (Schulz et al., 2018).

Our metagenomic and metatranscriptomic datasets from Harvard Forest have led to the discovery of:

• Novel DNA viruses (Graham et al., 2024)
• RNA phages (Neri et al., 2022)
• Viroid-like circular RNAs (Lee et al., 2023)
• Virophages (Lotun et al., in prep)
• New protein families (Fremin et al., 2022; Pavlopoulos et al., 2023)

Now, we’re taking this research a step further.

In collaboration with Prof. Amir Mitchell's Lab at UMass Chan Medical School, we’re screening these well-characterized soils for antimicrobial activity using an E. coli library of barcoded single-gene deletions. This approach, based on the pooled genetic screen in Noto Guillen et al., 2024), allows us to pinpoint which bacterial genes and traits are targeted by antimicrobial compounds found in soil.

By combining this genetic screen with our rich metagenomic data, we aim to identify the biosynthetic pathways responsible for producing these natural antimicrobials—potentially leading to new antibiotics or therapeutic agents.