Microscale microbial ecology

What does the world look like to a microbe?

Microbial evolution

How do microbes diversify their metabolic capabilities, and how does this influence their population dynamics?

Computational methods

Improving how we do microbial ecology, one R package at a time

Selected Publications

Here, we introduce a new approach for quantifying composition in synthetic bacterial communities based on Sanger sequencing. Using synthetic communities of marine bacterial isolates, we show that this approach yields accurate and reproducible abundance estimates for two-, four-, and seven-strain bacterial communities. Furthermore, this approach can provide results within one day and costs ~5 USD per sample.
bioRxiv, 2018

Here, we track the taxon and trait dynamics of bacteria attached to model marine particles and demonstrate that particle-attached communities undergo rapid, reproducible successions driven by ecological interactions. These results suggest that primary successions may shape particle-attached bacterial communities in the ocean and that rapid community-wide metabolic shifts could limit rates of marine particle degradation.
Nature Communications, 2016

In this study, we have used a yeast experimental system to explore the effect of range expansions on the maintenance of cooperative behaviors, which commonly display frequency- and density-dependent selection and are widespread in nature. We found that range expansions favor the maintenance of cooperation in two ways: (i) through the enrichment of cooperators at the front of the expanding population and (ii) by allowing cooperators to outrun an invading wave of defectors.
Proceedings of the National Academy of Sciences of the United States of America, 2013

Recent Publications

More Publications

. Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology. The ISME Journal, 2018.


. Modular assembly of polysaccharide-degrading microbial communities in the ocean. bioRxiv, 2018.