How do soil bacteria interact, and what happens when they do?

Bacteria seldom live alone. Despite this fact, most microbiology research is done with single bacterial species living in isolation. While this has proven to be a powerful approach, it is becoming clear that by reducing the complexity of the bacterial world, we are missing out on observing some fascinating bacterial behaviors. Outside of the laboratory, bacteria live in environments in which their lives are influenced by fluctuations in abiotic conditions, and by the other organisms surrounding them. We are broadly interested in how bacteria interact with their environment and with each other.

An exciting focus of the lab is on emergent traits which arise during interaction between bacteria, which would be difficult (or impossible) to predict based on the study of each organism in isolation. The system we work on focuses on the soil bacteria Pseudomonas fluorescens and Pedobacter. Under our experimental conditions, neither is capable of movement across the surface of an agar plate. However, in this particular environment, interaction between these bacteria triggers the ability to migrate together. We are using genetic, genomic, and classic microbiology tools to learn about how these bacteria interact, and how the “social motility” works.

Social motility (the big colony) compared to growth of Pedobacter and P. fluorescens mono-cultures (the small colonies on top).


Evolutionary resurrection of flagella production.

How bacteria function and evolve new functionality remains a major question in microbiology. Studying microbial evolution provides an opportunity to observe evolution in real time and ask questions about the mechanisms underlying the observed phenotypic changes. With collaborators, we recently showed that Pseudomonas fluorescens strains which were defective for flagellum production due to loss of a regulator (FleQ), were able to repurpose a related regulator (NtrC) and thus rewire the flagellum regulatory system. The adaptation occurred in a reproducible two-step process in which mutations are thought to alter the activation and specificity of a regulatory protein, resulting in it replacing the missing regulator of flagella gene expression. Our current work seeks to define the mechanism by which NtrC substitutes for FleQ, and explore the role of environmental conditions in the selection of strains with resurrected flagella.

Non-motile fleQ mutant of P. fluorescens (left). A motile sector swims away from the the fleQ mutant colony, indicating resurrection of motility (right).

The publication of this work (here) was featured in The Scientist and Nature Reviews Microbiology, and attracted the interest of “intelligent design” proponent Michael Behe, who penned a commentary for the Discovery Institute website “Evolution News” (here).

Quorum sensing inhibition by marine bacteria.

A new area of interest in the lab is the identification of molecules which inhibit quorum sensing of the Gram negative pathogen Pseudomonas aeruginosa. Cultivation of marine microbes has allowed us to establish a collection of several hundred bacteria, which we have screened for the ability to inhibit quorum sensing. Several promising candidates have been identified, and we are now working to decipher the structure of the molecule(s) responsible. We are interested in the therapeutic potential of anti-virulence by disrupting quorum sensing, and in the role of molecules which inhibit quorum sensing in the ecology of bacterial communities.