Our fundamental scientific interest lies in understanding the processes (biological or otherwise) that constrain the evolution of microbes in the environment, and by extension, the biosphere. Because no organism lives in isolation but in diverse multispecies communities, addressing this challenge requires us to understand the selective pressures that emerge within such collectives. To this end, we focus our studies on the physiological constrains that govern the dynamics of microbial community assembly and disassembly in nature.
The context in which we address this fundamental problem is provided by the microbial communities that specialized in degrading complex forms of particulate organic matter (e.g. glycans) in the environment, and in particular, the ocean. This choice of context allows us to establish a link between the micro-scale ecology of bacteria and processes of global impact, such as the recycling of complex organic matter that sustains the C cycle.
Our research is enabled by a suit of resources built over the last few years: a large and diverse collection of marine bacteria (representative of most well-known particle associated organisms), genetic tools, ecological arenas for synthetic ecologies, mathematical models and hundreds of newly sequenced genomes.
A few of the key questions we are currently exploring are:
- ‘Collective action’ in microbes: division of labor, social and multicellular behaviors, cooperation, and their impact on relevant ecosystem processes.
- Glycan-bacteria interactions: the evolution of specialists and their exploiters; community assembly on glycan-rich particles.
- Inferring function from genomes in an annotation-free manner.
- Metabolic complementarities and mutualisms among marine microbes.
In addition to our focus on marine microbes, we have extended our work to include other systems such as synthetic pitcher plant microbiomes, or waste treatment biofilm granules. We also apply our methods in collaborations with industry aimed at understanding the mechanisms of (synthetic) biopolymer degradation in the environment.