At a fundamental level, we are interested in understanding the physiological and ecological constrains of microbial life that lead to the emergence of structure in microbial ecosystem. We address this fundamental problem in the context of the microbial communities that digest complex forms of organic matter in the environment, and in particular, the ocean. This choice of context allows us to establish a link between the micro-scale community dynamics and processes of global impact, such as the C cycle. Moreover, COM-degrading communities have a large potential for applications in industry, especially as tools to unlock new biomass feedstocks.
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.
Genotype-phenotype mapping
Over the years we have built a biobank of marine bacteria, representative of the taxa that dominate coastal microbial communities. Using this resource, we are interested in understanding the link between physiology and ecology, asking questions like What determines carbon source preferences?, and how do organisms regulate substrate uptake when confronted with multiple substrates? Our goal is to (i) group organism into metabolic niches that help us “translate” taxonomic composition into functional information, and (ii) to learn how to predict metabolic preferences from genomes.
Meta-organisms and functional augmentation
We are exploring new approaches to engineer life by designing spatially structured microbial communities. We do this with a new technology that allows us to create programmable, DNA-guided multi-species consortia. We see these consortia as “meta-organisms” wherein spatial proximity facilitates interactions between metabolically complementary species.
Spatial Ecology of Bacteria
We develop microfluidic tools to visualize microbial colonization and community assembly at the microbe scale and in real time. We focus on communities that degrade complex organic materials, like chitin or cellulose, to understand how ecological interactions manifest in spatially structured environments and how fluid flow influences community assembly.
Host-microbiome interactions in the environment
Zooplankton mediate energy flow from phytoplankton to higher trophic levels, shaping carbon export and the coastal food webs that support aquaculture. We are developing a model system to identify how the zooplankton microbiome controls digestion, growth efficiency, disease resistance, and grazing/pellet production—mechanisms that matter both for carbon cycling and for sustainable, climate-resilient aquaculture.