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Interactions in the microbiome – the effect of spatial organisation

Principal Supervisor: Dr Orkun Soyer

Secondary Supervisor(s): Dr Richard Puxty

University of Registration: University of Warwick

BBSRC Research Themes:

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Deadline: 4 January, 2024


Project Outline

Microbiome research is expanding. This is a natural progression, as no microbe lives in isolation in Nature. From guts of animals, to the soil and the ocean, every environment inhabited by microbes contains 100s of species co-existing. These, so-called microbial communities or microbiomes are microscopic ecosystem where different species interact and co-exist. Understanding these interactions and their dynamics is a significant research frontier.

In Nature, microbes commonly live in spatially organised communities such as biofilms, mats, and granules. Such structures, and in particular granules and aggregates are found to form in various habitats such as the open ocean, freshwaters, and even bioreactors. In the open ocean and in freshwater, granules and aggregates are formed primarily by filamentous cyanobacteria. These emergent structures enable specific biogeochemical processes by cyanobacteria, including carbon and nitrogen fixation. We have developed a model cyanobacterial granule system, derived from a local freshwater reservoir. In this system, we have identified 15 species alongside the dominant cyanobacteria.

In this project, you will decipher the specific, metabolic interactions between these bacteria in the spatial context of the granule. We have already isolated several species from this system, allowing us to address both pairwise and higher-level interactions. Ideal candidates should have an interest in microbial ecology and application of quantitative methods to it.

Relevant Publications

Techniques

Metagenomics, proteomics, FISH, targeted metabolomics.