Microbial social lives: A multi-scale systems approach to decode microbial metabolic networks

"Methane (CH4), a potent greenhouse gas, is next only to CO2 with a global warming potential of 34. Microbes play an integral role in global CH4 cycling and it is well-established methanogenic archaea produce methane under anoxic conditions, while aerobic methane-oxidizing bacteria (MOB) present in the oxic-anoxic interface consume methane to limit emissions into the atmosphere. Aerobic MOBs can use methane as a sole carbon and energy source and have been studied extensively for their role in global methane cycle, biotransformation of halogenated hydrocarbons and valorisation of methane to biofuels and other platform chemicals.

Previously, our work has studied the ecophysiology of MOB in different environments e.g. chemosynthetic caves, landfills and rice paddies. However, little is known how these environmentally important bacteria interact with other microbial communities (e.g. sulfur/phosphorus cycles).

This project will use a model chemosynthetic cave ecosystem (Movile Cave, Romania www.deepakkumaresan.com/movile-cave.html) to develop a multi-scale systems approach to understand how eco-evolutionary adaptations and the environment (geochemistry/hydrogeology) constrain microbial interactions.

Specifically, the student will use:
i) molecular ecology tools (i.e. stable isotope probing enabled metagenomics/proteomics) to track isotopes within the microbial communities to identify metabolic networks.
ii) Genome-resolved metagenomics alongside isolation of novel MOB to study eco-evolutionary adaptations.
iii) Synthetic communities and CRISPR-mediated genome engineering strategies to study microbial interactions.
iv) State-of-the-art in situ monitoring of environmental conditions, including geochemical tools to identify metal speciation and hydrogeological base surveys to build a comprehensive framework of the subsurface physical environment. "