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

甲烷(CH4)是一种强有力的温室气体，仅次于二氧化碳，其全球变暖潜力为34。微生物在全球CH4循环中发挥着不可或缺的作用，它是公认的产甲烷古菌在缺氧条件下生产甲烷，而存在于氧-缺氧界面的好氧甲烷氧化细菌(MOB)消耗甲烷以限制向大气的排放。需氧暴徒可以将甲烷作为唯一的碳和能源，并因其在全球甲烷循环、卤代烃的生物转化以及甲烷转化为生物燃料和其他平台化学品中的作用而得到广泛研究。此前，我们的工作已经研究了不同环境中的暴徒的生态生理学，例如化学合成洞穴、垃圾填埋场和稻田。然而，人们对这些对环境重要的细菌如何与其他微生物群落(如硫/磷循环)相互作用知之甚少。该项目将使用一个化学合成洞穴生态系统模型(罗马尼亚Movile Cave，www.dedeakkumaresan.com/movile-ave.html)来开发一种多尺度系统方法，以了解生态进化适应和环境(地球化学/水文地质学)如何约束微生物的相互作用。具体地说，学生将使用：i)分子生态学工具(即稳定同位素探测实现的元基因组学/蛋白质组学)来跟踪微生物群落中的同位素，以确定代谢网络。ii)基因组解析的元基因组学，同时分离新的MOB来研究生态进化适应。iii)合成群落和CRISPR介导的基因组工程战略，以研究微生物的相互作用。iv)最先进的环境条件的现场监测，包括用于确定金属形态的地球化学工具和水文地质基础调查，以建立地下物理环境的全面框架。“

"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. "