Rules of life in CO2-driven microbial communities: Microbiome engineering for a Net Zero future

微生物群落（通常称为微生物组）无处不在;在我们的皮肤上，在我们的肠道中，在我们赖以生长食物的土壤中，实际上几乎在地球上的每一个可居住的环境中。微生物组的成员以无数种方式相互作用，我们才刚刚开始欣赏，这在很大程度上要归功于我们掌握的强大的新工具。在这个雄心勃勃的多学科项目中，我们汇集了专业知识，使用这些工具来挖掘管理微生物群落成员之间相互作用的“生命规则”，以期开发出可以帮助我们理解和控制微生物组功能的预测方法。利用居住在地热泉的低多样性社区，我们将询问社区成员之间的代谢，生态和进化相互作用，共同管理二氧化碳转化为增值产品。这些产品涵盖了由直接微生物生长产生的初级代谢产物（并作为制造业的平台化学品和生物燃料具有价值），以及不直接喜欢生长但在微生物群落中发挥不明确作用的次级代谢产物，并且通常具有对社会具有高价值的生物活性特性（例如抗生素，抗癌剂）。我们将使用合成生物学方法来设计微生物组及其感兴趣的代谢途径，既作为一种学习工具来测试代谢产物产生和功能的假设，也作为一种手段来增强系统的CO2生物转化能力，以用于未来的生物技术发展。同时，我们将应用生态和代谢建模方法，继续生成可以用我们的模型系统进行测试的假设，并将其整合到新的预测工具中，以准确地从微生物组基因组数据中推断功能。至关重要的是，这些方法将协同工作，以帮助解决驱动这个模型系统的微生物-微生物相互作用，我们特意选择了这个模型系统，以最大限度地实现我们雄心勃勃的目标。通过解开这些低多样性系统中的生命规则，我们将朝着了解影响我们种植食物和过健康生活的能力的更复杂的社区迈出重要的第一步。与此同时，我们的项目承诺提供新的方法，将废弃的二氧化碳排放转化为废物，实现更可持续和净零的未来。

Microbial communities (often called microbiomes) are everywhere; on our skin, in our gut, in the soil we rely on to grow our food, indeed in almost every habitable environment on the planet. Members of microbiomes interact with one another in myriad ways which we are only just beginning to appreciate, thanks largely to powerful new tools at our disposal. In this ambitious, multidisciplinary project, we bring together expertise to use these tools to unearth the 'rules of life' that govern the interactions between microbial community members, with the view to develop predictive approaches that can help us to understand and control microbiome function. Drawing on low diversity communities that inhabit geothermal springs, we will interrogate the metabolic, ecological and evolutionary interactions between community members that collectively govern the conversion of CO2 into value-added products. These products span primary metabolites that result from direct microbial growth (and hold value as platform chemicals for manufacturing industries and as biofuels), as well as secondary metabolites that are not directly liked to growth but that play ill-defined roles in microbial communities, and often harbour bioactive properties of high value to society (e.g. antibiotics, anticancers). We will use synthetic biology approaches to engineer the microbiome and its metabolic pathways of interest, both as a learning tool with which to test hypotheses on metabolite production and function, and as a means to augment the CO2 bioconversion capacity of the system for future biotechnological development. In parallel, we will apply ecological and metabolic modelling approaches to continue to generate hypotheses that can be tested with our model system, and which will be integrated into new predictive tools to accurately infer function from microbiome genomic data. Crucially, these approaches will work in tandem to help resolve the microbe-microbe interactions that drive this model system, which we have deliberately chosen to maximise the success of our ambitious goals. By unravelling the rules of life in these low-diversity systems, we will take the first major step towards understanding the more complex communities that impact our ability to grow food and live healthy lives. At the same time, our project promises to deliver new ways to turn waste CO2 emissions into waste, towards a more sustainable and Net Zero future.