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

微生物群落(通常被称为微生物群)无处不在；在我们的皮肤上，在我们的肠道里，在我们赖以种植食物的土壤中，实际上在地球上几乎每一个宜居的环境中。微生物群的成员以无数种方式相互作用，我们才刚刚开始欣赏这些方式，这在很大程度上要归功于我们可以使用的强大的新工具。在这个雄心勃勃的多学科项目中，我们汇集了专业知识，使用这些工具来揭示支配微生物群落成员之间相互作用的“生命规则”，以期开发出能够帮助我们了解和控制微生物组功能的预测方法。利用居住在地热泉水中的低多样性群落，我们将询问群落成员之间的新陈代谢、生态和进化互动，这些互动共同管理着二氧化碳转化为增值产品的过程。这些产品包括直接由微生物生长产生的初级代谢物(作为制造业和生物燃料的平台化学品具有价值)，以及不直接喜欢生长但在微生物群落中扮演不明确角色的次生代谢物，并且往往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的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检验关于代谢物生产和功能的假说，也作为一种手段来为未来的生物技术发展增加系统的二氧化碳生物转化能力。同时，我们将应用生态和代谢建模方法来继续生成假说，这些假说可以用我们的模型系统进行测试，并将被集成到新的预测工具中，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，帮助解决驱动这个模型系统的微生物-微生物相互作用，我们故意选择这个模型系统，以最大限度地实现我们雄心勃勃的目标的成功。通过解开这些低多样性系统中的生命规则，我们将朝着理解更复杂的社区迈出重要的第一步，这些社区影响我们种植粮食和健康生活的能力。与此同时，我们的项目承诺提供新的方法，将废物二氧化碳排放转化为废物，迈向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.