NSFDEB-BSF: Ecological networks and ecosystem function in the cow rumen microbiome: a multi-scale approach

牛、绵羊和山羊等反刍动物在人类农业中是必不可少的，它们完全依赖上消化道或瘤胃中的微生物群落将植物纤维转化为营养物质。这些群落被称为微生物群落，它们进行一连串的化学反应，分解(发酵)植物纤维。发酵的副产物可以作为营养物质被动物吸收，或者被微生物进一步加工。这最终导致二氧化碳和甲烷的产生，这两种强有力的温室气体随后进入大气。研究表明，发酵过程中的能量通过微生物群流动的方式在各个动物之间存在很大差异。这个项目将研究这些差异及其后果：化学反应如何不同，由群落中的不同微生物执行，对发酵有不同的影响，在某些情况下，不同之处在于它们是否比甲烷生产更有利于动物饲养效率，还是反过来。更详细地了解这项工作将导致的瘤胃微生物区系中的生态相互作用及其功能影响，将有助于研究人员确定更好的微生物组控制策略，并开发更有针对性的干预技术，以更环境可持续的方式提高食品安全。将对学生进行培训，并促进国际和跨学科合作。该项目将结合微生物基因组学、厌氧微生物学和微生物群落生态学来研究瘤胃微生物物种之间的生态相互作用，以及它们如何控制具有不同功能效率的替代微生物群的建立。研究人员将以高时间和遗传分辨率揭示微生物组的群落组装动态，并确定替代群落状态通过优先效应在瘤胃中聚集的可能性。当某些物种由于其生态相互作用而预先规定了群落的未来状态时，就会产生优先效应，刺激特定物种子集的生长，并抑制其他物种的生长。然后，研究人员将把由此产生的群落组成差异与瘤胃微生物组代谢效率的变化联系起来。通过这些努力，他们将建立群落结构和物种间相互作用之间的联系，主要发生在微观尺度上，以及重要的生态系统功能，如奶牛瘤胃中植物纤维材料的降解。

Ruminants such as cows, sheep and goats are essential in human agriculture and are fully dependent on microbial communities in their upper digestive tract, or rumen, to transform plant fiber into nutrients. These communities, known as microbiomes, carry out a cascade of chemical reactions that break down (ferment) the plant fiber. By-products of fermentation can be absorbed as nutrients by the animal or be further processed by microbes. This ultimately leads to the production of carbon dioxide and methane, potent greenhouse gases that then go into the atmosphere. Studies have shown that there is much variation among individual animals in the way energy from the fermentation process flows through their microbiomes. This project will look at these differences and their consequences: how the chemical reactions can differ, be performed by different microbes in the communities, have different effects on fermentation, and in some cases, differ in whether they favor animal feeding efficiency over methane production or the other way around. The more detailed understanding of the ecological interactions and their functional impacts in microbiomes of the rumen that will result from this work will help researchers identify better microbiome control strategies and develop more targeted intervention techniques to increase food security in a more environmentally sustainable manner. Students will be trained, and international and cross-disciplinary collaborations will be fostered. This project will bring together microbial genomics, anaerobic microbiology and microbial community ecology to study ecological interactions among the microbial species in the rumen, and how they control the establishment of alternative microbiomes with different functional efficiencies. Researchers will reveal the community assembly dynamics of the microbiome in high temporal and genetic resolution, and identify the potential for alternative community states to assemble in the rumen via priority effects. Priority effects occur when certain species precondition future states of the community due to their ecological interactions, stimulating the growth of a specific subset of species and inhibiting others. Researchers will then map resulting community composition differences to changes in the metabolic efficiency of the rumen microbiome. Through these efforts, they will establish the links between community structure and inter-species interactions, mainly happening at micro-scales, and important ecosystem functions such as the degradation of plant fiber material in the cow rumen.