Exploring how species interactions shape adaptive evolution in soil microbial communities

农业土壤微生物群落提供重要的生态系统服务，如为作物提供养分、防止病原体、分解有毒重金属和碳储存。然而，这些社区越来越多地面临人类活动造成的恶劣环境条件，例如农药的密集使用、海平面上升导致的盐度增加以及养猪场的抗生素径流。虽然体外实验表明，微生物可以迅速进化出对这些压力源的抗性，但这些研究仅限于在高度人工的实验室环境中，在单一压力源存在下的单一物种进化。然而，在一个复杂的自然群落中，进化反应可能受到阻碍，因为适应其他竞争物种的存在比适应环境更重要。微生物在面对人为压力时持续存在的能力对于维持依赖于稳定和高效微生物群落的生态系统功能具有明显的后果。我提议的研究将使用土壤微生物群落的实时实验进化，来测试复杂土壤微生物群落中的物种相互作用是否以及如何影响对压力环境的进化反应。我将重点关注与农业高度相关的压力源：广谱唑杀菌剂，猪场的抗生素径流以及气候变化导致的盐度和温度升高。由于环境压力因素通常是结合在一起的，我将测试这些压力因素单独和组合的影响。这项研究将在利物浦大学综合生物学研究所进行，该研究所是英国罗素集团的成员，在进化生物学、生态学和微生物学领域拥有前沿研究。最先进的技术，如16s rRNA，内部转录间隔（ITS）宏基因组学和全基因组测序将补充这项研究，由利物浦基因组研究中心支持。我将使用MicroResp系统来测量进化微生物产生的二氧化碳，从而突出进化适应与微生物生态系统功能之间的联系（与兰开斯特大学的Emma Sayer博士合作）。我提出的研究将深入了解自然土壤群落中是否以及如何发生对农业压力的进化反应。在我们面临气候变化和日益严重的农业害虫威胁等挑战，同时需要在2050年之前养活全球90多亿人口之际，这些问题尤为重要。这项研究将通过深入了解微生物进化适应在密集农业环境中的作用，迎接与BBSRC战略重点“可持续农业和食品的生物科学”相关的挑战。这种基本的理解将为未来的研究提供信息，旨在利用和操纵微生物群落，以实现高效、环保的食品生产。BBSRC将整合微生物组研究作为2019年响应模式的优先事项，强调了对基础、因果、微生物组研究的需求。

Agricultural soil microbial communities provide vital ecosystem services such as providing nutrients to crops, protection against pathogens, breaking down toxic heavy metals and carbon storage. However, these communities are increasingly faced with harsh environmental conditions imposed by human activity - such as intensive use of pesticides, increased salinity from rising sea levels, and antibiotic run-off from pig farms. While experiments in vitro reveal that microbes can rapidly evolve resistance to such stressors, such studies are limited to a single species evolving in the presence of a single stressor in a highly artificial laboratory environment. In a complex natural community, however, evolutionary responses may be impeded because adapting to the presence of other competing species is more important than adapting to the environment. The ability of microbes to persist in the face of anthropogenic stress has clear consequences for maintaining ecosystem functions that rely on stable and efficient microbial communities. My proposed research will use real-time experimental evolution of soil microbial communities, to test if and how species interactions in complex soil microbial communities influence evolutionary responses to a stressful environment. I will focus on stressors highly relevant to agriculture: a broad-spectrum azole fungicide, antibiotic run-off from pig farms and increasing salinity and temperatures driven by climate change. Since environmental stressors are commonly encountered in combination, I will test the impact of these stressors individually and in combination.This research will be conducted at the Institute of Integrative Biology at the University of Liverpool, a member of the UK Russell Group with cutting-edge research in the fields of evolutionary biology, ecology and microbiology. State-of-the-art technologies such as 16s rRNA, internal transcribed spacer (ITS) metagenomics and whole genome sequencing will complement this research, supported by the Centre for Genomic Research at Liverpool. I will employ the MicroResp system to measure CO2 production by evolved microbes, thus highlighting the link between evolutionary adaptation and microbial ecosystem functioning (collaborating with Dr Emma Sayer, Lancaster University). My proposed research will yield insights into if and how evolutionary responses to agricultural stress occur in natural soil communities. Such questions are particularly relevant as we face challenges such as climate change and growing threats from agricultural pests, while simultaneously needing to feed over 9 billion people worldwide by 2050. This research will meet challenges associated with the BBSRC strategic priority 'Bioscience for sustainable agriculture and food', by gaining fundamental insights into the role of microbial evolutionary adaptation in an intense agricultural setting. Such fundamental understanding will inform future research that aims to harnass and manipulate microbial communties for efficient, environmentally friendly, food production. The need for fundamental, causal, microbiome research is highlighted by BBSRC prioritising Integrative Microbiome Research as a responsive mode priority in 2019.