Evolutionary adaptation in Archaea

生物多样性在大多数自然环境中是巨大的，并且在全球范围内对维持生态系统功能至关重要。高多样性被认为是由于对无数结构化环境和生物生态位的适应以及对替代资源的专业化而产生的。多样性反映了进化和生态之间的相互作用，因为生物适应环境变化而创造生物多样性，而生物多样性又被选择用于维持生态系统功能。因此，适应是一个对地球上的生命至关重要的进化过程。微生物（包括三个生命领域中的两个，即细菌和古细菌）是地球上最丰富的生物，在微生物适应过程中，有三种机制被认为是重要的：重组，允许遗传物质的横向交换（获得或失去）；正选择，有利于有利突变的增加；以及基因的差异表达。微生物由于其产生时间短，基因组小，体积小，是研究适应环境的有用生物。温古菌在中温环境中占原核生物丰度的重要比例，在全球氮的生物地球化学循环中起着重要作用。它们负责硝酸盐的浸出和氧化亚氮的产生，既参与温室气体的产生，又参与水/土壤的污染，因此具有重要的生态作用。在陆地环境中研究的所有非生物因子中，pH值对不同生态系统中三个空间尺度（世界范围、英国范围和农业pH样地）的古细菌群落组成的影响似乎最大。因此，thaumarchaea是研究环境适应性的一个很好的模型，本文将针对两种主要方法进行研究。首先，由于培养的thaumarchaea数量有限，人们对这些生物的了解严重有限，但是单细胞测序等新技术的发展将使人们能够使用一种不需要实验室培养的方法来比较它们的基因组。研究人员将对从不同pH值土壤中获得的细胞进行基因组测序，并用于比较它们的重组和选择水平，以了解高温古细菌受pH影响的原因和方式。其次，将采用实验进化方法在实验室中驱动高温古细菌在不同严格控制的pH压力下的进化，以分析它们的适应性。Thaumarchaea将在生长2.5年后进行比较，以评估它们随时间的进化适应以及不同pH值制度的功能。这将为进化速度、它们的专业化和适应的基因组基础等关键问题提供答案。这个项目将是第一个通过重组和选择来分析陆地古细菌的适应性的项目，也是第一个对古细菌的长期进化实验。因此，它将影响我们对农业、水和环境污染中重要的微生物群的生态学和进化之间联系的理解，也将为其他重要环境微生物的生态学和进化研究提供信息。

Biological diversity is vast in the majority of natural environments and, globally, is essential for the maintenance of ecosystem function. High diversity is believed to have arisen from adaptation to the myriad of structured environmental and biotic niches and specialisation to alternative resources. Diversity reflects the interaction between evolution and ecology, as organisms adapt to environmental change to create biological diversity, which, in turn, is selected for maintenance of ecosystem function. Therefore, adaptation is an evolutionary process of crucial importance to life on earth. Microorganisms (comprising two of the three domains of life, namely the bacteria and the archaea) are the most abundant organisms on earth and three mechanisms are seen as important in the process of microbial adaptation: recombination, allowing lateral exchange (gain or loss) of genetic material; positive selection, favouring the increase of advantageous mutations; and differential expression of the genes. Microorganisms are useful organisms to study adaptation to the environment due to their short generation time, their small genome and their small size.The thaumarchaea represent a significant proportion of prokaryotic abundance in mesophilic environments and play an important role in the global biogeochemical cycling of nitrogen. They are responsible for nitrate leaching and nitrous oxide production, participating in both greenhouse gas production and water/soil pollution, and thus play an important ecological role. Of all the abiotic factors investigated in terrestrial environments, pH appears to have the strongest influence on thaumarchaeal community composition at three spatial scales (world-wide, UK-wide and on a agricultural pH plot) in different ecosystems. Therefore, thaumarchaea represent a good model for studying adaptation to the environment and two main approaches will be targeted in this proposal.First, the limited number of cultivated thaumarchaea has seriously limited knowledge on these organisms, but development of new technologies such as single-cell sequencing will enable comparison of their genomes using an approach that does not require laboratory cultivation. Genome sequencing of cells obtained from soils with different pH will be developed and used to compare their levels of recombination and selection, in order to understand why and how thaumarchaea are influenced by pH.Second, an experimental evolution approach will be adopted to drive evolution of the thaumarchaea in the laboratory under different tightly controlled pH pressure in order to analyse their adaptation. Thaumarchaea will be compared after growth for 2.5, to assess their evolutionary adaptation over time and as a function of different pH regimes. This will provides answers to key questions on the speed of evolution, on their specialization and on the genomic basis of adaptation. This project will be the first to analyse adaptation of terrestrial thaumarchaea by recombination and selection and will also be the first long-term evolution experiment on archaea. It will therefore impact on our understanding of the links between ecology and evolution of a microbial group important in agriculture, water and environmental pollution, and will also inform ecological and evolutionary studies of other important environmental microorganisms.