Evolutionary adaptation in Archaea

古细菌的进化适应

• 批准号: NE/J019151/1
• 负责人: Cecile Gubry-Rangin
• 金额: $ 31.43万
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ019151%2F1
• 关键词: Evolutionary; adaptation; Archaea

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.

生物多样性在大多数自然环境中占有重要地位，在全球范围内，生物多样性对于维持生态系统功能至关重要。高度多样性被认为是由于对无数结构化环境和生物小生境的适应以及对替代资源的专门化而产生的。多样性反映了进化与生态学之间的相互作用，生物适应环境变化，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体，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（获得或损失）;积极选择，有利于增加有利的突变;基因的差异表达。微生物是研究环境适应性的重要生物，其世代时间短，基因组小，体积小，在中温环境中占原核生物的重要比例，在全球氮的生态地球化学循环中起着重要作用。它们负责硝酸盐淋溶和一氧化二氮的产生，参与温室气体的产生和水/土壤污染，因此发挥重要的生态作用。在陆地环境中调查的所有非生物因素中，pH似乎对不同生态系统中三个空间尺度（全球范围内，英国范围内和农业pH图）的thaumarchaeal群落组成的影响最大。因此，thaumarchea是研究适应环境的一个很好的模型，本提案将针对两个主要方法：首先，培养的thaumarchea数量有限，严重限制了对这些生物体的了解，但新技术的发展，如单细胞测序，将能够使用不需要实验室培养的方法来比较它们的基因组。将开发从不同pH值的土壤中获得的细胞的基因组测序，并用于比较它们的重组和选择水平，以了解为什么和如何thaumarchaea受到pH值的影响。第二，将采用实验进化方法，在实验室中驱动thaumarchaea在不同严格控制的pH值压力下的进化，以分析它们的适应性。将在生长2.5年后比较Thaumarchaea，以评估它们随时间的进化适应性以及不同pH制度的功能。这将为关于进化速度、它们的专门化和适应的基因组基础等关键问题提供答案。该项目将是第一个通过重组和选择来分析陆地thaumarchaea适应性的项目，也将是第一个关于古菌的长期进化实验。因此，它将影响我们对农业，水和环境污染中重要的微生物组的生态学和进化之间的联系的理解，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。

项目成果

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

• DOI: 10.1111/1462-2920.13971
• 发表时间: 2017-12
• 期刊: Environmental microbiology
• 影响因子: 5.1
• 作者: Herbold CW;Lehtovirta-Morley LE;Jung MY;Jehmlich N;Hausmann B;Han P;Loy A;Pester M;Sayavedra-Soto LA;Rhee SK;Prosser JI;Nicol GW;Wagner M;Gubry-Rangin C
• 通讯作者: Gubry-Rangin C

Seqenv: linking sequences to environments through text mining.

• DOI: 10.7717/peerj.2690
• 发表时间: 2016
• 期刊: PeerJ
• 影响因子: 2.7
• 作者: Sinclair L;Ijaz UZ;Jensen LJ;Coolen MJL;Gubry-Rangin C;Chroňáková A;Oulas A;Pavloudi C;Schnetzer J;Weimann A;Ijaz A;Eiler A;Quince C;Pafilis E
• 通讯作者: Pafilis E

Temperature responses of soil ammonia-oxidising archaea depend on pH

• DOI: 10.1016/j.soilbio.2016.12.007
• 发表时间: 2017-03-01
• 期刊: SOIL BIOLOGY & BIOCHEMISTRY
• 影响因子: 9.7
• 作者: Gubry-Rangin, Cecile;Novotnik, Breda;Prosser, James I.
• 通讯作者: Prosser, James I.