Evolution of thaumarchaeotal metabolism under contrasting oxygen conditions

对比氧条件下奇菌代谢的进化

• 批准号: NE/R001529/1
• 负责人: Cecile Gubry-Rangin
• 金额: $ 66.16万
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FR001529%2F1
• 关键词: Evolution; thaumarchaeotal; metabolism; under; contrasting

Many of the important ecological processes essential for life on earth and for the sustainability of our environment are performed by microbes (the bacteria and archaea) that are astonishingly abundant and diverse on the planet. Their functional diversity has arisen through many millions of years of adaptation to environmental change. Despite the contribution of microbial activity to global nutrient cycles and environmental stability, our inability to grow most microbes in the laboratory has severely limited our understanding of the ways in which they adapt to change and evolve. Recent technological innovations remove this limitation and allow us to study adaptation in microbes. The first innovation is the ability to sequence genomes of microscopic single cells extracted from the environment, allowing identification of genetic changes involved in adaptation and inference of how genomes have changed through deep evolutionary time. The second is the use of this genetic information to improve our ability to cultivate microbes, enabling physiological studies.This project aims to use these cutting-edge technological advances to answer key questions about the mechanisms that generate this vast microbial functional diversity in nature, one of the greatest and most exciting challenges in biology. It will focus on a microbial group, the Thaumarchaeota, which are very diverse and abundant and have enormous environmental and economic impacts because of their role in oxidising ammonia fertilisers (resulting in greenhouse gas production and annual loss of >$70 billion of nitrogen fertilisers). As not all Thaumarchaeota perform ammonia oxidation, it is important to understand the distribution and activity of other Thaumarchaeota in the environment. This project will therefore address important environmental concerns about soil security and environmental change.In this project, soil will be incubated at varying oxygen concentrations to determine the Thaumarchaeota that are active under different conditions. Novel thaumarchaeotal genomes will be extracted from soils with different oxygen preferences using a cutting-edge technology, single-cell genomics, which enables sequencing of the genome of individual microscopic cells. This will establish the genetic basis for the differences in these oxygen preferences. We will compare these new genomes with those previously available to trace the evolutionary origin of the genes and metabolic pathways implicated. We will test our evolutionary inferences using physiological studies of laboratory cultures, using novel techniques and genomic information, to isolate organisms never previously grown in the laboratory. Finally, the relative abundance and activity of these groups will be assessed in several ecosystems to determine their ecological relevance. The project will address the crucial and exciting scientific and technological challenge of understanding the processes leading to the enormous functional diversity of microbes in terrestrial ecosystems, and will have broad environmental and socio-economic impact. It will increase our ability to predict the impact of environmental change on microbial diversity and ecosystem functions and will ensure better management of soil by facilitating the development of improved strategies for fertilisation utilisation and reduced greenhouse gas production. As the microbes studied in this proposal are unexplored, limited current information is available but their role in biogeochemical cycles and potential involvement in plant-microbe interactions is likely, offering novel scope of environmental and ecosystem understanding. Through various events, the scientific findings of this project will be disseminated to the public of all ages and to governing bodies and policy makers to communicate the importance of understanding adaptation in the face of environmental change and the need for better management of natural capital for ecosystem services.

许多对地球上的生命和我们环境的可持续性至关重要的生态过程都是由微生物（细菌和古细菌）完成的，它们在地球上的数量和种类惊人。它们的功能多样性是经过数百万年对环境变化的适应而产生的。尽管微生物活动对全球营养循环和环境稳定做出了贡献，但我们无法在实验室培养大多数微生物，这严重限制了我们对它们适应变化和进化的方式的理解。最近的技术创新消除了这一限制，使我们能够研究微生物的适应性。第一个创新是能够对从环境中提取的微观单细胞的基因组进行测序，从而识别与适应有关的遗传变化，并推断基因组如何在深度进化时间中发生变化。第二个是利用这些遗传信息来提高我们培养微生物的能力，使生理学研究成为可能。该项目旨在利用这些前沿技术来回答有关产生自然界中巨大微生物功能多样性的机制的关键问题，这是生物学中最伟大和最令人兴奋的挑战之一。它将重点关注一种微生物群，即Thaumarchaeota，这种微生物种类繁多，数量众多，由于它们在氧化氨肥（导致温室气体的产生和每年700亿美元的氮肥损失）中的作用，对环境和经济产生了巨大的影响。由于不是所有的Thaumarchaeota都进行氨氧化，因此了解环境中其他Thaumarchaeota的分布和活性是很重要的。因此，该项目将解决有关土壤安全和环境变化的重要环境问题。在这个项目中，土壤将在不同的氧气浓度下孵育，以确定在不同条件下活跃的Thaumarchaeota。新的古细菌基因组将从不同氧偏好的土壤中提取，使用尖端技术，单细胞基因组学，这使得单个微观细胞的基因组测序成为可能。这将为这些氧气偏好的差异建立遗传基础。我们将把这些新的基因组与以前可用的基因组进行比较，以追踪基因的进化起源和所涉及的代谢途径。我们将使用实验室培养的生理学研究来测试我们的进化推断，使用新技术和基因组信息，分离以前从未在实验室中生长的生物体。最后，将在几个生态系统中评估这些类群的相对丰度和活动，以确定它们的生态相关性。该项目将解决关键和令人兴奋的科学和技术挑战，了解导致陆地生态系统中微生物巨大功能多样性的过程，并将产生广泛的环境和社会经济影响。它将提高我们预测环境变化对微生物多样性和生态系统功能的影响的能力，并将通过促进改进施肥利用和减少温室气体生产战略的发展，确保更好地管理土壤。由于本提案中研究的微生物尚未被探索，目前的信息有限，但它们在生物地球化学循环中的作用和植物-微生物相互作用的潜在参与可能为环境和生态系统的理解提供了新的范围。通过各种活动，本项目的科学发现将传播给各年龄段的公众、理事机构和决策者，以宣传在面对环境变化时理解适应的重要性，以及为生态系统服务更好地管理自然资本的必要性。

项目成果

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota.

• DOI: 10.1038/s41467-022-31847-7
• 发表时间: 2022-07-15
• 期刊: Nature communications
• 影响因子: 16.6

Genomic determinants of soil depth niche partitioning in Gagatemarchaeaceae, a novel family of deeply-rooted Thaumarchaeota

• DOI: 10.1101/2023.03.08.531495
• 发表时间: 2023-03
• 期刊: bioRxiv
• 作者: Paul O. Sheridan;Yiyu Meng;T. Williams;C. Gubry-Rangin

Selective inhibition of ammonia oxidising archaea by simvastatin stimulates growth of ammonia oxidising bacteria

• DOI: 10.1016/j.soilbio.2019.107673
• 发表时间: 2020-02
• 期刊: Soil Biology & Biochemistry
• 影响因子: 9.7
• 作者: Jun Zhao;M. Bello;Yiyu Meng;J. Prosser;C. Gubry-Rangin

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota.

• DOI: 10.1038/s41467-020-19132-x
• 发表时间: 2020-10-30
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Sheridan PO;Raguideau S;Quince C;Holden J;Zhang L;Thames Consortium;Williams TA;Gubry-Rangin C
• 通讯作者: Gubry-Rangin C

Oxygen preference of deeply-rooted mesophilic thaumarchaeota in forest soil

• DOI: 10.1016/j.soilbio.2020.107848
• 发表时间: 2020-09-01
• 期刊: SOIL BIOLOGY & BIOCHEMISTRY
• 影响因子: 9.7
• 作者: Biggs-Weber, Eva;Aigle, Axel;Gubry-Rangin, Cecile
• 通讯作者: Gubry-Rangin, Cecile