Macro-evolution in microorganisms: marine-terrestrial transitions as a case-study for adaptive radiations in bacteria

微生物的宏观进化:海洋-陆地转变作为细菌适应性辐射的案例研究

基本信息

  • 批准号:
    NE/T008083/1
  • 负责人:
  • 金额:
    $ 70.51万
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Research Grant
  • 财政年份:
    2021
  • 资助国家:
    英国
  • 起止时间:
    2021 至 无数据
  • 项目状态:
    未结题

项目摘要

Understanding the ecological and evolutionary drivers of biodiversity is of central importance to biology. However, knowledge on the extent, tempo, mode, and drivers of bacterial diversification greatly lags behind that of animals and plants. This knowledge gap is problematic, as bacteria are fundamental to biogeochemistry and ecosystem functioning, agriculture, industry, and human health, but also because there is great intrinsic value in understanding the evolution of the most ancient and diverse group of organisms on the planet.Adaptive radiations arguably form the best examples of the power of natural selection to generate biodiversity. These evolutionary bursts of diversification occur when a single ancestral type is faced with ecological opportunity enabling diversification into a multitude of specialised types. Unique colonisation events of virgin ecosystems, often the cause of adaptive radiations in animals and plants, are highly improbable in bacteria because of their large population sizes and high dispersal capacity. However, adaptive radiations could also be spurred by the evolution of 'key innovations' that open up new ecological opportunity (e.g. the evolution of the pharyngeal jaw allowing radiation of Rift Lake cichlids). It can be hypothesised that the extraordinary ability of bacteria to acquire novel traits via Lateral Gene Transfer (LGT) could make the evolution of key innovations and thus subsequent adaptive radiations especially prevalent. However, despite having a long history of research in multicellular organisms, it remains unknown whether adaptive radiations are an important driver in natural bacterial populations.One of the most drastic environmental transitions for metazoans and bacteria alike is that between marine and terrestrial environments. Marine-terrestrial transitions occasionally occur in bacterial taxa and are accompanied by significant rewiring of central metabolism. These transitions thus present an excellent model for the exploration of novel adaptive zones through key innovations. We will sample the ecologically versatile Myxobacteria from a range of terrestrial and marine habitats in Cornwall, U.K. to systematically study adaptive radiations in bacteria. First, we will estimate the frequency whereby myxobacterial lineages transition from marine to terrestrial habitats or vice versa. To do so, we will sequence a marker gene in replicated environmental samples to build a high-resolution evolutionary tree on which habitat preferences of lineages are mapped. Second, we hypothesise that lineages that colonise new habitats undergo adaptive radiations, leaving an imprint of increased branching rate in the phylogenetic tree compared to lineages that remain in their ancestral habitat. Third, we will retrieve genomes through isolate-based genome sequencing and by assembling genomes from metagenomes to identify the key adaptation(s) underlying marine-terrestrial transitions, elucidate whether they are the result of LGT events, and to explore the genomic consequences of a transition and subsequent radiation. There is a rich tradition of studying adaptive radiations in eukaryotes. Although theory and empirical data suggest that bacteria could likewise experience bursts of adaptive evolution, this will be the first largescale, purpose-designed analysis of adaptive radiations in bacteria. Results generated in this pioneering project will pave the way for studies in other bacterial taxa colonising different environments through different mechanisms and more generally provide impetus for the detailed study of macro-evolutionary patterns generating prokaryote diversity which ultimately underlies the functioning of all ecosystems.
了解生物多样性的生态和进化驱动因素对于生物学至关重要。然而,关于细菌多样化的程度、节奏、模式和驱动因素的知识远远落后于动植物的知识。这种知识差距是有问题的,因为细菌是生物地球化学和生态系统功能、农业、工业和人类健康的基础,而且还因为了解地球上最古老和多样化的生物体群体的进化具有巨大的内在价值。辐射可以说是自然选择产生生物多样性的力量的最佳例子。当单一祖先类型面临能够多样化为多种专门类型的生态机会时,就会发生这些多样化的进化爆发。原始生态系统的独特定植事件通常是动植物适应性辐射的原因,但由于细菌种群规模大且传播能力强,因此在细菌中极不可能发生这种定植事件。然而,“关键创新”的进化也可能刺激适应性辐射,这些创新开辟了新的生态机会(例如,咽颌的进化允许裂湖慈鲷的辐射)。可以假设,细菌通过横向基因转移(LGT)获得新特征的非凡能力可能使关键创新的进化以及随后的适应性辐射特别普遍。然而,尽管多细胞生物的研究历史悠久,但适应性辐射是否是自然细菌种群的重要驱动因素仍然未知。对于后生动物和细菌来说,最剧烈的环境转变之一是海洋和陆地环境之间的转变。细菌类群偶尔会发生海洋-陆地转变,并伴随着中枢代谢的显着重新连接。因此,这些转变为通过关键创新探索新的适应区域提供了一个优秀的模型。我们将从英国康沃尔郡的一系列陆地和海洋生境中对生态上多功能的粘细菌进行采样,以系统地研究细菌的适应性辐射。首先,我们将估计粘细菌谱系从海洋栖息地过渡到陆地栖息地的频率,反之亦然。为此,我们将对复制的环境样本中的标记基因进行测序,以构建高分辨率的进化树,在其上绘制谱系的栖息地偏好。其次,我们假设殖民新栖息地的谱系会经历适应性辐射,与保留在祖先栖息地的谱系相比,在系统发育树中留下分支率增加的印记。第三,我们将通过基于分离的基因组测序和从宏基因组组装基因组来检索基因组,以确定海洋-陆地转变背后的关键适应,阐明它们是否是 LGT 事件的结果,并探索转变和随后的辐射。研究真核生物适应性辐射有着丰富的传统。尽管理论和经验数据表明细菌同样可以经历适应性进化的爆发,但这将是对细菌适应性辐射的首次大规模、专门设计的分析。这一开创性项目产生的结果将为研究通过不同机制在不同环境中定植的其他细菌类群铺平道路,更广泛地为详细研究产生原核生物多样性的宏观进化模式提供动力,而原核生物多样性最终是所有生态系统功能的基础。

项目成果

期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Myxococcus xanthus.
黄色粘球菌。
  • DOI:
    10.1016/j.tim.2021.03.006
  • 发表时间:
    2021
  • 期刊:
  • 影响因子:
    15.9
  • 作者:
    Vos M
  • 通讯作者:
    Vos M
Accessory microbiomes.
  • DOI:
    10.1099/mic.0.001332
  • 发表时间:
    2023-05
  • 期刊:
  • 影响因子:
    2.8
  • 作者:
    Vos, Michiel
  • 通讯作者:
    Vos, Michiel
Adaptive radiations in natural populations of prokaryotes: innovation is key.
  • DOI:
    10.1093/femsec/fiad154
  • 发表时间:
    2023-11-13
  • 期刊:
  • 影响因子:
    4.2
  • 作者:
  • 通讯作者:
A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection.
  • DOI:
    10.1371/journal.pbio.3001645
  • 发表时间:
    2022-06
  • 期刊:
  • 影响因子:
    9.8
  • 作者:
    Soni, Vivak;Vos, Michiel;Eyre-Walker, Adam
  • 通讯作者:
    Eyre-Walker, Adam
Copper selects for siderophore-mediated virulence in Pseudomonas aeruginosa.
  • DOI:
    10.1186/s12866-022-02720-w
  • 发表时间:
    2022-12-13
  • 期刊:
  • 影响因子:
    4.2
  • 作者:
    Lear, Luke;Hesse, Elze;Buckling, Angus;Vos, Michiel
  • 通讯作者:
    Vos, Michiel
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Michiel Vos其他文献

Michiel Vos的其他文献

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{{ truncateString('Michiel Vos', 18)}}的其他基金

The effect of recombination on incipient speciation in bacteria
重组对细菌初期物种形成的影响
  • 批准号:
    NE/L013177/1
  • 财政年份:
    2014
  • 资助金额:
    $ 70.51万
  • 项目类别:
    Research Grant
Sex and Death: testing the evolutionary benefit of recombination using a bacterium and bacteriophage model
性与死亡:使用细菌和噬菌体模型测试重组的进化益处
  • 批准号:
    NE/K000926/1
  • 财政年份:
    2013
  • 资助金额:
    $ 70.51万
  • 项目类别:
    Research Grant

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基于微生物生态进化和生境改良整合技术的高效石油降解菌群构建及其土壤适应性识别
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