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：
Michiel Vos
金额：
$ 70.51万
依托单位：
UNIVERSITY OF EXETER
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

来源：
https://gtr.ukri.org/projects?ref=NE%2FT008083%2F1
关键词：
Macro evolution microorganisms marine terrestrial

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生物学至关重要。然而，知识在细菌多样化的程度，速度，模式和驱动因素方面极大地落在了动物和植物的背后。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，这也是因为在理解地球上最古老和多样化的生物体的演变方面具有巨大的内在价值。适应性辐射的最古老和多样化的生物体的演变可以说是生成自然选择的最佳实例。当单个祖先类型面临生态机会，使多样化成为多种专业类型时，就会发生这些多元化的进化爆发。维珍生态系统的独特殖民事件，通常是动物和植物适应性辐射的原因，由于其人口较大和高分散能力，因此在细菌中极不可能。然而，“关键创新”的演变也可以刺激自适应辐射，从而开辟了新的生态机会（例如，咽下颌的演变允许裂谷丽夫湖塞奇利德湖的辐射）。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以使关键创新的演变发展，从而特别普遍。然而，尽管在多细胞生物中有悠久的研究史，但尚不清楚自适应辐射是否是天然细菌种群中的重要驱动力。在海洋和陆地环境之间，对后生动物和细菌的最急剧环境过渡之一。海洋事物过渡偶尔发生在细菌分类单元中，并伴随着中央代谢的大量重新布线。因此，这些过渡为通过关键创新探索新型自适应区域提供了一个极好的模型。我们将对英国康沃尔郡的一系列陆地和海洋栖息地进行生态通用的粘菌病采样，以系统地研究细菌的适应性辐射。首先，我们将估计粒细菌谱系从海洋到陆地栖息地过渡，反之亦然。为此，我们将在复制的环境样品中对标记基因进行测序，以构建一棵高分辨率进化树，并在其上绘制栖息地的偏好。其次，我们假设将新栖息地的谱系经历了适应性辐射，与保留在祖先栖息地中的谱系相比，系统发育树的分支率提高留下了增加。第三，我们将通过基于分离株的基因组测序和组装来自元基因组的基因组来检索基因组，以识别海洋 - 事物过渡的关键适应性，从而阐明它们是否是LGT事件的结果，并探索过渡和后续辐射的基因组后果。在真核生物中研究适应性辐射有丰富的传统。尽管理论和经验数据表明细菌同样可以体验自适应演化的爆发，但这将是对细菌自适应辐射的第一个大刻度，专门设计的分析。该开创性项目中产生的结果将为其他细菌分类群的研究铺平道路，通过不同的机制在不同的环境中定居，并且通常为详细研究宏观进化模式提供了动力，从而产生了原核多样性，这最终是所有生态系统功能的基础。