Unravelling the diversity and function of fine root endophytes

植物与不同的微生物群落相互作用，构成其微生物组，并对其生长和发育产生重大影响。在大多数生态系统中，微生物组由菌根共生体主导，其中植物为真菌提供糖和脂质，以换取真菌从土壤中吸收的营养。最广泛的菌根共生是丛枝（AM）型，这被认为是生态系统过程的关键决定因素，通过其在生态地球化学循环和支持植物群落的多样性和生产力的作用。直到最近，人们认为形成AM的真菌包括球囊菌门，我们对AM生态系统作用的理解几乎完全基于这组真菌。然而，我们最近发现，形成独特的“细根内生菌（FRE）”AM形态型的真菌是毛霉门内的内生菌目的成员，因此AM共生实际上是由两个不同的真菌群形成的，它们在7亿多年前分道扬镳。尽管我们知道FRE在全球范围内分布，并且在生态系统中可能很丰富，但我们对多样性几乎一无所知。所涉及的真菌的生态学或生态系统功能。然而，有证据表明，FRE和球囊菌门与环境有着截然不同的相互作用，并可能在生态系统中发挥不同的功能作用。在这个项目中，我们将使用现有的DNA档案收集的NERC农村调查的一部分，以确定在英国主要的栖息地类型的FRES的多样性和丰富性，并比较环境，植被和气候因素，确定分布的FRES和球囊菌门。目前，FRE是“黑暗真菌”，仅被称为环境序列。我们的研究表明，FRES代表多个物种，我们将与澳大利亚和瑞典的研究人员合作，根据它们的遗传学和形态学来定义它们，并确定它们在全球分布模式中的程度。我们有证据表明，FREs和肾小球真菌与土壤磷有不同的相互作用，与FREs更丰富的条件下，磷的可用性非常低。我们将与爱尔兰研究人员合作，研究土壤磷状况如何影响FRES的多样性和丰富性，在韦克斯福德使用一个独特的50年牧场实验。我们将确定FREs是否作为促进植物生长和营养供应的互利共生体发挥作用，类似于球囊菌门与其宿主植物的相互作用。该计划的一个关键部分将是组装FRES的基因组，并利用这些基因组来了解FRES在生态系统中的功能作用，以及决定其在生态系统中分布的相互作用。由于FREs不能在没有植物或纯培养条件下生长，我们将利用新兴的长读段DNA测序技术，该技术现在打开了直接从环境宏基因组提取的DNA组装FRE基因组的令人兴奋的可能性。除了提供对FREs形成的AM的多样性和功能的基本理解，我们将提供技术进步，这将促进我们在鉴定微生物真核生物如真菌和原生生物的功能和生态意义方面的能力的重大进步，这些真核生物在很大程度上是不可培养的，迄今为止在环境基因组测序工作中一直被忽视。

Plants interact with diverse communities of microbes, which constitute their microbiome, and which have major impacts on their growth and development. In most ecosystems the microbiome is dominated by mycorrhizal symbioses, in which the plant provides the fungus with sugars and lipids in exchange for nutrients assimilated by the fungus from the soil. The most widespread mycorrhizal symbiosis is the arbuscular (AM) type, which is recognized as a key determinant of ecosystem processes, through its role in biogeochemical cycling and in supporting the diversity and productivity of plant communities. Until recently, it was assumed that the fungi which form AM comprise the phylum Glomeromycota, and our understanding of the ecosystem roles of AM is based almost exclusively on this group of fungi. However we have recently shown that fungi which form the distinctive 'fine root endophyte (FRE)' AM morphotype are members of the Order Endogonales within the phylum Mucoromycota so that the AM symbiosis is actually formed by two distinct groups of fungi which diverged over 700 million years ago.Although we know that FREs are globally distributed and can be abundant within ecosystems we know almost nothing about the diversity, ecology or ecosystem function of the fungi involved. However, evidence suggests that FRE and Glomeromycota have contrasting interactions with the environment and may perform different functional roles in ecosystems. In this project we will use existing DNA archives collected as part of the NERC Countryside Survey to determine the diversity and abundance of FREs across major British habitat types, and compare the environmental, vegetation and climatic factors which determine distribution of FREs and Glomeromycota. Currently FRE are 'dark fungi' known only as environmental sequences. Our research suggests that FREs represent multiple species, and we will collaborate with Australian and Swedish researchers to define these based on both their genetics and morphology, and determine the extent to which these have global distribution patterns. We have evidence to suggest that FREs and glomeromycota have different interactions with soil phosphorus, with FREs more abundant under conditions of very low phosphorus availability. We will collaborate with Irish researchers to investigate how soil phosphorus status affects diversity and abundance of FREs using a unique 50 year pasture experiment in Wexford. We will establish whether FREs function as mutualistic symbionts which promote plant growth and nutrient supply, similar to the interactions that Glomeromycota have with their host plants. A key part of the programme will be to assemble genomes of FREs and use these to understand the functional roles of FREs in ecosystems, and the interactions which determine their distribution across ecosystems. Since FREs can't be grown in the absence of plants, or under pure culture conditions, we will take advantage of emerging long read DNA sequencing technology which now opens the exciting possibility of assembling FRE genomes directly from DNA extracted from environmental metagenomes.In addition to providing fundamental understanding of the diversity and function of the AM formed by FREs, we will provide technological advances which will facilitate a major advance in our ability to characterise the function and ecological significance of microbial eukaryotes such as fungi and protists, which are largely unculturable and have been neglected in environmental genome sequencing efforts to date.