Unravelling the diversity and function of fine root endophytes

植物与不同的微生物群落相互作用，这些微生物构成了它们的微生物群落，并对它们的生长和发育产生了重大影响。在大多数生态系统中，微生物群是由菌根共生体主导的，在这个共生体中，植物为真菌提供糖和脂，以换取真菌从土壤中吸收的营养。最广泛的菌根共生类型是丛枝菌根(AM)，它被认为是生态系统过程的关键决定因素，因为它在生物地球化学循环中发挥作用，在支持植物群落的多样性和生产力方面发挥作用。直到最近，人们一直认为形成AM的真菌包括球菌门，而我们对AM生态系统作用的理解几乎完全基于这类真菌。然而，我们最近发现，形成独特的‘细根内生菌(FRE)’AM形态模式的真菌是毛霉门Endogonales的成员，因此AM共生实际上是由两个不同的真菌群形成的，这两类真菌在7亿多年前分开。尽管我们知道FRES是全球分布的，并且可以在生态系统中丰富，但我们对所涉及的真菌的多样性、生态学或生态系统功能几乎一无所知。然而，有证据表明，FRE和球菌门与环境的相互作用截然不同，可能在生态系统中扮演不同的功能角色。在这个项目中，我们将使用作为NERC乡村调查的一部分收集的现有DNA档案来确定英国主要栖息地类型的FRES的多样性和丰度，并比较决定FRES和Glmer mycota分布的环境、植被和气候因素。目前，FRE是一种仅被称为环境序列的“暗真菌”。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来定义这些物种，并确定它们具有全球分布模式的程度。我们有证据表明，FRES和Glommycota与土壤中的磷有不同的相互作用，在磷有效性很低的条件下，FRES更加丰富。我们将与爱尔兰研究人员合作，通过在韦克斯福德进行一项独特的50年牧场实验，研究土壤磷状况如何影响FRES的多样性和丰度。我们将确定FRES是否作为互惠共生体发挥作用，促进植物生长和养分供应，类似于球孢菌门与寄主植物的相互作用。该方案的一个关键部分将是收集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不能在没有植物或在纯培养条件下生长，我们将利用新兴的长读DNA测序技术，该技术现在开启了直接从环境元基因组提取的DNA组装FRE基因组的令人兴奋的可能性。除了提供对由FRES形成的AM的多样性和功能的基本了解外，我们还将提供技术进步，促进我们在表征微生物真核生物的功能和生态意义方面取得重大进展，例如真菌和原生动物，这些微生物在很大程度上是不可培养的，迄今在环境基因组测序工作中被忽视。

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.