Dimensions: Phylogenetic and Functional Diversity of Tripartite Plant-Fungal-Bacterial Symbioses

本项目研究了真菌的多样性、进化和生态功能，Mucoromycota。这些真菌在工业上对油脂生产和农业系统中的生物肥料具有重要意义。它们通过在植物组织内的生长创新与植物共同进化，并与植物成功入侵土地有关。这组真菌中的许多真菌是植物生长促进剂，并在其细胞内携带细菌内共生体，这些细菌属于仅从这些真菌中已知的细菌谱系。其中一些细菌会产生强效毒素。本研究探讨了这些内细菌在真菌宿主生长和代谢中的作用，以及内细菌对真菌与植物相互作用的影响。它将为其他科学家提供这些真菌的培养收集和数据库。参考DNA条形码和基因组序列将整合到基于序列的分类器中，作为更广泛社区的资源。该项目的一部分内容是关于“生物多样性和进化研究中的计算思维”的短期课程，以及确定传统农业和文化实践如何影响土壤中的毛霉菌真菌的研究。总的来说，这项研究将为博士后、研究生和本科生提供多样化和跨学科的教育、培训和推广。研究人员将比较和分析整个基因组，以确定在植物-真菌-细菌伙伴中共同进化的共生性状，并将通过亚转录组学评估细菌内共生体对真菌宿主功能的影响及其与植物的相互作用。寄主植物表型、代谢组、转录组和对非生物胁迫的恢复能力的变化将在旨在测试寄主、真菌和细菌遗传性状的实验中进行研究。系统发育维度将整合进化和基因组学，提供一个强大的系统发育框架和新的计算工具，用于估计毛霉菌及其细菌内共生体之间的共同进化和水平基因转移过程。遗传维度将应用植物-真菌-细菌共生体的基因组学和亚转录组学研究，在系统基因组学提供的指导下进行选择，以确定参与共生相互作用的关键基因。功能组件将剖析候选基因在不同植物-真菌/细菌伴侣和非生物应激源的背景下对植物寄主适应性的作用。这项综合研究将促进跨学科合作，为三方多王国共生的多样性、进化和功能提供新的见解。

This project investigates the diversity, evolution and ecological functions within a diverse lineage of fungi, the Mucoromycota. These fungi are industrially important for lipid production and as biofertilizers in agricultural systems. They have co-evolved with plants through innovations of their growth within plant tissues, and are implicated in the successful invasion of land by plants. Many of the fungi in this group are plant growth promoters and carry within their cells bacterial endosymbionts belonging to lineages of bacteria that are known only from these fungi. Some of these bacteria produce potent toxins. This research investigates the role of these endobacteria on their fungal host's growth and metabolism, and the impact of endobacteria on fungal-plant interactions. It will produce a culture collection and database of these fungi available to other scientists. Reference DNA barcodes and genome sequences from these collections will be integrated into sequence-based classifiers as a resource for the broader community. A short-course on "Computational Thinking in Biodiversity and Evolutionary Research", and studies to determine how traditional agriculture and cultural practices impact Mucoromycota fungi in the soil are part of the project. Overall, this research will provide diverse and cross-disciplinary education, training, and outreach to postdocs, graduate and undergraduate students.The researchers will compare and analyze entire genomes to identify symbiosis traits that have co-evolved in plant-fungi-bacteria partners, and will assess the impact of bacterial endosymbionts on the function of their fungal host and its interaction with plants through metatranscriptomics. Changes in host plant phenotype, metabolome, transcriptome, and resilience to abiotic stress will be studied in experiments designed to test genetic traits in the host, fungi and bacteria. The phylogenetic dimension will integrate evolution and genomics to provide a robust phylogenomic framework and new computational tools for estimating co-evolutionary and horizontal gene transfer processes between Mucoromycota and their bacterial endosymbionts. The genetic dimension will apply genomic and metatranscriptomic studies of plant-fungal-bacterial symbionts, selected with guidance provided by the phylogenomics, to identify critical genes involved in symbiotic interactions. The functional component will dissect the role of candidate genes for plant host fitness in the context of different plant-fungal/bacterial partners and abiotic stressors. Together this integrated research will foster interdisciplinary collaborations to provide novel insights into the diversity, evolution and functioning of tripartite multi-kingdom symbiosis.