Collaborative Research: Functional and evolutionary bases of substrate-specificity in wood-decaying basidiomycetes

木材是陆地生态系统中最丰富的碳库之一。木材的真菌分解是碳循环的一个关键组成部分，影响土壤生产力，并有潜力被开发用于生产生物燃料和其他“绿色”技术。主要的木材腐烂真菌是蘑菇形成（伞菌纲）。木材的物理特性和化学成分因植物种类而异，并且大多数木材腐烂的伞菌具有特征性的木材基质范围。然而，目前还不清楚为什么个别种类的木材腐朽真菌往往发生在特定的植物宿主。本项目将通过分析木材腐烂过程中表达的基因，以及腐烂过程的物理和化学特征，研究木材腐烂伞菌的底物特异性和底物转换机制。参与木材腐烂或降解的真菌酶在新兴的生物过程中具有潜在的应用，例如与能源有关的生物转化，包括生物燃料生产和生物修复。加强对不同种类真菌利用特定木材基质的机制的理解，有助于指导可用于此类应用目的的遗传资源的开发。该项目将支持一名博士后研究员和两名研究生，并将在美国的三个合作学术机构为本科生提供培训。为了向广大观众介绍有关真菌和木材分解的信息，该项目将在伍斯特生态博物馆（http：//www.ecotarium.org/）创建互动展览，并制定相应的公共方案，这是一个科学和自然博物馆，每年接待140 000多名游客，其中包括大量来自地区公立学校的学生。展品将展示真菌的多样性、腐烂过程以及真菌在碳循环中的作用。拟议的研究将集中在四种具有可用基因组序列的伞菌纲（具有不同的底物偏好）。真菌将在四种不同树种（两种针叶树和两种硬木）的固体薄片上培养。将使用Illumina HiSeq 2000平台进行转录组分析，重点关注编码已知或疑似参与木材腐烂的酶的基因，以及功能未知的共表达基因。系统基因组分析将利用所有可用的基因组的木材腐烂伞菌，重点是基因家族可能发挥作用的腐烂，表达谱的通知。衰变的物理和化学特性将使用显微镜，质谱仪和化学分析殖民基板。拟议的研究是在真菌系统学和分子进化，木材腐烂和森林产品病理学，真菌基因组学，以及腐烂系统的遗传学和生物化学方面具有专业知识的研究人员之间的合作。本计画将利用木材腐朽菌基因组学的最新进展。它将为森林生态系统中真菌的功能和进化提供深入了解，并为未来的研究创建一个框架，旨在了解影响特定真菌基因表达的特定植物衍生化合物。

Wood (lignocellulose) is one of the most abundant carbon pools in terrestrial ecosystems. Fungal decomposition of wood is a critical component of the carbon cycle, impacts soil productivity, and has the potential to be exploited in the production of biofuels and other 'green' technologies. The major wood-decaying fungi are mushroom-forming (Agaricomycetes). The physical characteristics and chemical composition of wood vary among plant species, and most wood-decaying Agaricomycetes have characteristic wood substrate ranges. However, it is not understood why individual species of wood decaying fungi tend to occur on specific plant hosts. This project will investigate the mechanisms of substrate specificity and substrate switching in wood-decaying Agaricomycetes using a combination of analyses of genes expressed during decay, and physical and chemical characterization of the decay process. Fungal enzymes that are involved in wood decay or degradation have potential applications in emerging bioprocesses, such as energy-related bioconversions, including biofuel production, and bioremediation. Enhanced understanding of the mechanisms that allow different species of fungi to exploit particular wood substrates could help guide development of genetic resources that could be used for such applied purposes. This project will support one Postdoctoral Fellow and two graduate students, and will provide training to undergraduates at three collaborating academic institutions in the US. To bring information about fungi and wood decomposition to a wide audience, this project will create interactive exhibits and develop accompanying public programs at the Worcester EcoTarium (http://www.ecotarium.org/), a science and nature museum which serves over 140,000 visitors annually including large numbers of students from regional public schools. Exhibits will illustrate fungal diversity, the decay process, and the role of fungi in the carbon cycle.The proposed research will focus on four species of Agaricomycetes (with distinct substrate preferences) with available genome sequences. The fungi will be cultured on solid wafers of four different tree species (two conifers and two hardwoods). Transcriptome profiling will be performed with the Illumina HiSeq 2000 platform, focusing on genes encoding enzymes known or suspected to be involved in wood decay, as well as co-expressed genes of unknown function. Phylogenomic analyses will make use of all available genomes of wood-decaying Agaricomycetes, focusing on gene families that are likely to play a role in decay, as informed by expression profiles. Physical and chemical characteristics of decay will be addressed using microscopy, mass spectrometry, and chemical analyses of colonized substrates. The proposed research is a collaboration between researchers with expertise in fungal systematics and molecular evolution, wood decay and forest products pathology, fungal genomics, and genetics and biochemistry of decay systems. This project will capitalize on recent advances in genomics of wood-decaying basidiomycetes. It will provide insight into the functioning and evolution of fungi in forest ecosystems, and create a framework for future studies aimed at understanding the specific plant-derived compounds that affect expression of particular fungal genes.