Collaborative Research: Molecular mechanisms and biogeochemical consequences of decomposer species interactions during succession in ecosystems

全球每年产生超过1000亿吨的陆地植物物质。其中90%的生物质进入土壤中死亡的有机物质池中。然而，我们对分解微生物群落如何处理这种材料的了解还不够清楚，无法预测土壤中碳和养分循环的速度。这是我们对生态系统稳定性知识的一个重大缺口，因为分解的生化过程决定了陆地上的碳储存和生物圈向大气释放的二氧化碳数量之间的平衡。分解者微生物是一个高度多样化的有机体群体：在任何时候，数百种微生物都可以生活在一块分解的木质碎屑上。这项研究的目的是确定这些分解者物种在植物物质腐烂过程中相互作用的特定生化方式，以及这些相互作用如何随着时间的推移塑造这些重要群落的物种组成和总活动。这项研究的结果将提供有关生物过程的详细信息，这些过程导致二氧化碳向大气的最大自然通量之一。该项目将包括为博士后学者、研究生和本科生提供培训机会。PIs将通过儿童暑期项目传播关于分解微生物的重要性的K-12课程。微生物是生态系统级生物地球化学循环的引擎，因此它们频繁的协同和拮抗相互作用可能决定这些过程的速度。一种被广泛观察到的微生物物种相互作用模式发生在死亡有机物(即凋落物)的腐烂过程中，分解真菌群落随着时间的推移相继出现，并跟踪凋落物化学物质丰度的变化。在整个系统中，在腐烂的每个阶段，相同的真菌目、属和种往往主导着分解者群落，然而这些单个物种持续占据主导地位的机制，以及它们如何影响系统的生物地球化学，尚不清楚。这项研究的目的是确定调控这些过程的分子水平的因素。虽然最初为大型生物开发的物种相互作用的经典理论可能适用于分解者，但关于微生物代谢策略的新信息，如物种之间的交叉喂养和对生长和代谢的预期调节，也可能解释这些群落的结构和活动。腐烂过程中凋落物和微生物化学的变化是自然界中微生物最可预测的刺激序列之一，但目前尚不清楚微生物如何对这些刺激做出反应，或者这些过程在各种真菌中是如何变化的。这项拟议的研究将通过利用最先进的转录组学、代谢组学和代谢通量模型与真菌-凋落物系统模型来解决这些问题，以1)确定调节竞争优势真菌物种和稀有真菌物种之间相互作用的分子刺激，2)建立代谢网络模型，预测物种相互作用、群落动力学和代谢产物在凋落物中循环的结果，以及3)测试分子水平的模型是否能够成功地概括先前在自然凋落物腐烂中观察到的群落和生物地球化学动力学。这项工作的潜在贡献将是对分解者真菌相互作用的完整的基因到生态系统水平的分析，扩大和建立分析化学、分子生物学、微生物学、群落生态学和生态系统生态学领域之间的联系。

Over 100 gigatons of terrestrial plant matter are produced globally each year. Ninety percent of this biomass enters the pool of dead organic matter in soils. However, our understanding of how communities of decomposer microorganisms process this material is not yet clear enough to predict the rate of carbon and nutrient cycling through soils. This is a major gap in our knowledge of ecosystem stability, as the biochemical process of decomposition determines the balance between carbon storage on land and the amount of carbon dioxide released from the biosphere to the atmosphere. Decomposer microorganisms are a highly diverse group of organisms: hundreds of species of microbes can live on a piece of decomposing woody debris at any one time. The objective of this research is to identify the specific, biochemical ways in which these decomposer species interact during the decay of plant matter, and how these interactions shape the species composition and total activity of these important communities over time. The results of this research will provide detailed information on the biological processes that give rise to one of the largest natural fluxes of carbon dioxide to the atmosphere. The project will include training opportunities for a postdoctoral scholar, and graduate and undergraduate students. The PIs will disseminate a K-12 curriculum about the importance of decomposer microorganisms through summer programs for children.Microbes are the engines of ecosystem-level biogeochemical cycling, such that their frequent synergistic and antagonistic interactions likely determine rates of these processes. A widely observed pattern of microbial species interactions occurs during decay of dead organic matter (i.e. litter), where communities of decomposer fungi succeed one another over time and track changes in the abundance of litter chemicals. Across systems, the same orders, genera, and species of fungi often dominate the decomposer community present at each stage of decay, yet the mechanisms by which these individual species consistently become dominant, and how they influence the biogeochemistry of the system, are unknown. The objective of this research is to identify the molecular-level factors that regulate these processes. While classic theories of species interactions originally developed for macroorganisms may apply to decomposers, new information on microbial metabolic strategies, such as cross-feeding between species and anticipatory regulation of growth and metabolism, may also account for the structure and activity of these communities. Changes in litter and microbial chemistry during decay constitute one of the most predictable sequences of stimuli for microorganisms in nature, yet it is not known how microbes respond to these stimuli, or how these processes vary across a diversity of fungi. The proposed research will address these questions by leveraging state-of-the-art transcriptomics, metabolomics, and metabolic flux modeling with a model fungal-litter system to 1) determine the molecular stimuli that mediates interactions between competitively dominant and rare fungal species, 2) develop metabolic network models that predict the outcomes of species interactions, community dynamics, and metabolite cycling through litter, and 3) test whether molecular-level models can successfully recapitulate community and biogeochemistry dynamics previously observed in natural litter decay. The potential contribution of this work will be a complete gene-to-ecosystem-level analysis of decomposer fungal interactions, expanding and building linkages between the fields of analytical chemistry, molecular biology, microbiology, community ecology, and ecosystem ecology.