Collaborative Research: IODP-enabled Insights into Fungi and Their Metabolic Interactions with Other Microorganisms in Deep Subsurface Hydrothermal Sediments

合作研究：借助 IODP 深入了解深层地下热液沉积物中的真菌及其与其他微生物的代谢相互作用

• 批准号: 2046799
• 负责人: Virginia Edgcomb
• 金额: $ 50.24万
• 依托单位: Woods Hole Oceanographic Institution
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-15 至 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2046799&HistoricalAwards=false
• 关键词: Collaborative; Research; IODP; enabled; Insights

The marine subsurface is one of the least explored habitats on Earth. International Ocean Discovery Program (IODP) Expedition 385 drilled into the seafloor in Guaymas Basin, Mexico, and was the first to drill directly into subsurface sediments and sediment-hosted basalt sill intrusions of an active hydrothermal basin. This expedition provides a direct microbiological window into a deep hydrothermal biosphere across an active plate spreading center where complex hydrocarbons are generated by heating of buried organic matter under high temperature and pressure. Mounting evidence suggests that Fungi constitute an active and ecologically important fraction of the subsurface biosphere community. This is especially true in organic-rich continental margin sediments that are ideal for colonization by aerobic and anaerobic Fungi, where fungal activities may contribute significantly to nutrient cycling. Major knowledge gaps in our knowledge of subsurface microbiota preclude our ability to estimate their full impact: how active Fungi are distributed along temperature and depth gradients, the range of substrates utilized by active cells, and how Fungi may cooperate with bacteria in degradation of complex organic matter, including hydrocarbons. Fungi are known to participate in degradation of refractory organics and cycling of metals and to produce novel metabolites with interesting properties. This project informs us on origins of different lineages of microbial life on Earth, the extent of marine subsurface carbon cycling, limits of life, how life adapts to environmental change, and the potential for Fungi to accelerate the biodegradation of complex hydrocarbons. Given the extent of the potential subsurface biosphere, Fungi likely play an important role in global nutrient cycling. The culture collection of fungal isolates created by this project will be available for exploration of their ecology and novel properties by other interested researchers, and may also yield insights into basal fungal lineages. These biogeochemical and potential evolutionary outcomes are of great interest to other research disciplines, educators, and students alike. The project’s K-16 education program capitalizes on programs aimed at increasing involvement of under-represented undergraduate populations in research. High school students, undergraduates, a graduate student, and postdoc are involved in the research. An art-in-science project with a local high school is being displayed at the community library along with education materials on marine Fungi and their ecological roles. This project examines how abundance, diversity and distribution of Fungi and co-inhabiting bacteria and archaea changes in subsurface sediment samples exhibiting a wide range of in situ temperatures and pressure, what the active fraction of cells is along these gradients, and whether/how Fungi impact carbon cycling in this biosphere by interacting metabolically with bacteria to break down hydrocarbon substrates. The project is assessing the activities of in situ microorganisms in this active hydrothermal subsurface biosphere using a cutting-edge combination of molecular approaches and culture-based studies of enrichments and microbial isolates applied to an extensive collection of samples from 8 sites in Guaymas Basin varying in temperature profile, presence of old, buried magmatic sills, and geochemical conditions. The investigators are examining 1) marker genes and metagenomes of sorted active cells using new bioorthogonal non-canonical amino acid tagging (BONCAT) approaches, 2) the distribution of bacterial, archaeal, and fungal cells and their marker genes along depth and geochemical gradients using microscopy, ‘meta-omics’ and lipid biomarker analyses, 3) substrate usage by fungal isolates, 4) metabolite pools, nutrients, and hydrocarbons with depth, and 5) fungal metabolism of complex organics (and syntrophies between Fungi and Bacteria) using time-course stable isotope probing of RNA from culture-based studies coupled with analyses of expressed genes and pools of metabolites.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

海洋地下是地球上最少探索的栖息地之一。国际海洋发现计划第385号考察队在墨西哥瓜伊马斯盆地的海底钻探，是第一个直接钻探地下沉积物和活跃热液盆地沉积物托管玄武岩岩床侵入体的考察队。这次考察提供了一个直接的微生物窗口，进入一个活动板块扩张中心的深层热液生物圈，在那里，复杂的碳氢化合物是通过在高温高压下加热埋藏的有机物而产生的。越来越多的证据表明，真菌构成了地下生物圈群落的一个活跃的和生态上重要的部分。在富含有机物的大陆边缘沉积物中尤其如此，这些沉积物是好氧和厌氧真菌定植的理想场所，真菌活动可能对营养循环有重大贡献。我们对地下微生物群的认识存在重大知识缺口，因此无法估计它们的全部影响：活性真菌如何沿沿着温度和深度梯度分布，活性细胞利用的底物范围，以及真菌如何与细菌合作降解复杂的有机物，包括碳氢化合物。已知真菌参与难降解有机物的降解和金属的循环，并产生具有有趣特性的新型代谢物。这个项目告诉我们地球上微生物生命的不同谱系的起源，海洋地下碳循环的程度，生命的极限，生命如何适应环境变化，以及真菌加速复杂碳氢化合物生物降解的潜力。考虑到潜在的地下生物圈的范围，真菌可能在全球营养循环中发挥重要作用。由该项目创建的真菌分离物的培养物收集将可用于其他感兴趣的研究人员探索其生态学和新特性，并且还可能产生对基础真菌谱系的见解。这些地球化学和潜在的进化结果对其他研究学科，教育工作者和学生都非常感兴趣。该项目的K-16教育计划利用旨在增加代表性不足的本科生参与研究的计划。高中生、本科生、研究生和博士后都参与了这项研究。 一个与当地一所高中合作的科学艺术项目正在社区图书馆沿着，同时展出的还有关于海洋真菌及其生态作用的教育材料。该项目研究了地下沉积物样品中真菌和共同居住的细菌和古菌的丰度，多样性和分布如何变化，表现出广泛的原位温度和压力，细胞的活性部分是沿着这些梯度，以及真菌是否/如何通过与细菌代谢相互作用来影响生物圈中的碳循环，以分解碳氢化合物底物。该项目正在评估这一活跃的地下热液生物圈中原地微生物的活动，采用先进的分子方法和基于培养的富集和微生物分离研究相结合的方法，对从瓜伊马斯盆地8个地点广泛收集的样品进行研究，这些地点的温度分布、是否存在古老的埋藏岩浆岩床以及地球化学条件各不相同。研究人员正在检查1）使用新的生物正交非规范氨基酸标记（BONCAT）方法分选的活性细胞的标记基因和宏基因组，2）使用显微镜，“元组学”和脂质生物标志物分析，细菌，古细菌和真菌细胞及其标记基因沿着深度和地球化学梯度的分布，3）真菌分离物的底物使用，4）代谢物池，营养物，碳氢化合物的深度真菌对复杂有机物的代谢（以及真菌和细菌之间的同养型）使用培养物中RNA的时程稳定同位素探测-该奖项反映了NSF的法定使命，并被认为值得通过利用基金会的智力价值和更广泛的影响进行评估来支持审查标准。

项目成果

Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation

• DOI: 10.1038/s41396-023-01492-z
• 发表时间: 2023-09-01
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Mara, Paraskevi;Zhou, Ying-Li;Edgcomb, Virginia
• 通讯作者: Edgcomb, Virginia