CAREER: The consequences of rarity for soil microbiome stability in structure and function

职业：稀有性对土壤微生物组结构和功能稳定性的影响

• 批准号: 1749544
• 负责人: Ashley Shade
• 金额: $ 80万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1749544&HistoricalAwards=false
• 关键词: CAREER; consequences; rarity; soil; microbiome

Microorganisms are the smallest life forms and yet they have large and critical roles in maintaining the health of ecosystems. Environmental microbial communities provide essential functions, including the cycling of key resources like carbon and nitrogen. In soils, microorganisms form diverse communities with thousands of distinct species, but the role of most of these species is unknown. In particular, it is not clear how microbial species that are not very abundant (rare) contribute to community functions. However, rare microorganisms are thought to be important when environmental conditions fluctuate because they provide functions that help their ecosystem resist change or to recover quickly. This project will investigate the diversity and functions of rare microorganisms in a soil ecosystem impacted by a long-term disturbance, and determine how they contribute to the system's resilience to this disturbance. The research will provide insights into the critical role of microbial diversity for environmental resilience, which has implications for broad national interests in energy and food security, environmental conservation and remediation, and the management of ecosystem services. The project will advance the fields of ecology and ecosystem science by investigating the links between microbial diversity and functions in the environment. It also will benefit society by providing classroom education in quantitative methods and training members of the scientific workforce in leading-edge technologies used in biology and chemistry.The three aims of this research are to: 1) quantify the contributions of rare microbial taxa to community stability after a long-term environmental disturbance; 2) evaluate the abilities of rare microbial taxa to a) persist given disturbance and b) respond to specific environmental changes that result from the disturbance; and 3) determine the impact of competition between rare and abundant microbial taxa on community stability and functions. The Centralia, Pennsylvania soil ecosystem is the site of a long-burning coal seam fire that will serve a model severe disturbance for this work. For Aims 1 and 2, surface soils will be collected annually from established sites along a fire-impact gradient so that community changes over time due to the influence of fire can be quantified. Soil microbial communities will be assessed using genetic markers of phylogenetic and functional diversity obtained from untargeted DNA and RNA sequencing. Rare microbial taxa will be identified using bioinformatics and their contributions to community stability will be quantified with ecological statistics. For Aim 3, bacteria isolated from field soils will be arrayed into synthetic microbial communities to assess outcomes of competition between rare and abundant microorganisms. Microbial community "goods", which include small, excreted molecules like enzymes and antibiotics, will be measured using sensitive mass spectrometry to determine how competition impacts their production. Together, these efforts will provide insights into the ecological roles of rare microbial taxa, and microbial biodiversity more broadly, for community stability and function.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.

微生物是最小的生命形式，但它们在维持生态系统的健康方面发挥着巨大而关键的作用。环境微生物群落提供基本功能，包括碳和氮等关键资源的循环。在土壤中，微生物形成了具有数千种不同物种的多样化群落，但其中大多数物种的作用尚不清楚。特别是，尚不清楚数量不是很丰富（稀有）的微生物物种如何促进群落功能。然而，当环境条件波动时，稀有微生物被认为很重要，因为它们提供了帮助生态系统抵抗变化或快速恢复的功能。该项目将调查受长期干扰影响的土壤生态系统中稀有微生物的多样性和功能，并确定它们如何促进系统对这种干扰的恢复力。该研究将深入了解微生物多样性对环境复原力的关键作用，这对能源和粮食安全、环境保护和修复以及生态系统服务管理等广泛的国家利益具有影响。该项目将通过研究微生物多样性与环境功能之间的联系来推进生态学和生态系统科学领域的发展。它还将通过提供定量方法的课堂教育和培训科学工作者使用生物学和化学的前沿技术来造福社会。这项研究的三个目的是：1）量化稀有微生物类群在长期环境干扰后对群落稳定的贡献；2） 2) 评估稀有微生物类群 a) 在给定干扰下持续存在和 b) 对干扰导致的特定环境变化作出反应的能力； 3）确定稀有和丰富的微生物类群之间的竞争对群落稳定性和功能的影响。宾夕法尼亚州森特勒利亚的土壤生态系统是长期燃烧煤层火灾的所在地，它将成为这项工作的严重干扰模型。对于目标 1 和 2，每年将沿着火灾影响梯度从已建立的地点收集表层土壤，以便可以量化由于火灾影响而引起的社区随时间的变化。将使用从非目标 DNA 和 RNA 测序中获得的系统发育和功能多样性的遗传标记来评估土壤微生物群落。将使用生物信息学来识别稀有微生物类群，并通过生态统计来量化它们对群落稳定性的贡献。对于目标 3，从田间土壤中分离出的细菌将被排列成合成微生物群落，以评估稀有微生物和丰富微生物之间的竞争结果。微生物群落“产品”包括酶和抗生素等小分子、排泄物，将使用灵敏的质谱法进行测量，以确定竞争如何影响其生产。这些努力将共同深入了解稀有微生物类群和更广泛的微生物生物多样性对群落稳定和功能的生态作用。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

A global survey of arsenic-related genes in soil microbiomes

• DOI: 10.1186/s12915-019-0661-5
• 发表时间: 2019-05-30
• 期刊: BMC BIOLOGY
• 影响因子: 5.4
• 作者: Dunivin, Taylor K.;Yeh, Susanna Y.;Shade, Ashley
• 通讯作者: Shade, Ashley

RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

• DOI: 10.1128/msystems.00349-18
• 发表时间: 2019-01-01
• 期刊: MSYSTEMS
• 影响因子: 6.4
• 作者: Dunivin, Taylor K.;Choi, Jinlyung;Shade, Ashley
• 通讯作者: Shade, Ashley

Resource Competition and Host Feedbacks Underlie Regime Shifts in Gut Microbiota

• DOI: 10.1086/714527
• 发表时间: 2021-07-01
• 期刊: AMERICAN NATURALIST
• 影响因子: 2.9
• 作者: Guittar, John;Koffel, Thomas;Litchman, Elena
• 通讯作者: Litchman, Elena

Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop

培养支持微生物组分析的计算技能的策略：EDAMAME 研讨会的五年视角

• DOI: 10.1128/msystems.00297-19
• 发表时间: 2019
• 期刊: mSystems
• 影响因子: 6.4
• 作者: Shade, Ashley;Dunivin, Taylor K.;Choi, Jinlyung;Teal, Tracy K.;Howe, Adina C.;Greene, Casey S.
• 通讯作者: Greene, Casey S.

Microbiome rescue: directing resilience of environmental microbial communities

微生物组拯救：指导环境微生物群落的恢复力

• DOI: 10.1016/j.mib.2022.102263
• 发表时间: 2023
• 期刊: Current Opinion in Microbiology
• 影响因子: 5.4
• 作者: Shade, Ashley