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

微生物是最小的生命形式，但它们在维持生态系统健康方面发挥着重要的作用。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，微生物形成了不同的群落，有数千种不同的物种，但这些物种中的大多数物种的作用尚不清楚。特别是，不是非常丰富(稀有)的微生物物种如何对群落功能做出贡献还不清楚。然而，当环境条件波动时，稀有微生物被认为是重要的，因为它们提供了帮助其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，并确定它们如何有助于系统对这种干扰的适应能力。这项研究将深入了解微生物多样性对环境复原力的关键作用，这对能源和食品安全、环境保护和修复以及生态系统服务管理方面的广泛国家利益具有影响。该项目将通过调查微生物多样性与环境功能之间的联系，推动生态学和生态系统科学领域的发展。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性的贡献；2)评估稀有微生物类群对a)在给定干扰下持续存在的能力；b)对干扰导致的特定环境变化做出反应；以及3)确定稀有和丰富微生物类群之间的竞争对群落稳定性和功能的影响。宾夕法尼亚州森特拉利亚的土壤生态系统是一场长期燃烧的煤层大火的现场，这将为这项工作提供一个严重干扰的模型。对于目标1和目标2，将每年沿着火灾影响梯度从已建立的地点收集表层土壤，以便能够量化由于火灾影响而导致的社区随时间的变化。将使用从非定向DNA和RNA测序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。将利用生物信息学识别稀有微生物类群，并用生态统计数据量化它们对群落稳定的贡献。对于目标3，从田间土壤中分离出的细菌将被排列到合成微生物群落中，以评估稀有和丰富微生物之间的竞争结果。微生物群落的“商品”，包括酶和抗生素等排泄出来的小分子，将使用灵敏的质谱仪进行测量，以确定竞争如何影响它们的生产。总之，这些努力将提供对稀有微生物类群的生态作用的洞察，以及更广泛的微生物生物多样性，以促进社区的稳定和功能。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.