CAREER: Soil Microbial Ecology and Evolution in a Warming World

微生物是每个生态系统的重要组成部分。 它们在自然界中几乎从不孤立地生活;只是作为与其他微生物共同体的一部分。土壤微生物群落是地球元素循环的主要参与者，它们对环境变化的反应可以决定微生物是否有助于土壤保留更多的化合物，如碳，或者是否会以气态形式排放。随着地球环境的变化，土壤有效储存碳的能力也在变化，减少了土壤提供的有益生态系统服务，并将储存的碳气体释放到大气中。在马萨诸塞州中部的温带森林中进行的一项长达25年的野外实验中，温度的升高导致土壤碳以二氧化碳气体的形式大量流失。这种损失主要是由于微生物造成的，土壤碳衰减的时期会被微生物群落组成的变化所打断。土壤碳损失的这种循环性质表明，土壤中存在长期的微生物控制碳。在这个实验中，温度的升高对土壤真菌产生了负面影响，但对细菌没有影响，这表明细菌正在适应这些新的环境条件，并且有可能进一步适应长期的环境压力。 随着时间的推移，碳化合物的质量已经退化，对数百种细菌分离物的研究表明，来自长期加热土壤的细菌代谢降解形式的碳的能力增加。 展望未来，在这个NSF CAREER项目中，研究将从长期变暖实验中研究土壤细菌的生态学和进化，以更好地预测环境压力对陆地生态系统的影响。通过在课堂环境中进行大量研究，该项目还将有助于培养下一代环境微生物学学生。这项研究旨在评估核心假设，即土壤细菌已经获得了与适应数十年土壤温度慢性升高相关的特征。第一个目的是直接测量与土壤有机质质量和数量下降几十年的慢性温度胁迫相关的原位微生物群落特征的可塑性。实验室培养实验将使用稳定同位素探测来测量从长期变暖实验中收集的土壤中微生物的温度敏感性。田间实验是对长期研究中关闭热量之前、期间和之后收集的土壤进行分析。将对生物质和微生物产品（如酶和胞外多糖）的不同组分进行测量，并评估长期温度升高造成的变化。第二个目标是了解单个细菌对长期变暖的进化适应。将筛选分离株的与寡养相关的性状（适应低数量底物）和与复合碳降解相关的性状（适应低质量底物，包括木质素类似物）。将对具有生态生理学数据的一个物种子集的基因组进行测序，以研究与寡养或降解复杂底物的能力相关的性状进化。这些生物也将是一个共同的花园实验的一部分，旨在将与长期温度胁迫相关的基因组特征与土壤适应性的变化联系起来。总之，这些数据将被用来估计进化适应土壤碳建模重要的微生物参数的速度。该项目将为研究生提供研究和教学培训，并为本科生和高中生提供微生物生理学、生态学和基因组学培训。了解细菌的适应性可能有助于解释土壤碳损失的非线性模式在几十年的慢性温度上升，并将定义如何在碳循环的环境控制可能会在一个非线性的作用在更长的时间scales.This奖项反映了NSF的法定使命，并已被认为是值得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的支持。

Microorganisms are important components of every ecosystem. They virtually never live in isolation in nature; only as part of communities with other microbes. Soil microbial communities are major actors in the Earth's elemental cycles, and their response to environmental change can determine whether microbes help soil to retain more of compounds such as carbon, or whether it will be emitted in gaseous forms. As Earth's environment changes, so does the ability for soil to effectively store carbon, reducing the beneficial ecosystem services that soils provide, and releasing stored carbon gas into the atmosphere. In a 25-year long field experiment ongoing in a temperate forest in central Massachusetts, increases in temperature have resulted in a large loss of soil carbon as carbon dioxide gas. The loss is mostly due to microbes, with periods of soil carbon decay punctuated by changes in microbial community composition. This cyclic nature of soil carbon loss over decades suggests the existence of long-term microbial control over carbon in soil. In this experiment, increases in temperature have negatively affected soil fungi but not bacteria, suggesting that bacteria are adapting to these new environmental conditions, and that further adaptations to long-term environmental stress are possible. Over time, the quality of carbon compounds has been degraded, and examination of hundreds of bacterial isolates showed that the bacteria from chronically heated soils have an increased ability to metabolize degraded forms of carbon. Going forward, in this NSF CAREER project, research will examine the ecology and evolution of soil bacteria from the long-term warming experiment, in an effort to better predict the effect of environmental stress on terrestrial ecosystems. By doing much of the research in the classroom setting, this project will also help train the next generation of students in environmental microbiology. This research is designed to evaluate the central hypothesis that soil bacteria have acquired traits associated with adaptation to decades of chronic increases to soil temperature. The first aim is to directly measure the plasticity of in situ microbial community traits associated with declining soil organic matter quality and quantity over decades of chronic temperature stress. A laboratory incubation experiment will use stable isotope probing to measure temperature sensitivity of microbes associated with soils collected from a long-term warming experiment. The field experiment is an analysis of soils collected from before, during and after the heat is turned off for three months in the long-term study. Measures of different components of biomass and microbial products like enzymes and exopolysaccharides will be made and evaluated for changes due to long-term temperature increases. The second aim is to understand evolutionary adaptation of individual bacteria to long-term warming. Isolates will be screened for traits associated with oligotrophy (adaptation to low quantity substrate) and traits associated with degradation of complex carbon (adaptation to low quality substrate, including lignin analogs). The genomes of a subset of species with ecophysiology data will be sequenced for a study of trait evolution associated with oligotrophy or ability to degrade complex substrates. These organisms will also be part of a common garden experiment in an effort to link genomic features associated with long-term temperature stress to changes in fitness in soils. Altogether, these data will be used to estimate a rate of evolutionary adaptation for microbial parameters important to soil carbon modeling. This project will provide graduate student training in research and teaching, as well as undergraduate and high school student training in microbial physiology, ecology and genomics. Understanding bacterial adaptation might help to explain the non-linear pattern of soil C loss over decades of chronic temperature increase, and would define how environmental controls over the carbon cycle may act in a non-linear over longer time scales.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.