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。它们实际上从未在自然界中与世隔绝地生活过；只是作为与其他微生物共处的群落的一部分。土壤微生物群落是地球元素循环中的主要参与者，它们对环境变化的反应可以决定微生物是帮助土壤保留更多的化合物，如碳，还是以气体的形式排放。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的生态系统服务，并将储存的碳气释放到大气中。在马萨诸塞州中部的一片温带森林中进行的一项长达25年的野外实验中，气温的上升导致了土壤碳以二氧化碳气体的形式大量流失。损失主要是由微生物造成的，土壤碳的衰变期间不时会出现微生物群落组成的变化。几十年来土壤碳损失的这种周期性特征表明，微生物对土壤中的碳存在长期的控制。在本实验中，气温上升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，进一步适应长期环境压力是可能的。随着时间的推移，碳化合物的质量已经下降，对数百个细菌分离物的检查表明，来自长期加热土壤的细菌代谢降解形式的碳的能力增强。展望未来，在这个NSF职业项目中，研究人员将研究长期变暖实验中土壤细菌的生态和进化，以努力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，该项目还将帮助培训下一代学生环境微生物学。这项研究旨在评估核心假设，即土壤细菌已经获得了与数十年来土壤温度的长期上升相适应的特征。第一个目标是直接测量与数十年慢性温度胁迫下土壤有机质质量和数量下降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的同位素探测来测量与长期变暖实验收集的土壤相关的微生物的温度敏感性。田间试验是对长期研究中停热三个月前、中、后采集的土壤进行分析。将对生物质的不同成分以及酶和胞外多糖等微生物产品进行测量，并对长期气温上升造成的变化进行评估。第二个目标是了解单个细菌对长期变暖的进化适应。将筛选与寡养相关的特性(适应低数量底物)和与复杂碳降解相关的特性(适应低质量底物，包括木质素类似物)。具有生态生理学数据的一组物种的基因组将被测序，用于研究与寡养或降解复杂底物的能力相关的特征进化。这些生物也将是一个普通花园实验的一部分，该实验旨在将与长期温度胁迫相关的基因组特征与土壤适合性的变化联系起来。总之，这些数据将被用来估计对土壤碳模拟重要的微生物参数的进化适应速度。该项目将提供研究生研究和教学方面的培训，以及本科生和高中生在微生物生理学、生态学和基因组学方面的培训。了解细菌适应可能有助于解释几十年来慢性气温升高时土壤碳损失的非线性模式，并将定义对碳循环的环境控制如何在较长时间范围内以非线性方式发挥作用。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 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.