RUI: Mechanisms of Microbial Elemental Sulfur Reduction at the Community, Cellular and Enzymatic Levels

地球表面之下是微生物群落，它们独立于太阳驱动的表面生活，并与大气中的氧气隔绝。因为地下与大气中的氧气是隔绝的，这些微生物需要寻找替代化合物来“呼吸”(还原)，以便进行驱动生命所需的能量循环。硫和氧有许多共同的特征，包括它们作为“可呼吸的”化合物的能力。为了更好地了解硫的减少，这个项目将结合不同的研究，这些研究将着眼于硫化学、蛋白质生物化学以及在炎热、富含石油的地下环境中基于硫的“呼吸”(呼吸)的遗传学。总而言之，这些研究将有助于理解这些生命系统如何能够在地球深处发展，生命可能是如何在早期无氧地球上进化的，甚至生命可能是如何在宇宙中其他地方进化的。本科生研究人员将进行这些研究，经验丰富的本科生将通过成功的项目指导年轻的研究人员，这些项目旨在留住未被充分代表的低收入学生，从而创建一个更强大的多元文化科学教学和研究社区。这些研究还将被整合到微生物生态学和生物信息学的本科课程中，其中微生物生态学实验室实验获得的数据将由生物信息学课程的学生进行分析。硫磺呼吸被认为是地球上最早的生命能量守恒途径之一。它对大气、海洋、沉积物和地下深处的硫和元素循环仍然很重要。由于微生物产生的硫化物具有极强的腐蚀性和毒性，因此在石油化工和其他领域也特别令人感兴趣。目前还不清楚哪些硫形态对微生物硫呼吸的代谢机制有贡献，也不清楚这些酶是如何机械地实现这一转化的。许多环境中硫还原酶和微生物的相对水平尚不清楚。将通过关注特定环境--一个深热、富含碳氢化合物的油气藏--并通过以下综合研究来解决这些首要问题：(1)在微生物群落水平，确定深热地下环境中微生物的特征，并通过元基因组学和元转录组学确定硫还原微生物和酶；(2)酶水平，通过动力学和结构技术确定硫还原酶的机制；(3)在地球化学水平，利用循环伏安法原位确定硫的化学形态以及在微生物和酶还原过程中硫的化学形态。这项工作的一个变革性方面是，循环伏安法将被用来获得酶还原硫磺过程中存在的整个硫物种、分离的微生物物种和微生物种群的“快照”。这项工作还将提供存在于深层地下流体中的硫化学物种的原地视图。对地下深层硫代谢的清楚了解将拓宽我们对生物地球化学硫循环、极端环境中的生命以及演化过程的理解。据估计，地下环境中含有地球上40%-60%的细菌细胞，至少占地球碳生物量的三分之一。然而，由于其隐蔽的性质，这一巨大的生物多样性储藏库才刚刚开始勘探。

Beneath the surface of the earth are microbial communities that live independent from the sun-driven surface and are sealed off from the atmosphere's oxygen. Because the subsurface is shut off from oxygen in the atmosphere, these microbes need to find alternative compounds to "breathe" (reduction), in order to carry out the energetic cycles necessary to drive life. Sulfur and oxygen share many characteristics, including their ability to serve as "breathable" compounds. To better understand sulfur reduction, this project will incorporate different studies that will look at sulfur chemistry; protein biochemistry; and the genetics of sulfur-based "breathing" (respiration) in a hot, petroleum-rich subsurface environment. Together, these studies will help with understanding how these living systems are able to develop deep in the earth, how life might have evolved on the early oxygen-free earth, and even how life might evolve in other places in the universe. Undergraduate researchers will conduct the studies, with experienced undergraduates mentoring young researchers through successful programs designed for the retention of underrepresented and lower income students in science; therefore creating a stronger multicultural scientific teaching and research community. These studies will also be integrated into undergraduate courses in Microbial Ecology and Bioinformatics, in which data obtained in the Microbial Ecology laboratory experiments will be analyzed by the students in the Bioinformatics course.Sulfur-based respiration is suggested to have been one of the earliest energy conserving pathways for life on earth. It remains important to the sulfur and elemental cycles in the atmosphere, oceans, sediments, and deep subsurface. It is also of specific interest in petrochemical and other fields due to the extremely corrosive and toxic effect of microbially-produced sulfides. It is not at all clear which forms of sulfur contribute to the metabolism mechanisms of microbial sulfur respiration in situ, or how these enzymes mechanistically carry out this transformation. The relative levels of sulfur-reducing enzymes and microbes in many environments remain unknown. These overarching questions will be approached by focusing on a specific environment - a deep, hot, hydrocarbon-rich reservoir - and by integrating studies: (1) at the level of the microbial community by characterizing the microbes in the deep, hot subsurface environment and identifying sulfur-reducing microbes and enzymes through metagenomics and metatranscriptomics; (2) at the enzymatic level by determining the mechanisms of sulfur-reducing enzymes by kinetic and structural techniques; and (3) at the geochemical level by using cyclic voltammetry to determine the chemical speciation of sulfur in situ and during reduction by microbes and enzymes. A transformative aspect of this work is a way in which cyclic voltammetry will be used to obtain a "snapshot" of the entire range of sulfur species present during the reduction of sulfur by enzymes, isolated microbial species, and microbial populations. This work will also provide a view of the sulfur chemical species present in deep subsurface fluids in situ. Having a clear picture of sulfur metabolism in the deep subsurface will broaden our understanding of biogeochemical sulfur cycling, life in extreme environments, and evolutionary processes. It has been estimated that the subsurface environment contains 40-60% of the bacterial cells on earth, accounting for at least one third of the earth's carbon biomass. However, because of its hidden nature, this huge reservoir of biodiversity has only begun to be explored.