CAREER: The Carbon Concentrating Mechanism of the Deep-sea Hydrothermal Vent Chemolithoautotroph Thiomicrospira Crunogena

化学自养细菌通过氧化硫化物、氨和铁等无机化合物获得能量，并利用这些能量为二氧化碳和碳酸氢盐的固定提供动力。这些生物具有很大的生态和环境相关性；例如，它们是热液喷口食物网的基础，在全球氮循环中占据关键作用，并使受尾矿影响的地区酸化。它们的一些栖息地的二氧化碳和碳酸氢盐浓度长期或间歇性较低，这使在低碳条件下生长能力增强的生物处于明显的优势。可以合理地预测，许多化石型自养生物具有广泛的适应能力来应对“低碳”条件。热液喷口的化学自养细菌Thiommicrospira crungena最近被证明起到了‘二氧化碳真空’的作用。它能够在浓度极低的碳酸氢盐和二氧化碳的存在下快速生长，并能以某种方式用碳酸氢盐填充细胞，使细胞内的碳酸氢盐浓度比细胞外高出100倍。此外，克鲁根霉的基因组最近已经测序，这将极大地促进发现负责其“二氧化碳真空”能力的基因。该项目的总体目标是从生理学和遗传学的角度描述克拉诺根霉将大量碳酸氢盐和二氧化碳‘泵入’其细胞的能力。为了实现这一目标，将同时使用传统的生理学方法和尖端的分子工具。化学自养生物催化具有深远的生态和地球化学重要性的过程；发展对它们如何应对明显的环境应激源的了解将极大地增强我们预测它们在现场的活动的能力，以及它们可能如何受到大气二氧化碳浓度增加的影响。更广泛的影响这些研究目标在很大程度上依赖于由K·斯科特基因组学课程的本科生和研究生手工注释的基因组数据。由于选修本课程的学生异常热情，以及基因组水平分析在生物学研究中的重要性与日俱增，首席研究员打算将基因组学教育扩展到次要水平。教育部分的目标是1。为中等科学教育工作者开设微生物基因组学夏季研讨会。在每年夏季入学的20名教育工作者中，有5名将从主要招收少数族裔学生的学校中挑选。创建一个基于网络的界面，允许中学生与PI及其研究生和本科生研究人员互动，以了解更多关于微生物基因组的知识。将定量逆转录聚合酶链式反应纳入上层微生物生理学实验室。这种综合的研究和教育方法将产生对化学自养生理学的基本见解，为未来环境样本的分析提供目标基因，并为解释来自其他微生物的基因组数据提供关键见解，并为中学生加入基因组学革命做好准备。

Chemolithoautotrophic bacteria obtain energy by oxidizing inorganic compounds such as sulfide, ammonia, and iron, and use this energy to power carbon dioxide and bicarbonate fixation. These organisms are of great ecological and environmental relevance; for example, they are the base of the food web at hydrothermal vents, occupy critical roles in the global nitrogen cycle, and acidify areas impacted by mine tailings. Some of their habitats have chronically or episodically low concentrations of carbon dioxide and bicarbonate, which puts organisms with an enhanced ability to grow under 'low carbon' conditions at a distinct advantage. It is reasonable to predict that many chemolithoautotrophs have extensive adaptations to cope with 'low carbon' conditions. The hydrothermal vent chemolithoautotroph Thiomicrospira crunogena has recently been demonstrated to act as a 'carbon dioxide vacuum'. It is capable of growing rapidly in the presence of vanishingly low concentrations of bicarbonate and carbon dioxide, and can somehow pack its cells with bicarbonate, to the point where the concentration of bicarbonate inside the cells is 100X higher than outside. Furthermore, T. crunogena's genome has recently been sequenced, which will greatly facilitate the discovery of the genes responsible for its 'carbon dioxide vacuuming' ability.The overall objective of this project is to physiologically and genetically characterize T. crunogena's ability to 'pump' vast quantities of bicarbonate and carbon dioxide into its cells. To meet this objective, both traditional physiological methods and cutting-edge molecular tools will be utilized. Chemolithoautotrophs catalyze processes of profound ecological and geochemical importance; developing an understanding of how they cope with an obvious environmental stressor will substantially enhance our capability to predict their activities in situ, and how they may be impacted by increasing concentrations of atmospheric carbon dioxide.Broader impactsThese research objectives rely heavily on genome data manually annotated by the undergraduate and graduate students enrolled in K. Scott's Genomics class. Spurred by the extraordinary enthusiasm of the students enrolled in this course, and by the growing importance of genome-level analyses in biological research, the principal investigator intends to expand genomics education to the secondary level. The objectives of the educational component are1. To create summer workshops in microbial genomics for secondary science educators. Five of the twenty educators enrolling per summer would be selected from schools with predominantly minority enrollment.2. To create a web-based interface allowing secondary students to interact with the PI and her graduate and undergraduate researchers to learn more about microbial genomics.3. To incorporate QRT-PCR into an upper-level Microbial Physiology Lab. This integrated approach to research and education will yield fundamental insights into chemolithoautotroph physiology, provide target genes for future analyses of environmental samples and key insights into the interpretation of genomic data from other microorganisms, and prepare secondary students to join the genomics revolution.