Collaborative Research: Establishing the Hydrogen Isotopic Window into Archaeal Lipid Biomarkers

生命有三大类群--真核生物、细菌和古生菌。这项工作的重点是经常被忽视的古生菌。它们是对地球上物质和能量循环至关重要的微生物。在整个地球历史上，它们一直发挥着这一重要作用。像地球上的所有生命一样，古生物是由碳、氧和氢等元素组成的。这些元素形成了所有生命所需的更大的有机分子，如DNA、蛋白质和脂质。地球生物学家研究这些有机分子是为了了解地球上现在和过去的生命。然而，并不是所有的这些都能长期保存下来。大多数DNA和蛋白质迅速分解，只能用来研究今天的地球。脂类通常更坚硬，因此对地质生物学家很有用，因为它们可以在岩石中保存数千年。古生菌中的脂类特别耐寒，不容易分解。这意味着他们可以存储有关微生物居住的地方的信息。在它们死后很久，古生菌产生的脂肪可以从泥、油和岩石中提取出来。为了了解地球的过去，地球生物学家研究了数百万年前由古生菌建造的这些脂类的结构和原子。然而，要正确破译死亡已久的微生物脂质中的信息并非易事。要做到这一点，重要的是在现代系统和实验室中研究这些相同的脂类。这个项目将在实验室中研究几个重要的古生菌，并阐明古生菌如何利用不同种类的氢原子来制造脂类。这一结果将有助于解释古生菌中的脂肪能告诉我们它们最近生活过的地方以及过去数百万年的情况。拟议的项目强调对各级学生的培训，这包括高级研究生(博士和硕士实习生)以及本科生、高中生和中学生。为了吸引服务不足地区的高中生和中学生，项目成员将使用一个由毕业生和本科生领导的名为ManyMentors的点对点指导网络。这是一个基于APP的辅导平台，将服务不足的教室中对STEM表现出兴趣的学生与寻求STEM学位的本科生和研究生进行匹配。具体的教学活动都是为了培养可移植的技能。这包括批判性思维、书面和口头交流以及编程素养。所有项目成员都将参加这些活动。古生菌是生命的一个领域，对今天和整个地球历史上低温(150摄氏度)环境中物质和能量的循环至关重要。该项目的主要目标是揭示古生物类脂生物标志物的氢(H)同位素组成如何记录地球化学和地质微生物过程，并可用于重建现代环境系统和现代地质过去。要阅读这些记录，需要对古生代生物标志物H同位素分馏进行受控的实验校准，这一点目前还不存在。这项工作将通过校准代表古菌在不同氧化还原制度、碳源和能量通量上的脂氢同位素特征来解决这一知识差距，以反映自然界遇到的一整套环境。具体地说，它将检验这样一种假设，即古细菌脂类的结构和氢同位素组成记录了古细菌生物标志物(能量和碳的可用性以及营养/能量通量)变化的主要假想的地球化学驱动因素。为了实现这一目标，拟议的工作将采用混合培养方法，包括速率控制的稳态(化学恒定)实验，结合古菌脂肪特性，化合物特定的氢同位素分析，以及建模工作。这项工作的成果将是一个基于过程和机制的解释框架，用于古生物类脂H同位素分馏，以响应环境压力。也就是说，拟议的工作将能够在广泛的时间和空间尺度上对过去和现在的生物地球化学过程进行(重新)解释，从行星(外圈氧化还原)到区域(盆地氧化还原)再到界面(孔隙水氧化还原)。该项目将培训两名低温地球化学和地球微生物学的博士生，并提供无数机会让来自不同背景的本科生参与基础科学研究。学生的参与将以强调批判性思维、实验室和分析技能的培养以及接触地球微生物学中的新想法和问题为指导。这将使学生获得可移植的技能，如合理的实验设计、假设构建和检验，以及地球科学中的编程素养。这些都是21世纪劳动力的必备技能，无论是在地球科学领域还是在地球科学领域之外。科普夫联合计划致力于开放源码、数据收集和分析软件，并在课堂上部署了这些模块，作为在地球科学课程中提高编码素养的更大努力的一部分。为了扩大科罗拉多大学博尔德分校开发的编码模块的影响，Co-Pi Leavitt将在达特茅斯大学的地球微生物学和生物地球化学课程中测试和实施它们。这两家私人投资机构都致力于试验性的预注册(通过开放科学框架)以及所有数据产品的长期存档和保存。所有PI和团队成员都将参与ManyMentors网络。这一奖项反映了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。

Life has three major groups - the eukaryotes, bacteria and archaea. This work focuses on the often-overlooked archaea. They are microbes critical to the cycling of matter and energy on Earth. They have played this important role throughout the history of the planet. Like all life on Earth, archaea are made up of elements such as carbon, oxygen and hydrogen. These elements form larger organic molecules that are required by all life such as DNA, proteins, and lipids. Geobiologists study these organic molecules to learn about life on Earth today and in the past. However, not all of these are preserved over long periods of time. Most DNA and proteins break down quickly and can only be used to study Earth today. Lipids are often much hardier and so are useful to geobiologists because they can be preserved in rocks for millennia. Lipids from archaea are particularly hardy and do not break down easily. This means that they can store information about the place in which the microbe lived. Long after they die, the lipids made by archaea can be extracted from muds, oils, and rocks. Geobiologists examine the structures and atoms of these lipids built by archaea millions of years ago to learn about Earth's past. However, it is not easy to decode the information in the lipids of long dead microbes correctly. To do this well, it is important to study these same lipids in modern systems and in the lab. This project will study several important archaea in the lab and shed light on how the different kinds of hydrogen atoms are used by archaea to build their lipids. The results will lead to advances in interpreting what lipids from archaea can tell us about the places they lived recently, and millions of years in the past. The proposed project emphasizes training of students at all levels and this includes advanced graduate (PhD and MS trainees) as well as undergraduate, high-school and middle school students. To engage high-school and middle school students in underserved districts, project members will use a graduate and undergraduate led peer-to-peer mentoring network called ManyMentors. This is an app-based mentoring platform that matches students in underserved classrooms who show interest in STEM with undergraduate and graduate students seeking STEM degrees. Specific teaching activities are all aimed at fostering transferrable skills. This includes critical thinking, written and verbal communication, and coding-literacy. All project members will participate in these activities. Archaea are a domain of life central to the cycling of matter and energy in low temperature (150 Celsius) environments today and throughout Earth's history. The primary objective of this project is to uncover how the hydrogen (H) isotopic composition of archaeal lipid biomarkers records geochemical and geomicrobial processes and may be used to reconstruct modern environmental systems and the recent geologic past. To read these records requires controlled experimental calibration of archaeal biomarker H isotope fractionation, which does not yet exist. This work will address this knowledge gap by calibrating the lipid H-isotopic signature of representative archaea across different redox regimes, carbon sources and energy fluxes reflecting the full suite of environments encountered in nature. Specifically, it will test the hypothesis that the structural and H-isotopic composition of archaeal lipids records the main hypothesized geochemical drivers of variability in archaeal biomarkers (energy and carbon availability, as well as nutrient/energy flux). To achieve this, the proposed work will employ a mixture of culturing methods including rate-controlled steady-state (chemostatic) experiments, combined with archaeal lipid characterization, compound-specific H isotope analysis, and a modeling effort. The output of this work will be a process- and mechanism-based interpretive framework for archaeal lipid H isotope fractionation in response to environmental forcings. That is, the proposed work will allow for (re)interpretations of past and present biogeochemical processes across wide temporal and spatial scales, from planetary (exosphere redox) to regional (basinal redox) to interfacial (pore-water redox). This project will train two PhD students in low temperature geochemistry and geomicrobiology and provide myriad opportunities to engage undergraduate students from diverse backgrounds in basic scientific research. Student engagement will be guided by an emphasis on critical thinking, lab and analytical skills building, and exposure to new ideas and questions in geomicrobiology. This will allow student to gain transferrable skills, such as rational experimental design, hypothesis construction and testing, and coding-literacy in the geosciences. These are requisite skills in the 21st century workforce, both in and out of the geosciences. Co-PI Kopf has a demonstrated commitment to open-source code, data collection and analysis software and has deployed such modules in the classroom as part of a larger effort to increase coding-literacy in geoscience courses. To expand the impact of coding modules developed at CU Boulder, Co-PI Leavitt will test and implement them in geomicrobiology and biogeochemistry courses at Dartmouth. Both PIs are committed to experimental pre-registration (via Open Science Framework) and the long-term archiving and preservation of all data products. All PIs and team members will participate in the ManyMentors network.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.