Collaborative Research: Metaproteomics: Linking Natural Microbial Community Structure and Function Via Protein identification

就生物量而言，微生物是地球上最丰富的生物，其碳含量是整个人类碳含量的5000倍。一茶匙的海水通常含有超过100万个微生物细胞。考虑到大小和形状的有限差异，在显微镜下区分一个物种和另一个物种是困难的。将特定功能与单个细胞或群体联系起来更具挑战性。海洋微生物驱动碳、氮、氧和其他对生物圈功能至关重要的元素的生物地球化学循环。了解微生物多样性、微生物代谢和生物地球化学之间的关系是当今微生物生态学家面临的巨大挑战之一。宏蛋白质组学是一种新的、未经尝试的方法来鉴定存在于微生物群落中的蛋白质。蛋白质是驱动细胞中所有化学反应的引擎，可以用来识别特定的微生物，因为每种微生物都含有独特的蛋白质谱。因此，鉴定微生物群落中的蛋白质将提供关于在给定样品中存在什么微生物以及它们在采样时正在做什么的信息。本研究将宏蛋白质组学应用于海洋微生物群落，以期：1)比较不同地理和时间尺度下的蛋白质表达模式；2)从特定样品中鉴定出特别感兴趣的蛋白质；3)将特定的微生物功能与单个微生物群联系起来。从微生物群落样品中提取的蛋白质将根据质量和电荷进行分解，以提供群落蛋白质剖面的图像。通过比较这些图像，可以量化不同样本之间的异同。将收集感兴趣的特定蛋白质的序列信息，并用于鉴定蛋白质和最可能的蛋白质微生物来源。该项目将首次对动态和高度复杂的海洋微生物组合进行深入的元蛋白质组学研究。宏蛋白质组学是元基因组学和环境转录组学的一种替代和补充方法。虽然在海洋中发现了许多新的微生物，但绝大多数海洋微生物仍然不能在实验室中培养。作为一种与培养无关的方法，宏蛋白质组学将解决微生物群落中实际表达的蛋白质，而不是由宏基因组学和转录组学提供的潜在表达测量。该项目将资助两名研究生，并为他们提供微生物多样性、生物海洋学、分析化学和生物信息学等领域的跨学科培训。

Microbes are the most abundant organisms on the planet in terms of biomass, containing ~5,000 times the amount of carbon found in the entire human population. A single teaspoon of ocean water often contains over 1 million individual microbial cells. Given limited differences in size and shape, distinguishing one species from another under the microscope is difficult. Associating specific functions with individual cells or populations is even more challenging. Marine microbes drive biogeochemical cycles of carbon, nitrogen, oxygen and other elements that are critical to the function of the biosphere. Understanding relationships between microbial diversity, microbial metabolism and biogeochemistry is one of the great challenges facing microbial ecologists today. Metaproteomics is a new and untried approach to identify proteins present in microbial communities. Proteins are the engines that drive all chemical reactions in cells and can be used to identify specific microbes as each contains unique protein profiles. Thus, identifying proteins in microbial communities will provide information about what microbes are present in a given sample and what they are doing at the time of sampling. This research will apply metaproteomics to marine microbial communities to: 1) compare the protein expression patterns over geographic and temporal scales; 2) identify proteins of particular interest from specific samples; and 3) link specific microbial functions with individual microbial groups. Proteins extracted from microbial community samples will be resolved based on mass and charge to provide an image of the community protein profile. Similarities and differences between different samples will be quantified by comparing these images. Sequence information for specific proteins of interest will be gathered and used to identify both the protein and most probable microbial source of the protein. This project will provide the first in depth metaproteomic study of a dynamic and highly complex marine microbial assemblage. Metaproteomics is an alternative and complementary approach to metagenomics and environmental transcriptomics. Although many novel microorganisms have been detected in the ocean, the vast majority of marine microbes still cannot be grown in the laboratory. As a culture-independent approach, metaproteomics will address what proteins are actually expressed in microbial communities rather than the potential expression measurements provided by metagenomics and transcriptomics. This project will support two graduate students and provide both with highly interdisciplinary training spanning the fields of microbial diversity, biological oceanography, analytical chemistry, and bioinformatics.