Collaborative Research: Linking microbial diversity, gene expression, and the transformation of terrestrial organic matter in major U.S. rivers

合作研究：将美国主要河流的微生物多样性、基因表达和陆地有机质的转化联系起来

• 批准号: 1457794
• 负责人: Byron Crump
• 金额: $ 82.6万
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1457794&HistoricalAwards=false
• 关键词: Collaborative; Research; Linking; microbial; diversity

Rivers and streams are the major conduits for transporting of Earth's carbon from the land to the oceans. Much of the carbon is in a dissolved organic form, and it serves as food for aquatic microorganisms. The challenge is that the chemical diversity of dissolved organic carbon is very great, and the genetic diversity of aquatic microbes is also immense. Accordingly, this project will use state-of-the art genomic methods to study the diversity and specific functions of these microorganisms. The results will fill a critical gap in understanding the specific metabolic capabilities of these microbes and how they carry out the key ecosystem function of transforming and metabolizing highly complex, riverborne dissolved organic carbon. The data that will be collected are important for predicting the impacts of land-use change, nutrient use, and shifting climate on freshwater quality across the USA. The research involves a collaboration with the Yale Peabody Museum Evolution program for inner-city New Haven high-school students to train interns and develop an interactive museum exhibit on U.S. rivers. The project will also train a postdoctoral researcher, and undergraduate and graduate students, including members of underrepresented groups in science.The goal of the project is to describe interactions and feedbacks between watershed diversity, microbial functional diversity, and dissolved organic matter (DOM) chemistry in 36 large U.S. rivers, and to experimentally link gene expression with DOM degradation in five of them (the Altamaha, Columbia, Mississippi, St. Lawrence and Yukon). River sampling will be conducted in collaboration with a U.S. Geological Survey stream network. This research will address the concept that microbial genetic mechanisms in river ecosystems are closely linked to climate and landscape features that control river environmental conditions, particularly DOM quality. This concept implies that microbial function is shaped by DOM composition, climate, and river chemistry. These shaping forces alter the functional genetic capabilities required for competitive success within riverine microbial communities, and, thus, drive shifts in functional gene expression and phylogenetic composition, that, in turn, increase the efficiency of DOM metabolism and biogeochemical processes. Three hypotheses are to be tested: (1) the functional genetic composition and gene expression patterns of riverine microbial communities are correlated with the composition of riverine DOM; (2) community gene expression patterns vary predictably in response to shifts in the available forms of DOM; and, (3) the composition of riverine bacterial communities correlates with the composition of riverine DOM over space and time, and varies with watershed-specific climatic factors. The first hypothesis will be addressed with an empirical study of microbial community gene content (metagenomics), gene expression (metatranscriptomics), and DOM diversity (high-resolution analytical chemistry) during four seasons in five rivers that encompass a broad range of DOM composition. The second hypothesis will be addressed with an experimental study to identify active organisms and genes expressed by freshwater microbial metabolism. The third hypothesis will be addressed with an empirical study of microbes, DOM, and river chemistry in 36 major U.S. rivers. Statistical approaches being developed through a Microsoft-sponsored international working group (BioGeoChemistry Data System) will be applied to link microbial and DOM data.

河流和溪流是将地球碳从陆地输送到海洋的主要渠道。 大部分碳以溶解的有机形式存在，是水生微生物的食物。 挑战在于溶解有机碳的化学多样性非常大，水生微生物的遗传多样性也非常大。 因此，该项目将使用最先进的基因组方法来研究这些微生物的多样性和特定功能。 这些结果将填补了解这些微生物的特定代谢能力以及它们如何执行转化和代谢高度复杂的河流溶解有机碳的关键生态系统功能的关键空白。 将收集的数据对于预测土地利用变化、养分利用和气候变化对美国各地淡水质量的影响非常重要。 该研究涉及与耶鲁大学皮博迪博物馆进化计划合作，为纽黑文市中心的高中生提供培训实习生并开发关于美国河流的互动博物馆展览。该项目还将培训一名博士后研究员、本科生和研究生，包括科学界代表性不足群体的成员。该项目的目标是描述流域多样性、微生物功能多样性和溶解有机物 (DOM) 化学之间的相互作用和反馈在美国 36 条主要河流中，并通过实验将基因表达与其中 5 条河流（阿尔塔马哈河、哥伦比亚河、密西西比河、圣劳伦斯河和育空河）的 DOM 降解联系起来。河流采样将与美国地质调查局河流网络合作进行。这项研究将探讨河流生态系统中微生物遗传机制与控制河流环境条件（特别是 DOM 质量）的气候和景观特征密切相关的概念。这个概念意味着微生物功能是由 DOM 组成、气候和河流化学决定的。这些塑造力改变了河流微生物群落竞争成功所需的功能遗传能力，从而推动功能基因表达和系统发育组成的变化，进而提高 DOM 代谢和生物地球化学过程的效率。需要检验三个假设：（1）河流微生物群落的功能遗传组成和基因表达模式与河流DOM的组成相关； (2) 群落基因表达模式可预测地随着 DOM 可用形式的变化而变化； (3)河流细菌群落的组成与河流DOM的组成在空间和时间上相关，并随着流域特定的气候因素而变化。第一个假设将通过对包含广泛 DOM 组成的五条河流的四个季节期间微生物群落基因内容（宏基因组学）、基因表达（宏转录组学）和 DOM 多样性（高分辨率分析化学）的实证研究来解决。第二个假设将通过实验研究来解决，以确定淡水微生物代谢表达的活性生物体和基因。第三个假设将通过对美国 36 条主要河流的微生物、DOM 和河流化学的实证研究来解决。微软赞助的国际工作组（BioGeoChemistry Data System）正在开发的统计方法将用于链接微生物和 DOM 数据。