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

河流和溪流是将地球上的碳从陆地输送到海洋的主要管道。 大部分碳以溶解的有机形式存在，它是水生微生物的食物。 面临的挑战是，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是巨大的。 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。 这些结果将填补理解这些微生物的特定代谢能力以及它们如何实现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，营养物质使用和气候变化对美国淡水质量的影响非常重要。 这项研究涉及与耶鲁皮博迪博物馆进化计划的合作，该计划旨在为纽黑文市中心的高中学生培训实习生，并开发一个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的群体的成员。该项目的目标是描述美国36条大型河流中流域多样性、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，并通过实验将其中5条河流的基因表达与DOM降解联系起来（阿尔塔马哈、哥伦比亚、密西西比、圣劳伦斯和育空地区）。河流采样将与美国地质调查局河流网络合作进行。这项研究将解决这一概念，即河流生态系统中的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。这一概念意味着微生物的功能是由DOM组成，气候和河流化学。这些塑造力量改变了在河流微生物群落中竞争成功所需的功能遗传能力，因此，驱动功能基因表达和系统发育组成的转变，这反过来又增加了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）群落基因表达模式随着DOM可用形式的变化而发生可预测的变化;（3）河流细菌群落组成与河流DOM的时空组成相关，并随流域特有的气候因素而变化。第一个假设将解决与微生物群落基因含量（宏基因组学），基因表达（元转录组学），DOM多样性（高分辨率分析化学）在四个季节在五条河流，包括一个广泛的DOM组成的实证研究。第二个假设将通过一项实验研究来解决，以确定淡水微生物代谢所表达的活性生物和基因。第三个假设将解决与微生物，DOM和河流化学在36个美国主要河流的实证研究。通过微软赞助的一个国际工作组（生物地球化学数据系统）正在开发的统计方法将被用于连接微生物和DOM数据。

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.