Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems

沿海海洋生态系统中细菌类群的增长率

• 批准号: 1261359
• 负责人: Barbara Campbell
• 金额: $ 77.4万
• 依托单位: Clemson University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-10-01 至 2017-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1261359&HistoricalAwards=false
• 关键词: Growth; Rates; Bacterial; Taxa; Coastal

Prokaryotic organisms in marine systems are highly diverse and carry out many types of metabolic processes important in biogeochemical cycles. However, the contribution of individual bacterial taxa to biochemical processes is not well understood. Similarly, previous studies have had limited success in understanding the regulation of bacterial communities by looking at correlations between abundance of individual taxa and environmental factors. Estimates of growth rates will help understand both problems. The contribution of specific bacterial taxa to biogeochemical cycles is likely to scale with growth rate as well as abundance, and these rates are also likely to be more sensitive to environment fluctuations than abundance. This project will examine the following questions and hypotheses about a fundamental property of organisms, growth rates: 1) what is the relationship between growth rate and abundance of specific bacterial taxa in controlled experiments? Do 16S rRNA:rDNA ratios or other growth-regulated transcript:gene ratios reflect real differences in growth rates? The PIs hypothesize that growth responsive transcript:gene ratios will correlate with growth rates independent of metabolic strategy and phylogeny, even though ratios and absolute rates will vary among bacterial species or within a taxa growing under different conditions. This hypothesis will be explored in environmentally relevant isolated bacteria whose genomes have been sequenced as well as in individual taxa in natural communities, whose genomes will be sequenced via a single cell approach. 2) What is the relationship between growth rate and abundance in situ? How are variations in the environment reflected in bacterial growth rates? The PIs hypothesize that growth rates, estimated by either 16S rRNA:rDNA ratios or by other growth responsive transcript:gene ratios, will be better correlated to environmental factors than abundance alone. Variation in growth rates within and between taxa will correlate with changes in the environment, especially with light and nutrients. The project will test this hypothesis by analyzing three well-­studied diverse marine ecosystems: a coastal Microbial Observatory site which has been sampled since 2006, and the Delaware and Chesapeake Bays. To investigate the questions and hypotheses outlined above, the PIs will use a combination of single cell genomics, high throughput sequencing, and QPCR approaches to examine levels of 16S rRNA and other growth-regulated transcripts as well as their corresponding genes under various nutrient conditions and different in situ temporal and spatial scales. High throughput sequencing avoids amplification and cloning artifacts and is cost effective. Growth-­responsive transcript:gene ratios, microbial abundance, and biogeochemical properties will be examined over hourly, daily, weekly and monthly time scales to investigate the influence of environmental factors on growth rates of individual bacterial taxa and to explore bottom-­up control of microbial communities. Intellectual MeritThe results from this project will do much to alter our perception of microbial processes in the oceans and estuaries by providing answers to long-­standing questions about relationships between activity and standing stocks of bacterial populations. It will begin to link quantitative rate measurements of specific bacterial taxa to the extensive genomic data now becoming available. Broader Impacts The project will support a graduate student and involve underrepresented undergraduates in summer research projects, including at sea fieldwork. The results from this project will be incorporated into an environmental genomics web site and used in courses taught by Kirchman. The Kirchman and Campbell labs are featured in lab tours open to the public (~ 1000 visitors per year) and the PIs are also involved in Coast Day, an annual open house that attracts about 10,000 visitors. Finally, the PIs will be involved in K-­12 teacher training workshops and other Delaware Environmental Institute outreach activities.

海洋系统中的原生生物具有高度多样性，并进行许多类型的代谢过程，这些代谢过程在海洋地球化学循环中非常重要。然而，单个细菌类群对生物化学过程的贡献还不清楚。同样，以前的研究通过观察个体分类群丰度与环境因素之间的相关性，在理解细菌群落的调控方面取得了有限的成功。对增长率的估计将有助于理解这两个问题。特定细菌类群对生物地球化学循环的贡献可能与生长速率以及丰度成比例，并且这些速率也可能比丰度对环境波动更敏感。 本项目将研究以下关于生物体基本特性-生长速率的问题和假设：1）在受控实验中，生长速率与特定细菌类群丰度之间的关系是什么？16 S rRNA：rDNA比率或其他生长调节转录物：基因比率是否反映了生长速率的真实的差异？PI假设生长响应转录本：基因比率将与生长速率相关，而与代谢策略和代谢发生无关，即使比率和绝对速率在细菌物种之间或在不同条件下生长的分类群内会有所不同。这一假设将在基因组已测序的环境相关的分离细菌以及自然群落中的个体类群中进行探索，其基因组将通过单细胞方法进行测序。 2)增长率和原地丰度之间的关系是什么？ 环境的变化如何反映在细菌的生长速度上？PI假设，生长速率，估计由16 S rRNA：rDNA的比例或其他生长反应转录：基因的比例，将更好地与环境因素比丰度单独相关。类群内部和类群之间生长速率的变化与环境的变化有关，特别是与光照和营养物质有关。该项目将通过分析三个经过充分研究的多样化海洋生态系统来验证这一假设：一个自2006年以来一直进行采样的沿海微生物观测站，以及特拉华州和切萨皮克海湾。 为了研究上述问题和假设，PI将使用单细胞基因组学，高通量测序和QPCR方法的组合来检查16 S rRNA和其他生长调节转录物的水平，以及在各种营养条件和不同的原位时空尺度下相应的基因。高通量测序避免了扩增和克隆假象，并且具有成本效益。将在每小时、每天、每周和每月的时间尺度上检查生长-增殖反应转录物：基因比率、微生物丰度和微生物地球化学性质，以研究环境因素对单个细菌分类群生长速率的影响，并探索微生物群落的自下而上控制。 知识价值这个项目的结果将大大改变我们对海洋和河口微生物过程的看法，为长期存在的关于细菌种群的活动和现存量之间关系的问题提供答案。它将开始将特定细菌分类群的定量速率测量与现在可用的广泛的基因组数据联系起来。该项目将支持一名研究生，并让代表性不足的本科生参与暑期研究项目，包括海上实地考察。该项目的结果将被纳入一个环境基因组学网站，并用于Kirchman教授的课程。Kirchman和坎贝尔实验室是向公众开放的实验室图尔斯之旅的特色（每年约1000名游客），PI也参与了海岸日，这是一个每年吸引约10，000名游客的开放日。最后，PI将参与K-12教师培训讲习班和其他特拉华州环境研究所的外联活动。