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: 1233271
• 负责人: Barbara Campbell
• 金额: $ 77.4万
• 依托单位: University of Delaware
• 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 2013-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1233271&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.

海洋系统中的原核生物高度多样化，并进行多种类型的生物地球化学循环中重要的代谢过程。然而，单个细菌类群对生化过程的贡献尚不清楚。同样，之前的研究通过观察单个类群的丰度与环境因素之间的相关性来了解细菌群落的调节，但取得的成功有限。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会随着生长速率和丰度而扩大，而且这些速率也可能对环境波动比丰度更敏感。 该项目将研究以下有关生物体基本特性（生长速率）的问题和假设：1）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？ 16S 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差异？ PI 假设生长响应转录本：基因比率将与独立于代谢策略和系统发育的生长速率相关，尽管比率和绝对速率在细菌种类之间或在不同条件下生长的分类单元内会有所不同。这一假设将在与环境相关的分离细菌（其基因组已被测序）以及自然群落中的单个分类群（其基因组将通过单细胞方法进行测序）中进行探索。 2）生长速率和原位丰度之间有什么关系？ 环境的变化如何反映在细菌生长率上？ PI 假设，通过 16S rRNA:rDNA 比率或其他生长响应转录本：基因比率估计的生长率将比单独丰度更好地与环境因素相关。类群内部和类群之间生长速率的变化将与环境的变化相关，尤其是光和营养的变化。该项目将通过分析三个经过充分研究的不同海洋生态系统来检验这一假设：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湾和切萨皮克湾。 为了研究上述问题和假设，PI 将结合使用单细胞基因组学、高通量测序和 QPCR 方法来检查 16S rRNA 和其他生长调节转录本及其相应基因在各种营养条件和不同原位时间和空间尺度下的水平。高通量测序可避免扩增和克隆假象，并且具有成本效益。生长响应转录本：将在每小时、每天、每周和每月的时间尺度上检查基因比率、微生物丰度和生物地球化学特性，以研究环境因素对单个细菌类群生长速率的影响，并探索微生物群落的自下而上控制。 智力价值该项目的结果将在很大程度上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活动和现有种群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已可用的广泛基因组数据联系起来。更广泛的影响 该项目将支持一名研究生，并让代表性不足的本科生参与夏季研究项目，包括海上实地考察。该项目的结果将被纳入环境基因组学网站，并在基希曼教授的课程中使用。 Kirchman 和 Campbell 实验室参加了向公众开放的实验室参观活动（每年约 1000 名参观者），PI 还参与了海岸日活动，这是一项每年吸引约 10,000 名参观者的开放日活动。最后，PI 将参与 K-12 教师培训研讨会和特拉华环境研究所的其他外展活动。