Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems

海洋系统中的原核生物种类繁多，在生物地球化学循环中进行多种重要的代谢过程。然而，单个细菌分类群对生物化学过程的贡献尚不清楚。同样，以前的研究通过观察单个分类群的丰度与环境因素之间的相关性，在理解细菌群落的调节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和丰度成比例，并且这些速率也可能比丰度对环境波动更敏感。本项目将研究以下问题和假设，关于生物体的基本特性，生长速率：1)在控制实验中，生长速率与特定细菌类群的丰度之间的关系是什么？16S rRNA:rDNA比率或其他生长调节转录基因比率是否反映了生长速率的真正差异？pi假设生长响应转录：基因比率将与生长速率相关，独立于代谢策略和系统发育，即使比率和绝对比率在不同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。这一假设将在环境相关的分离细菌中进行探索，这些细菌的基因组已经测序，以及在自然群落中的单个分类群中，它们的基因组将通过单细胞方法进行测序。2)生长速率与原地丰度的关系是什么？环境的变化是如何反映在细菌生长速率上的？pi假设，通过16S rRNA:rDNA比率或其他生长应答转录基因比率估计的生长速率将比单独的丰度更好地与环境因素相关。类群内部和不同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有关。该项目将通过分析三个研究良好的不同海洋生态系统来验证这一假设：一个自2006年以来一直取样的沿海微生物观测站，以及特拉华和切萨皮克湾。为了研究上述问题和假设，pi将结合单细胞基因组学、高通量测序和QPCR方法，检测不同营养条件和不同原位时空尺度下16S rRNA和其他生长调节转录物及其相应基因的水平。高通量测序避免了扩增和克隆产物，并且具有成本效益。生长响应转录：基因比率、微生物丰度和生物地球化学特性将在每小时、每天、每周和每月的时间尺度上进行检查，以研究环境因素对单个细菌分类群生长速度的影响，并探索微生物群落的自下而上控制。这个项目的结果将通过回答长期存在的关于细菌种群活动和存量之间关系的问题，大大改变我们对海洋和河口微生物过程的看法。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夏季研究项目，包括海上实地考察。这个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Campbell实验室是向公众开放的实验室之旅的特色（每年约有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展活动。

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.