Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems

海洋系统中的原核生物种类繁多，进行许多类型的代谢过程，在生物地球化学循环中占有重要地位。然而，单个细菌分类群对生化过程的贡献还没有被很好地理解。同样，以前的研究通过考察单个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的成功也有限。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度和丰度成正比，而且这些速率也可能对环境波动比丰度更敏感。这个项目将检验关于生物体的一个基本属性，生长速度的下列问题和假设：1)在对照实验中，生长速度和特定细菌分类群的丰度之间有什么关系？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度的真正差异？PI假设生长反应转录本：基因比率将与增长率相关，而不受代谢策略和系统发育的影响，即使比率和绝对率在不同条件下生长的细菌物种或分类群中会有所不同。这一假设将在与环境相关的分离细菌中进行探索，这些细菌的基因组已经被测序，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。2)生长速度与原位丰度有什么关系？环境的变化如何反映在细菌的生长速度上？PI假设，通过16S rRNA：rDNA比率或其他生长反应转录本：基因比率估计的生长速度将与环境因素更好地关联，而不是仅仅与丰度相关。类群内部和类群之间生长速度的差异将与环境的变化相关，特别是与光照和营养物质的变化有关。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验证这一假设：自2006年以来一直在采样的沿海微生物观测站，以及特拉华州和切萨皮克湾。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方法相结合的方法，在不同的营养条件和不同的原位时间和空间尺度下检测16S rRNA和其他生长调节转录本及其相应基因的水平。高通量测序避免了扩增和克隆人工产物，并且具有成本效益。生长反应转录本：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性质，以调查环境因素对单个细菌分类群生长速度的影响，并探索对微生物群落的自下而上的控制。智力价值这个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，因为它为长期存在的关于细菌种群数量和活动之间的关系的问题提供了答案。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，并让未被充分代表的本科生参与夏季研究项目，包括在海上的实地考察。该项目的结果将被纳入环境基因组学网站，并用于Kirchman教授的课程。Kirchman和Campbell实验室向公众开放(每年约1000名游客)，PI还参与了每年吸引约10,000名游客的海岸日开放参观活动。最后，专业人员将参加K-12教师培训讲习班和特拉华州环境研究所的其他外联活动。

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.