Genomic and Transcriptomic Comparison of Iron and Light Physiology in Coastal and Oceanic Diatoms

沿海和海洋硅藻铁和光生理学的基因组和转录组比较

• 批准号: 0962208
• 负责人: Bethany Jenkins
• 金额: $ 70万
• 依托单位: University of Rhode Island
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2015-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0962208&HistoricalAwards=false
• 关键词: Genomic; Transcriptomic; Comparison; Iron; Light

Intellectual Merit: Diatoms are among the most important primary producers in the ocean. Coastal species can respond to dynamic inputs of nutrients into the surface ocean and form large biomass blooms. Phytoplankton growth in much of the ocean is limited by one nutrient or another, and species that persist in these environments must be able to function under these low nutrient conditions. Oceanic diatom species have lower Fe requirements for growth and may have evolved to subsist in low Fe environments by changing the composition of Fe-demanding metabolic pathways. Iron and light responsive pathways are intimately linked because of the large Fe requirement of photosynthesis and the potential for both to limit growth and the efficiency of the biological carbon pump. Physiological and field studies have shown that many diatoms are susceptible to Fe/light co-limitation, but we lack information on the biochemical basis for co-limitation and how this differs between diatom species. This project will use a combination of genomics tools to investigate how coastal and oceanic diatoms in the ecologically important Thalassiosira genus respond to differing conditions of Fe and light. The investigators will compare the genome sequence of the oceanic diatom T. oceanica, which has recently been sequenced by the PI in collaboration with Illumina, Inc., to published diatom genomes to identify potential differences and similarities in the Fe and light metabolism in oceanic and coastal diatoms. They will use normalized libraries of Expressed Sequence Tags (EST) to characterize the transcriptome of T. oceanica, an oceanic strain of T. weissflogii, and the coastal diatom T. rotula grown in a matrix of Fe-limiting and replete conditions and at low and growth-saturating light levels. And they will quantify gene expression levels for the transcriptome-wide response in these experiments using digital gene expression (DGE), and use the EST data to map the DGE tags. Data from the DGE and EST experiments will be used to compare how diatom metabolism responds to variable light and Fe concentrations and to identify target genes for following limitation in natural diatom populations. Expression of these genes will be monitored in time-course experiments with additional manipulations of Fe and light levels to identify gene markers indicative of different physiological states using quantitative PCR (qPCR). The investigators will also design antibodies to a select number of proteins to monitor protein expression, and they will use qPCR and antibodies to follow responses in diatom communities in field samples collected from a cruise transitioning between Fe-replete and Fe-limiting environments as part of other funded research efforts. This work will further our understanding of how diatoms are adapted to different environments and what the genetic basis for their ecological success may be. Results from this work will help us predict how diatoms may respond to changing light regimes as a result of increased stratification due to climate change and help predict if species from different habitats will have similar or varied responses.Broader Impacts: The project will build genomic infrastructure for ecologically important species. PI Jenkins teaches a course in genome sequence analysis and the analysis tools developed and tested during the proposed work will be incorporated into this course. Students in the course will participate in the annotation of the T. oceanica genome. The project will support a graduate student and a new female postdoctoral investigator. Video for outreach to high school students will be developed. The investigators and students will record video episodes on the importance of phytoplankton, how iron and light control ocean photosynthesis, and how genomics tools can be used to understand ecological questions. Content aimed at a high school audience will be uploaded to their sites on SciVee (http://www.scivee.tv/user/bjenkins,http://www.scivee.tv/user/dreuxchappell), a site supported by NSF and others. The work benefits society because it will help us understand how organisms that mediate carbon cycling in the ocean respond to scenarios of changing climate and changing nutrient dynamics. Results from the proposed work will provide us with a much better view of diatom metabolism and further our understanding of their ecology

智力优势：硅藻是海洋中最重要的初级生产者之一。沿海物种可对海洋表层营养物质的动态输入作出反应，形成大量生物量水华。 在海洋的大部分地区，浮游植物的生长受到一种或另一种营养物质的限制，在这些环境中生存的物种必须能够在这些低营养条件下发挥作用。海洋硅藻的生长对铁的需求较低，可能已经进化到通过改变铁代谢途径的组成来在低铁环境中生存。铁和光响应途径密切相关，因为光合作用需要大量的铁，并且两者都有可能限制生长和生物碳泵的效率。生理和实地研究表明，许多硅藻容易受到铁/光的共同限制，但我们缺乏信息的生化基础共同限制，这是如何不同的硅藻物种。该项目将使用基因组学工具的组合来研究具有重要生态意义的海链藻属中的沿海和海洋硅藻如何对不同的铁和光条件作出反应。研究人员将比较海洋硅藻T.最近PI与Illumina公司合作对oceanica进行了测序，发表的硅藻基因组，以确定潜在的差异和相似之处，铁和光代谢在海洋和沿海硅藻。他们将使用表达序列标签（EST）的标准化文库来表征T。oceanica，一个海洋性的T. weissflocculus和海岸硅藻T.在铁限制和充满条件的基质中以及在低的和生长饱和的光水平下生长的圆藻。他们将在这些实验中使用数字基因表达（DGE）量化全转录组响应的基因表达水平，并使用EST数据绘制DGE标签。从DGE和EST实验的数据将被用来比较硅藻代谢如何响应于可变的光和铁浓度，并确定目标基因以下限制在天然硅藻种群。这些基因的表达将在时程实验中进行监测，并使用定量PCR（qPCR）对Fe和光水平进行额外操作，以鉴定指示不同生理状态的基因标志物。研究人员还将设计针对选定数量的蛋白质的抗体来监测蛋白质表达，他们将使用qPCR和抗体来跟踪硅藻群落中的反应，这些硅藻群落是从一次在铁丰富和铁限制环境之间过渡的巡航中收集的实地样本，作为其他资助研究工作的一部分。这项工作将进一步让我们了解硅藻如何适应不同的环境，以及它们生态成功的遗传基础可能是什么。这项工作的结果将帮助我们预测硅藻如何应对由于气候变化而增加的分层而导致的光照变化，并帮助预测来自不同栖息地的物种是否会有相似或不同的反应。更广泛的影响：该项目将为生态重要物种建立基因组基础设施。PI Jenkins教授基因组序列分析课程，在拟议工作期间开发和测试的分析工具将被纳入本课程。本课程的学生将参与T.海洋生物基因组。该项目将资助一名研究生和一名新的女博士后研究员。将制作向高中生宣传的录像带。研究人员和学生将录制有关浮游植物重要性的视频片段，铁和光如何控制海洋光合作用，以及如何使用基因组学工具来理解生态问题。针对高中观众的内容将上传到他们在SciVee上的网站（http：//www.scivee.tv/user/bjenkins，http：//www.scivee.tv/user/dreuxchappell），这是一个由NSF和其他人支持的网站。这项工作有益于社会，因为它将帮助我们了解介导海洋碳循环的生物如何应对气候变化和营养动态变化的情景。从拟议的工作结果将为我们提供一个更好地了解硅藻代谢和进一步了解他们的生态