NSFOCE-BSF: Microbial ecosystems in silico, in the lab and in the field: understanding interactions between abundant marine bacterial taxa

NSFOCE-BSF：计算机模拟、实验室和现场的微生物生态系统：了解丰富的海洋细菌类群之间的相互作用

基本信息

批准号：
1635070
负责人：
Daniel Segre
金额：
$ 40万
依托单位：
Trustees of Boston University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-01 至 2019-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1635070&HistoricalAwards=false
关键词：
NSFOCE BSF Microbial ecosystems silico

项目摘要

Every drop of seawater contains around one million microorganisms (bacteria, small algae and other organisms such as ciliates and diatoms). These marine microbes feed the entire marine ecosystem, modulate global cycles of carbon and other elements, and impact climate. With the advances in genome-sequencing technology, we can now identify the microbes and assess their genetic and metabolic capacities, yet we still cannot deduce from the genomes of these organisms how they will grow - and interact - in nature. This project will tackle this challenge through a tightly integrated combination of mathematical modeling, laboratory experiments and field work in the Eastern Mediterranean, to identify genes and pathways dictating how environmentally-relevant microbes grow and interact in the sea. The project will produce genome-scale mathematical models of the metabolism of Prochlorococus, the numerically-dominant photosynthetic bacteria in large swaths of the ocean, and of Alteromonas, abundant marine bacteria which make their living by consuming and respiring organic molecules produced by Prochlorococcus and other photosynthetic microbes. These models will be tested using laboratory cultures of these organisms grown alone and together, and determine to what extent the models and laboratory cultures represent the growth and death of these organisms in the Eastern Mediterranean. This study will be useful for scientists of many disciplines, including not only marine biology, oceanography and ecology but also genetics, medicine and agriculture. Results will shed light on the dynamics of some of the most common organisms in the world, responsible for the production of up to 20% of the oxygen we breathe. This collaborative study will foster the development and training of the next generation of marine scientists, and will be used in outreach activities designed to share with high-school students and the general public the excitement of marine research and the need to responsibly utilize and sustain the oceans for the sake of future generations. The strong human impact on marine ecosystems, and the need for quantitative and predictive understanding of how they will respond to a changing environment, calls for interdisciplinary research and training for the next generation of scientists and decision makers. Models and data generated by this work will be integrated into a novel educational exploration-focused, web- and field-based educational module. This module will introduce key concepts in microbiology, environmental sciences and oceanography to intermediate- and high-school students.This project will tackle the challenge of understanding microbial interactions from the underlying genetic data through a tightly integrated combination of genome scale modeling, laboratory experiments and field work in the Eastern Mediterranean. The investigators aim to identify genomic traits dictating how environmentally-relevant primary producers and heterotrophic bacteria interact. Genome-scale (dynamic flux balance analysis, dFBA) models of Prochlorococus MED4 and of Alteromonas HOT1A3 will be produced and calibrated using high-throughput measurements of growth and physiological parameters in laboratory batch cultures, combined with detailed analysis of specific metabolites. The dFBA models will be combined in-silico and the results compared to laboratory co-cultures. Model-data discrepancies will provide opportunities to revisit the models, suggesting the mediation of alternative processes such as allelopathy or other types of chemical signaling. Finally, time-series data on the community composition and function during the summer/fall Prochlorococcus bloom in the hyper-oligotrophic Eastern Mediterranean, combined with field experiments (microcosms), will provide a test of hypotheses generated in the lab. This study will provide the first detailed "roadmap" linking genomic traits (genes and metabolic pathways) and rate measurements with species interactions in environmentally-relevant marine microbes. Genome-scale models will likely be embedded in a not-so-distant future in global-scale models of the Earth System, and the study will provide a critical stepping-stone towards predicting how marine microbial systems will evolve in a changing world.

每一滴海水都包含大约一百万个微生物（细菌，小藻类和其他生物，例如纤毛和硅藻）。这些海洋微生物为整个海洋生态系统提供了调节碳和其他元素的全球周期，并影响气候。随着基因组测序技术的进步，我们现在可以识别微生物并评估它们的遗传和代谢能力，但是我们仍然无法从这些生物的基因组中推断出它们在自然界中如何成长和相互作用的基因组。该项目将通过在地中海东部的数学建模，实验室实验和现场工作的紧密整合结合来应对这一挑战，以识别基因和途径决定了与环境相关的微生物在海中的生长和相互作用。该项目将产生基因组规模的数学模型，以实现氯氯氯氯此的代谢，这是大海洋中的数值优势光合细菌，以及拟南天异的替代品，丰富的海洋细菌，通过prococcus and Photosecocus和其他photosecentic microbess产生的有机分子，从而使它们的生存和呼吸有机分子生存。这些模型将使用这些生物的实验室培养物进行测试，并确定模型和实验室培养物在多大程度上代表这些生物在东地中海的生长和死亡。这项研究将对许多学科的科学家有用，不仅包括海洋生物学，海洋学和生态学，还包括遗传学，医学和农业。结果将阐明世界上一些最常见的生物的动态，负责我们呼吸的20％的氧气产生。这项合作研究将促进下一代海洋科学家的发展和培训，并将用于旨在与高中生和公众共享海洋研究的兴奋，以及为子孙后代而进行负责任地利用和维持海洋的兴奋。人类对海洋生态系统的强烈影响，以及对它们将如何应对不断变化的环境的反应，呼吁对下一代科学家和决策者进行跨学科研究和培训的需求。这项工作生成的模型和数据将集成到一个新型以教育探索为中心的，基于网络和现场的教育模块中。该模块将在中级和高中生中介绍微生物学，环境科学和海洋学的关键概念。该项目将通过基因组规模建模，实验室实验，实验室实验和现场工作的基础遗传数据的微生物相互作用的挑战应对挑战。研究人员旨在确定基因组特征决定了与环境相关的原发性生产者和异养细菌如何相互作用。基因组规模（动态通量平衡分析，DFBA）的核酸核Med4和Alteromonas Hot1a3的模型将使用实验室批次培养物中生长和生理参数的高通量测量以及详细分析的特定代谢物的详细分析来产生和校准。与实验室共文化相比，DFBA模型将合并在核中，结果。模型数据差异将为重新访问模型提供机会，这表明替代过程（例如化学病或其他类型的化学信号传导）进行了调解。最后，在夏季/秋季氯环球菌中，地中海东部的夏季/秋季氯环球菌在地中海东部的夏季 - 氯环球菌上开花的时间序列数据将提供实验中产生的假设的测试。这项研究将提供第一个详细的“路线图”，将基因组特征（基因和代谢途径）与与环境相关的海洋微生物中的物种相互作用进行速率测量。基因组规模的模型可能会嵌入地球系统的全球尺度模型中，这将为预测海洋微生物系统将如何在不断变化的世界中发展而来，为预测海洋微生物系统将如何发展。