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

每一滴海水都含有大约100万个微生物（细菌、小型藻类和其他生物，如纤毛虫和硅藻）。这些海洋微生物为整个海洋生态系统提供食物，调节全球碳和其他元素的循环，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，但我们仍然无法从这些生物体的基因组中推断出它们将如何在自然界中生长和相互作用。该项目将通过数学建模、实验室实验和地中海东部实地工作的紧密结合来应对这一挑战，以确定决定与环境相关的微生物如何在海洋中生长和相互作用的基因和途径。该项目将为原绿球藻（原绿球藻是海洋中数量上占主导地位的光合细菌）和异单胞菌（大量的海洋细菌，通过消耗和呼吸原绿球藻和其他光合微生物产生的有机分子为生）的代谢建立基因组尺度的数学模型。这些模型将使用单独和共同培养的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了东地中海这些生物的生长和死亡。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，而且包括遗传学、医学和农业。结果将揭示世界上一些最常见的生物体的动态，这些生物体负责生产我们呼吸的氧气的20%。这项合作研究将促进下一代海洋科学家的发展和培训，并将用于外联活动，旨在与高中生和公众分享海洋研究的兴奋，以及为了子孙后代负责任地利用和维持海洋的必要性。人类对海洋生态系统的强烈影响，以及对海洋生态系统如何应对不断变化的环境的定量和预测性理解的需求，要求对下一代科学家和决策者进行跨学科研究和培训。这项工作产生的模型和数据将被整合到一个以教育探索为重点的、基于网络和实地的教育模块中。本单元将向中学生和高中生介绍微生物学、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、实验室实验和东地中海实地工作的紧密结合，解决从潜在遗传数据中理解微生物相互作用的挑战。研究人员的目标是确定基因组特征，这些特征决定了与环境相关的初级生产者和异养细菌如何相互作用。将制作原绿球菌MED4和Alteromonas HOT1A3的基因组尺度（动态通量平衡分析，dFBA）模型，并使用实验室批量培养中生长和生理参数的高通量测量，结合特定代谢物的详细分析进行校准。dFBA模型将在硅中结合，并将结果与实验室共培养进行比较。模型数据的差异将为重新审视模型提供机会，表明化感作用或其他类型的化学信号传导等替代过程的中介作用。最后，在超少营养东地中海夏季/秋季原绿球藻华期间的群落组成和功能的时间序列数据，结合实地实验（微观世界），将为实验室产生的假设提供检验。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）和速率测量与环境相关的海洋微生物物种相互作用联系起来。基因组尺度的模型很可能在不久的将来嵌入到地球系统的全球尺度模型中，这项研究将为预测海洋微生物系统在不断变化的世界中如何进化提供一个关键的垫脚石。

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.