Collaborative Research: Predicting the Spatiotemporal Distribution of Metabolic Function in the Global Ocean

预测海洋化学和生物将如何应对全球变化是社会的一个紧迫问题。这个项目将开发新的建模技术，利用热力学中关于能量如何在系统中运动的分支学科中的物理学思想来预测这种变化。随着时间变化的系统热力学的最新进展表明，系统将在内部组织起来，以便最大限度地流动和耗散能量。例如，夏季海洋和大气之间形成的温差推动了飓风(有组织的结构)的形成，飓风的存在加速了温差的消散。该项目利用了这一基本特性，但将其扩展到微生物群落，如细菌和浮游植物，它们构成了海洋食物网的基础，并强烈影响海洋化学。基于生物如何利用太阳能和化学能从环境中的碳、氮、磷和其他元素中构建自己的信息，该模型可以预测新陈代谢功能，如光合作用或大气中的固氮，是如何在海洋中的时间和空间表达的。这些预测可以与现有的海洋观测相比较，包括新开发的依赖DNA和RNA测序来确定微生物群落代谢功能的技术。该项目将支持一名博士后学者在海洋生物地球化学建模、热力学和分子观察之间的这种新的接口。该项目还将支持暑期实习，作为伍兹霍尔伙伴教育计划的一部分，该计划是一个机构联盟，致力于增加伍兹霍尔的学生多样性，并支持每年两个独立的本科生研究项目，作为海洋生物实验室(MBL)环境科学学期计划的一部分。将在该项目的第二年举办一次讲习班，以扩大对海洋生物地球化学热力学方法的了解，并探讨其在新陈代谢模型和理论最新进展的更广泛背景下的地位。在项目期间开发的海洋模型代码将是开源的并公开传播。该项目建立在达尔文项目的基础上，达尔文项目是一种基于特征和选择的建模方法，用于描述海洋浮游生物群落和生物地球化学循环。这种方法依靠当地竞争从不同的种群中进行选择，并确定调节生物地球化学循环的微生物的功能特征。该项目将把这种基于选择的建模方法与先前开发的分布式代谢网络视角结合起来，以便于计算反应热力学。这将提供对关键代谢功能的机械和定量描述，并允许新模型直接映射到基于组学的观察。该项目将利用基于最大熵产生(MEP)猜想的新的建模设计标准来确定新陈代谢机制的分配及其表达，如代谢在固氮和氨吸收之间的切换。模型试验将依赖于现有的海洋调查和观测。一旦得到验证，耦合模型将被用于调查功能生物多样性的损失、通才与专家、时间浮游策略以及生态系统生物地球化学中群落互补性的损失。该项目的一个重要成果将是代谢功能和表达(如固氮和氨氧化)的预测全球生物地理图，可以用定向组学观察进行测试并用于解释。

Predicting how marine chemistry and biology will respond to global change is a pressing issue for society. This project will develop new modeling techniques for predicting such changes using ideas derived from physics in the subdiscipline of thermodynamics that concerns how energy moves in a system. Recent advancements in the thermodynamics of systems that change over time indicate that systems will internally organize so as to maximize the flow and dissipation of energy. For example, the temperature difference that develops between the ocean and atmosphere over the summer drives the formation of hurricanes (the organized structures) whose presence hastens the dissipation of the temperature difference. This project utilizes this fundamental property but extends it to microbial communities, such as bacteria and phytoplankton, which form the base of the ocean food web and strongly influence ocean chemistry. Based on information on how biology utilizes solar and chemical energy to construct itself from carbon, nitrogen, phosphorus and other elements in the environment, the model can predict how metabolic functions, such as photosynthesis or nitrogen fixation from the atmosphere, are expressed over time and space within the ocean. These predictions can be compared to existing oceanographic observations, including newly developed techniques that rely on DNA and RNA sequencing to determine metabolic function of the microbial community. This project will support one postdoctoral scholar in this new interface between ocean biogeochemistry modeling, thermodynamics and molecular observations. The project will also support summer internships as part of the Woods Hole Partnership Education Program, a consortium of institutions committed to increasing student diversity in Woods Hole, as well as support two independent undergraduate research projects per year as part of the Semester in Environmental Science Program at the Marine Biological Laboratory (MBL). A workshop will be held in year 2 of the project to broaden exposure of thermodynamic approaches in marine biogeochemistry and explore its place in the broader context of recent advances in metabolic modeling and theory. Ocean model code developed during the project will be open source and publicly disseminated.This project builds upon the Darwin Project, a trait and selection based modeling approach for describing marine plankton communities and biogeochemical cycles. The approach relies on local competition to select from a diverse population and determines the functional characteristics of microorganisms that mediate biogeochemical cycles. The project will combine this selection-based modeling approach with a distributed metabolic network perspective previously developed to facilitate calculating reaction thermodynamics. This will provide mechanistic and quantitative description of key metabolic functions and allow the new model to be directly mappable to omics-based observations. The project will utilize new modeling design criteria based on the maximum entropy production (MEP) conjecture to determine allocation of metabolic machinery and its expression, such as metabolic switching between nitrogen fixation and ammonium uptake. Model testing will rely on existing oceanographic surveys and observations. Once validated, the coupled model will be used to investigate losses of functional biodiversity, generalist versus specialists, temporal planktonic strategies as well as losses in community complementarity on ecosystem biogeochemistry. A significant output from the project will be a predicted global biogeography map of metabolic function and expression (such as nitrogen fixation and ammonium oxidation) that can be tested with, and used to interpret, directed omics observations.