NSF-BSF: Cell death, metabolism and the emergency of long-term survival through microbial interactions in Prochlorococcus, a globally abundant marine model cyanobacterium

该项目旨在了解微生物细胞因营养饥饿而死亡-这是生物学中一个基本而复杂的过程。这一点至关重要，因为微生物及其分子过程会对更广泛的生态系统产生重大影响，对地球化学和地球气候产生重大影响。当微生物细胞死亡时，它们会释放出分子，这些分子可以喂养其他生物体，或者作为强大的有机物质存在于环境中。在这个研究项目中，研究人员将专注于原绿球藻的细胞死亡，原绿球藻是一种广泛分布的海洋光合微生物，对海洋生物地球化学循环至关重要，其死亡率知之甚少。拟议的研究将结合联合收割机创新的计算模型和实验室实验，以研究细胞代谢和细胞死亡之间错综复杂的相互作用，死亡后细胞生物量的命运，以及原绿球藻和其他细菌之间的相互作用如何影响原绿球藻死亡率。这项研究的结果将有助于阐明海洋中有机物质的命运，有助于我们了解海洋动力学，并对应对新出现的疾病和环境可持续性等全球挑战产生影响。此外，该项目以其融合生物学、生物化学、物理学和生态学的综合方法，为前沿的跨学科研究铺平了道路。除了直接的科学影响，这项奋进将促进学生的科学素养。特别是，该项目将开发一个以探索为重点，基于网络和实地的教育计划，向来自低收入家庭的初中和高中学生介绍微生物学，环境科学和海洋学的关键概念，旨在帮助他们成功地接受STEM高等教育。当微生物细胞死亡时，它们的生物量被释放出来，促进其他生物的生长，或者作为持久的、可分解的有机物留在生态系统中。反过来，与共存生物的代谢相互作用可以缓解营养饥饿，降低死亡率。虽然我们对一些模式生物用来减少营养胁迫和延缓死亡的机制了解很多，但细胞死亡过程本身仍然是一个“黑匣子”。具体而言，很少有人知道如何通过特定的代谢途径减少流量诱导细胞活力的损失。此外，目前还不清楚微生物相互作用如何有助于降低死亡率和促进微生物生态系统的紧急恢复力。该项目将整合基因组规模的代谢建模和实验室实验，包括通量分析，使用丰富的海洋蓝藻原绿球藻和两个异养伙伴-交替单胞菌和Roseovarius。要解决的三个主要问题是：（i）导致细胞死亡的代谢条件是什么？(ii)当细胞死亡时，细胞生物量的命运如何？和，（iii）什么是代谢的相互作用，一些异养菌（交替单胞菌），但不是其他（玫瑰），降低原绿球藻死亡率？该研究项目的关键是在基因组规模的通量平衡分析（FBA）模型中开发极端饥饿和死亡的新数学公式。然后将通过详细测量细胞的生理学、其生化组成和周转、基因表达以及大分子和代谢物的关键细胞内和细胞环境通量，对模型进行实验验证。该项目将揭示生物体生命周期的重要组成部分，细胞死亡，以及有机物质的命运和周转，这对生物地球化学循环有重大影响。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project aims to understand the death of microbial cells due to nutrient starvation - a fundamental yet complex process in biology. This is crucial as microbes and their molecular processes significantly impact the broader ecosystem, with major implications for biogeochemistry and Earth’s climate. When microbial cells die, they release molecules that may feed other organisms or persist in the environment as robust organic matter. In this research project, the investigators will focus on cell death of Prochlorococcus, a widespread marine photosynthetic microbe critical to oceanic biogeochemical cycles, and whose mortality is poorly understood. The proposed research will combine innovative computational modelling and laboratory experiments to examine the intricate interplay between cellular metabolism and cell death, the fate of cellular biomass after death, and how interactions between Prochlorococcus and other bacteria affect Prochlorococcus mortality. The results of this research will help illuminate the fate of organic matter in the ocean, contributing to our understanding of oceanic dynamics, with implications for addressing global challenges such as emerging diseases and environmental sustainability. Furthermore, the project, with its integrated approach bridging biology, biochemistry, physics, and ecology, paves the way for cutting-edge interdisciplinary research. Beyond the immediate scientific impact, the endeavor will foster scientific literacy among students. In particular, the project will develop an exploration-focused, web- and field-based educational program, that introduces key concepts in microbiology, environmental sciences and oceanography to intermediate- and high-school students from low-income backgrounds, with the goal of helping them pursue successful higher education in STEM.When microbial cells die, their biomass is released, fueling growth of other organisms, or remaining in the ecosystem as long-lasting, recalcitrant organic matter. In turn, metabolic interactions with co-occurring organisms can alleviate nutrient starvation, reducing mortality. While much is known about the mechanisms employed by some model organisms to reduce nutrient stress and delay mortality, the process of cell death itself remains a “black box”. Specifically, little is known about how reduction of flux through specific metabolic pathways induces the loss of cell viability. Moreover, it is still unclear how microbial interactions can help reduce mortality and promote the emergent resilience of microbial ecosystems. The project will integrate genome-scale metabolic modelling and laboratory experiments, including flux analysis, using the abundant marine cyanobacterium Prochlorococcus and two heterotrophic partners – Alteromonas and Roseovarius. The three major questions to be addressed are: (i) What are the metabolic conditions leading to cell death?; (ii) What is the fate of cell biomass as the cells die?; and, (iii) What are the metabolic interactions with some heterotrophs (Alteromonas) but not others (Roseovarius) that reduce Prochlorococcus mortality? Key to the research project is the development of new mathematical formulations of extreme starvation and death within genome-scale, flux balance analysis (FBA) models. The models will then be validated experimentally, through detailed measurements of the physiology of the cells, their biochemical composition and turnover, gene expression and key intracellular and cell-environment fluxes of macromolecules and metabolites. This project will shed light on an important part of an organism's life cycle, cell death, and the fate and turnover of organic matter, which has major implications for biogeochemical cycling.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.