OCE-PRF Predicting OMZ and seasonal microbial activity from community structure using machine learning and novel measurements of ATP turnover

该奖项全部或部分由《2021年美国救援计划法案》（公法117-2）资助。海洋微生物，包括单细胞细菌、古细菌和真核生物，是海洋中碳和能量转化的主要驱动力。微生物环在将溶解的营养物质转化为生物量和向上的食物网方面的效率是由微生物群落的个体活动决定的。不幸的是，目前表征海洋环境中微生物活动的方法是有偏差的，大多数直接测量都集中在氧合水域中呼吸二氧化碳的异养微生物上。这些测量排除了在海洋营养循环中起主要作用的大量微生物的多样性，包括光合作用和化养生物，以及低氧、缺氧水域中的微生物。该项目将通过腺苷酸能量系统的新应用来测量微生物的活性，腺苷酸能量系统被所有生物体和几乎所有代谢途径所使用。这项工作将集中在加州当前生态系统的站点，具有广泛的海洋条件和可变的微生物群落。这些地点包括代表氧气最低带（OMZs）的低氧峡谷、反映东部边界流的上升流地点和时间动态的沿海地点。在计划的采样范围内，将为本科生提供支持，让他们加入船上的工作，帮助进行海水采样，并获得进行海洋学研究的经验。从这些采样工作中产生的数据集将用于开发微生物代谢（活动）的预测模型，该模型可应用于其他海洋区域，基于群落结构，丰度和地球化学参数，跨越时间和环境浓度。高产的加利福尼亚洋流生态系统受到浮游植物群落季节性演替的影响，硅藻和鞭毛藻的优势与上升流相吻合。这些浮游植物群将营养物质转化为生物量的能力对初级生产力、生物地球化学循环和微生物循环有影响。缺氧环境将微生物群落转向厌氧菌和化养菌，它们具有独特的代谢和不同的效率，将获得的碳源转化为生物量和能量。因此，微生物群落结构可能会直接影响omz中微生物环的效率，但由于采样技术的偏差，精确定义微生物活性的差异一直受到阻碍。本项目将探讨季节性上升流系统中浮游植物群落结构和丰度与能量储存、代谢率和生长率等微生物活动直接相关的假设。此外，omz中的微生物活动与厌氧代谢策略的实施直接相关，因此可以通过群落结构的变化来预测。微生物活性将通过高通量应用的能量电荷和三磷酸腺苷（ATP）周转率的新措施来表征，而微生物群落结构将通过16S和18S rRNA基因扩增子测序来定义。将进行两次专门的一日游，前往位于加利福尼亚湾的拉霍亚和斯克里普斯峡谷，并包含已知的omz。此外，微生物活动测量结果将被纳入正在进行的时间序列中，该时间序列将在加利福尼亚州拉霍亚的斯克里普斯海洋研究所码头每周两次采样微生物群落结构。从巡航和时间序列中获得的测量结果将用于开发微生物代谢的预测模型，该模型基于群落结构、丰度和地球化学参数，并使用自组织图（SOMs）和随机森林回归。因此，该项目将产生可以推广到更广泛的海洋区域的预测模型，以及具有前所未有的自然微生物活动跨时间和环境条件分辨率的数据集。该奖项反映了美国国家科学基金会的法定使命，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 award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).Marine microbes, including single-celled bacteria, archaea, and eukarya, are the main drivers of carbon and energy transformations in the ocean. The efficiency of the microbial loop at transforming dissolved nutrients into biomass and up the food web is defined by the individual activities of the microbial community. Unfortunately, current methods for characterizing microbial activities in the marine environment are biased, with most direct measurements focusing on heterotrophic microbes that respire carbon dioxide in oxygenated waters. These measurements exclude a large diversity of microbes that play major roles in ocean nutrient cycles, including photosynthesizes and chemotrophs as well as microbes in low oxygen, anoxic waters. This project will measure the activity of microbial organisms through novel applications of the adenylate energy system, which is used by all organisms and in almost all metabolic pathways. This work will focus on sites in the California Current Ecosystem with a wide range of oceanographic conditions and variable microbial communities. These locations include low oxygen canyons representative of oxygen minimum zones (OMZs), upwelling locations reflecting eastern boundary currents, and temporally dynamic coastal sites. Within the planned sampling, support will be allocated for undergraduate students to join shipboard efforts to help with seawater sampling and gain experience conducting oceanographic research. The datasets produced from these sampling efforts will be used to develop predictive models of microbial metabolism (activity) that can be applied to other oceanographic regions, based on community structure, abundance, and geochemical parameters across time and environmental concentrations.The highly productive California Current Ecosystem is subjected to seasonal successions of phytoplankton communities, with diatom and dinoflagellate dominance coinciding with upwelling. The ability of these phytoplankton groups to convert nutrients into biomass have impacts on primary productivity, biogeochemical cycles, and the microbial loop. Hypoxic environments shift the microbial community towards anaerobes and chemotrophs, which have unique metabolisms and differential efficiencies converting acquired carbon sources into biomass and energy. Therefore, the microbial loop efficiency in OMZs is likely to be directly impacted by microbial community structure, but precisely defining these differences in microbial activity has been hampered by biased sampling techniques. This project will address the hypotheses that microbial activity, in terms of energy storage, metabolic rates, and growth rates will be directly liked to and predicted by phytoplankton community structure and abundances in seasonal upwelling systems. Additionally, microbial activities in OMZs are linked directly to the implementation of anaerobic metabolic strategies and can thus be predicted by changes in community structure. Microbial activity will be characterized using high throughput applications of novel measures of the energy charge and adenosine triphosphate (ATP) turnover rates while the microbial community structure will be defined with 16S and 18S rRNA gene amplicon sequencing. Two dedicated, single day cruises to the La Jolla and Scripps Canyons located within the California Bight, and containing known OMZs will be conducted. Additionally, microbial activity measurements will be incorporated into an on-going time-series that is sampled for microbial community structure twice-a-week at the Scripps Institute of Oceanography pier in La Jolla, CA. Measurements from the cruises and time-series will be used to develop predictive models of microbial metabolism based on community structure, abundance, and geochemical parameters across time and within known OMZs using self-organizing maps (SOMs) and random forest regression. Therefore, this project will produce predictive models that can be generalized to broader ocean regions in addition to datasets with unprecedented resolution of natural microbial activity across time and environmental conditions.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.