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

该奖项的全部或部分资金来自《2021年美国救援计划法案》(公法117-2)。海洋微生物，包括单细胞细菌、古生菌和真核细菌，是海洋碳和能源转化的主要驱动力。微生物环路将溶解的营养物质转化为生物量并沿食物链向上的效率由微生物群落的个体活动决定。不幸的是，目前表征海洋环境中微生物活动的方法是有偏见的，大多数直接测量侧重于在含氧水域中呼吸二氧化碳的异养微生物。这些测量排除了在海洋营养循环中发挥主要作用的大量微生物，包括光合作用和化学营养素，以及低氧、缺氧水域中的微生物。该项目将通过腺苷能量系统的新应用来测量微生物的活动，所有有机体和几乎所有的代谢途径都使用腺苷能量系统。这项工作将集中在加州当前生态系统中具有广泛海洋条件和可变微生物群落的地点。这些地点包括以氧气最少区(OMZ)为代表的低氧峡谷、反映东部边界流的上升流地点，以及时间上动态的沿海地点。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，并获得开展海洋研究的经验。这些采样工作产生的数据集将被用来开发微生物代谢(活动)的预测模型，该模型可以应用于其他海洋区域，基于群落结构、丰度和随时间和环境浓度变化的地球化学参数。加州目前的高生产力生态系统受到浮游植物群落的季节性演替，硅藻和甲藻的优势与上升流相吻合。这些浮游植物群体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都有影响。低氧环境使微生物群落转向厌氧菌和趋化菌，它们具有独特的新陈代谢和不同的效率，将获得的碳源转化为生物质和能源。因此，OMZ中的微生物环效率可能直接受到微生物群落结构的影响，但准确确定微生物活动的这些差异一直受到有偏见的采样技术的阻碍。这个项目将解决这样的假设，即在能量储存、代谢率和生长率方面的微生物活动将直接受到季节性上升流系统中浮游植物群落结构和丰度的影响和预测。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能量电荷和三磷酸腺苷(ATP)周转率的新测量来表征，而微生物群落结构将通过16S和18S rRNA基因扩增序列来确定。将进行两次专门的、单日航行，前往位于加利福尼亚州海湾内的拉霍亚峡谷和斯克里普斯峡谷，其中包含已知的OMZ。此外，微生物活性测量将被纳入正在进行的时间序列中，该时间序列每周在加利福尼亚州拉霍亚的斯克里普斯海洋研究所码头进行两次微生物群落结构采样。来自游轮和时间序列的测量将被用来利用自组织映射(SOM)和随机森林回归，基于随时间和已知OMZ内的群落结构、丰度和地化参数开发微生物新陈代谢预测模型。因此，除了具有前所未有的自然微生物活动随时间和环境条件的分辨率的数据集之外，该项目还将产生可推广到更广泛海洋区域的预测模型。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.