Alteromonas macleodii MIT1002 growth on and uptake of Prochlorococcus-derived metabolites

This data package contains the results from a series of experiments designed to test the response of a heterotrophic, copiotrophic, gammaproteobacterium, Alteromonas macleodii strain MIT1002, to a range of metabolites released by the phytoplankton Prochlorococcus. A. macleodii MIT1002 was isolated from co-culture with Prochlorococcus, and so we hypothesized that A. macleodii MIT1002 would be able to grow on the full range of substrates tested. Instead, we found that A. macleodii MIT1002 could only grow on a narrow range of substrates, and data suggest that this substrate specificity may be related to transporter specificity. We performed two types of experiments: growth experiments and uptake experiments. Data from growth experiments are labeled with the name of the substrate being tested (e.g., “Leu,” for leucine, or “3m2ob”, for 3-methyl-2-oxobutanoic acid). For these experiments, we grew A. macleodii MIT1002 on either pyruvate (as a positive control), a selected Prochlorococcus-related substrate, or a mix of pyruvate and the metabolite. We measured growth in 96-well plates by OD600 using a plate reader which took a measurement every 0.5h for 48h. Uptake experiments are labeled with either “KHU7” (an experiment which tested A. macleodii MIT1002 growth on and uptake of 3-methyl-2-oxobutanoic acid) or “KHU8” (an experiment which tested the A macleodii MIT1002 growth on and uptake of 3-methyl-2-oxopentanoic acid -or lack thereof). For these experiments, we measured growth by flow cytometry. We measured the change in dissolved (i.e., extracellular) metabolite concentration by filtering samples, extracting organic carbon from the filtrate by solid phase extraction, and quantifying selected metabolites from the filtrate by targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS). This data package includes the peak areas for targeted metabolites generated by LC-MS/MS, the peak areas for our standard curves used for quantification, and the dissolved metabolite concentrations quantified by this analysis. These experiments (both growth and uptake) were performed from January 2019 – June 2021, and this is a completed data package.

本数据包包含一系列实验的研究结果，旨在检测异养、富营养型γ-变形菌门（Gammaproteobacterium）菌株*Alteromonas macleodii* MIT1002对浮游植物原绿球藻（Prochlorococcus）释放的各类代谢物的响应。该菌株分离自与原绿球藻的共培养体系，因此我们曾推测其可在所测试的全部底物上完成生长。但实验结果显示，*Alteromonas macleodii* MIT1002仅能在狭窄范围的底物上生长，数据表明该底物特异性可能与转运蛋白的特异性相关。
本研究开展了两类实验：生长实验与摄取实验。生长实验的数据以所测试底物的名称进行标注（例如“Leu”代表亮氨酸，“3m2ob”代表3-甲基-2-氧代丁酸）。此类实验中，我们将*Alteromonas macleodii* MIT1002培养于三类体系：丙酮酸（作为阳性对照）、特定原绿球藻相关底物，以及丙酮酸与该代谢物的混合培养基。我们采用酶标仪在96孔板中通过测定OD600值监测菌株生长，每0.5小时采集一次数据，连续监测48小时。
摄取实验以“KHU7”或“KHU8”进行标注：其中KHU7实验检测了*Alteromonas macleodii* MIT1002在3-甲基-2-氧代丁酸上的生长与摄取情况；KHU8实验则检测了该菌株在3-甲基-2-氧代戊酸上的生长、摄取情况（或无生长/摄取现象）。此类实验中，我们通过流式细胞术监测菌株生长。我们通过过滤样本、采用固相萃取从滤液中提取有机碳，并通过靶向液相色谱-串联质谱（LC-MS/MS）对滤液中的目标代谢物进行定量，以此测定溶解态（即胞外）代谢物浓度的变化。
本数据包包含LC-MS/MS分析得到的目标代谢物峰面积、用于定量的标准曲线峰面积，以及通过该分析得到的溶解态代谢物浓度数据。本系列实验（包括生长实验与摄取实验）于2019年1月至2021年6月间完成，本数据包为完整数据集。