Data underlying the PhD thesis: The Pulse of Metabolism: Analysing “Candidatus Accumulibacter” dynamic flows

***Data underlying the PhD thesis: The Pulse of Metabolism: Analysing “Candidatus Accumulibacter” dynamic flows"***Authors: T. Paez-Watson, M.C.M. van Loosdrecht, S. A. WahlDepartment of Biotechnology, Faculty of Applied Sciences, Delft University of Technology<br><br>*** General description ***Data that has been used for the publication of the PhD thesis.<br>All software and simulation data has been previously published with each chapter in GitHub. This dataset includes non-available experimental data from the reactor analysis of each publication.<br><br>References from publication:<br>- https://pubs.acs.org/doi/10.1021/acsestwater.4c00247?r- Metabolic implications for dual substrate growth in “Candidatus Accumulibacter”. Article under review in Environmental Science and Technology<br><br>This work was supported by SIAM Gravitation Grant 024.002.00, the Netherlands Organization for Scientific Research (NWO).<br><br><br>*** Data collection and file description ***<br>1) ------ Sweet Secrets qFISH ------<br>Microscopic images from the 2 bioreactor enrichments of "Candidatus Accumulibacter"probed with the FISH oligonucleotides PAOmix, GAOmix and EUBacteria. Together with the FISH images, the python code that was developed and used to quantify the cellsof different colors for qFISH. More details regarding the experiments and the microscopic images at:are available at https://doi.org/10.1021/acsestwater.4c00247?urlappend=%3Fref%3DPDF&amp;jav=VoR&amp;rel=cite-as<br><br>2) ------ Sweet Secrets Reactor Operation ------<br>The operational data of the long term bioreactot enrichments run for the publication.Both bioreactor enrichments were operated under the exact same parameters except for the rotational speed at 400 and 800 rpms respectively. <br>Available files:- Time_samples.xsls Cycle analyses on the reactors at steady state- TSS.VSS measurements on the biomass concentration of the reactors over time- HPLC results.xsls HPLC results and phosphate measurements of cycle analysis.<br><br>3) ------ Experiments Mix Substrates ------<br>The operational data of the long term bioreactor enrichment run for the publication.Bioreactor was enriched under acetate as the only carbon source, but was tested in batch mode for it's uptake capacities of acetate, aspartate and a mix. Files containdata regarding the batch tests with mixed substrate.<br>Available files:- FISH images of the community- Cycle studies performed in January and February during problems of the reactor operation.- Batch tests 2023. Batch tests of the mixed substrates. Results indicate PHAs, glycogen, polyphosphate and acetate/aspartate consumption over time.

** 博士论文配套基础数据集：《代谢脉动：解析“候选积磷菌属（Candidatus Accumulibacter）”的动态代谢流》**
作者：T. Paez-Watson、M.C.M. van Loosdrecht、S. A. Wahl
代尔夫特理工大学应用科学学院生物技术系

** 数据集概述 **
本数据集为对应博士论文所使用的全部实验数据。所有软件代码与仿真数据已随论文各章节在GitHub平台公开发表。本数据集包含各已发表论文中未公开的反应器分析实验原始数据。

参考文献：
- https://pubs.acs.org/doi/10.1021/acsestwater.4c00247?r 《“候选积磷菌属（Candidatus Accumulibacter）”双底物生长的代谢启示》，目前已提交至《Environmental Science and Technology》期刊待审。

本研究得到SIAM引力项目基金（编号024.002.00）与荷兰科学研究组织（NWO）资助。

** 数据收集与文件说明 **
1) **“甜蜜机密”系列定量荧光原位杂交（qFISH）实验**
包含两批经PAOmix、GAOmix及EUBacteria荧光原位杂交（Fluorescence In Situ Hybridization, FISH）寡核苷酸探针标记的“候选积磷菌属（Candidatus Accumulibacter）”生物反应器富集物的显微图像。同步配套用于量化qFISH图像中不同颜色细胞数量的自研Python代码。实验与显微图像的详细信息可访问：https://doi.org/10.1021/acsestwater.4c00247?urlappend=%3Fref%3DPDF&jav=VoR&rel=cite-as

2) **“甜蜜机密”反应器运行数据**
包含为发表论文开展的长期生物反应器富集实验的运行参数。两批生物反应器富集实验除转速分别设置为400与800转每分钟外，其余运行参数完全一致。
可用文件：
- `Time_samples.xsls`：反应器稳态条件下的周期分析数据
- `TSS.VSS measurements`：随时间变化的反应器生物质浓度总悬浮固体（TSS）、挥发性悬浮固体（VSS）检测结果
- `HPLC results.xsls`：周期分析的高效液相色谱（High Performance Liquid Chromatography, HPLC）检测结果与磷酸盐浓度数据

3) **混合底物实验**
包含为发表论文开展的长期生物反应器富集实验的运行数据。该反应器以乙酸盐作为唯一碳源进行富集，但后续以批次模式测试了其对乙酸盐、天冬氨酸及混合底物的摄取能力。本部分文件包含混合底物批次实验的相关数据。
可用文件：
- 群落荧光原位杂交图像
- 反应器运行故障期间1月与2月开展的周期研究数据
- 2023年批次测试：混合底物的批次实验数据，结果涵盖聚羟基脂肪酸酯（PHAs）、糖原、聚磷酸盐及乙酸盐/天冬氨酸随时间的消耗情况。