Data for: Linking cell size, Vmax, and Km in phototrophs and chemotrophs: Insights from Bayesian inference

Microbial growth is often described in terms of resource uptake rates, making the understanding and parameterization of these rate-limiting processes critical for microbial modeling. In phototrophic plankton, theoretical studies suggest that nutrient uptake is limited by mechanistic processes involving membrane transporters, and it has been observed that the cell-specific maximum resource uptake rate (Vmax) follows a power-law relationship with cell size, as well as a trade-off between Vmax and the half-saturation constant (Km). These constraints may also apply to chemotrophic microorganisms; however, many datasets lack direct cell-size measurements. We therefore leveraged the assumption that prokaryotic cell sizes, Vmax, and Km each follow log-normal distributions, drawing parallels with established phytoplankton scaling laws. Our analysis suggests that chemotrophic organisms generally exhibit higher maximum uptake rate per dry weight (VmaxDW) and Km ..., , , # Data for: Linking cell size, Vmax, and Km in phototrophs and chemotrophs: Insights from Bayesian inference

This repository contains all data and scripts required to reproduce the analyses and figures presented in the study.

## Directory Structure

Data_and_Programs
├── README.md
├── Original_data
│ ├── README.md
│ ├── Microbial_Parameter_database_kinetics.csv
│ └── Phytoplankton_Data
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Aost15.xlsx
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Aost16.xlsx
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Baltic.xlsx
│ ├── Marañón_et_al_2012_Ecol_Lett.xlsx
│ ├── Perrin_et_al_2015_Biogeosciences.xlsx
│ └── Rees_2014_Mar_Ecol_Prog_Ser.xls
├── Derived_data
│ ├── README.md
│ ├── chain.csv
│ ├── dataAll.json
│ ├── KmDB.csv
│ ├── logLikes.csv
│ ├── VmaxDB.csv
│ └── vol_weight.json
└── Scripts
├── README.md
├── DataProcessingAndPDFs.wl
├── Generate_Figure1.nb
├── Generate_Other_Figures.nb
├── Hartigans_dip_test.R
└── ...,

微生物生长通常以资源摄取速率进行表征，因此对这些限速过程的理解与参数化，是微生物建模的关键所在。在光合浮游生物（phototrophic plankton）中，理论研究表明其营养摄取过程受细胞膜转运蛋白介导的机械过程限制；同时已有观测显示，细胞特异性最大资源摄取速率（cell-specific maximum resource uptake rate，Vmax）与细胞大小呈幂律关系，且Vmax与半饱和常数（half-saturation constant，Km）之间存在权衡特性。上述约束或许同样适用于化能营养微生物（chemotrophic microorganisms），但多数现有数据集缺乏直接的细胞大小测量数据。为此，我们假设原核生物的细胞大小、Vmax及Km均服从对数正态分布（log-normal distributions），并结合已确立的浮游生物缩放定律开展类比分析。本分析表明，化能营养生物通常表现出更高的单位干重最大摄取速率（maximum uptake rate per dry weight，VmaxDW）与Km……

# 关联光合与化能营养生物的细胞大小、Vmax及Km：基于贝叶斯推断（Bayesian inference）的研究洞察
本仓库包含复现本研究中所有分析与图表所需的全部数据与脚本。

## 目录结构
Data_and_Programs
├── README.md
├── Original_data
│ ├── README.md
│ ├── Microbial_Parameter_database_kinetics.csv
│ └── Phytoplankton_Data
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Aost15.xlsx
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Aost16.xlsx
│ ├── Brandenburg_et_al_2018_Ecol_Lett_Baltic.xlsx
│ ├── Marañón_et_al_2012_Ecol_Lett.xlsx
│ ├── Perrin_et_al_2015_Biogeosciences.xlsx
│ └── Rees_2014_Mar_Ecol_Prog_Ser.xls
├── Derived_data
│ ├── README.md
│ ├── chain.csv
│ ├── dataAll.json
│ ├── KmDB.csv
│ ├── logLikes.csv
│ ├── VmaxDB.csv
│ └── vol_weight.json
└── Scripts
├── README.md
├── DataProcessingAndPDFs.wl
├── Generate_Figure1.nb
├── Generate_Other_Figures.nb
├── Hartigans_dip_test.R
└── ...