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
└── ...,

微生物生长常以资源摄取速率进行表征，因此对这类限速过程的理解与参数化，是微生物建模的核心关键。在光合浮游生物（phototrophic plankton）中，理论研究表明营养盐摄取受膜转运蛋白（membrane transporters）参与的机制性过程限制；已有观测证实，细胞特异性最大资源摄取速率（Vmax）与细胞大小遵循幂律关系，且Vmax与半饱和常数（Km）之间存在权衡效应。上述约束或许同样适用于化能营养微生物（chemotrophic microorganisms），但多数数据集缺乏直接的细胞大小测量数据。因此我们假设原核生物（prokaryote）的细胞大小、Vmax及Km均服从对数正态分布（log-normal distribution），并借鉴已确立的浮游植物尺度律开展研究。本团队的分析显示，化能营养生物通常展现出更高的单位干重最大摄取速率（VmaxDW）与Km……
# 关联光合与化能生物的细胞大小、Vmax与Km：贝叶斯推断的启示
本代码库包含复现该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
└── ...