Soil Carbon

Document

Enzyme

BRENDA Enzyme Database

Expasy - ENZYME

Microbiome

微生物组实验手册：架起各领域通向微生物组世界的桥梁_Bio-protocol

Model

CBM-CFS3: Carbon Budget Model

cat-cfs/libcbm_py: Carbon budget model library based on CBM-CFS3

IBIS: ORNL DAAC INTEGRATED BIOSPHERE SIMULATOR MODEL (IBIS), VERSION 2.5

ED2: GitHub - EDmodel/ED2: Ecosystem Demography Model

Ecosystem heterogeneity determines the ecological resilience of the Amazon to climate change | PNAS | 生态系统异质性决定了亚马逊对气候变化的生态复原力
GMD - The biophysics, ecology, and biogeochemistry of functionally diverse, vertically and horizontally heterogeneous ecosystems: the Ecosystem Demography model, version 2.2 – Part 2: Model evaluation for tropical South America

ROTHC: Rothamsted Carbon Model (ROTHC) | Rothamsted Research

Theoretical Ecosystem Ecology | Run the RothC model for a site

Python version of RothC Official Rothamsted Research Release

DNDC: GRAMP: Home (ags.io)

Global DNDC Network

MIMICS: GitHub - wwieder/MIMICS: MIMICS Code Repository

GMD - Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0) GMD - Modeling boreal forest soil dynamics with the microbially explicit soil model MIMICS+ (v1.0)

Millennial Version 2: Improved global-scale predictions of soil carbon stocks with Millennial Version 2 - ScienceDirect

rabramoff/Millennial: This is a repository for the newly developed Millennial model

APSIM: APSIMInitiative/APSIM710： APSIM | APSIM

APSIMInitiative/ApsimX: ApsimX is the next generation of APSIM

⭐Yasso: Soil carbon model Yasso - Finnish Meteorological Institute

Century Model: Century – Natural Resource Ecology Laboratory at Colorado State University

ICBM: Olof Andrén: Ecology, Environmental Conservation & Soil Biology

rCTOOL: francagiannini/rCTOOL: C-TOOL a simple and flexible SOM turnover model

Modelling and validating soil carbon dynamics at the long-term plot scale using the rCTOOL R package - ScienceDirect

CASMOFOR: CASMOFOR - CArbon Sequestration MOdel for FORestations

CO2Fix: EuropeanForestInstitute/CO2Fix-distribution: CO2Fix model software

3-PG: 3-PG Forest Growth Model | Process Introduction

⭐iLand: iLand | startpage | 基于个体的景观森林和干扰模型

LANDIS-II: LANDIS-II Forest landscape model

The LANDIS-II Foundation

FORCCHN V2.0: JingF1/FORCCHN2_model: These files includes the run code, DLL package, and datasets of FORCCHN2 model.

GMD - FORCCHN V2.0: an individual-based model for predicting multiscale forest carbon dynamics

LPJ-GUESS Ecosystem Model: LPJ-GUESS home page at Lund University | 基于过程的动态植被-陆地生态系统模型，包含冻土、野火模块

forestat: caf-ifrit/forestat: forestat: Forest Carbon Sequestration and Potential Productivity Calculation 森林碳汇计量和潜力计算 | 森林碳汇，不包括土壤

LukeEcomod/SoilCarbon: Soil Carbon models

LukeEcomod/SpaFHy_v1: Spatial Forest Hydrology (Launiainen et al. Hydrological and Earth System Sciences, 2019)

bsulman/INTERFACE-model-experiment-synthesis: Code from soil carbon model-experiment synthesis project coming out of INTERFACE workshop

SoilR: Models of Soil Organic Matter Decomposition

Theoretical Ecosystem Ecology

Organization

VEMAP

Thesis

Black Carbon Stability In Soil

Black Carbon In Soil Organic And Mineral Matter

MODELING THE DYNAMICS OF CARBON SEQUESTRATION: INJECTION STRATEGIES, REMOBILIZATION, AND CAVITATION

Uncertainties in Soil Model Projections

OATD: Maas, Ellen DvL - Uncertainties in Soil Model Projections

Biogeochemical controls and spatial modeling of CO2 and CH4 fluxes in a complex forest landscape | 温室气体结合数字土壤制图

"Towards a paradigm shift in the modeling of soil organic carbon decomp" by Yujie He

"Three-Dimensional Water and Carbon Cycle Modeling at High Spatial-Temp" by Chang Liao

Selected Topics of Deep Learning Application in Forest Research

Microbial and Mineral Controls over Soil Carbon Cycling and Storage: Process-based Modeling, Observational Syntheses, and Global Implications

Soil carbon sequestration: factors influencing mechanisms, allocation and vulnerability

"Merging Ecology and Earth System Modeling: Biotic and Abiotic Controls" by Emily Kyker-Snowman

"The Effect of Sample Grinding on Color-based Predictions of Soil Organ" by Mason Rutgers

Article

Global turnover of soil mineral-associated and particulate organic carbon | Nature Communications | 使用DSM方法

Chengjie Ren

Code for "Global turnover of soil mineral-associated and particulate organic carbon"

Global soil organic carbon–climate interactions: Why scales matter - Jungkunst - 2022 - WIREs Climate Change - Wiley Online Library | 土壤有机碳预测的尺度

A global meta-analysis of soil organic carbon in the Anthropocene | Nature Communications | Meta分析；方法详细可参考

A trade-off between plant and soil carbon storage under elevated CO2 | Nature | 小样本Meta分析

Cesarterrer/SoilC_CO2 | 包含完整数据和代码 R Code

Global Distributions of Reactive Iron and Aluminum Influence the Spatial Variation of Soil Organic Carbon | 使用glmm.hp, 方法可参考 | CRAN: Package glmm.hp

Divergent accumulation of microbial necromass and plant lignin components in grassland soils-All Databases

氨基糖和木质素酚作为微生物坏死物质和植物木质素成分的示踪剂

Isolating organic carbon fractions with varying turnover rates in temperate agricultural soils – A comprehensive method comparison - ScienceDirect

土壤有机碳分组
作者：Somfractionation: Somfractionation
机构：Thünen: Home

SOM fractionation methods: Relevance to functional pools and to stabilization mechanisms - ScienceDirect | 土壤有机质分组，较为详细

Microbial models with minimal mineral protection can explain long-term soil organic carbon persistence | Scientific Reports

Domwoolf/Somic1 | SOMic 微生物土壤碳模型
ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)

Emergent temperature sensitivity of soil organic carbon driven by mineral associations | Nature Geoscience | 使用MIMICS-CN，代码可用

由于土壤较浅且岩石含量过高，南部的一些采样点的采样范围仅限于 60 厘米以内。在 S6 站点，由于深度为 >15 cm 的连续岩石，仅对上部 0-15 cm 进行了采样。

MBC

An extraction method for measuring soil microbial biomass C - ScienceDirect

Measurement of soil microbial biomass C by fumigation-extraction—an automated procedure - ScienceDirect

MAOM and POM

10g干土 → 0.5% 六偏磷酸钠（质量百分比） → 加入珠子 → 震荡18h → 53μm筛子冲洗 → 保留POM

mineral-associated organic matter | particulate organic matter

53-2000μm POM；<53μm MAOM

Global Change Biology | Environmental Change Journal | Wiley Online Library

10g干土 → 0.5% 六偏磷酸钠 → 加入珠子 → 震荡18h → 53μm筛子冲洗 → 保留MAOM和POM → 测定OC（盐酸熏蒸）、C/N

https://onlinelibrary.wiley.com/doi/10.1111/gcb.17070

盐酸熏蒸：12-20mg样品 → 去离子水润湿 → 25ml浓盐酸 → 放入清洗并使用HCl预处理的玻璃干燥器 → 熏蒸6-12h → 50°C干燥3h+

Soil carbon storage informed by particulate and mineral-associated organic matter | Nature Geoscience

5g 2mm干土 → 0.5% 六偏磷酸钠 → 加入珠子 → 震荡18h → 53μm筛子冲洗 → 保留MAOM和POM → 60°C干燥至恒重 → 测定OC（酸化）、N

RF方法估算LUCAS数据库中碳组分

酸化参考：Acid fumigation of soils to remove carbonates prior to total organic carbon or CARBON‐13 isotopic analysis - Harris - 2001 - Soil Science Society of America Journal - Wiley Online Library

30mg干土 → 50μL银箔胶囊，50μL水润湿 → 100mL 12M 浓盐酸 → 放入真空干燥器6-8h → 60°C干燥4h

酸化补充参考：Carbonate removal by acid fumigation for measuring the δ13C of soil organic carbon

300mg 球磨干土 → 20mL玻璃瓶，150μL去离子水润湿 → 100mL 12M 浓盐酸 → 真空干燥器80kPa → 完全去除30-56h（0-50cm） → 取出烧杯后抽真空1-1.5h排除HCl蒸汽 → 60°C干燥16h

Where and why do particulate organic matter (POM) and mineral-associated organic matter (MAOM) differ among diverse soils? - ScienceDirect

10g 2mm筛分干土 → 50ml 0.5% 六偏磷酸钠 → 震荡18h → 53μm筛子冲洗 → 保留MAOM和POM → 进一步分离2-53μm、<2μm → 测定OC（pH>7 部分HCl熏蒸72h）、N

土壤中碳相关分析方法--中国科学院东北地理与农业生态研究所分析测试部

20g 2mm筛分干土 → 100ml 0.5% (5g/L) 六偏磷酸钠 → 90r/min 震荡18h → 53μm筛子冲洗 → 保留MAOM和POM → 60°C干燥10h+（过夜） → 测定OC

Does microbial carbon use efficiency differ between particulate and mineral‐associated organic matter? - Ma - 2024 - Functional Ecology - Wiley Online Library | Xiaojuan Feng: microbial Carbon use efficiency did not consistently differ between particulate and mineral-associated organic matter – Functional Ecologists

2mm筛分干土 → 1：5 土水比 → 180r/min 震荡30min → 53μm筛子冲洗 → 冷冻干燥 → 保留MAOM和POM → 微生物培养