<table><thead><tr><th>Model Name</th><th>References</th><th>Factor of weaknesses</th><th>C-Cycle Model structure</th><th>C-Cycle Scale of analysis</th><th>N-Cycle Model structure</th><th>N-Cycle Scale of analysis</th><th>Type of weaknesses</th><th>Cause of weaknesses</th><th>Possible explanation</th></tr></thead><tbody><tr><td rowspan="12"></td><td rowspan="2">Shirato and Yokazawa (2005)</td><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>General discrepancies (C)</td><td>Management</td><td>Disturbances (i.e. clearing and burning of pulled vegetation)</td></tr><tr><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td rowspan="2">Zimmermann et al. (2007)</td><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Underestimation of SOC content</td><td>Management</td><td>Slow decomposition rate of SOM in Rice when submerged soils are waterlogged and subjected to anaerobic conditions (RothC is not usable for waterlogged soil, Rice)</td></tr><tr><td>Pedo-climatic</td><td>1</td><td>0</td><td>0</td><td>0</td><td>General discrepancies (SOC)</td><td>Soil properties (general) - Climate</td><td>Soil properties - Air temperature</td></tr><tr><td rowspan="2">Liu et al. (2009)</td><td>Management</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td rowspan="3">Rampazzo Todorovic et al. (2010)</td><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Overestimation of SOC content</td><td>Management (Fertilization)</td><td>Stubble (i.e. using the conventional setting of stubble retention factor)</td></tr><tr><td>Pedo-climatic</td><td>1</td><td>0</td><td>0</td><td>0</td><td>General discrepancies (SOC content)</td><td>Soil properties (general) - Climate</td><td>Soil properties</td></tr><tr><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td></td><td>Management (Fertilization - Crop type)</td><td>Type of crop and straw</td></tr><tr><td rowspan="2">Nieto et al. (2010)</td><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Overestimation of SOC content</td><td>Management (Tillage)</td><td>C losses due to soil erosion</td></tr><tr><td rowspan="2">Xu et al. (2011)</td><td>Pedo-climatic</td><td>1</td><td>0</td><td>0</td><td>0</td><td>General discrepancies (SOC content)</td><td>Soil properties (general) - Climate</td><td>Soil properties</td></tr><tr><td>Management</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td rowspan="3">Gonzalez-Molina et al. (2011)</td><td>Pedo-climatic</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Overestimation of SOC content</td><td>Soil properties (general) - Climate</td><td>Type of ecosystem (rangelands complexity, erosion, type of soil, etc.)</td></tr><tr><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td></td><td>Management (general)</td><td>Residues, overgrazing, etc.</td></tr><tr><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td rowspan="2">Nieto et al. (2013)</td><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Overestimation of SOC content</td><td>Management (Tillage)</td><td>Tillage (erosion)</td></tr><tr><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr><tr><td rowspan="2">Wang et al. (2013)</td><td>Management</td><td>1</td><td>0</td><td>0</td><td>0</td><td>Overestimation of SOC content</td><td>Management (Fertilization)</td><td>Fertilization (N + straw)</td></tr><tr><td>Pedo-climatic</td><td>0</td><td>0</td><td>0</td><td>0</td><td>---</td><td>---</td><td>---</td></tr></tbody></table>
<table><caption>Table 7 – Analysis of type and cause of modelling weaknesses and the relative possible explanation for single modelling study. For each study, the specific factor of weaknesses and the biogeochemical cycle involved (i.e. C or N) have been considered</caption><thead><tr><th>Model Name</th><th>References</th><th>Factor of weaknesses</th><th>C-Cycle Model structure</th><th>C-Cycle Scale of analysis</th><th>N-Cycle Model structure</th><th>N-Cycle Scale of analysis</th><th>Type of weaknesses</th><th>Cause of weaknesses</th><th>Possible explanation</th></tr></thead><tbody><tr><td rowspan="2">STICS</td><td>Farina et al. (2013)</td><td>Pedo-climatic<br>Management</td><td>1<br>1</td><td>0<br>0</td><td>0<br>0</td><td>0<br>0</td><td>Under/Overestimation of GPP and Reco</td><td>Climate<br>Management (general)</td><td>Dry condition<br>Rotation with fallow</td></tr><tr><td>Schnebelen et al. (2004)</td><td>Pedo-climatic<br>Management</td><td>0<br>0</td><td>0<br>0</td><td>1<br>1</td><td>0<br>1</td><td>Overestimation of soil N absorption</td><td>Soil properties (general)<br>Management (Crop type)</td><td>Type of soil (soil lying on cryoturbated material cannot be parametrized).<br>Type of crop (inadequate predication root density in some particular soil i.e. cryot.)</td></tr><tr><td rowspan="3">Justes et al. (2009)</td><td>Pedo-climatic<br>Management</td><td>0<br>0</td><td>0<br>0</td><td>0<br>1</td><td>0<br>0</td><td>---<br>Underestimation of N mineralization</td><td>---<br>Management (Fertilization)</td><td>---<br>Default values of the decomposition module (Analysis on 25 catch crops residues).</td></tr><tr><td>Pedo-climatic<br>Management</td><td>0<br>0</td><td>0<br>0</td><td>0<br>0</td><td>0<br>0</td><td>---<br>General discrepancies (N mineralization and organic N sequestered in soil)</td><td>---<br>Management (Fertilization)</td><td>---<br>Lack of sensitivity of N uptake to N mineralization (lack of synchrony between extra mineralization due to catch crops and crop N demand in the model).</td></tr><tr><td>Constantin et al. (2012)</td><td>Management</td><td>0<br>0</td><td>0<br>0</td><td>1<br>1</td><td>0<br>0</td><td></td><td></td><td></td></tr></tbody></table>
**Figure captions**

Figure 1 – Top-down approach focused at gaining insight into compositional sub-systems of the most important processes and approaches implemented into the 9 biogeochemical models used in the analysis. Classification was built according to three levels of detail: i) Low: five general classes (level 1); ii) Medium: 20 main processes (level 2); iii) High: 196 approaches (methods/options/components, level 3).
<table><caption>Fig. 1</caption><thead><tr><th colspan="3">Level 1 – General Classes</th></tr></thead><tbody><tr><td>Mostly simulated discrete units considered in agricultural modelling<br/>N° of units: 5<br/>Level of detail: LOW</td><td colspan="2">Level 2 – Main Processes</td></tr><tr><td></td><td>Mostly simulated main processes considered in agricultural modelling<br/>N° of processes: 20<br/>Level of detail: MEDIUM</td><td>Level 3 – Main approaches</td></tr><tr><td></td><td></td><td>Mostly simulated modelling approaches considered in agricultural modelling<br/>N° of approaches: 196<br/>Level of detail: HIGH</td></tr></tbody></table>