Relationship between soil CO2 and other gas compositions

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CO2 and CH4 Dynamic in Critical Zone

One of the most essential zones determining the gas exchange rate is called the critical zone, where a holistic framework integrates the studies of air, soil, rock, water, and biological sources in the near-surface of the terrestrial ecosystem. These permeable layers represent complex and heterogeneous processes from the top of the tree to the aquifers’ bottom (Lin, 2010). The gas exchange within a critical zone represents a significant part of the CH4 and CO2 atmospheric budget. The figure below describes the process involved in the CO2 transfer process.
Fig 1. (A) The schematic processes diagram of soil gas CO2 in a critical zone (Hasenmueller et al., 2015) and (B) CO2 and CH4 production and consumption in soil (Dalal and Allen, 2008).
Fig 1 demonstrates that various processes are driving the soil atmosphere pCO2, which includes i) The production of CO2 by the soil microbes, ii) The diffusion of the CO2 downward to the groundwater or upward to the atmosphere, iii) the mineral dissolution causing the CO2 degassing or drawdown to pore-fluids, iv) advection of DIC (Dissolved Organic Carbon) containing fluid out or into the system, v) advection of the carbon dioxide into air-filled soil pore spaces. Soil pCO2 distribution was also found to be varied predictably with the topographic position.
The CO2 efflux (Fsoil) commonly refers to soil respiration (Rs) from the surface of the soil to the atmosphere, which may come from multiple sources, including respiration of the root system (Rr), respiration of the soil fauna, and CO2 production from non-biological source (Rn). Although both terms, Fsoil and Rs, are used interchangeably, several findings have challenged this assumption. Some argued that respired CO2 might be dissolved in soil solutions (Xu and Shang, 2016; Sánchez-Cañete, Barron-Gafford, and Chorover, 2018). The high soil pCO2 was found in a wet and deep level in swale slopes and valleys. Meanwhile, the low level of soil pCO2 was found in dry and shallow levels in planar slopes and ridges (Hasenmueller et al., 2015).
The CO2 gas exchange can be categorized into three types consisted of (i) soil respiration, which includes root and microbial respiration, (ii) ecosystem respiration involving aboveground plant respiration, and (iii) Net Ecosystem Exchange [NEE], which is the differences between photosynthesis and ecosystem respiration where the positive values reveal the soil as a source and negative value indicate a CO2 sink. As for methane, it is naturally originated from microorganisms belonging to the domain archaea when anoxic microsites are formed. Methanotrophy (oxidation of CH4) and methanogenesis (production of CH4) are two biogenic processes driving the concentration, especially in the soil compartment (Oertel et al., 2016). Three main possible transport mechanisms rule temporal and spatial variations of CH4 production within the critical zone, which include i) diffusion of dissolved CH4 along the concentration gradient, ii) the release due to ebullition (CH4 contained in the bubbles), iii) plant mediated-transport. Meanwhile, the CH4 originating from anthropogenic sources results from agriculture, waste, energy, and industrial activity (Serrano-Silva et al., 2014).


The anaerobic condition is strictly required by the CH4 producing bacteria, which correlate positively with the soil’s water content. Besides, the soil acts as a sink of CH4 during this aerobic condition (Smith et al., 2003; Gao et al., 2015; Oertel et al., 2016). The soil organic matters strongly affect the moisture content that further has a proportional effect on soil CH4 oxidation and its retention in the soil. The activity of the methanotrophs is affected by the moisture content by controlling the diffusion of the gas in and through the soil (Hiltbrunner et al., 2012; Tate, 2015). The distribution of grain size in the soil also affects the amount of moisture occupied in the soil.
Moreover, the emission of the gasses produced aerobically is fostered when the soil has a high proportion of large pores that retain less water and more oxygen (Van Der Weerden, De Klein and Kelliher, 2010). Meanwhile, The CH4 formation emitted during anaerobic conditions is more extensive in the soil whose dominant fine pore (Dutaur and Verchot, 2007). It also promotes the N2O formation during a similar anaerobic condition (Gu et al., 2013). During the warm period, the Lower CO2 emission was identified in the sandy soils compared with the fine-textured soils (Dilustro et al., 2005).
The higher soil emission was found in the unstable soil aggregates because C and N are more available for soil microbes (Kögel-Knabner et al., 2010). Precipitation contributes to the evolution of gas emission from the soil, also known as the Birch effect (Birch, 1958). Driven by the availability of readily decomposable material and renewed mineralization, the soil emission rises within minutes or hours of precipitation. Within the next few days, the level of emission returns to the baseline (Ludwig et al., 2001; Borken and Matzner, 2009). Nonetheless, this Birch effect decrease as it has a more intensive wet-dry cycle (Borken and Matzner, 2009). The decomposition of the soil organic matter has been widely reported to be influenced by high solar radiation. Also known as the photodegradation process, ultraviolet light stimulates a direct breakdown of organic matter to CO2 occurs mainly during the low moisture season (Brandt, Bonnet, and King, 2009; Yanni, Suddick and Six, 2015).


The effect of the soil temperature on the CO2 outgassing has been calculated since the early 1990s. For instance, Silvola et al., (1996) have concluded that temperature is the most critical factor controlling the outgassing of CO2 from the soil. Based on the laboratory experiment, Moore and Dalva (1993) found that the CO2 emission from the peat soil was increased more than doubled when the temperature was increased from 10 to 23 °C. The sensitivity factor of Q10 is widely used to describe the dependency of gas emissions from the soil, both biological and chemical, with the temperature change of 10°C (Berglund, Berglund and Klemedtsson, 2010) as well as an increase of the depth (Tang et al., 2003). The rise of the soil temperature causes higher soil emissions and respiration rates due to the increase of microbial metabolism. Besides, soil respiration rates affecting CH4 and N2O emissions are forced by increasing soil temperature, leading to the decrease of O2 concentration in the soil (Butterbach-Bahl et al., 2013; Oertel et al., 2016). During the field measurement campaign, even though the soil respiration rate showed an exponential increase with the temperature (Tang et al., 2003), it is difficult to distinguish the degree of moisture and temperature contribution due to their overlapping effects (Fang and Moncrieff, 2001). The rates of CH4 oxidation tend to rise with the soil temperature due to its association with the enzymatic process. The higher exchange of CH4 at high altitudes is found due to rapid warming. This exchange occurs mainly from a switch between CH4 oxidation and loss with soil thawing (Serrano-Silva et al., 2014; Tate, 2015). Nonetheless, in less extreme environments, the soil temperature does not play a significant role in controlling CH4 oxidation.

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Soil pH Value

The changes in soil bacteria community can be indicated by the pH value changes that are often subject to more intensive management practice, for instance, lime and fertilizer application (Lauber et al., 2008; Tate, 2015). Even though, in general, acidic soil conditions lead to lower soil emission, the optimal pH value to optimize CH4 production (Methanogenesis) is ranging from a pH value of 4 to 7. In contrast, the oxidation of CH4 is usually identified over various pH values between 2.5 to 8 (Oertel et al., 2016). However, pH is suspected to be a less crucial controlling variable because, in some studies where most soils exhibit a soil pH’s value of 6, the consumption of atmospheric CH4 is frequently high and observed at various pH values. It is almost certain that over time methanotrophic communities in a different ecosystem can accommodate a broad range of soil pH (Tate, 2015). As for the CO2, the most massive emission was identified at neutral pH-values (Cuhel et al., 2010; Oertel et al., 2016). Moreover, insignificant correlations were found between the emission of NO and N2O and pH value (Pilegaard et al., 2006; Oertel et al., 2016).


It is a widely held view that nutrient plays an essential role in the microbial and respiratory process. The sources range from natural N and C available in the soil, atmospheric deposition, and manure or fertilizer (Oertel et al., 2016). The emission of CO2 and CH4 are mostly positively correlated with the C/N ratio (Shi et al., 2014). However, the CH4 production might be decreased in the presence of Fe3+, Mn4+, SO42−, and NO3− acting as electron donors, especially in (sub)tropical soils and paddy fields (Oertel et al., 2016). On the contrary, the N2O emission is negatively correlated with the C/N-ratio (Pilegaard et al., 2006). Generally, the increase of soil N content results in higher soil respiration and higher NEE. Nonetheless, the amount of Carbon (C) is restricted, causing limited influence on soil respiration. The application of N fertilizer also affects the enormous sensitivity on soil respiration relative to the soil moisture and reversal effects again soil temperature (Peng et al., 2011).

Exposure and Air Pressure

The site exposure that may consist of the elevation, morphological position, and the plant cover affects the soil emission indirectly by influencing soil temperature. Besides, the lower air pressure encourages more significant soil emission due to reduced counter-pressure on the soil (Reicosky et al., 2008; Oertel et al., 2016). It is a widely held view that the CO2 dissolution and ventilation process plays a significant role in storing a large amount of CO2 for more than 50000 ppm of CO2 in subsurface cracks, pores, and cavities. Furthermore, it has the most significant effect on limestone and karst soil and can be transferred to the atmosphere. The impact of wind speed and wind gustiness on subsurface gas vertically and horizontally has been simulated experimentally. It is indicated that the gas transport near the wind-exposed surface is considerably affected by wind speed and wind gustiness (Poulsen, Furman, and Liberzon, 2018). However, it is unclear whether this happens on the deep layer of soil (greater than 6 m). Previous research conducted in the CCS Total pilot, Lacq-Rousse, France, on the monitoring and modeling aspects showed that the soil CO2 concentration at the deep layer of soil was negatively correlated with changes in the piezometric level groundwater in seven seasonal cycles. Specifically, the fluctuation is caused by CO2 dissolution or release process by the perched water table acting as a pump.

Land Use Changes

The land-use change plays a significant role in GHG emissions from the soils, especially when the land covered with the vegetation (forests, grass, peatlands) is converted into agricultural land. 30% to 35% of the soil carbon occupying the top 7 cm of the soil will be lost during the first 30 years after the land-use change (Degryze et al., 2004; Oertel et al., 2016). Land-use changes generally affect the quantity and the quality of the organic matter that further proportionally changes the general population of microbial biomass, including methanotroph communities and smaller methanogen. Typically, the soil organic matter changes also influence soil properties, including water retention and soil fertility. It indirectly affects the methanotroph community’s activity and the oxidation of CH4 (Tate, 2015).

Table of contents :

Chapter 1: General Introduction
1.1. Global Carbon cycle
1.2. Scientific Context of the Thesis: DEEPSURF Project
1.3. Aims of the thesis
1.4. Chapters Structure
1.5. CO2 and CH4 Dynamic in Critical Zone
1.5.1. Humidity
1.5.2. Temperature
1.5.3. Soil pH Values
1.5.4. Nutrients
1.5.5. Exposure and Air Pressure
1.5.6. Land Use Changes
1.5.7. Stand and Plant types
1.5.8. Hydrobiogeochemical Processes
1.5.9. Measurement methods for gas exchange
Chapter 2: Metrology
2.1. Fundamental and Instrumental Generalities: Application to Gas Studies
2.1.1. FTIR Spectroscopy (FTIRS)
2.1.2. Cavity Ring-Down Spectroscopy (CRDS)
2.1.3. Gas Chromatography (GC)
2.2. Laboratory Gases Analysis
2.2.1. Gas Analyzers and Gas standard Preparation
2.2.2. Calibration Strategy
2.3. Results
2.3.1. Calibration results of CO2 and CH4
2.3.2. Cross-Validation
2.4. Intermediate Conclusion
Chapter 3: Subsoil CO2 and Micrometeorological Monitoring
3.1. Introduction
3.2. Materials and Methods
3.2.1. Study site description
3.2.2. In-situ Subsoil Gases and Auxiliaries Data Measurements
3.2.3. Micrometeorological Measurement
3.2.4. Principal Component and Wavelet Analysis
3.2.5. In-situ Subsoil Gases Measurement
3.2.6. Seasonal, Daily, and Hourly Variations
3.3. Discussion
3.3.1. CO2 molar fraction dynamics
3.3.2. Analysis of Wind Turbulence and Soil moisture Content
3.3.3. Analysis of Pressure pumping Effect due to Wind Turbulence
3.4. Conclusion
Chapter 4: Long-Term Eddy Covariance Analysis
4.1. Introduction
4.2. Materials and Methods
4.2.1. The Fundamental of Eddy Covariance Technique
4.2.2. Instrumentation and Measurements
4.2.3. Data Processing
4.2.4. The flux footprint
4.2.5. Drought Index and Vegetation State
4.3. Results
4.3.1. Seasonal variations in environmental variables
4.3.2. Variations of Carbon Exchange
4.3.3. Vegetation State
4.3.4. Thinning and Fluxes
4.4. Discussion
4.4.1. Soil and atmospheric dryness across the years
4.4.2. Ecosystem Respiration Responses
4.4.3. Gross Primary Productivity Response
4.5. Intermediate Conclusion
Chapter 5: Subsoil Gases and Eddy Covariance Analysis
5.1. Introduction
5.2. Materials and Methods
5.2.1. CO2 storage calculation
5.2.2. Ecosystem Respiration and Flux Footprint
5.2.3. Soil Gases Sampling and Analysis
5.3. Results
5.3.1. Ecosystem Respiration, CO2 Storage, and Environmental Driver Dynamics
5.3.2. Isotopic Composition
5.3.3. Relationship between soil CO2 and other gas compositions
5.4. Discussion
5.4.1. Change in Soil CO2 storage Due to Subsoil Ventilation
5.4.2. Controlling Processes on Subsoil CO2 in Temperate Forest
5.5. Conclusion
Chapter 6: General Discussion and Conclusion
7.1 Installation of Borehole Instrument
7.2. Percentage of filtered and missing data from flux tower
7.3. Half-hourly Measurement of Borehole and Flux Tower Data (2019-2020)


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