Biogenic Gas Bubbles Produced within Soil Macropores

Simultaneous measurement of gas bubble size and CO2 concentration with VisiSens A3

Yuhong He, Cameron Proctor, and Alex Tong
Department of Geography and Planning, University of Toronto, Canada

Greenhouse gas measurements in wetlands note considerable spatial and temporal variability in biogenic gas bubbles, suggesting microscale heterogeneities influence formation and realease. However, traditional techniques can only measure volumes several orders of magnitude greater than individual gas bubbles. To inspect discrete bubbles in the laboratory and field, the VisiSens™ A3 system was utilized against gas bubbles from highly organic wetland soils. Biogenic bubbles from an anaerobically incubated soil core ranged in size from 0.02 - 2 mL and revealed a CO2 concentration range from 0.7 - 8.5 %, even between adjacent bubbles less than 5 cm apart. Biogenic gas bubbles associated with ebullition events from a stagnant pond could also be quantified by VisiSens™ A3 in the field, offering a unique opportunity to coincidentally record ebullition timing, size and CO2 concentration at previously unavailable fidelity.

Owing to the predominance of anaerobic conditions, wetlands are the strongest biogenic contributors to atmospheric emissions of greenhouse gases. Organic matter decomposes in saturated soil primarily through methanogenesis, generating methane, carbon dioxide, hydrogen sulphide and hydrogen as biogenic gases. Over time the gases accumulate forming a separate gas phase that eventually coalesces into bubbles trapped within the soil macropore spaces. Pressure changes can trigger the release of trapped bubbles, allowing the gases to escape past the sediment-atmosphere interface in an event known as ebullition. Understanding biogenic gas and ebullition processes is challenging because the scale at which the controlling variables are measurable (landscape to plot) is mismatched with the scale of biogenesis (microscale). Gradients in soil structure and composition have been implicated in influencing multiple biogenic gas processes such that gas concentrations in evolved bubbles are spatially heterogeneous. However, the strength of the relationship between explanatory variables and the build-up and release of gases within the soil matrix has not been quantified. Recently, there has been considerable interest in investigating biogenesis processes at microscale in order to explain the variability witnessed at larger scales. Traditional technologies provide little information on the distribution of gases in the soil at microscales and are therefore of little use in helping understand biogenic gas bubble dynamics. In contrast, the VisiSens™ system has no minimal sample volume and permits 2-dimensional visualization and development of CO2 concentration profiles from objects down to 20 µm. This novel technology may permit the examination of biogenic gas bubbles at scales previously unavailable. Our primary objective is to determine whether the VisiSens™ A3 system can assess individual biogenic gas bubbles and to utilize this system to examine their CO2 concentration conformity or heterogeneity in relation to variables such as bubble size, depth of bubble formation and proximity to sources of labile carbon. Our secondary objective is to assess the utility of the VisiSens™ A3  system for monitoring ebullition events in the field.

Materials & Methods

A soil core was extracted from Cranberry Marsh, Ontario, Canada. The sediment was primarily comprised of sand with high concentrations of organic matter from detritus captured during flood events. The core was extracted from sediment below the water table and promptly incubated for 30 days to allow anaerobic conditions to develop. Water levels were maintained at + 2 cm over the sediment for the duration of the experiment. A plastic syringe was used to extract soil water containing the biogenic gas bubbles from the sediment. A separation vessel (Fig. 1 B) was constructed out of long glass tubes filled with CO2 free water. The sensor foil (SF-CD1R, PreSens) was attached to one end of the separation vessel with a thin layer of Kwik-Sil epoxy. Care was taken to ensure sufficient epoxy was utilized to guarantee a good seal around each tube end. For measurements the separation vessel was immersed in a large water reservoir, inverted such that gases could escape out of the unsealed end, and then righted under water to ensure no gases re-entered the tubes. The camera was mounted on top facing towards the separation vessel. The distance of camera and sensor foil was adjusted such that the ends of four tubes (shape drawn in permanent marker, Fig. 1 A) were within the camera´s field of view. Four bubbles were extracted from the soil core in rapid sequence. The VisiSens™ AnalytiCal 3 software was utilized to record images every 10 seconds for 6.6 minutes (40 pictures). Once a few baseline pictures were captured the four bubbles were injected in sequence into a unique tube of the separation vessel (one bubble per tube). To monitor ebullition events, a modified set-up was placed in a stagnant pond for four hour duration. The separation vessel was replaced by a funnel ending at the SF-CD1R sensor foil. Not subdividing the foil by tubes allowed biogenic gas bubbles of larger size to be assessed. Large bubbles had previously been visually witnessed to occur. A four hour measurement with 10 second picture capture interval was conducted. The funnel was checked for captured ebullition bubbles every 10 minutes. After a bubble was captured, the camera was permitted to take approx. 7 pictures. Afterwards the funnel was tipped to eject the ebullition bubble and then placed back in position.


Gas bubbles tended to form throughout the soil core in all macropore spaces, with the largest bubbles present in the spaces near organic matter as opposed to hot spots of high sand concentration. Gas bubbles conformed to the irregular shape of the macropores and bubble size ranged from 0.02 - 20 mL. Over 40 bubbles were extracted and successfully assessed via VisiSens™. Overall, the CO2 concentrations within gas bubbles ranged from 0.7 - 8.5 % of air volume. Although it was not uncommon for adjacent bubbles to have similar CO2 concentrations, spatial heterogeneity at spatial scales less than 5 cm was observed (Fig. 2). Bubble size appeared to be negatively related to CO2 suggesting larger bubbles may permit more CO2 accumulation, possibly due to the longer residence time of the bubble in the soil matrix. Depth of bubble formation also appeared correlated to CO2 concentration, with deeper soil featuring lower CO2 concentration in formed bubbles. Top layers of sediment typically feature freshly deposited organic matter which is very labile compared to the partially decayed matter in deeper sediments whose labile components were preferentially consumed. Field monitoring over the four hour period captured three ebullition events within the column of water underneath the funnel. The first event occurred at 54 minutes. Two small ebullition bubbles precede the emission of a large bubble much greater than the surface area of the sensor foil. The CO2 concentration of the initial bubbles is not much greater than the dissolved concentration in the pond water. The latter bubble is much larger, and consumes the initial bubbles. The second event occurs after 2 hours and 41 minutes of monitoring. A small ebullition bubble of high CO2 concentration can be discretely observed. The last ebullition observation occured shortly after, at three hours and one minute. Picture quality during this event was hindered by upstream sedimentation increased due to higher outflow from a weir.


Utilizing the VisiSens™ system, the CO2 content of individual biogenic gas bubbles was determined. To our knowledge this is the first instance in which individual bubbles have been quantified. Thus, the VisiSens™ system represents a novel new approach for investigating biogenic gases at scales not previously available to the scientific community. Understanding how biogenic gas production and accumulation vary spatially within wetland soil is of critical importance since accumulated bubbles partially regulate the total quantity of greenhouse gases released to the atmosphere. In the future, the VisiSens™ system might become a key tool for scientists to investigate biogenic gas dynamics. In particular, the ability to assess individual bubbles is critical for microscale exploration of the links between biogenic gas production and environmental drivers. The VisiSens™ system proved to be a powerful new technology to capture ebullition events and provided valuable information about the frequency and magnitude of CO2 emission. The ability to monitor episodic ebullition while retaining the fidelity to capture crucial data about individual bubbles are two great advantages. The system is inexpensive, easy to use and could assist climate modeling efforts in the near future.


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