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Advanced measurements & analyses of GHG fluxes from soils & ecosystems (AMAGS)
Provider: Faculty of Science

Activity no.: 5451-26-00-00There are 30 available seats 
Enrollment deadline: 24/06/2026
PlaceDepartment of Geoscience and Natural Resource Management
Date and time24.08.2026, at: 09:00 - 28.08.2026, at: 16:00
Regular seats30
LecturersKlaus Steenberg Larsen
Jesper Riis Christiansen
ECTS credits2.50
Contact personKlaus Steenberg Larsen    E-mail address: ksl@ign.ku.dk
Enrolment Handling/Course OrganiserPhD Administration SCIENCE    E-mail address: phdcourses@science.ku.dk
Enrolment guidelines
This is a specialised course where 50% of the seats are reserved to PhD students enrolled at the Faculty of SCIENCE at UCPH and 50% of the seats are reserved to other applicants. Seats will be allocated on a first-come, first-served basis and according to the applicable rules.

Anyone can apply for the course, but if you are not a PhD student at a Danish university (except CBS), you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.


Aim and Content
Aim:
The course will focus on teaching the students how to measure and calculate the exchange of GHG’s between the soil/ecosystem and the atmosphere using state-of-the-art chamber and analyzer technologies.
The course will highlight the conceptual, technological and analytic challenges involved in obtaining the “true” measure of the GHG flux between the soil and the atmosphere and how these data can be used to address fundamental knowledge gaps related to biogeochemical feedbacks to current and future climate.
Background: The chamber method is the most widely used for GHG flux measurements, but comes with the downside of being extremely time consuming. However, recent development in combining novel chamber design with real-time GHG analyses now allows for automation of the flux measurements using very short time scales, compared to earlier technologies. These advances now rival the temporal resolution of eddy covariance measurements often considered as the golden standard in GHG flux measurements.
This development represent a significant advantage as it is known that long measurement times using chambers severely biases the flux measurements meaning that flux quality is greatly improved. Another advantage of automated chambers is the potential to resolve spatiotemporal patterns in much higher detail than possible with other GHG flux techniques. Because chambers target small areas they can be deployed to measure spatial patterns which are highly needed to understand soil physical, chemical and biological drivers of GHG fluxes.


Content:
The course will be based on field work done at our state-of-the-art GHG facilities, Brandbjerg and Højbakkegård, where the students will be introduced to and work with highly advanced technologies to quantify exchange of greenhouse gases in agriculture, grassland/heatland and forest ecosystems (i.e. 15 h of practical exercises over two days in the field, KSL, JRC, JP, SB, AB). Automatic chamber systems in operation at the sites allow students to get an insight in to real research projects dealing with GHG exchange and will work as a basis for class room discussion and learning.
Another 15 hours will be spent working with the data obtained in the field (i.e. 15 h theoretical exercises). Remaining time during the course will be spent on lectures by RK, JP, KSL, JRC, and AB (5 h) and class instructions for the theoretical exercises and summaries by RK, JP, KSL, and JRC (5 h). The 30 hours of preparation time will be spent on reading the suggested reading and an e-learning pre-assignment (10 h, KSL and JRC) to familiarize themselves with the R software and two specific R packages typically used for calculating the GHG fluxes, i.e. the HMR package (co-developed by JP) and the goFlux package (co-developed by KSL and JRC).


Learning outcomes
Intended learning outcome for the students who complete the course:

Knowledge
• describe commonly used chamber methods and equipment for measuring greenhouse gas fluxes from soils/ecosystems/water surfaces
• demonstrate the field use of the chamber method with different gas analyzers
• discuss theory of sampling design

Skills
• work independently with the chamber methods under field conditions
• evaluate the pros and cons of using specific designs to measure greenhouse gas fluxes
• apply the sampling methodology in the field
• design a problem-oriented scientific field sampling protocol for greenhouse gas fluxes

Competences
• project-oriented group work in the field
• choose the correct techniques to obtain a representative flux of greenhouse gases
• analyze field data using graphic and statistical techniques in R
• synthesize results in a written report


Target Group
The course target group is PhD students, who wants to learn about technologies and data analytical tools for measuring and calculating the exchange of one or more greenhouse gases between soils / ecosystems and the atmosphere.
The course is relevant to many PhD students studying various aspects of plant-microbe processes, interactions, and responses to changes in land use management, pollution, and climate across multiple ecosystem types spanning from intensive agricultural systems to more complex natural ecosystems.


Recommended Academic Qualifications
The PhD student should be working with some aspect of greenhouse gas exchange between soil/water surface/ecosystem and the atmosphere in their PhD project. A master’s degree with previous experience is an advantage but not a requirement.


Research Area
It is critical for environmental scientists to quantify the major sources and sinks of the most common greenhouse gases (GHG) as well as to disentangle the processes involved in GHG exchange in terrestrial ecosystems including streams, rivers and lakes. Such data and knowledge are essential for the development of national and international strategies for sustainably managing energy production and land use.


Teaching and Learning Methods
AMAGS focuses on hands-on experience for the students by measuring the exchange of GHG’s between the soil and the atmosphere using the chamber methodology. It is a key element of the course that participant will perform fieldwork testing the theoretical basis of the course at a real field site under the guidance of the course teachers. Furthermore, it is central to the course that collected data are integrated into the theoretical exercise part of the course (i.e. 15 h in total). With this emphasis on doing science the course will highlight the conceptual, technological and analytic challenges involved in obtaining the “true” measure of the GHG flux between the soil/ecosystem and the atmosphere.
Key concepts of the course will be presented by keynote lectures by RK, JP, AB, JRC and KSL, as well as discussed on the background of presentations by the students, group work and fieldwork. The course starts with establishing a knowledge base by reviewing current literature within the research field prior to course start. This will form the basis for an active involvement of PhD students in the specific theoretical and methodological problems, how to construct a research question and carry out a field sampling design with hands-on experiments and evaluate the data collection techniques through actual analyses of field data. The course is finalized by group presentation by students and a written report submitted after the course presenting and discussing the collected data and results.
The proposed PhD course expands the scope of our collaboration with RK by taking advantage of his unique competences in biogeochemistry and GHG measurements with his expertise as a teacher.


Type of Assessment
Participants must hand in a written report summarizing and discussing the results of data obtained and analysed during the course


Literature
Manual chambers:
Christiansen, J. R., Korhonen, J. F. J., Juszczak, R., Giebels, M., & Pihlatie, M. (2011). Assessing the effects of chamber placement, manual sampling and headspace mixing on CH4 fluxes in a laboratory experiment. Plant and Soil, 343(1–2), 171–185. https://doi.org/10.1007/s11104-010-0701-y.
Pihlatie, M. K., et al. (2013). Comparison of static chambers to measure CH4 emissions from soils. Agricultural And Forest Meteorology 171-172: 124-136. 10.1016/j.agrformet.2012.11.008
Xu, L., Furtaw, M. D., Madsen, R. A., Garcia, R. L., Anderson, D. J., & McDermitt, D. K. (2006). On maintaining pressure equilibrium between a soil CO2 flux chamber and the ambient air. Journal of Geophysical Research Atmospheres, 111(8), 1–14. https://doi.org/10.1029/2005JD006435.
Christiansen, J. R., Outhwaite, J., & Smukler, S. M. (2015). Comparison of CO2, CH4 and N2O soil-atmosphere exchange measured in static chambers with cavity ring-down spectroscopy and gas chromatography. Agricultural and Forest Meteorology, 211–212, 48–57. https://doi.org/10.1016/j.agrformet.2015.06.004.
Thalasso, F., Riquelme, B., Gómez, A., Mackenzie, R., Aguirre, F. J., Hoyos-Santillan, J., Rozzi, R., and Sepulveda-Jauregui, A.: Technical note: Skirt chamber – an open dynamic method for the rapid and minimally intrusive measurement of greenhouse gas emissions from peatlands, Biogeosciences, 20, 3737–3749, https://doi.org/10.5194/bg-20-3737-2023, 2023.

Automated chambers:
Brændholt, A., Larsen, K.S., Ibrom, A., and Pilegaard, K.: Overestimation of closed-chamber soil CO2 effluxes at low atmospheric turbulence, Biogeosciences, 14, 1603–1616, https://doi.org/10.5194/bg-14-1603-2017, 2017.
Lee, JS. Comparison of automatic and manual chamber methods for measuring soil respiration in a temperate broad-leaved forest. j ecology environ 42, 32 (2018). https://doi.org/10.1186/s41610-018-0093-0.
Flux calculation:
Hutchinson, G. L., & Mosier, A. R. (1981). Improved Soil Cover Method for Field Measurement of Nitrous Oxide Fluxes. Soil Science Society of America Journal, 45(2), 311. https://doi.org/10.2136/sssaj1981.03615995004500020017x.
Pullens J.W.M., etal. (2023) Identifying criteria for greenhouse gas flux estimation with automatic and manual chambers: A case study for N2O. European journal of soil science, 74:e13340. https://doi.org/10.1111/ejss.13340.
Rheault et al. (2024). goFlux: A user-friendly way to calculate GHG fluxes yourself, regardless of user experience. Journal of Open Source Software, 9(96), 6393. https://doi.org/10.21105/joss.06393 (https://qepanna.quarto.pub/goflux/)
Hüppi, R., Felber, R., Krauss, M., Six, J., Leifeld, J., & Fuß, R. (2018). Restricting the nonlinearity parameter in soil greenhouse gas flux calculation for more reliable flux estimates. PLOS ONE, 13(7), e0200876. https://doi.org/10.1371/journal.pone.0200876.
Chamber guideline papers (for reference):
Pavelka M., et al (2018) Standardisation of chamber technique for CO2, N2O and CH4 fluxes measurements from terrestrial ecosystems. International Agrophysics, 32, 569-587. doi: 10.1515/intag-2017-0045.
Maier M., et al. (2022) Introduction of a guideline for measurements of greenhouse gas fluxes from soils using non-steady-state chambers. J. Plant Nutr. Soil Sci. 2022;185:447–461. doi: 10.1002/jpln.202200199.


Course coordinator
Klaus Steenberg Larsen (KSL), Associate Professor, ksl@ign.ku.dk
Jesper Riis Christiansen (JRC), Associate Professor, jrc@ign.ku.dk


Guest Lecturers
RK (Senior scientist and head of division at Karlsruhe Institute of Technology, IMK-IFU, Germany) is an expert on GHG measurements (CO2, CH4 and N2O) and feedback mechanisms of global environmental changes on terrestrial ecosystems. He has worked for >25 years with measuring and modelling C and N turnover and associated matter fluxes in natural and managed ecosystems at site and landscape scale. RK contributes to the course with lectures and instructions during theoretical exercises.

JP (Tenure Track Assistant Professor, Dept. of agroecology, Aarhus University) is an expert on eddy co-variance measurements of GHG exchange as well as on the calculations of fluxes using R software and flux calculation packages. In particular, an expert on the HMR package, where he was a co-developer of the latest version. JP contributes to the course with lectures and instructions during theoretical exercises as well as partially in the field.

The proposed PhD course expands the scope of our collaboration with both RK and JP by taking advantage of their unique knowledge in the field of biogeochemical cycling of ecosystems and GHG measurement expertise.


Dates
24 – 28 August 2026


Course location
KU-IGN, Rolighedsvej 23, 1958 Frederiksberg C – and at field sites in Jægerspris and at Højbakkegård.



Course fee
• Participant fee: 1000 DKK (All participants)
• PhD student enrolled at SCIENCE: 0 DKK
• PhD student from Danish PhD school Open market: 0 DKK
• PhD student from Danish PhD school not Open market: 3000 DKK
• PhD student from foreign university: 3000 DKK
• Master's student from Danish university: 0 DKK
• Master's student from foreign university: 3000 DKK
• Non-PhD student employed at a university (e.g., postdocs): 3000 DKK
• Non-PhD student not employed at a university (e.g., from a private company): 8400 DKK

Cancellation policy
• Cancellations made up to two weeks before the course starts are free of charge.
• Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000
• Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000
• No-show will result in a fee of DKK 5.000
• Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000

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PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types.
In addition to the course fee, there might also be a participant fee.
If the course has a participant fee, this will apply to all participants regardless of participant
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