• Soil respiration

    Hi all,

    I am experiencing logistical difficulties downloading the soil respiration data from the EGM. Therefore, I wonder if more people are just using flux data from the spreadsheets and not downloading the curves?


    • Thumb_erika
      Almost 3 years ago

      Brill! Thanks a lot, Cécile!

    • Thumb_cg_profile_photo
      Almost 3 years ago

      That's right, we are just using flux data from the spreadsheets. You can find the code we use to convert from raw EGM data to flux data on github:
      https://github.com/OxfordEcosystemsLab/GEMcarbon.R It is called "EGM_raw_to_flux_option1" (or option 2, depending on your experimental layout - see RAINFOR-GEM manual for descriptions of options).
      Let me know if you need help, Cécile

  • Toby MarthewsCarbon dynamics of representative ecosystems in nortwestern Peruvian AmazonSoil respiration

    Master Toby,

    The EGM-4 we are using for assessing soil respiration have showed an strange behaviour during this week. In normal conditions (we assume that) the SRC chamber sounds during the pre-measurement calibration but suddenly it stopped to do that. I am not sure if that is OK, apparently the measurements look good. What do you think about it?

    Another question is regarding partitioning experiment. The manual indicates that it is necessary to measure the initial emission: putting 10cm-long-tubes on the places where it will be put the 9 tubes, moving the litter in each tube content as they correspond and then measuring the soil respiration in each one. The point what should I do if I do not have that initial measurement. Can I do the procedure beside the already-installed tubes and consider them as initial measurements?

    Hope you can help me with this.


    • Thumb_photo0133
      Over 2 years ago

      Happy new year to you!

    • Thumb_photo0133
      Over 2 years ago

      Hear the fan is a good option, we did not realize it, but we will take this into account.
      No, I do not have access to another one. In fact we have another “old/recycled one” which was used in Allpahuayo plots and stopped working in 2013. It would be great to send it to you in Oxford. Maybe people of PP Systems can do something with it. Is that possible? We bought the EGM we are using in at the end of 2013 and it had been working very well before this problem. The soda lime is still green so it is ok. I think the problem is solved, hence thank you for your help.
      We have the problem of NV in partitioning respiration experiment data of Allpahuayo. If we ran the analysis (data collected in 2011) without the NV data some values are negative and we are bricking against the wall with that. We did not know that it was needed to collect the NV, so we will collect it and look what happens next.
      Thanks for the analysis.

    • Thumb_sam_0693
      Over 2 years ago

      Hi Jhon - Happy New Year!

      As far as I'm aware, the high pitched sound has no other purpose other than to indicate that the chamber is flushing, hold in air. More important is that you can here the fan in the SRC whirring, indicating that it is working and indeed mixing the air inside the SRC.

      Do you have access to another EGM and SRC unit? If so, it would be nice to take repeat measurements and check for agreement. If not, do you know when the EGM was last serviced/re-calibrated? Have you troubleshooted everything else (p73 of manual) such as checking if the soda lime needs replacing? It should be replaced if 2/3's of it in the tube is turning brown. It's hard to know if what you are seeing is the machine or indeed real measurements, but if you suspect it to be faulty, you can send it back to Oxford and we can get it fully serviced by PP Systems for you.

      For the control experiment in order to calculate NV or pre-existing spatial variation, I don't think it matters too much that you are measuring this at a later date - we can assume that the spatial variation is the same now as it was then - perhaps just try to carry out the measurements in a similar time of year so that soil moisture levels are similar.

      As for the analysis, I will try to find out where this is described in detail and get back to you.


    • Thumb_photo0133
      Over 2 years ago

      Hi Sam,
      Sorry for the slow feedback.
      1. When I select the plot number, appears a message: “CHAMBER FLUSHING, HOLD IN AIR". At the same time, the chamber should sound for around 15 seconds but it had not been sounding. I just opened the SRC chamber and cleaned it inside and now it is sounding again. There was some dust in it. Something curious: this device is a “new one”. When I was working at Allpahuayo plots I had used a recycled one and never heard that sound, so I do not know if that is normal. The data looks a bit lower than usual but I am not sure if that is due to machine or it is a real measurement.
      2. In the last manual, there is a proportion of ambient (NV) or pre-existing spatial variation. This is measured before collar installation, so what should I do if I do not have this data. Shall I do the procedure beside the already-installed tubes and consider them as initial measurements?
      3. One last question is how to analyze the data of partitioning experiment using the protocol 2. The manual omits this chapter. I am going to set up these tubes and the protocol 2 looks interesting.

    • Thumb_sam_0693
      Almost 3 years ago

      Hi Jhon,

      I'm sat next to Toby and he asked me to try and answer this for you as I've been using them far more recently than he has.

      Firstly, when you say it sounds during pre-measurement, are you referring to the high pitched tone, or the sound of the fan flushing the chamber? I've never experienced not hearing the high pitched tone before, but I think so long as you can hear the fan flushing the chamber, that is the most important part of pre-measurement calibration and it should be OK and if the results look reasonable, then this is encouraging.

      Secondly, it sounds as though you are implementing partitioning experiment protocol 1 (with 4 sets of 9 tubes)? I'm not absolutely clear what your question is, but essentially, if you have removed litter before taking an initial emission measurement, you can replace the litter that was removed (same amount) from the tube, wait for some time and take another measurement, which will include the flux from the litter. Then you can remove the litter again, wait some time, and take another measurement. The difference between these two measurements is attributable to the litter.

      I hope this helps, but please tell me if it wasn't what you were asking for and I'll get back to you again.
      All best from Oxford,

  • Soil depth profileDendrometer bandsCoarse litter fallRAINFOR methodologiesGround coarse litter massStem respirationCensusIngrowth coresFine litter fallSoil respiration partitionningSoil respirationRhizotrons

    Dear All,

    A new version of the RAINFOR-GEM manual is now out and here is the link: http://www.tobymarthews.com/rainfor-gem-manual-v30.html (it'll move across to the permanent URL at http://gem.tropicalforests.ox.ac.uk/page/resources very soon).

    I hope this is useful!

    Best regards,

  • CensusIngrowth coresSoil respiration

    Hello again,

    As part of my job at Peruvian Amazon Research Institute (IIAP), the last December it was organized a training workshop in GEM methods for cuantifying carbon stocks and fluxes in tropical forests. Several students and professionals with climate change interest learnt our protocols.

    Pictures show part of the data collection and analysis.


    Thumb_p1020901 Thumb_p1020904 Thumb_p1020909 Thumb_p1020919 Thumb_p1020932 Thumb_p1020937 Thumb_p1020938 Thumb_p1020952 Thumb_p1020962
  • Understanding the carbon cycle of Andean ForestsCarbon dynamics from Andes to AmazonRAINFOR Intensive sitesSoil respiration

    Dear All

    Would anyone have a spreadsheet that shows how to calibrate the soil water content measured with the Hydrosense? I have taken the required measurements in the lab (weights and water contents of a determined volume of soil), and I just want to be sure about the calculations that I have to do.

    Thanks a lot!
    Have a good weekend!

  • RAINFOR methodologiesStem respirationSoil respiration partitionningSoil respiration

    Hi Jhon,
    I put a schematic of the adapter ring in Appx. II of the RAINFOR-GEM manual (footnote, p.72). If you extract that image and blow it up, you get the attached. With that, you should be able to get an adapter ring made up in any workshop (best to take an SRC-1 with you to the workshop so that they can make it fit exactly).

  • Yadvinder MalhiWalter Huaraca HuascoSoil respiration

    Another thing , we are looking for a adapter ring of the SRC-1 chamber. Anyone knows how to design it or where can I get it?

    Thanks again


  • Soil respirationTambopata

    Hi Darcy and the Tambopata team. Great work and thank you for the pictures.
    Just one comment: your soil respiration collars appear to be quite high above the ground. They could probably be half that height above the ground. Making the collars lower reduces the air space volume, and therefore increases the sensitivity of the CO2 flux measurement.
    No need to change the collars now they are installed, but in future it is good to remember this (the same goes for all the other GEM sites). Keep up the great work and I look forward to visiting Tambopata in August!

  • Soil respiration

    Hi all,
    I would like to most informations as far as soils partitioning respiration is concerned. Give some details.

  • Stem respirationSoil respirationIngrowth coresComprehensive description of the carbon cycle of African forests

    If you have had problems downloading data from your EGM-4, it may be that your computer has an old version of the PP Systems software (see message from Kathryn Jeffery). Try installing this software instead.

  • Soil respiration partitionningSoil respirationStem respirationComprehensive description of the carbon cycle of African forests

    Installing the USB to serial converter for the EGM-4

    We’ve had some installation problems with the EGM-4: these have been linked to the IOGEAR USB serial adapter (GU232A) not installing properly. Note the installation disk with the USB to serial adapter is not compatible with 64 bit operating systems. If you’re having problems installing the USB to serial adapter follow these instructions:

    1. Check your system software in System Properties; System type (32 or 64 bit) and operating system
    2. Go to this site: http://www.iogear.com/support/dm/driver/GUC232A
    3. Choose the correct driver software for your computer. Click download and when finished, unzip the zipped file and save to a known location.
    4. For Windows 7 64 bit; now plug in the USB to serial adapter to your computer (important: please remember which USB port you have used) and wait for several minutes- windows should automatically install the driver. To check, go to Computer, System Properties, Device Manager, Click next to Ports (COM and LPT) and you should see “ATEN USB to Serial Bridge”. If nothing has happened after several minutes, look in Device Manager and you should see an exclamation mark next to “USB serial converter D”; right click on this and a window should appear with an option to select the driver manually; you can navigate to the folder where you saved the driver and install it. Once it is installed you should see the name has changed to “ATEN USB to Serial Bridge in Device Manager”.
  • Soil respirationAkwasi Duah-Gyamfi

    Hi Akwasi,
    I got the following response from Dan regarding the soil moisture probes:
    The probe should be set to the "mineral" setting since the soil is mainly mineral. The organic setting is designed more for peats etc. These two settings just apply different generic conversion factors to the same raw sensor readings. These generic conversion factors are OK but ultimately, it'd be good to calibrate every sensor to the actual soils at the sites. Not sure if you've done this before but it just involves taking a big soil core, sealing the plastic tube at the bottom, inserting the sensor into the soil at the top and then gradually drying out the core. As the core dries you should take sensor readings and simultaneously weigh the entire core. Keep drying until constant mass (when all the water has evaporated), then you know the mass of the whole dry core and so can go back to the previous mass measurements and work out the mass/volume of water that had been present beforehand. There should be a good correlation (probably not 1:1 though) correlation between the sensor estimate and the directly measured soil moisture content.
    Is that clear? Let me know if you need any more assistance!
    All best

  • Soil respirationAkwasi Duah-Gyamfi

    Hi Akwasi,
    I'm afraid I don't have the answer to your question right now, but I am looking into it. Meanwhile, here is a link to the Theta Probe (ML2x) manual - ftp://ftp.dynamax.com/manuals/ML2x_Manual.pdf
    - refer to page 14 - I will get back to you in due course when I find the answer!
    All best,

  • Soil respiration

    Dear Colleagues, I have been using the TDR 100 soil moisture meter for determining volumetric water content (VWC). the instrument is not working properly and so i decided to use a Theta Probe Soil moisture sensor type ML2x. However, the ML2x has two options for taking soil moisture: % moisture mineral soil and % moisture organic soil. My question which of these options should i select to represent VWC as measured by the TDR 100?

  • Soil depth profileDendrometer bandsCoarse litter fallRAINFOR methodologiesGround coarse litter massStem respirationCensusIngrowth coresFine litter fallSoil respiration partitionningSoil respirationRhizotrons

    Apologies for cross-posting: After much debate and revisions between here and Leeds, the new version (2.2) of the RAINFOR-GEM Intensive Plots manual has now been uploaded on a new subpage of http://gem.tropicalforests.ox.ac.uk/ (see "Resources" on the left).

    This replaces the version 2.0 uploaded on GEM in February and also Dan Metcalfe's original v1.0 of the manual uploaded on http://www.geog.leeds.ac.uk/projects/rainfor/pages/manuals_eng.html (under “Measuring tropical forest carbon allocation and cycling”) and http://www.eci.ox.ac.uk/research/ecodynamics/carbon-balance.php (under “Online Materials” halfway down).

    Hope this is useful for everyone!

  • Soil respiration

    Would anyone know what does it mean when you are measuring soil respiration with the EGM and some values of T and H appear on the screen? It has happened when it has been raining.
    Thank you very much!

  • SAFE subprojectSoil respiration

    Soil respiration equipment

  • Carbon dynamics in Wytham WoodsSoil respiration

    Soil respiration