• J. R. Jones added an answer:
    How does one collect pore water samples from coal seams and is there any standard protocol?

    Aerobic and anaerobic conditions.

    J. R. Jones · Massey University

    Presumably the coal seam is not saturated with water.  If it were, then a core will fill with water simply due to the pressure gradient.  For an unsaturated coal seam, using a double action pressure swing to first locally infuse the seam with water, then extract it, will obtain enough for later analysis.  A device will need to be invented for this purpose to lower into the core, however.  The alternative is to extract a core sample and then analyse in the laboratory.


    Jim R. Jones

  • Luiz Carlos Cotovicz Junior asked a question:
    What are the thresholds of DO supersaturation that can make possible the spontaneous bubble formation?

    The high primary production at hypertrophic environmentals  can produce oxygen at so high levels that spontaneous bubble formation can occur. What are these DO thresholds (depence with temperature, etc)? Can someone indicate to me readings about this theme? Thank you.

  • Michel Vorenhout added an answer:
    Is it important to get new information on the biogeochemical role of biogenic (biological) detritus in water ecological systems?

    Biogeochemistry is an interesting interdisciplinary science. New data on biogeochemistry are often difficult to interpret; it is a challenge to find their significance to ecology.

    Michel Vorenhout · University of Amsterdam

    As you are refering to your own paper, it might make sense to specify your question a bit more. As Dr Farrington states: the issue is too wide to be simple.

  • Michel Vorenhout added an answer:
    Diel periodicity in soil redox potential.
    I've been reviewing redox potential (Eh) data taken at twenty minute intervals in wetland mesocosms. When plotted over time, it exhibits a pretty obvious diel wave with a mid-day peak and flat-bottomed troughs. The daily variation is pretty high, around 200 mV. My first thought was that it was caused by enhanced rhizosphere oxidation during peak photosynthesis, because the graph closely resembled that of photosynthesis (a few published studies have proposed this mechanism before). The only problem was that the graph looked almost the same in an unplanted mesocosm. Is there any way benthic algae or photosynthetic bacteria could be oxidizing the sediment at depths of 10 cm?
    Michel Vorenhout · University of Amsterdam

    Maybe an old question, but hope this still helps.

    Even though you will have an unplanted mesocosm, there is a lot happening in the sediment/water interface. Most work is done by the microbes, and daily variations you mention are rather normal in my experience. The depth is a bit much, but not too strange.

    For explanations, it is first of all important to describe how you measured the redox potential, and describe the possible microbial activity in your system. Note that you will need a very good measurement device to do the mesurements.

    Did you publish your findings? Maybe the attach paper is of interest to you.

  • Tom P. Rippeth asked a question:
    What are the relative impacts of diapycnal mixing vs surface mixing layer deepening on sea surface pCO2?

    Here we have only calculated the impact of diapycnal fluxes on the sea surface pCO2 - however significant entrainment of deep water into the surface mixed layer will also impact on the sea surface value of pCO2. Given this change will essentially be a "shock" when compared to the much slower changes due to diapycnal fluxes - has anyone considered the relative timescales of the growth (ie. DIC/ NO3 utilisation) and equilibration on pCO2 - and whether it is even important when compared to the slow diffusion of CO2 across the sea surface?

  • Sara Vicca added an answer:
    Can anyone suggest a good review article on soil nutrient (major nutrients: N, Ca, Mg, K, P, S) bioavailability?

    I'm looking into bioavailability mechanisms in soil. A lot has been done to understand P availability but what has been done to estimate the bioavailable pools of other nutrients?

    Sara Vicca · University of Antwerp

    Here's an overview report from the FAO. Among others, they specify what factors affect the bioavailability of various nutrients.

  • Abdelgawad Elsaadany asked a question:
    Does anyone know any research which finds some relationship between cyanbacterium spirulina and biogeochemistry?


  • Dannielle S. Green added an answer:
    Does anyone know what this Marine Organism is?

    It was found at in an Irish marsh exposed to fresh and marine water (depending on the tide) and was living on top of mud. It is not flat (picture can be deceiving) and is shaped like half a lemon. It is about 2mm long. Looks like some sort of slug, but I have no idea where to start. When alive it moves like a slug across the surface of the mud. The one in the pic is preserved in alcohol. Any help would be very much appreciated!!

    Dannielle S. Green · Trinity College Dublin

    Thank you for taking the time to respond! I shall take your advice Jeff and send them off just to be sure. 



  • Eucharia O Nwaichi added an answer:
    How does one grind leaf samples to a fine powder for analysis by ICP-MS?
    I am struggling to grind my samples to a fine powder, possibly because they have a very high sap/resin content. The samples have been freeze dried under vacuum, which should make them brittle but they are not!

    So far I have tried:

    - a Zirconium Oxide ball mill;
    - Agate mortar and pestle and liquid nitrogen;
    - inside an Orbital shaker in seal jars with glass balls;
    - An Agate Mill mortar and pestle mill.

    I can't proceed with the analysis until these samples are powdered, and I am running out of ideas and would appreciate any suggestions from people who have successfully powdered their samples.
    Eucharia O Nwaichi · University of Port Harcourt

    I agree with Sen

  • Jörg Schaller added an answer:
    Is anyone performing an experiment analyzing the potential of a wetland in recovery of metals/metalloids/rare earth elements as suggested by our review?
    Schaller, J., Vymazal, J., Brackhage, C., 2013. Retention of resources (metals, metalloids and rare earth elements) by autochthonously/allochthonously dominated wetlands: A review. Ecol. Eng. 53, 106-114.?
    Jörg Schaller · University of Bayreuth

    Please see our new paper on this issues:

    Schaller, J., T. Headley, S. Prigent, and R. Breuer. 2014. Potential mining of lithium, beryllium and strontium from oilfield wastewater after enrichment in constructed wetlands and ponds. Science of the Total Environment 493:910-913.

  • Michael Moisseeff added an answer:
    How can I measure terpenoids in resin?
    What affects the composition of resin? Is the ratio of sesquitepenoids and diterpenoids in a resin always the same, or does it change due to external or internal influences on the plant?
    Michael Moisseeff · Institut National Polytechnique de Toulouse

    Also, if you are working with frankincense or myrrh, those are gommo-oleo-résins, meaning there is an hydrophile component (gum) that might trap more or less water. (the oleéo part is essential-oil)

  • Ibrahim M. J. Mohialdeen added an answer:
    Can fatty acid exist in the lower Paleozoic hydrocarbon source rock?
    The most common biomarkers in old hydrocarbon source rock are various alkanes, but I found a series of fatty acid from our GC-MS data. So I am not sure they are modern contaminant or not. I am a novice in the scope of organic geochemistry, so I hope some one can give me some advice and I'll be very appriciative!
    Ibrahim M. J. Mohialdeen · University of Sulaimani

    Yes, it  exists. 

    You can return to published articles related to organic geochemistry in Paleozoic sediments

  • Boreddy Suresh Kumar Reddy asked a question:
    Can anthropogenic nss SO4 contribute to more CCN over Chichijima than that of marine nss SO4?

    Which sulfate (anthropogenic or marine biogenic) will contribute to more CCN over a remote marine island in the western North Pacific.

  • Qicheng Bei added an answer:
    Does anyone measure nitrogen fixation in forest ecosystems?
    There are big gaps in quantifying the total N fixation which holds us back to assess the whole ecosystem N budget. Although there have been modeling work of N fixation, observational results are very limited. Let's discuss the methods.
    Qicheng Bei · Chinese Academy of Sciences

    Obviously, very few now due to the measure technique. SEE the newest paper in PNAS. BNF is notorious for its measure problem. However, we are trying to measure forset free-living BNF next year using 15N2-feeding developed by our group. See my paper. Write to or call me, and we can cooperate in the future if you are interest.

  • Klara Rehakova added an answer:
    Freeze-thaw impacts on soil phosphorus: possible collaboration for multi-site comparison?
    I've been doing some work on how freeze-thaw events cause pulse losses of phosphorus from soils, and am currently writing a short paper on this. I would like to see if anybody is interested in carrying out a common-methodology study to look at this across a range of systems. We would manipulate soils to a common protocol involving leaching of mesocosms, followed by bicarbonate extractions of soil and litter P, as well as microbial biomass P. Solutions can then be sent to me for analysis if you don't have access to a UV-vis spec. You can also send me the soils for the incubation if you don't have the capacity to do the manipulations. Basic background information on soils would be the only other requirement, and a synthetic approach would allow a neat paper among all contributors. please message me if of interest. Rob.
    Klara Rehakova · Academy of Sciences of the Czech Republic
    Hello Rob,
    we are group working in Wester Himalays on the interaction soil/microbial assemblages/plant. Your research sounds interesting for us. If you will be interested to get some samples from altitude 4000-6000 m.a.s, pH of soil 7-8 from nival and subnival zone we woul be glad to sample some for you. We aslo could bring some samples from Svalbard, deglaciated, undeveloped soils.
    Good luck with your work.
  • B.W. Murphy added an answer:
    How can I clearly track the source of formation of soils?
    I have analyzed a soil sample from a deltaic region and found higher concentrations of Fe, Cu, Cr, Ni. It seems to me that there was some exposed ultramafic rock which has undergone intense weathering to form such soils and transported to the lower regions. How can I clearly track the source that might have given rise to formation of these soils. Any papers or suggestions?
    B.W. Murphy · Office of Environment and Heritage
    the soils are from a deltaic region which indicates the soils are not in situ??? At the broad scale it can be useful to understand the geomorpholgy of the soils as this will help identify the provenaces of the parent materials. Maps of the radiometric emissions can be very useful in identifying the sources of materuials at the broad scale. Oftten the radiometrics can she the depositional sequences of materials in alluvial. colluvial environments.
    At the more detailed geochemical level the signatures of different heavy metals and isotpoes as discribed by other contributers can confirm the sources of parent materials. Particle size distributions and the mineralogy of the sand fractions can also give some indication of the sources of parent materials.
    There are numerous refernces on radiometrics and soil, eg Wilfred 2012, Geoderma 1783 -184, 124 - 142.
  • Natella Mirzoyan added an answer:
    Which septum is best to take for water and gas samples and can septa be cleaned and reused?
    I want to take samples for DOC, sulphate, and dissolved gases (CH4 and CO2).
    For the dissolved gases, the vial is only half filled with water and has an Argon headspace with overpressure (1.5 atm). It might have to wait several days for analysis (max. 1 week), hence the septum has to be gas tight. For DOC the vial will be filled with water without any headspace, hence bleaking should be low.
    Has anyone experience about this? Can septa be re-used e. g. through ultrasonic cleaning?

    Thanks for answers.
    Natella Mirzoyan · Weizmann Institute of Science
    I have been using butyl stoppers for the gas collection: 7ml serum vials with 20mm butyl stoppers capped with aluminium seals. They were quite good, but I would use them only one time and I would still try to analyse the gasses at my first convenience.
  • Pradipta Mohapatra added an answer:
    Can an aquatic system release CO2 and O2 at the same time?
    The System is shallow and has high benthic chlorophyll content.
    Pradipta Mohapatra · Utkal University
    It is not possible. I cite two extreme cases as argument.1. in eutrophicated conditions there will be much photosynthesis and more requirement of CO2 and more evolution of oxygen. There will be only net release of O2 and absorption of CO2 from air. 2. In waters with organic load or in any water body at night, there will be high respiration and net demand of O2. So there will be absorption of O2 and possibly evolution of CO2 if the concentration exceeds the solubility limit. Since there is a high solubility of CO2 in water, water bodies are generally the CO2 sinks. On the other hand O2 has a low solubility in water resulting in net release of O2. Therefore in all photosynthetically active water bodies there is evolution of O2 and absorption of CO2 during day time and in night the reverse is true if the concentration of these gases in water exceeds their solubility.
  • Carlos Enrique Daza added an answer:
    Is there a difference between TRIS and Trizma?
    I plan to prepare buffer solutions for pH analyses.
    Carlos Enrique Daza · National University of Colombia
    They are the same compound, TRIS and TRIZMA are different forms of nomenclature.

    TRIS: tris(hydroxymethyl)aminomethane
    TRIZMA: 2-Amino-2-(hydroxymethyl)-1,3-propanediol
  • Arash V. Moradi added an answer:
    Which factors influence the S4 (RC) peak of Rock-Eval 6?
    I am investigating the role and effect of OM and its type in the uptake of trace elements in sediment-water interfaces. I would like to know why there are differences in the S4 value (measured in 850 C) of samples with the same kerogen type (I) and homogeneous lithology (marl)? Which factors influence the residual carbon content of samples? Does the S4 or residual carbon content still have potential to generate petroleum (theoretically) or do we consider it as a dead (Type IV) carbon?
    Arash V. Moradi · Ankara University
    Thank you so much Atif, Ahmed and Nicolaj.
  • Jebril Hadi added an answer:
    What is the best way to extract cations from the organic cation exchanger of the forest floor or litter?
    I am interested in nutrient cations such as Magnesium, calcium and potassium in the litter-layer of forest soils. Analyzing total Mg, Ca and K content of the litter is quite straight forward (acid digestion), but extracting the exchangeable cations from the litter-layer is more tricky. For soil samples, I use KCl or NH4 acetate as an extractant but I carry out 2 sequential extractions. For litter samples, I haven't found a way to do 2 sequential extractions because organic matter floats and it is difficult to recover the entire solid sample after the first extraction. Does anyone know which protocols have the best extraction recovery?
    Jebril Hadi · Bureau de Recherches Géologiques et Minières
    Dear Dr Van der Heijden,

    I suggest that you should try the hexaamminecobalt(III) trichloride method.

    A standard method exists (ISO 23470:2007), but you can adapt this method (amount of sample, concentration and volume, S/L ratio, pH.. ), depending on the situation . For your kind of sample, a single extraction (30 minutes) followed by filtration (0.1µm) should be sufficient to extract all the exchangeable cations (including organic matter). The CEC can be cross-determined by colorimetric analysis and major cations (Na, K Ca, Mg, NH4...) analysis of the extract solution. If major cations analysis overtakes colorimetric value, this means that your sample contains solubles salts. You can correct this discrepancy, either by proceeding to leaching assays (pure water) on the sample, or by first washing it prior to CEC measurements. I would recommend the first option.

    You should not encounter the reverse situation (i.e. colorimetry > major cations), unless you are working on preserved samples containing reductive species (e.g. reduced clays). This is the object of my next paper ..

    One must note that this method may be aggressive for biological systems, because it used as well for DNA crystallographic studies. Hexaamminecobalt(III) replaces barely all major counter-ions, including Mg in DNA. But this worth a try!

    Best regards
  • Mark Edward Brigham added an answer:
    What is the lifetime of methylmercury in deep ocean waters?
    Better constraining the numbers for both, MMHg and DMHg, could help understanding the production, degradation, and cycling of these species in the global oceans. What do we already know and what would you think are the best approaches to get a better hand on the estimates?
    Mark Edward Brigham · United States Geological Survey
    Lars-Eric, Look at the paper "Mercury sources, distribution, and bioavailability in the North Pacific Ocean: Insights from data and models" by Elsie Sunderland et al. (Global Biogeochemical Cycles, 2009, I suggest scanning some of Elsie Sunderland's other papers as well (you can view her profile here on Research Gate). Robert Mason from University of Connecticut (also on ResearchGate) would be another contact; start with his recent paper "Mercury biogeochemical cycling in the ocean and policy implications" (R.P. Mason et al, Environmental Research, 2012, Both of these individuals are interested in the question you pose, and would be useful for you to contact directly if you are doing research in this area.
  • Xiao-Jun Allen Liu added an answer:
    Which is the best way to express amount of substrate and CO2 respiration rate?
    I have been reading many papers about adding glucose, sugar or other complex substates (cellulose, litter, crop residues) to soil to analyze soil organic matter decomposition and soil respiration. The confusing issue I ran into was: how to express the amount of C from substates added to soil? For example, some report the ug or mg C per g soil, and some simply use the percentage of C based on the soils used. For the respiration, some use the ug CO2-C per g per h, some ug CO2-C per g per day or week, and some even use mg CO2-C per g per h/day/week.

    Other than the inconsistent report of the amount of substrate, different papers have different experiments periods or lengths. I am wondering if it is better to express the amount of C from substrates using a time scale? For instance, two papers report the same amount of 1000 ug C per g soil, but they have different duration, let's say 10 days and 100 days. By using the time scale, we see the C addition is completely different: 10 ug C/g soil/day vs 100 ug C/g soil/day. But I don't know which way is best for respiration.

    Does anyone agree or disagree that we should propose a common way to specify the expression of substrate input and respiration? Feel free to leave your comments and suggestions below. Thank you.
    Xiao-Jun Allen Liu · Northern Arizona University
    Bt report the unit (mg C kg-1 h-1) would cause very small numbers which are difficult to read and interpret for readers.
  • Thomas Petzoldt added an answer:
    How important is iron and sulfur in the ecosystems you study?
    I just came across a paper that is very interesting discussing iron - sulfur dynamics in the presence of iron reducing bacteria. In the Everglades, the system I am interested in, iron concentrations are relatively low (generally) while in some areas sulfur (as sulfate) is extremely high.
    Thomas Petzoldt · Technische Universität Dresden

    Iron and sulfur are very important in aquatic systems by controlling anoxic phosphorus release from sediments. This is generally well known, but the details are more complicated - as always.

  • Thomas Starnes added an answer:
    Is somebody familiar with regulations for shipping plants and soils within EU or from non-EU countries to EU countries?
    I would like to ship autochthonous plants and soils from EU and non-EU countries to Spain for experimental purposes. Is there many regulations to do this? Is it actually possible? Thank you.
    Thomas Starnes · Amphibian and Reptile Conservation
    You might find these pages helpful:

    Assuming they are not CITES listed, a Photosanitary Certificate is usually required.
  • Fikrat Hassan added an answer:
    Does anyone know of a paper discussing nutrient starvation in an ecosystem?
    I am looking for a paper which discusses the potential negative effects of extreme nutrient limitation. The majority of the literature focuses solely on enrichment or excessive loading of nutrients. While eutrophication can be harmful for ecosystems, I assume that nutrient starvation could also be bad, unless it is an adapted ultra oligotrophic system. Just wondering if anyone has stumbled upon any papers.
    Fikrat Hassan · University of Baghdad
    Dear Julian,
    You can look for F. P. Healey manuscripts about nutrient limitation; he discussed all status of limitation. Also Maestrini et al. 1999 and Rothhaupt 1995 will be useful.
  • Denise Akob added an answer:
    Question about experimental results: metal dynamics in an iron-rich creek soil.
    Dr. Akob,
    I am curious if in your study you saw an eventual decrease of Fe(II) in solution, due to potential sorption onto the soils or formation of Fe(II) minerals? And were you able to analyze the sediment at the end of the experiments?
    Denise Akob · United States Geological Survey

    We did not measure Fe(II) past the time frame presented in the ES&T paper. The sediment at the end of the experiment was used for XANES and EXAFS analysis. We did not analyze Fe(II) minerals.

    Denise Akob
  • Fatemeh Babaei added an answer:
    Extracting data from a raster using a polygon shape?
    I have done a kriging for Organic Matter in soil in a forest plot. Afterwards I export the data to a Raster. Now I have a polygon shape (done in QGIS) with the tree canopy projection, I would like to extract the data of the points under canopy and out the canopy in order to analyse the effect of canopy in soil characteristics. How can I do that?
    Fatemeh Babaei · University of Zanjan
    I m late too. In using Fishnet, Xtools plugin on ArcGIS is more better and easier to use than Fishnet tool in ArcGIS. I guess you have found the way already. Good luck for you.

About Biogeochemistry

Biogeochemistry is the scientific discipline that involves the study of the chemical, physical, geological, and biological processes and reactions that govern the composition of the natural environment (including the biosphere, the hydrosphere, the pedosphere, the atmosphere, and the lithosphere).

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