• Abhijit Mitra added an answer:
    How to estimate the population variance part (lambda) of the MSEP decomposition?

    I am working on identify which explanatory variables could be interesting to add in a mechanistic model on soil carbon dynamic.

    I am able to calibrate a simple model on experimental data from several sites. This model is like an average model without explanatory variables and so don't simulate the variability existing between the different sites. I have some informations about the different sites (soil properties) which could improve the predictive quality of my model.

    I can estimate the MSEP of the "average" model and I'd like to estimate the population part (lambda) of the MSEP decomposition according to Bunke and Droge (1984) or Wallach and Goffinet (1987). This part represent the minimum MSEP we can get with the explanatory variables present in the model. The bigger this part is (relatively to the MSEP) the most we have to add explanatory variables to improve the predictive quality of the model. This term depends on how much the predicted variable (y) varies for fixed values of the explanatory variables (X) in the model : lambda=E[var(y|X)].

    I found that when the explanatory variables are categorial, we can estimate lambda by the mean square error of the residuals of a linear model between y and X which seems logical for me. I first thought that we can do it the same way with continuous explanatory variables but I doubt now because of the linear hypothesis which can be a contribution of the squared biais part of the MSEP decomposition (Delta).

    Have you any suggestions of how I estimate the lambda part of the MSEP decomposition?

    Thanks for the help!


    Abhijit Mitra · University of Calcutta

    It will be better if you just tell the specific objectives and your target.

  • Paul A Macklin added an answer:
    Are there scientific equipment distributors near or in Bali?

    I will be conducting one year groundwater/CO2 flux research in Bali starting in a couple of months. Do you know of any suppliers for scientific equipment such as pH cal solutions/DIC vials/Hg or CO2 calibration gases? Any help would be appreciated. I am in the process of gaining a Research Visa. Best regards. Paul

    Paul A Macklin · Southern Cross University

    Thank you so much Ari and Andre.......very helpful information for me

    All the best ,


  • Yash Gupte added an answer:
    I’m planning to investigate Al and Si co-deposition in silicophytoliths. Can anyone send me information about this subject?

    I am especially interested on papers about elemental anlaysis of silicophytoliths

    Yash Gupte · Ramnarain Ruia College

    diatoms & scanning electron microscope with AAS, dats all u need

  • Alan P Newman added an answer:
    Anyone familiar with Henry's constant of CO2 at different pH?

    I am trying to estimate the total amount of CO2 evolution from an abiotic reaction at pH 2. I measured the headspace concentration, and am trying to calculate the aqueous concentration using Henry's constant, which is 1.1 at 20C (dimensionless). Is this number still valid at pH 2? Does the Henry's constant of CO2 change upon pH change?

    Intuitively, yes. We usually strip out dissolved CO2 by acidification, and collect it using NaOH. However, it is very hard to find a table of Henry's constant of CO2 at different pH. 

    Alan P Newman · Coventry University

    Actually  the obvious way to determine the Henry's law constant would be at a pH which suppresses the ionisation of the hydrated carbon dioxide. If you look at the equilibrium diagrams this would be at pH 4.5 or less.

    This is a matter of the formal definition of the constant which considers only gas phase carbon dioxide and the solvated carbon dioxide molecule.

    By way of a practical application of this. The UK used to have a standard method for measuring sulphur dioxide in air based on an acid base titration of a bubbler solution.

    The pH of this solution was set to 4.5 at the start of the experiment so as to prevent interference from carbon dioxide. Obviously sulphur dioxide also dissolves to form a weak acid but this gas was oxidised as soon as it dissolved because the bubbler solution contained hydrogen peroxide and thus sulphuric acid, a strong acid, was formed.

    At the pH you are working at you should find that the literature value of  Henry's law constant would predict very closely the distribution of gas phase and dissolved carbon dioxide.

    Hope this helps.

  • Paul R Bartholomew added an answer:
    What is this mineral as depicted in the Raman spectrum below?

    We measured this Raman spectrum on a secondary mineral speleothem of a lava tube ( The main body was Thenardite and additionaly this spectrum appears occasionaly. Do you know it ?

    Thanks for your help.

  • Mikhail I Makarov added an answer:
    Why does the intensive soil frost increase the nitrogen concentration in leaves?

    I recently found in a peatland that the plants (both mosses and sedges) that experienced more intensive winter frost (colder soil with deeper frost) for more than 10 years have a higher N concentration in the leaves or capitula. Usually, a decrease in the plant N uptake is suggested after enhanced soil frost by many studies. Can anyone provide me some reference that is in line with my finding or provide me some possible explanations? Thank you!

    Mikhail I Makarov · Lomonosov Moscow State University

    Concentration of N-NH4+ increases in the soil after its freezing. The mechanism of this phenomenon is other question.

  • Kenneth M Towe added an answer:
    Is there anyone with research experience and interest in investigation of biogenic calcium carbonate polymorphs?

    I am looking for someone, who is expert and interested in investigation of cacopolymorphs formation through microbial activity, for cooperation in writing a research paper (as an co-author). I have the results of SEM, XRD, FTIR and light microscopy of microbially induced caco3 precipitates which I did for some other reasons than morphology. I need the expert person for interpretation of the data in view point of a specialist.

  • Nancy Falxa Sonti added an answer:
    Are there any studies that quantify nutrient removal from native woody plants in stormwater management systems?

    I know a group that is trying to get credit for planting native woody species in storm water management features because logically this should remove more nutrients but they need a study to provide evidence in order to get TMDL credit.  Please let me know if there are any studies they can cite.  Thanks!

    Nancy Falxa Sonti · US Forest Service

    This citation may be useful as well -

  • Asmeret Asefaw Berhe added an answer:
    How do I measure the enzymatic activity inside and on the surface of soil aggregates?

    I want to separately value enzymatic activity within the soil aggregate and on the surface of it. I can not find literature on this topic. Thank you. 

    Asmeret Asefaw Berhe · University of California, Merced

    I agree with the suggestions given above. I would just like to add that you do not want to use water to separate your aggregates of different sizes. Water based separation is obviously the easiest esp when you are working with small aggregates. But the rewetting and drying will very likely change the enzyme activity, and microbial community composition and abundance significantly, etc and your data will really not be useful. We recently reviewed the effect of rewetting and drying during routine soil lab analyses and the findings are pretty serious ... these procedures introduce a lot of bias and/or errors to experimental results. see the attached file

  • Antler Gilad 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.
    Antler Gilad · University of Cambridge

    low iron in surface water is more likely due to oxidation of iron with oxygen. 

    In the subsurface, Fe(2+) can interact with H2S. if you can smell H2S it should be good indication for low dissolve iron(+2) concentration as this reaction is fast. (And by the smell of H2S pretty much indicate that H2S is in excess) 

  • Alexander Galushko added an answer:
    Why anammox and nitrification need additional electrons for the ammonium reaction?

    These two processes are involved in the nitrogen cycle. I wonder why these two pathways need additional electrons !

    Alexander Galushko · University of Vienna

    Oxidation state of N in nitrite is +3 and N in ammonia is -3. Therefore, net change of electrons in annamox reaction is 0.

    In the first step of nitrification (oxidation of ammonia to nitrite) there is no need in additional electrons. BUT there is "hidden" requirement of electrons to "prepare" oxygen for hydroxylation of ammonia. Ammonium monooxygenase does not use O from water for hydroxylamine formation it does use O from O2. For this it needs to bring O with zero oxidation state to O with -2 oxidation state. Here additional electrons are required. However, in general equation this is "hidden" by the usage O2 as electron acceptor.

    What both processes require is so called reverse electron transfer: to bring electrons released at higher redox potential reaction into lower redox potential reaction. In both cases that are reactions of assimilation of CO2. That normally is achieved by ATP hydrolysis (or any other reactions) that brings up the proton motive force and makes energetically unfavorable reaction to occur.

  • Javier Sánchez España added an answer:
    Can anyone recommend literature on biogeochemical characterization of artificial lakes through dissolved nutrients?

    Besides the collection of macroscopic invertebrates, I also measured dissolved nutrients during the assessment of a gravel pit lake. I would like to characterize the water of the lake using this data, but I've found no reference on methodology, yet. I would be grateful if anyone could give me advice to start out. Thank you in advance.

    Javier Sánchez España · Instituto Geológico y Minero de España

    Dear Peter,

    I attach a comprehensive study which may is not so easily available (it is a chapter from a recent book by Springer).

    Here you will find lots of data and highly constructive discussions on biogeochemistry, biogeochemical cycling, food webs, trophic state and nutrient fluxes in a very special type of artificial lakes - mine pit lakes. I would specially recommend Section 3.3 (Biology and Ecosystems, starting on p. 107), since it includes information from many lakes, specially from Germany.

    Probably the complexity is rather different than in a gravel pit lake, but the principles and scientific background behind their biogeochemical characterization (including the influence of dissolved nutrients on lake ecology) are the same, and thus they could be equally useful for you.

    I hope this can help,



  • Pete Manning added an answer:
    Why was the litter decomposition rate positively correlated with N content in the early stages of litter decomposition?

    Many studies found that plant litter decomposition rate is related with litter concentration of nutrients ,such as N. But there is no a clear reason. I want to ask how the N concentration of litter influence on the litter decomposition.

    Pete Manning · Universität Bern

    Because nitrogen lmits microbial growth. 

  • A. R. Karbassi added an answer:
    Can someone suggest a review about "pore water chemistry" in marine/lake core sampling?

    Especially, biogeochemistry or hydrogeochemistry in pore water of marine core deposite!

    A. R. Karbassi · University of Tehran

    Dear Emre

    You may see the following links:-

  • Clinton Rissmann added an answer:
    Why is the ratio of aqueous sulfate to chloride in aquatic systems related to sulfate reduction?

    I am trying to understand what mechanism(s) account for the fact that the [SO42-]:[Cl-] ratio in water can be indicative of the level of activity of sulfate-reducing bacteria in aquatic ecosystems.

    Clinton Rissmann · Environment Southland

    Hi Meredith, I relate to C. Brannon Andersen's answer. Having some understanding of the [Cl] would be very useful. If there is data from the lake from other studies you could compile an average or median [Cl]. Here in New Zealand we see considerable variation in freshwater Cl concentrations depending on the distance from the coast. However, under stable conditions the Cl concentration is usually very consistent for a given lake.  With respects to redox assignments I use a field portable colorimeter to measure Total Sulfide (TS), a handheld meter for D.O., Eh, SpC, pH  as well as taking samples for the main terminal electron accepting species (TEAS: NO3, Mn, Fe, SO4). If you were interested the redox assignment workbook of Jurgen et al. (USGS) is useful. Measuring total sulfide helps to discriminate as to whether FeIII or SO4 reduction is the dominant terminal electron accepting process. Kind regards, Clint

  • Kenneth M Towe added an answer:
    Are there cost-effective ways of capturing and harvesting 'biogenic' combustible gases from seeps in the seafloor?

    In the current 'climate change' syndrome, we are constantly looking for ways of ridding the atmosphere of accumulating radiative gases (so-called 'greenhouse gases, GHGs': H2O, CO2, and CH4). Over the last 3 decades, we have found thousands of locations in the seafloor, where one of the strongest GHGs is escaping, namely methane, CH4. These are active gas vents, or seeps, which are easily tracked acoustically, their manifestations known as mid-water gas plumes, or just 'flares'. I have recently found a way of harvesting such gas seepage, with a device (or system) called SUMECO: "submarine methane collector" (see my latest written contribution, in my profile). I belive this to be a viable and cost-effective way of harvesting methane from the seafloor, for use as a resource.

  • Pascal Badiou added an answer:
    What is the best way to quantify the phosphorus contribution by in-lake biogeochemical cycling?

    We know the internal P loading is a big contributor to algal bloom for many eutrophic lakes. But there is a lack of studies that can identify and quantify the amount of P from sediment resuspension in a eutrophic lake. Any idea or suggestion?

    Pascal Badiou · Ducks Unlimited Canada


    Another potential for examining this issue is to look at the maximum phosphorus sorption capacity of the sediments as well as the equilibrium phosphorus concentration. These will allow you to determine if the sediments in your system still have the capacity to bind P and at what water column P concentration your sediment acts as a sink or source of P. This will only identify the P fraction that is being released or taken up through biogeochemical interactions and will not provide information on P resuspension.

    In terms of P resuspension there are a number of studies that have examined the impacts of benthivorous fish and wind driven sediment resuspension on TP in the water column.

  • Amokrane Athmane added an answer:
    Are there any national-scale (US) land-use regression models for CO or SO2 that are publicly available?

    I'm thinking of something along these lines:

    But for SO2 or CO

    Thanks in advance LUR experts!

    Amokrane Athmane · Université de Khemis Miliana

    Not to my knowledge, and also this is not my area of research, mine is soil parameter.

  • Mark Krause added an answer:
    What is the optimum weight of carrier based inoculum to apply and the frequency of application for cleaning 1ha soil contaminated with 4-5% crude oil?

    The carrier is charcoal. It contains a consortium of efficient bacteria (10 to power 8-9 CFU/g). The soil was contaminated 7 years ago. The soil is clay loam, pH 8.2, low N, P and organic matter content.

    Mark Krause · Austin Analytical, LLC

    At that level it is completely dependent upon the bacteria. If the bacteria are aerobic it is doubtful that you will get treatment at that level of contamination. You might look into an alternative:  

    Look at the Piranha mix. We have successfully used their product to treat crude oil in the 5-10% loading range on soil; I have never found another product that would approach that level. it also has the added benefit of a single application and no further tilling.

  • John R. Helms added an answer:
    Does filtration of sea water result in loss of dissolved gaseous mercury (DGM) species (Hg0 and DMHg)?

    Measurements of dissolved gases (oxygen, CFCs,..) in sea water samples is usually done on unfiltered samples, and tedious protocols need to be followed to avoid any bias (must be first sample to be taken, quickly after collection, no bubbles, overflow bottles 3x volume,...).  DGM measurements are done on both, filtered and unfiltered samples. Could filtration result in any loss of Hg(0) or dimethylmercury?

    John R. Helms · Morningside College

    The issue isn't filtration per say as of course they are not particles. It's the sparing solubility and significant vapor pressure of the analytes. Under vacuum filtration conditions they can partition into the headspace and be evacuated by the vacuum system. That's why using capsule filters under positive pressure (or esp. gentle gravity pressure with no pump cavitation to generate bubbles) is recommended, *if filtration is needed*. If measurements are made immediately, there is no reason to filter. If samples are to be stored, they need to be preserved in a way that preserves the Hg speciation somehow and sometimes filtration is used to remove microbes.

  • Alexandre Castagna added an answer:
    Which method(s) can I use to smooth stacked curves of oxygen isotope?

    I want to use Cramer et al. (2009) raw data of oxygen and carbon isotopes for a very specific time period (around 2 Ma long) to compare it to my oxygen and carbon isotopes from terrestrial record. My aim is to show that my site is affectd by global factors by comparing Cramer's data with mine. I don't have the same sample resolution as Cramer's: he has about 1000 data points while I have about 300. How can I solve the problem of difference in data resolution? Which methods would you suggest to address this issue?

    I also would like to statistically compare my data with Cramer's, but my data is terrestrial so the oxygen isotope values are much lower (around -7 per mil). I would like to be able to compare the trends, not the actual values. Would anyone know which test(s) I could use?

    Alexandre Castagna · University of São Paulo

    Very nice Julie,

    I would suggest to you R as very flexible and powerful tool and you can always count on its large community of users to help you out. There are a number of e-mail groups dedicated to specific research areas with R. Good luck with your research.

  • Amit Kumar added an answer:
    How can I make an anaerobic environment in a 250 ml tight bottle contain Soil:water(1:1) to get methane ?

    Degradation of carbon at a certain temperature and humidity evolve methane. Only methods are require to maintain anaerobic Environment in small bottle.

    Amit Kumar · Indian Institute of Technology Roorkee

    Siyue Li...after conformation i will let you know ...but we can measure ch4 concentration ??

  • Per Hagelia added an answer:
    Can anyone recommend updated solubility constants for minerals associated with ARD?

    I basically need access to reliable solubility constants of sulfates which are associated with acid rock drainage, acid sulfate soils and acid mine drainage.

    Perhaps someone has made a recent compilation?

    Per Hagelia · Norwegian Public Roads Administration

    Thank you both for swift response.

  • Harald G. Dill added an answer:
    Dear fellows, Do you know any comprehensive review about soil weathering indexes?

    Weathering indexes are useful to estimate the intensity or the duration of a weathering process in geological materials as soils. But what are the pros and cons? What are the methodological issues about these indexes? And, finally, why aren't they popular? For soils there are two interesting indexes: the Ki (Silicate to Al-oxides ratio) and the Kr (Silicate to oxides ratio). In simple words: How intenser and/or longer the weathering process, more intense the loss of silicates will be and more oxides will remain in the soil. Therefore, higher the Kr or Ki ratio. As a rule of thumb, soils with Ki < 2 (devoid of 2:1 phyllosilicates) are the highly weathered ones. The highly weathered soils from Brazil very often presents Ki and Kr < 1.

    Harald G. Dill · Leibniz Universität Hannover

    Dear Mr. Sobrinho,

    the approach you will have to take, strongly depends on the mineral assemblage of your weathering profile. I have used clay minerals and heavy minerals. The latter group is rather sensitive and even can show you the intensity by the crystal morphology (see file attached). In your environment, newly formed APS minerals may also be of help (Aluminium-Phosphat-Sulfate minerals/ crandallite group), which can be used in combination with sequioxides (Al oxides) and phyllosilicates (kandite-group + halloysite). The following paper may give you an introduction into the matter

    DILL, H.G. (1998) A review of heavy minerals in clastic sediments with case studies from the alluvial fan through the near-shore marine environments.- Earth Science Review, 45: 103-132.

    DILL, H.G. (1995) Heavy mineral response to the progradation of an alluvial fan: implications concerning unroofing of source area, chemical weathering, and paleo-relief (Upper Cretaceous Parkstein fan complex / SE Germany).- Sedimentary Geology, 95: 39-56

    DILL, H.G. (2001) The geology of aluminium phosphates and sulphates of the alunite supergoup: A review.- Earth Science Reviews, 53: 35-93.

    Should you have further questions feel free to contact me on this matter.

    Best regards
    Harald G. Dill

  • Margarete Maria Kalin added an answer:
    Is somebody working in humic substances of riverbed sediments and their interaction with metals?

    Im working in La Matanza River and study the interaction between humic substances and metals and their mobilization influenced by dissolved organic mater in water column. I want to modelize it 

    Margarete Maria Kalin · Boojum Research Limited

     check out Christian Steinberg  work it is extensive in this area, including I believe a book on it. 

    greetings margarete

  • Victoriano Urgorri 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!!

    Victoriano Urgorri · University of Santiago de Compostela

    Dannielle, I think it's a juvenile of Alderia modesta (Lovén, 1844) a gastropod mollusc (Order Sacoglossa; Family Limapontiidae). This little sacoglossan (10 mm long) is associated with Vaucheria in saltmarshes and it is resistant to salinity changes. You can to check if the animal has a radula.

  • Harry ten Brink added an answer:
    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.

    Harry ten Brink · Energy Research Centre of the Netherlands

    I gave a reply 2 days ago, but it is not in the list.

    1. Regional models give an estimate of the concentration of sulfate at the site. Then you can use a formula of Doug Lowenthal to estimate the CCN number. Greg(ory) Carmichael of University of Iowa

    2. Natural sulphate can be assessed from an isotope measurement; perhaps there are data at your site. Example is the work of Len Barrie in Canada

    3. I checked the site: this is NOT REMOTE: it is in the east-Asian plume?!

  • Vahid Chamanara added an answer:
    What is the correct approach in calculating the average pH values measured by a combined electrode?
    Is it a directed ordinary mean or taking the anti-log values at first then getting the average and return to the log values again? I think if we measured it by electrode that is fair to calculate the ordinary mean from the pH values but if we measured the H ion activity which is so difficult then we can use the anti-loge approach. Am I correct?

    Thank you guys, 

    can we use the mean values in the SPSS output report? 

  • Igo F. Lepsch added an answer:
    Does anyone know how to stain (blue, red or other) silica-phytoliths (or biogenic opal)?

    Plant silica bodies (also callled silicophytoliths and plant opal) can be extracted from plant tissues or from soils. I wonder about the best method to stain these small particles in order to visualise and photograph them better under the petrographic microscope.

    Igo F. Lepsch · Federal University of Minas Gerais

    Olá Fernando,

    Já experimentamos colorir com Violeta Genciana ( methyl violet ) e obtivemos bons resultados

  • Nicolai S Panikov 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.
    Nicolai S Panikov · Harvard University

    The respiration rate must be expressed as amount of CO2 (ug or mg or g of CO2-C or mmol of CO2) per amount of soil (g, kg) per unit time (min, hr, day or even week/month/year).

    If you see the published data with the missed time units, then it is qualified as error made by authors and editors.

    What is better, mg of CO2-C or mmol of CO2? In a C-balance studies mass units of carbon are better. In the studies of metabolic pathways (e.g. degradation of PCB in soil), the molar concentration is preferable.

    What is better, ug, mg or g of CO2? g or kg of soil? hr or day? No strict rules, just make your numbers easy to read. There was a tendency to unify the units to international standard but it is not always justified.

    Finally, per g of soil or per m^2 of soil surface? Depends on technique you use, whether you measure a flux of CO2 by chambers or incubate few g of soil in a vessel.

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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