# Biogeochemistry

3
Does anyone have protocols for carbonate removal from freeze-dried dissolved organic matter?

The aim is to eliminate inorganic carbon for isotopic analysis (13C an 14C) of organic C. DOM  has been concentrated by reverse osmosis from river water samples.

For fluffy freeze dried samples, some times you can just 'fume' the sample with HCL vapor for a bit (I've used ~8hrs, but probably overkill) and re-lyophilize the sample or just put it under vacuum for a while to remove any water or HCL adsorbed.

A simple method for fuming just uses a glass desiccator. pour a mL or so of conc. HCL in the bottom put the sample tray and sample (unsealed so the HCL vapor can reach it) in, close the lid to the desicator and let diffusion do it's thing.

You can also pH adjust (very carefully) your samples before freezedrying them to ensure the DIC volatilizes during sublimation.

Good Luck!

3
What is the most popular method to measure Methane emission from agricultural activities?

In this case, I want to measure Nitrogen cycle including N fixed in soil, N uptake by plant, N leaching and N emission.

Other than the methods to measure the gases, often researcher overlook on the spatial effect (soil type and other variations). Most of the study related to the agriculture i.e. farm land only focused at only one location. In my study I utilized the proximal soil sensing technology to study the field heterogeneity. Once we have a knowledge about the field and the hotspot to measure the GHG, then we can place the chamber or the tower.

4
Could anyone recommend a paper on the relationship between d13C(org) stable isotope and Paleoproductivity in black shales (Lacustrine setting)?

I have read in several papers that lighter d13C(org) may be indicative of terrigenous input (landplant) and/or microbial activity (Biodegradation). Some scientists also use d13C(org) value as a proxy for paleoproductivity suggesting that lighter (more 12C) values are indicative of Paleoproductivity and eutrophication. I wonder, to what extent, d13C(org) could be used as a paleoproductivity indicator RELIABLY? Is there any published work on this issue?

You may be interested in the attached articles that relates the 13C-isotopic fingerprint of Pinus pinaster Ait. and Pinus sylvestris L. wood with the quality of standing tree
mass (forest productivity) as well as  the d13C values of trees with the 13C signature of the corresponding soil.

+ 1 more attachment

14
What is a good Atomic Absorption Spectrometer to use for exchangeable cation analysis in your opinion?

I think the title says it all, but I am in the market for an Atomic Absorption Spectrometer to run exchangeable cations as extracted by ammonium acetate, and would like to hear peoples comments about machines they have used.  Thank you.

Usually a proper AAS has also the option to function as a flame photometer (emission mode) which allows you to analyze Na and K. Say for this elements no extra hollow cathode lamp is needed, The only you have to care then is that the burner operates usually with propane for emission modes and acetylene for absorption mode (Mg, Ca, Fe, Mn, Zn, Cu....). With restricted bodget you may have a look to the Japanese manufacturer RIGACU, or consider to buy a refurbished used one. Older Instruments have much less gimmicks implemented and can be serviced nearly completely by your own. Newer generations of AAS depend very much on manufacturers service availability and therefore come up with another source of eventual costs.

8
What controls the reserves of base cations and the concentration of Ca, Mg, K and P in soil solution?

Hi hoping for people’s thoughts/comments on the generalised relationship between soil horizons (sensu lato soil depth) and the concentration of exchangeable bases as well as the regulation of inorganic ion concentrations (esp. K+ and P species) in soil solution? Specifically, is it fair to say that: (i) reserves of Ca, Mg, K and P species are highest within the subsoil due to a greater abundance of layer silicates and sesquioxides, and; (ii)  that the greater abundance of layers silicates and sesquioxides results in stronger/greater regulation of the concentration or these ions in soil solution (buffering?)  I realise that organic matter has by far the highest charge density (pH dependent) and yet I did not think it was particularly effective at regulating/retaining K, P or base cations relative to clays. I’m thinking particularly of fine texture (leossial) soils developed a temperate-humid climate. Clint

Thanks Paul. I hope to get it published next year. Cheers, Clint

4
What is the best method for measuring in situ soil Eh/ORP?

I would like a simple method to measure in situ soil reduction potential. Does anyone know of a durable sensor/probe that can be inserted into the soil profile for a reading of ORP? I'm reluctant to make a slurry or paste and measure with an Eh/ORP sensor as this will introduce atmospheric oxygen.

Thanks for your help/advice.I have been looking at the literature as suggested. I see various products on the market. I'm looking to install probes at 10 - 20 soil moisture and climate stations across an area of Southern New Zealand. We have a minimum of 2 and up to  10 years continuous soil moisture, soil and air temperature and precipitation at these sites. Idea is to deploy for 12 months or more and integrate into our data logging platform at each site. The question is now one of cost. This will determine how many sites we can install. Carla very interested in the needle sensors. Do you have a brand name. Stephen and Junghong thanks for your advice on reference electrodes and meter types. Regards,  Clint

8
Can anyone comment on this map made by me presenting increased likelihood of methane in the southern Baltic?

The map is  calculated on  the basis of  acoustic  observations of  the methane expulsions and  correlated type  of the  seabed - the  chart  of the  most probable  zones of  methane presence was calculated by me for  the  southern Baltic  Sea.  The methane  area is  well correlated with deeper stagnation areas.

New fig. The Methan expulsion from the  baltic  seabed observed at  the  echogram.

More  details  in:

Acoustic Tracking Dynamic Phenomena in Marine Ecosystem

BOOK in LECTURE NOTES IN ELECTRICAL ENGINEERING 146 · JANUARY 2012 with 8 READS
Impact Factor: 0.11 · DOI: 10.1007/978-3-642-27638-5_13
Publisher: Springer, Editor: S. C. Mukhopadhyay, ISBN: 978-3-642-27637-8

+ 1 more attachment

thanks Jan Schulz. The area is  indicating the  horizontal range  of  methane ebulitions, based on  acoustic  observations and  measurements of the  sebed  properties. The area can  be  correlated with  the  small dynamics  of the  currents and correlated very  soft  sediments. Generally  it  is indicating  the  deposits of the decomposition of  materials produced  due  to  increase  of the  eurtophisation.

2
Does anyone have any advice on Raman vs Vitrinite data?

Dear all,

I have Raman and vitrinite data and I would like to use the data to determine thermal overprint in my samples. When I calculate the T°C by Beyssacs equation. Temperatures are between 350-450°C. Vitrinite Data ranges between 2.17% to 2.68%. Using Barker and Pawlewicz equation for temperature calculation I get roughly 200°C.

Does someone have an idea what the reason for this might be?

Thanks for the help!

Inga

see attachment may be useful

6
Alpine Serpentinites: Can You Suggest a good overview article?

Can anyone suggest a good overview article on what makes Alpine Type serpentinites different from others? I know that plots of Cr# vs Mg# have different fields, but what else is different and why? Mineralogy? Any estimates of P-T conditions, or are they variable?

Thanks!

4
Where are current non-agricultural field experiments on biochar being conducted?

For purposes of scientific reviews and to obtain a better sense of the state of biochar implementation outside of broad-field agriculture, I am interested in learning about any prior or ongoing field experiments on biochar effects on plant productivity, soil processes, and biogeochemistry.  A brief "meta-data" description would be valuable (location; year implemented; size of treated areas; biochar dosage(s); plot replication; type of biochar used including feedstock, pyrolysis method, and peak temperature; soil type, including texture and pH; ecosystem or target plant species examined).

Depending on responses, I would consider collaboration on a review with contributors.

I have attached a file with my lab's ongoing field trials as a template.

Sean,

see those locations :

http://biochar-us.org/biochar-forest-ecosystems

http://www.biochar-international.org/sites/default/files/Hailong_Wang.pdf

5
Could anyone point me to protocols for running substrate induced respiration (SIR) via lab flask incubations on a LICOR-8100A?

I am trying to get a sense of how long I should run the LICOR after glucose addition to get a good estimate of CO2 flux. These are dry alpine soils with low OM.

and thank you Carolyn I found the flask application note very helpful!

5
How do I measure the amount of Nitrogen in a spay dried powder?

Dear all,

I would like to know if anyone can suggest a method of measuring the amount of nitrogen in a powder. The powder can and will be dissolved in hot water.

One of my starting points is, to dissolve the powder with deoxygenerated water under vacuum and cotinue with a headspace analysis.

Is there any other method thanusing a GC?

I really appreciate!

4
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

You may want to contact Wendy Zellner at USDA-ARS Toledo.

wendy.zellner@ars.usda.gov

http://www.ars.usda.gov/pandp/people/people.htm?personid=48449

2
Has anyone ever determined the microbial Fe(III) reduction-coated sand in the presence of DOM to distribute of Pb in soil?

I found many publications, but no one has reported the detailed protocol for this question.

Could you give me a detailed protocol?

Thank you Dr Sirvastava for explanation.

16
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?

Hi Boris, I agree that there is no sense of transformation if

arithmeticMean(pH)=geomean(H+)

The approach I am using is the one described in your link. However, when the measured pH values are very similar (within one pH unit), the difference in averaging is insignificant and this old article is showing some good example:

http://jeb.biologists.org/content/84/1/335.full.pdf

9
Which sediment dating method will be best suited for young sediment?

The lake has continually received sewage effluent  and is less than 75years old?

210 Pb  plus 226Ra

7
How can I measure nutrient recycling in arboricultural systems?

Many studies claim one of the benefits of arboriculture is the increased uplift, retention, and recycling of mineral nutrients. However, quantification of this topic tends to be limited to very rudimentary techniques, such as simply quantifying the total nutrients redelivered to the soil surface through litter.  I am interested to attempt to quantify the uplift and recycling of nutrients in arboricultural systems.  The only way I can think to do it is to define a ratio of isotope fractionation for the tree crop (which will likely change with the ratio on isotopes in the soil), and to assess the isotope ratios in the soil and tree over time.  Any thoughts, suggestions, citations, etc. along this topic?

Thank you for your contribution Abhishek, but I really donʻt see how that paper gets at my question.  It is a broad overview of root physiology and how it relates to plant growth, but does not get at any techniques for actually measuring uptake and recycling rates nor does it even get into the physiology specifically enough for me to think critically of how those measurements might be made.

To be clear I think what I want to do it really quite novel and cutting edge, and as far as I can envision so far will have to be using isotopes to understand the relative and absolute amounts of nutrients in the cycle.  Most interesting to me will be how the use of arboriculture decreases (or does not decrease) the amount of nutrients lost in very young soils, and increases the nutrient capture and use at an ecosystem scale. There is an emerging technique of using isotope fractionation to quantify phosphorous that has been biologically cycled or not that I think might be useful in this context.

26
Any better methods to remove carbonate from soils?

Hi All:

I am working on some alkaline soils which have high inorganic carbonates. Yet I need to analyze the soil C content, microbial biomass C, and the 13C isotopic signature of both. Are there any classical methods for removing those inorganic carbonates? In doing so I can get clear results after the carbonate removal.

Thanks very much.

Fernandes M, Krull E. 2008. How does acid treatment to remove carbonates affect the isotopic and elemental composition of soils and sediments? Environ. Chem. 5: 33-39 .

Harris D, Horwath W R, van Kessel C. 2001. Acid fumigation of soils to remove carbonates prior to total organic carbon or carbon-13 isotopic analysis. Soil Sci. Soc. Am. J. 65: 1853-1856 CrossRef

http://www.medwelljournals.com/fulltext/?doi=rjbsci.2009.858.865

7
How can I avoid reabsorption of trace metals into solid CaCO3 during hydrogen peroxide treatment?

In preparation of aragonite shell samples for trace metals analysis, I use buffered hydrogen peroxide to remove organic matter.  while this step is effective in reducing concentration of many elements, It seems that with regard to Al, Fe, Zn. Pb and perhaps a few other elements the sample becomes enriched during this process.

I will try the techniques for removing the adsorbed ions, and will try to use a week acid leach as well, after the H2O2 step.

After a talk with Steve Weiner I realized that I will not be able to separate the intra-crystaline organic matter. However, the trace elements signal from this part seems stable, so I am not that worried about it. mainly concerned about remains of soft tissue and algae inside and between shells.

Thank you all again

5
How would one determine the spectral slope for dissolved organic carbon at a given wavelength range?
How can I determine the spectral slope for DOM quality using UV-VIS spec data? Most literatures just mention the use of a standard equation method (non-linear fitting). Does the equation determine "S" at each wavelength using exponential curve for a given range (S275-S295, S290-S350 and S350-S400 nm) or can one use some software to determine the spectral slope at each wavelength?

Here is an important quesiton: How to decide the reasonable reference wavelenght, (lambda r)? Because currently a lot of literatures reported by using Helms et al(2008), but they didn't give the reference wavelength values specifically, this is why it's hard to results comparison.

93
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.

Dear Miranda, I will like to know if this is for elemental analysis?

4
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.

From literature I found that the optimum weight of the carrier based inoculum is  2% from soil weight in a pot experiment and the frequency of application was once for 150 days and the degradation% of TPH was satisfactory.

1
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!

Benjamin

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

3
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

• Source
##### Article: Biogeochemistry of the Dumai River Estuary, Sumatra, Indonesia, a Tropical Black-Water River
[Hide abstract]
ABSTRACT: The biogeochemistry of the Dumai River estuary in eastern Sumatra, Indonesia, was studied in order to obtain information on the sources, transformation, and fate of organic matter. Between October and December 2003, water, total suspended matter (TSM), and sediments were sampled along a salinity gradient during four campaigns, and plants and soils were collected from the catchment. Water samples were analyzed for dissolved inorganic nutrients and dissolved organic carbon (DOC). The concentrations of organic carbon (C<sub>org</sub>) and total nitrogen (N) and the stable carbon (δ<sup>13</sup>C<sub>org</sub>) and nitrogen (δ<sup>15</sup>N) isotope distributions were determined in TSM, sediments, plants, and soils. The pH as well as the concentrations of dissolved inorganic nutrients and TSM were very low in the river and increased toward the sea. A maximum DOC concentration of $5,050 \mu mol L^{-1}$ was measured in the river, and concentrations decreased toward the sea. Low-gradient relief and a dense vegetation cover, and hence little weathering and erosion, appear to be responsible for low river loads of dissolved nutrients and TSM in this black-water river. Leaching from extensive peat soils in its catchment may account for the high DOC content of the Dumai River. Peat swamps drained by numerous small rivers are estimated to cover $3.3 times 10^{4} km^2$ in eastern Sumatra, suggesting that leaching of DOC may be a significant source of carbon to the adjacent coastal seas. A comparison with "normal" rivers shows that black-water rivers can export similar amounts of DOC from catchments that are orders of magnitude smaller. Thus, export from small black-water rivers may be quantitatively more significant for the global DOC input into the ocean than previously thought.
Full-text · Article · Nov 2007 · Limnology and Oceanography

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

All the best ,

Paul

8
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.

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.

7
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 (https://www.researchgate.net/publication/265952424_RAMAN_STUDY_OF_SECONDARY_MINERALS_IN_A_RECENT_LAVA_TUBE). The main body was Thenardite and additionaly this spectrum appears occasionaly. Do you know it ?

+ 1 more attachment

7
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!

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

5
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.

5
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!

This citation may be useful as well -

http://www.nrs.fs.fed.us/pubs/jrnl/2007/nrs_2007_nowak_002.pdf