# Biogeochemistry

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.

4
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

All, thank you for your replies. Some more thinking for comment… One of the main reasons I ask this question is for an assessment of water (ground and surface) chemistry/quality. Specifically, waters I have collected the top soils (Teflon suction cups), interflow, subsoil drainage, and overland flow (soil zone) show much higher concentrations of K, SO4, DOC, NH4, and E.coli counts but low Si concentrations when contrast with groundwater and groundwater derived baseflow. Groundwaters show tightly regulated K concentrations, much lower and less variable DOC and SO4 no E.coli and elevated Si. This all makes sense to me in terms of the vertical filtering of DOC and selective retention of and regulation of ions as waters percolate deeper into the soil and unsaturated zone before reaching the underlying aquifer. In other words waters reaching the underlying aquifer have been subject to more regulation (interacted with far greater volumes of fine textured materials) than waters derived from shallow (upper 600 mm) lateral movement of water. So although concentrations of ‘nutrients’ (K, SO4, TAM, P etc) may be higher within the upper 600 mm they do not appear to be as strongly regulated by ion exchange or sorption processes. It would therefore appear that buffering (regulation) of ‘nutrients’ is proportionately greater within the subsoil and unsaturated zone than within the upper 600 mm of the soil profile.. not necessarily the concentration of ‘nutrients’.  To me this suggest either that organic matter is poor at regulating ion concentrations and or at retaining ions or that the shear abundance of nutrients from intensive land use overwhelm the regulatory (buffering) capacity of the upper portion of the soil. Regards, Clint.

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.
Limnology and Oceanography 11/2007; 52(6):2410-2417. DOI:10.2307/4502390

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

10
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.

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

• Source
##### Article: How air-drying and rewetting modify soil organic matter characteristics: An assessment to improve data interpretation and inference
[Hide abstract]
ABSTRACT: Air-drying and wetting of air-dried soil samples with water (i.e., rewetting) are widely used sample treatments in soil analyses. It is recognized that both air-drying and rewetting of soil samples affect the characteristics of organic matter (OM), but systematic evaluations are scarce. In this review, we syn-thesize what is known in the scientific literature concerning the types and magnitudes of effects resulting from air-drying and rewetting with respect to i) characteristics of aggregate-associated and water-extractable OM, ii) soil microbiota, and iii) decomposition of OM. Air-drying of soil samples results in the formation of new and/or stronger OM-mineral interactions as well as increased hydrophobicity and mineral surface acidity. The formation of new and enhancement of existing OM-mineral interactions may lead to an increase in perceived aggregate stability, potentially affecting estimates of amount and persistence of OM associated with soil aggregates. Compared to field moist samples, air-dried samples had 8e41% higher relative dry mass proportions in the 2-0.25 mm aggregate size fraction. Pronounced changes in the amount and composition of the water-extractable OM and soil microbiota are also detected during the course of air-drying and rewetting with the potential to affect the conclusions derived from OM decomposition experiments. Air-dried soil samples were found to have 2-10 times higher amounts of water extractable organic carbon and a decrease between 3% and 69% in the microbial biomass carbon (using the substrate-induced respiration technique) compared to field moist samples. The magnitude of air-drying and rewetting derived effects on sample characteristics appears to be site and soil type specific.
Soil Biology and Biochemistry 01/2015; 80:324-340. DOI:10.1016/j.soilbio.2014.10.018
7
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.

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)

2
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 !

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.

6
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.

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,

Cheers,

Javier

5
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.

Because nitrogen lmits microbial growth.

3
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!

Dear Emre

You may see the following links:-

http://water.usgs.gov/osw/techniques/workshop/winger.html

http://toxics.usgs.gov/definitions/pore_water.html

6
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.

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

12
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.

3
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?

Hi,

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.