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For example, total acidity decreased from 1.15 to 0.8 cmol∙kg-1 after 30 days and even less after 60 and 90 days. Exchangeable Al content dropped from 1.02 to 0.4-0.6 cmol∙kg-1 during incubation, that is more than 50%. At the same time, exchangeable H demonstrated 2-3-fold increase. CEC showed about 25% decrease.
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Can you please elaborate your experimental condition? What were your initial CEC and OC values and what were the values after incubation. How the soil was incubated e.g. moisture content etc.?
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I mean, I can use XRD to determine the crystal structure of minerals/identify them and see if they're changed during an experiment, and I can use SEM to 'see' the surface of a mineral or soil sample. But as far as I can tell neither of these techniques is very good for identifying or 'visualizing' organic molecules/material sorbed or otherwise associated with the material.
I am doing column experiments with organic material, and I can measure what's going in and what's coming out, but I am not sure how to 'see' or characterize what is retained in the soil. Is there a method for doing so? (I am looking for one besides a solvent extraction+characterization; I am hoping for something that allows me to see not just what is in the soil but how it's in the soil)
Any suggestions would be appreciated.
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Dear Alexandra, this is a very interesting technical question. As an inorganic chemist I'm not a proven expert in this field. However, I can suggest to you a few potentially useful articles which might help you in your analysis. Please have a look e.g. at the following papers:
In situ visualisation and characterisation of the capacity of highly reactive minerals to preserve soil organic matter (SOM) in colloids at submicron scale
Unfortunately this article has not been posted as public full text on RG. However, most of the authors have RG profiles. Thus there is a good chance to request the full text directly from the authors via RG.
Organo–organic and organo–mineral interfaces in soil at the nanometer scale
This paper has been published Open Access and can be freely downloaded as pdf file (see attached).
A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces
(also attached)
I hope this helps. Good luck with your work!
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Hello everyone, I have conducted a research on topic assessment of soil fertility and nutrient status under different cropping system. there are almost four cropping system. 25 soil samples from each cropping system was taken. CV value of my parameters like total N content, available P , Available K, soil organic matter content is more than 30. How can i reduce them ? I am looking for effective feedbacks from you all. Thank you.
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CV is dependent on errors committed during measurements. If errors are less CV should be acceptable. So for your case to reduce the high CV may be analyze the samples again and get new values and observe there will be a variation to the previous ones.
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Now a days many techniques are available on crop nutrition such as soil testing, plant testing, foliar diagnosis, soil test crop response method and colour chart method etc. Though many number of methods are available to diagnose deficiency or toxicity of nutrients either in soil or on crop plants , identification of type and level of nutrient deficiency or toxicity is difficult for recommending nutrient application. In this connection, discussion on soil mineral resource identification, nutrient release from the particular mineral and quantity of elements release my give better idea on nutrient management for agri / horti /forestry crops especially in organic agriculture.
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Yes , there is every possibility to keep soil pollution on guard. Unfortunately , the guiding riders are not so robust enough to interface soil test-based fertilizer recommendation to soil pollution -related issues...
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Hello,
I am looking for the average trace element concentrations in agricultural soils around the world. Do you know of a good place to start?
Thank you all immensely,
Xavier
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They are indeed available for this as this is a very important sector. Although they have been depleted in a few cases, they are being revived with the traditional methods.
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Prolific Earth Sciences developed and markets microBIOMETER a rapid test for microbial biomass (MB) and fungal to bacterial ratio which we have shown correlated r = 0.94 with CFE. We want to fund an independent University study. That can be published. The study must include at least 50 agricultural soil samples that range from high MB to low MB and cover a wide variety of soil types. [email protected]
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interested
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I conducted potential nitrous oxide emission assessment from soil samples following the method previously used by Zhong et al 2018. The samples were incubated for 48 hours, taking gas samples at 0, 24 and 48 hours respectively.
I have read the N2O concentrations from the gas samples collected using GC, and this data is available. Also, available is the soil-dry weight of the soil samples used in the assessment.
I feel somehow stuck at the procedure for final calculation of the potential N2O production using the available concentration readings from the GC.
Has anyone previously undertaken such, or a similar study, and can quickly unstuck me?
How do i proceed to determine the final N2O emitted from the soil samples ?
Thanks in advance
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Best wishes and interested
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Please I am trying to determine the exact amount of biochar that was added to each pot. Please kindly help me check if my calculation is right.
Biochar applied at 20 t -ha−1
Height of pot = 20cm
1 hm = 10000 meter square
Assuming density soil bulk density of 1.2 g/cm3
Volume = 10000 m2 x (20cm x 10-2) = 2.0 x 103m3
m = p X v
m = 1.2 g/cm3 x (2.0 x 103 x 1 x 106) cm3
m = 2.4 x 109
m = 2.8 x 106 kg
So for 20 t per ha biochar
Biochar = 20 t x 1 / (2.8 x 106 kg/ha) x 106 g
Biochar = 7.14 g/kg
So for 5 kg of soil Biochar added was = 7.14 x 5 =35.7g
Please if my calculations are not right can you kindly assist with the calculations.
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The calculation process is correct. As shown by several RG members above, the correct amount is 41.5 g per 5 kg soil.
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Hi,
I wonder if it is possible to find natural soil carbonates (calcite, dolomite, etc.), not coming from liming, in soils naturally having a low pH (4-5.5).
Is it possible to find these mineral forms of C in acidic tropical soils?
I am asking because while measuring both total C and inorganic C (after acid dissolution) of tropical soil samples from Indonesia with an Elementar, I sometimes get a gap between the two measurements.
Sometimes the gap is positive (total C > organic C), and other times the gap is negative (organic C > total C !?). Generally, total C is equal to organic C, meaning most samples do not show these confusing 2-way gaps, and suggest the absence of inorganic forms of C.
In both cases, I wonder if discrepancies are just technical (noise), or if the gaps between samples are due to the natural variability of my samples, or in some cases, there could be some carbonates present in those soils (which have a relatively low pH of 4-5).
Best,
Thomas
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I dont think , it is possible to find any carbonates in acidic soils , considering the critical pH for precipitation of carbonates as 8.2 , except the pedogenic carbonates deposited deep into the sub-surafce of acidic soils . Ironically , maximum deposits of limes /dolomites are reported from acid soil belts only....
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Isolation of fungi from soil samples
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You can add Dichloran to the medium with a concentration of 1mg Dichloran per 1 liter medium to prevent the growth of Rhizopus significantly.
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The question is about how smallholder farmers can have soil sampling and testing services at reduced or affordable costs
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Your question connects so well with soil test- based fertilizer recommendation in small farms where farmers don't have so much access to soil testing. In that case , farmers can follow the fertilizer prescription of those fields in that region which are known for high productivity. Can also take some clues from region specific demonstration trials on fertilizer response..
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If i m Having 3 soil sample than the blank titration value will be same in finding the organic carbon content for all the soil sample.
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Yes , blank value will not change...
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please tell any IS standards for permissible limit of heavy metals in soil?
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Please refer to this attached file. It might be helpful.
Regards
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Plant does not eat soil but take soil water, hence with the advent of recent technologies, the soil scientist should adopt soil water analysis methodology instead of dried soil analysis.
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Ajay Kumar Mishra the question is close to my heart as well and I feel there are some material available that might be in the interest of the question
https://www.nap.edu/read/2132/chapter/5 This book gave the details n explained in a much better way
https://www.nap.edu/read/2132/chapter/9 reading material from one chapter for your reference
https://www.nap.edu/read/2132/chapter/5 opportunities to improve soil and water quality
http://www.fao.org/3/i0131e/i0131e.pdf plant nutrient analysis guide for setting up and running a laboratory
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Are there any equations that show the role of shear stress in the scour depth prediction?
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Please see the attachment of Kiprotich Kiptum.
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Actually I found in previous research papers that both Cr forms i.e. trivalent and hexavalent are interconvertible. So I want to know the exact amount of both the forms of Cr in soil sample in which I have supplied only hexavalent Cr. It will help me to understand the mechanism behind toxic behavior of both the forms.
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Praveen Kumar Determine Cr(VI) by diphenylcarbazide (DPC) and then determine total Cr using ICP or AAS, if you have these instruments. DPC is specific to Cr (VI), while AAS/ICP measures total Cr (VI and III). subtract the difference, which gives Cr (III).
If you don't have access to these instrument, then try this method
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Permissible limit of different metals in soil, with reference to Indian standard
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Thank you, Dr. Frank T. Edelmann
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What are the latest techniques to access rhizospheric as well as endophytic microbial communities from soil sample.
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I am in agreement with Anoop. Nowadays, molecular techniques specially combined with stable isotope tracing analysis may be beneficial for soil microbial community monitoring in soil. Some interesting recent references linked below:
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I am preparing a metagenomics experiment from the soil sample. I will use Oxford Nanopore technology, which has only limited throughput (approx. 8 GB), so I need to discard all eukaryotic cells before the sequencing (because their genomes are really large, and would saturate the device quickly). So I am interested in the simple and reliable method, how to obtain only the prokaryotic and viral species. Is it a good idea to use some syringe filters? E.g. with the pore size 1 micron? So the eukaryotic cells will be stuck on the filter surface, and bacteria, archaea, and viruses will go through?
Thanks for all suggestions,
Martin
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For details of the possible methods to use, the article suggested hereunder refers.
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Hi all,
do you know about any commercial service which offers CryoMilling?
We have a few samples of plastics (including e.g. PET) and soils, which we need to cryomill, but since we do not need this service regularly, there is not so useful for us to buy a cryomill. 
Thanks in advance for suggestions,
Jan
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As a part of my doctoral research, I am testing soil samples for multiple elements (such as P, N, etc.). Because of COVID, I was not able to immediately test samples gathered in the field in the fall of 2020; instead, these samples have remained frozen. My question is - can I still get these samples tested, or has too much time passed? Another consideration is that the soil was quite wet when frozen, and large ice crystals have developed.
I'm returning to the field shortly, and will able to gather more samples, but ideally I would love to run these as well! Any help is appreciated.
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Yes, we do that. You can thaw them out and subject the samples through normal preparation and analysis.
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Dear all, I collected soil samples for estimating organic carbon. we heated the soil through combustion. Got lab results. I'm advised to use 'ginostart' or 'R' methods to further analyze lab results into meaningful results in line with the research study. Kindly help me with how to use Ginostart, and R methods. A link/explanations are all welcome.
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Hello everyone,
We recently adquired a Digiprep block digestion system in our lab and I wonder if it can be used for highly-carbonated soils decarbonization. I have been looking for similar protocols but I had no results.
Thanks in advance and kind regards.
Layla M. San Emeterio
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Just trying this exact same method on our Digi-Prep to remove carbonates from sediment samples for 13C analysis: 100 mg dried sediments, 60 Celsius, 15 hours of reflux, 30 ml HCL in a glass vial with watch glass. Repeat heating cycle with distilled water 3 times to remove acid traces.
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I have to determine dissolved organic carbon (DOC) in the soil. Can anybody tell me the complete procedure ?
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...another paper published by Jones & Willett in 2005:
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Generally forest ecosystems are often developed on poorly fertile soils where the plant available pools of nutrient cations are frequently very low, but the content of available potassium for a natural terrestrial forest stand shows a very high value of 671.89 kg/ha using the standard method for the soil chemical analysis, is it natural for the soils of a terrestrial forest patch?
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Dr Das, understandably, the soil sample presents more clay and perhaps even closer to the rock substrate. You may please check with your Geologist for details, please.
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I am growing bacteria from soil samples I obtained from mine tailings. I spread the samples on some nutrient, luria and tryptic soy agar plates. But, some of the colonies are growing just beneath the surface of the agar. Would it be ok if I just mash the agar to get to the colony and subculture that? I'm not sure how to do it otherwise.
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Nicole Botha Unfortunately, you can't extract multiple colonies.
You can extract single colonies and add them to their corresponding new plate for growing them. It's a long and exciting or tedious process but it will work.
Please let me know if this works! Good luck.
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Collected soil samples may be stored for a certain duration before they are tested in the laboratory. I would like to know if this storage time affects the test results of various parameters of soil.
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The best way of soil analysis is doing it as soon as possible. However, soil samples can be stored after air-drying and sieving through 2mm sieve in a paper bag. Removing the moisture helps to reduce the rate of bio-chemical reactions and change in soil properties will be minimal.
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As a function of dimensions of real projects?
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Feel free to get in touch with me for more explanation.
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Usually i had extracted DNA from soil sample using power soil Qigen kit and got upto 700 ng/ul of DNA.
I do have a soil sample which has pH of 2.3 higlhiy acidic and one with 12.3 which is highly alkaline
i performed same extraction and got DNA only 3-5 ng/ul... that is not suitable for my downstream tests.
Can some one suggested what to do to increase yield of DNA from such sample.
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Indirect DNA extraction method suitable for acidic soil with high clay content
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Samples were prepared in 2019 as follows. Each soil sample prepared of mass approximately equal to 0.500g was a added to 9ml of HCL (35-37%) and 3ml of HNO3 (70%). The samples were digested. Kindly assist if the samples would give give me same results in March 2021 as the results of November 2019. Argon was used in 2019, but in 2021 Helium (KED) was used.
Also is there a method/formula to correct for K-40 interferences by argon species????
Thanks!
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Dear Vaino:
Theoretically, for changes in measurement conditions and behaviour of the instrument, cones, use of KED mode, etc.. you can not expect to get the same "signal responses" on two different days. However, our fundamental assumption is that any such changes affect the samples and the calibration standards the same way, which is the main reason why we do a calibration for each measurement run. Then, regardless of the differences in "responses" or the absolute signal on different days, calculated concentrations based on corresponding calibrations should come out similar (within the statistical differences). So, do not make any quantitative comparisons of absolute intensities from the two days, other than the calculated concentrations.
- If your interference corrections (KED, etc.) affected samples and the standards differently on the two days for K, then the above assumption is not valid.
- If your measured values for U, Th are close to the Limit of Detection, there can be significant statistical differences that have to be tolerated.
- Usually, K is measured using K-39 (93.3% abundance), with possible interference from Ar38H1. Are you sure it was measured at mass 40, which is usually disallowed due to huge interference from Ar40?
Best wishes,
Nimal
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Dear colleagues,
I would like to seek your expert opinions on the optimal storage conditions for sediment/soil samples for microbial community analysis. How's your experience with -20C, 4C, and even room temperature and do they make a big difference? Thank you very much.
Regards,
Nathanael
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I would expect changes at that temperature and timeframe. The biological processes would be slowed down at lower temperatures but would still occur.
If you can, sample storage at -80°C should allow for long-term storage
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Can you help me find legislation in any country in the world that regulates the permissible limit concentrations of PBDE congeners in soil. Thank you!
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Only Norway has the normative values used to identify contaminated sites for PBDEs. The values for soil are 0.08 mg/kg for pentaBDE (BDE‐99) and hexaBDE (BDE‐154), and 0.002 mg/kg for decaBDE (NGU, 2007; UNEP 2015). Environment Canada has Federal Environmental Quality Guidelines (FEQGs) for PBDEs for risk management practice that describes guidelines for water, sediment and biological tissue to protect aquatic life and mammalian and avian consumers of aquatic life from adverse effects of PBDEs present in some commercial products (Environment Canada, 2013; http://www.ec.gc.ca/ese-ees/default.asp?lang=En&n=05DF7A37-1).
NGU (Norges geologiske undersokelse). Forslag til tilstandklasser for jord. Trondheim, December 2007.
UNEP (2015) Revised draft guidance for the inventory of polybrominated diphenyl ethers under the Stockholm Convention. UNEP/POPS/COP.7/INF/27
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For the purpose of determining water dispersible colloids (WDC) and colloidal phosphorus, can we use the soil samples that have been air-dried and sieved at 2 mm or should we use only the fresh field soil samples?
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A basic step in any soil analysis is to screen soil samples to eliminate gravel, Stone and other parts outside the volume range of soil, which may increase the reading of the required analysis. Drying is also necessary because the moisture in the soil increases the weight of the sample and therefore the sample has less readings than requested
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How to do acid digestion of soil sample with 3:1 aquaregia in an open vessel?
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Soil samples treated wit 3:1 hydrochloric acid and nitric acid provides the best results as nitric acid destroys organic matter and oxidizes sulphide material. Nitric acid converts metal ions into nitrate salts which are highly soluble. Sample digestion is ideal before AAS - to destroy the matrix which otherwise interfere during atomization. Digestion converts all form of metal into single oxidation state.
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Hello,
I'm trying to measure the physical and hydrological properties of organic substrate media.
Currently, I'm referring The book Soil sampling and Methods of Analysis by Carter and Gregorich. (Chapter 68)
Measurement of bulk density
The method recommends the substrates in the cores to be saturated and drained on a tension table at -1KPa. My question is if we don't have a pressure plate, can we let the cores drain by gravitation for a specific duration (1-2 hours) and take it as the saturation point?
And to obtain bulk density, air-filled porosity, water-filled porosity at saturation at that point?
Measurement of water holding capacity
Water retention curve is graphed as water content against the tension. Instead of tension, can we graph it against time? after letting the core samples drain from the bottom while closing the top of the core? (picture attached)
Can you please mention if there are any standardized procedures/ papers related to the question? Thank you very much.
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That will be very interesting. It primarily depends upon the nature of soil and porosity as organic matter (different varieties) would behave differently in filling up the gaps and enhance bulk density. Hydrological evaluation is greatly dependent upon the bulk density. May I request you to share your results. All the best.
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Our method consists of a potentiometric titration of a soil plus an electrolyte solution (0.01, 0.1 and 1.0 M KCl). Soil is stabilised during 1 hour and then HCl or NaOH is added in order to modify pH to 4.0 or 12.0 respectively. PZC should be found in the intersection of the three curves, but we are getting unexpected results. Could you recommend another method or a modification of the one I am performing. Thank you very much.
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Video link for determination of Point of zero charge (PZC)
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Soil microphology is all the efforts that are made to study soils or soil samples, but in a microscopic or microscopic field.
In the study, regular and polarized microscopes
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Since soils are derivatives of the existent geology, there is bound to be variations not only at the macro but even at micro levels. Although, macro is addressed generally, micromorphological understanding of soils presents complex process of nutrient potential and growth of either plants or agricultural produce. Better understanding would further facilitate appropriate planning.
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I took a sample to the laboratory and got a shocking result that shocking result.
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Hi all! Could anyone recommend some reading materials on this subject matter? Thanks!
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I want to test the chloride ion concentration in the soil sample where I am conducting a research, but I cannot find a procedure to proceed. Thanks in advance!
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Dear Ram,
This question is openly provided here to all RG members to be replied. Please I would cordially like to request if you have any opinion regarding this question just provide it here, then everybody can read your useful thought.
Many thanks for your understanding.
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I was testing soil samples for sporangia of Synchytrium endobioticum and noticed that every once in a while there are these strange 'jumps' in my curves. I repeated the test three times, the sample is from the same test tube, but one of the curves looks weird despite being undeniably positive like the rest. I included two screenshots, one of the target fluorescence signal and one of the respective control where the suspicious curve also shows a bump although a small one.
I'm trying to validate this method and am at a loss as to why this happens or how to prevent it. Has anyone ever seen something like it?
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Thank you for your contribution; in the end I've gotten rid of this phenomenon by choosing a different cleaning method which leaves a cleaner sample. I assume the problem was unspecific residual DNA from different soil organisms that affected amplification.
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My samples are very high in organic matter, and even small amounts of H2O2 cause the samples to foam up 4-5 times the beaker volume, spilling onto the lab bench. Is there anything that can be done to manage this, other than adding smaller volumes of H2O2 or digesting smaller soil samples?
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Place about 10 g air dry soil containing no particles larger than 2 mm in a polythene bottle. Add 50 ml of NaOAc solution (pH 5-6), warm on water bath. Then centrifuge and decant the supernatant. After removal of excess salts and CaCO3, follow the treatment of H2O2 for removal of organic matter. Add 5 ml of H2O2 in a sample previously treated to remove soluble salts and carbonates. Add H2O2 in increments of 5 to 10 ml or less, stir the suspension, and allow time for any strong effervescence or frothing to subside. Place it on a water bath to warm. Remove the centrifuge bottle from the water bath and allow it to cool. The reaction of soil with H2O2 is essentially complete when the soil sample loses its dark colour or when conspicuous effervescence ceases. Some effervescence will always be present due to the decomposition of the H2O2. Centrifuge the bottles and decant the supernatant. The sample is now ready for the next step.
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1. Please anyone tell me if I analyse my soil nitrogen through CHNS analyser and I get my reading in N% and according to the calculation if my reading is 0.07% then:
N Kg/hectare = 0.07*10000*2.24= 1568 kg/hectare which is too high in field soil sample.
So, please anyone tell what is the exact formula to convert field soil N% into kg/hectare if the sample was analysed through CHNS analyser.
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before answering your latest question I would like to confirm that the total value we got for your soil is within the range reported by Niels H. Batjes ( ). Table 4 reports a range of 1,500 to 21,000 kg TKN / ha.
Probably the most accurate way to know the amount of available N would be to extract soil with 2M KCl ( ) and analyze for NH4-N and NO3-N colorimetrically following the procedure of .
Alternatively, you need to assume a certain fraction of the total N, that is available to plants for uptake. Refer to Girijesh Kumar Sharma who mentioned that around a tenth of the total N is available. This value agrees well with Li Qian et al. (2014; ) who determined total N = 3.08 g / kg and available N = 0.21 g / kg for their soil.
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How deep should soil sampling be done in a rangeland ecosystem containing shrubs?
The aim is to study the effect of vegetation on soil texture and organic matter.
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@ Iman, I suggest to take soil samples up to 15 cm depth for grasses and up to 30 cm depth for shrubs.
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It is well known that micronutrients are equally important for plant growth and development, but they are required by plants in small quantities. If they are taken in excess amount, especially in soils having deficiency of major nutrients, they are harmful to plants. If micronutrients are applied in excess amount, they may produce a harmful level in soils, which may be more difficult to correct than a deficiency. Their deficiency can be determined bot by plant and soil tests. So, is that necessary to conduct an experiment to determine an appropriate rate or amount for micro-nutrients?
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Waiting for micronutrient deficiency to appear and then apply micronutrient , would be a faulty practice. The best course would be to get the soil and plant tested for micronutrient concentration and accordingly identify the micronutrient deficiency or sufficiency level . But most important is to have soil test rating or leaf nutrient standards to use them as interpretation tool. And t hereafter we need to have soil test or leaf nutrient - crop response relationship based fertilizer requirement prediction model to recommend amount of fertilizer to be given at a given yield level or for a target yield level.
So its quite a task while scientifically speaking...
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Hi,
I wonder if someone would share experience with building open-top chambers for surface heating of soil. My main question is what material can be used to build them? I found researchers using Sun-Lite HP panels and polycarbonate panels. The former seems to be used more often, but the latter seems to be more readily available.
Any input is appreciated!
Tamara
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interested
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I have soil samples that have been frozen for a while and I need to re-acclimate them for a series of analyses that require incubation at 25C. I have been looking for laboratory methods but seem to not find any or I am using the wrong terms "thawing methods".
How can I do this in a lab setting? I have an oven and incubator.
Thank you!
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Air drying soil samples for chemical analysis is the most common practice, but if you are conducting microbial analysis keeping them refrigerated at 4C before analysis could be done. There are a few good articles here that might lead you in the right direction:
Lee, Y.B., Lorenz, N., Dick, L.K., and Dick, R.P. 2007. Cold storage and pretreatment incubation effects on soil microbial properties. Soil Science Society of America, 71(4): 1299-1305.
Wu, L., and Ma, L.Q. 2001. Effects of sample storage of biosolids compost stability and maturity evaluation. Waste Management, 30(1): 222-228.
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I have 1851 soil samples data on pH covering a study area of 7482sq.km in northern Ghana and I am using 52 environmental long-term average variables (Relief, Climate, MODIS Reflectances and derived products) to fit a model in order to explain the variability for pH prediction. So far, all models tested have shown low explained variance and sometimes even gives negative.
How may I improve the Explained Variance below?
Kindly see attached, the spatial distribution of points, and metadata excel file showing details about the covariates used.
Below is the summary of my models explained variance.
Multiple Linear Regression: 0.03
Step-wise Multiple Linear Regression: 0.04
RandomForest: -7.02
ExtremeGradient Boosting: 0.03
Support Vector Machines with Polynomial Kernel: 0.03
Additional information about the sample data
  1. Avg. distance between two sample points using nearest neighbor analysis: 2551.29m
  2. Data source: Student research data
  3. Sampling method: Grid/Management Zone Hybrid Soil Sampling method. The grid size is 2-4sq.km, management zones are subdivisions within the grid.
My assessment so far
  1. Removed spatial outliers
  2. Removed value outliers
  3. Normality check was ok (please see attached)
  4. Variography shows a spatial structure (please see attached)
  5. Tried Recursive Feature Elimination to reduce the dimensionality but did not show any improvement
  6. Tried reducing dimensionality by removing highly correlated covariates at a threshold of 0.75
I would be most grateful for insights into any techniques that could help improve the model explained variance.
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Dear all,
Many thanks for helping me to think through my Digital Soil Mapping Analysis. Your references were also valuable.
In the end, Ordinary Kriging was the best estimator as the machine learning models were not able to capture enough variability in the observation data which was due to poor spatial dependence (i mean more points closer to each other have dissimilar pH values).
I reckon that if I have to use machine learning, I may need to use many hundreds of covariates where each covariate tries to explain a small portion of the variability and scale it down to the best predictors. This process is iterative and highly time-consuming but would be considered later.
I attach here, the Ordinary Kriging pH prediction results.
Thanks a lot!
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Dear colleagues!
I am trying to figure out how to do an extraction for soil microorganisms for further metabolomic analyses. I am only interested in the microbiota part, so I would like to discard any organic matter present in the samples.
Do you know any useful method for that? Any suggestions that could help me?
Thanks for your help!
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I am looking for soil tests including (PH EC and others tests) under salinity and foliar nano .
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Only EC give idea about soluble Salt further analysis of cation and anions give idea that which one is more dominate in cations gernally Na and in anions Cl dominancy was found in water samples some time SO4 dominancy was found in some samples EC (dS/m) × 10= Total Soluble salt peresent in solution
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We are doing the prediction of soil nutrients using spectral information by applying machine learning models. More than 300 soil samples were used from one district for analysis. We got the support vector machine model as best with less RMSE. Is it the same devolved model that holds good for other district soil nutrient prediction?
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According to the statistic, you are using a non parametric model, then the new data can be utilized with the trained learning model, unless the new data responds to other different reality. Then, the origin of the data must be considered to applying the trained model.
There is not an overwhelming reply.......
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Hey;
I am looking to work on clays in my soil samples, So I need to extract them first.
I know that I should first remove all the bending agents that make the clay sheets stay connected like ( Carbonates, Organic Matter ...) fur this purpose I have to attack the soil by Hcl 5N and H2O2;;, but I need The procedure any help, please. Thanks in advance
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Dear Soumaya,
You may refer to the document attached. You may find it useful for your intended purpose. Good day!
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Almost all the literature shows that the vertical distributions of soil organic carbon (SOC) & available nitrogen (N) is found decreasing with increased value of bulk density with respect to depth and all those values show uniformity in each layer of 20 cm and up to 1m depth, increasing or decreasing of such values are uniformly distributed for the soil samples found in the literature, is that uniformity maintained at every where, soil layer of the mother earth is so unique and maintain such identical uniformity, though I am waiting for the report for the values of distribution of these chemical parameters from the soil test laboratory, if the obtained values are uniformly distributed with depth, it will be really unique and identical.
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Dear Gautam,
In the case of this discussion, I am totally in agreement with the statements and thoughts of Shubham. He explained the issue as well. I am specifically a soil ecologist and zoologist and I am also concerned about issues related to physical and chemical properties of soil. Thank you for your precision. Good luck.
Best, Elaheh
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Sediment is relatively younger than the soil in the depositional environment as the sediments are consequence of the accretion of particles transported either by waters or by winds, whereas, soil profile is stable lacking any sort of movement. Soil profile is developed with time span which is a stable one, but the movement of the sediment particles developed those soil profiles in so many physiographic set up, are they (soils and Sediments) differed chemically, do they possess different chemical environment?
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yes its do it
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I am working on 16S rRNA sequences in soil and looking for best reference data base. Which one is best one greengene or RDP or SILVA or NCBI
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I advise you to use SILVA! SILVA has different similarity OTUs percentages, e.g. 99%, 97%, ..., and it is regularly updated.
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In one of my experiments, I am assessing root biomass from soil cores, in which I have the root dry weight data, the core parameters, and the respective bulk density and soil moisture values. I am confused during the cumulative measurement of root weight per unit soil surface, from the dry weight of roots collected on the sieve combinations. For calculating the root density, it is straightforward (root dry weight/ soil volume), but I am unable to comprehend the term "per unit soil surface"? Am I missing something "obvious" term in the calculations?
As this is a trivial measurement, manuscripts tend to skip the details and directly report the results. To search for hints, I tried to look into older journals, where they divided the total dry weight with the area under consideration (attached the source). What area should I consider, surface area, or the crossectional area of the soil core, or something else for the root biomass calculations, and why?
Thank you, and have a great day!
Rounak
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@Ali R A Moursy
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I have ion chromatgrahy by which different type of cation and anion can be determined . kjeldal nitrogen arrangement is also available but it is not convenient to me rather than ion chromatography. my question is if i test soil sample to determine nitrate instead of total nitrogen. it would be recomanded by guideline or not ?
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Plants absorb nitrogen in the form of nitrates and nitrites, and the forms of nitrogen in the soil are different between organic and mineral, in addition to being exposed to volatilization, washing and fixation ... etc. thanks to that total nitrogen measurement, and by means of the micro-kjeldahl method, Good luck, dear
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Bulk density of a forest soil sample in a community forest created under social forestry scheme in the district of Nadia, West Bengal is obtained as 0.81 gm/ cubic centimetre, comparatively too low from the other samples of the same forest stands collected from 500 meters distance, visibly the sample is silty in nature, and the implanted trees of the said community forest are mostly of teak categories, the forest stood in the alluvial plains of the lower Gangetic deltaic set up, is the obtained value of bulk density normal for the physical nature of the soils of the forest floors?
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Bulk density (BD) measurement needs to be done by core method for any comparison to other soils' BD. If the SOC is very high in soils under forest for a long time, BD may be really low.
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I am currently doing my final year project on Geochemical analysis of peat samples. I will be looking at parameters such as major and trace elements plus anions and cations. Should i take samples from the surface (0-5cm) or take deeper samples using auger sampler?
Thank you for your time.
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In my opinion, in addition to sampling from a depth of 0.5 cm, it is better to take a sample from a depth of 5-15 cm.
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Many researchers have given the values of OMC and MDD for bentonite based buffer materials corresponding to heavy compaction (higher compaction energy).
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In expansive soils, swelling increases with increasing dry density and decreasing moisture content. Therefore, standard compaction is better to be used for expansive soils to reduce swelling problem.
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We can measure exchangeable K, Ca using flame photometer. Is it possible to analyse these ion using spectral analysis
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@ Ashar, yes it is possible. Please have a look of the below link:
Soil Biol Biochem. 2008 Jul; 40(7): 1923–1930.
doi: 10.1016/j.soilbio.2008.04.003
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Dear all,
It is possible to determine ammonium and nitrate concentration on 2M KCl extracts by HPIC (Ion Chromatography)?
Can you suggest me some analytical protocol (or manuscript) to determine ammonium and nitrate by HPIC on 2M KCl soil extracts?
Thanks in advance.
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you might find the attached document interesting. Old, true, but at least food for thought.
I hope there is something in it for you.
Good luck with your research,
Detlef.
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Hello colleagues,
I would like to amply the lignin-degrading gene (i.e., LigX, LigY, LigZ, and LigW) from different types of soil. I have tried to find literature, but unfortunately, there are no articles available where they have quantified those genes from soil samples. There are some cloning/mutagenesis studies available where they amplified those genes and inserted them into E.Coli, but we are yet not successful amply from soil samples. Does anyone have an idea or someone working with ligning-degrading genes quantification? We are interested to quantify those genes from bacteria only.
Thank you and really appreciate your suggestions.
Milan
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Hi,
I am currently trying to determine rare earth and heavy metal concentration via ICP - OES. I have been preparing soil samples via digestion using solution B, however results obtained were illogical as the concentration of REE and heavy metal were too high to be considered as trace. Any suggestion on how to obtain more accurate results.
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Following
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I recently demonstrated an industrial sized horizontal centrifuge at a food manufacturing plant on their waste coming from their wastewater treatment plant (WWTP).  The WWTP plant manager now wants to know what the BOD coming from the centrate off the centrifuge, back to the WWTP would be.  We did not measure BOD or COD at the time but only total suspended solids (TSS mg/l) in the centrate going back to the WWTP.  Is there a way to maybe correlate the BOD from the information gathered from the influent coming from the manufacturing side to the WWTP, if the TSS and BOD were recorded, to our centrate TSS? 
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In typical municipal-domestic ww design, we adopt: a)BOD=295mg/l, b)COD=500ppm and c) TSS=BOD5=295 mg/l. The guides shd be applicable for most domestic ww. However, we also advocate water quality measurement.
However, for industrial wastewater there is no guidelines available as the compositions are totally different. Although said, there are still some variations even for domestic ww as we are what we eat and it also depends on what goes inside the sewer lines too.
In a recent case of a Leachate plant that I am working on, the characteristics were a)BOD5= 18g/l, b)COD=20g/l and c)TSS= 800mg/l. So to answer to your point, we cannot estimated BOD from TSS. Above writer has said rightly that BOD refers to soluble BOD. Cheers
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The fact that there are no proper laboratory equipments devised till date for direct tensile testing of soil, I'm looking for a simple indirect procedure that would help in determining tensile strength of soil samples reasonably well.
Your suggestions are solicited.
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Thank you Mr Jacob
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I have tried using PowerSoil Pro kit from Qiagen with slight modifications- incubating at 65 degree for 10 mins after adding solution CD1, increasing the number of washes with CD5 to 3 times and drying the tube for 15mins after washing.
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Thank you I'll try this kit !
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The purpose is to compare it with magnetic grain size data.
Thanks in advance
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Thank you
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The content obtained for the C & N in the soil samples of the forest floors is increased this time and in 2020 is 5 times more than that of the C & N obtained in 2008, simultaneously the same forest stands in four districts is increased by areas observed in the India State of Forest Report 2019, not only that the forest canopy is much lush green in comparison to 2008, is this change be considered as the evidence of the climate change, though the time span of only 12 years is very short for interpretation of the evidence of the climate change.
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I totally agree with Fazel Mohammadi-Moghadam that we need more studies to be done around the world to repeat the idea and evidence. It is a very interesting discussion we are countering here. During my PhD study, I have done a long-term research investigating the effects of 20 years climate influence on soil fauna and vegetation. I think 12 years can also be considered as a long-term research and these discussed obtained results maybe show the effect of higher temperatures on increasing the decomposition rates. Although this is a perception and it really needs to be studied in detail.
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Hi,
I'm working with a set of soil analyses obtained from an external laboratory.
Studying the results, I am highly confident that one of the analyses gave incorrect results because the values are extremely unlikely (in total disagreement with what is normally naturally occurring).
Besides, I have conducted additional analyses to triple-check this analysis.
The results I have obtained contradict, as I expected, the anomalous data.
The problem is, that the method I used is not the same as the initial method (unavailable at my lab), but is supposed to measure the same variable.
Now that it is time to write a research article, what would you do to overcome this problem?
Should I explain that for this particular analysis, results were abnormal and were not considered further?
Should it be done early in the results section, or later in the discussion section?
How have you dealt with unexpected/erroneous data with your research, when you cannot repeat the same analysis?
Will a journal accept to publish results which include one bad apple, while the rest of the basket is fine?
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First thing, I would present this to the external lab. Perhaps they can look back at notes, strip charts or other outputs to check for mistake. Then if that fails, present the truth with the possible erroneous value and cross checked with other methods, and discuss briefly in findings. Like suggested, if the whole journal paper has no value with this issue included, then you will probably get some bad marks from editor or reviewers, possible suggestions to recover. When you say the value from lab is extremely unlikely or unnatural, it is likely the lab just made a mistake, it happens. It would be better for them to review the circumstance and your cross checking, and agree there was a mistake and then use your value based on their agreement, with a footnote perhaps briefly mentioning this attached to the value. Other issues can develop such as if your cross checking followed much later in time and samples were not preserved and/or stored properly. You may have to justify your work too.
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Suppose we need to develop a new method for routine soil test (a reference one already exist).
After developing the new one, we found that the two methods are highly correlated (for example, R2=0.996). However, the difference between the two methods are large, and the correlation line is much deviated from the 1:1 line (see figure attached). Can this new method be used as a replacement of the reference method ?. Thanks
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This question is out of my field...
I have no idea about it
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This is wondering me as how the process of soil sampling for both NH4 and NO3 ? what was the reason to not analyze fresh soil samples for both parameters ? the dry soil sample change the state of both forms of N during storage.
Reviewer ask me this question?
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Asif Ali Khan In fact, by drying the soil, we intend to obtain the concentration of ammonia nitrogen present in the solid matrix. Avoiding quantifying that found in the water.
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Dear colleagues, I am trying to simulate a strip foundation on a cohesionless soil with a friction angle of 30 degrees. However, I obtain convergence problems. I am using a geostatic step.
The error in the simulation states:
Time increment required is less than the minimum specified
Too many attempts made for this increment
I am new modelling soils in Abaqus, therefore, I'm not sure if I'm ignoring some basic concepts or if there is something I missed when inputting the soil parameters.
Thanks in advance
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This may help to locate the problem:
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After soil chemical analysis, obtained result for the content of organic carbon and nitrogen in kg/ha shows 0.00, whereas potassium content is 55.20 kg/ha for a surface soil sample collected in the Panagarh forest patches under the Bardhaman Forest Division of West Bengal, the soil was collected in the depth of 15 cm and the bulk density of the soil is 1.3 gm/cubic cm, visibly the sampled soil is the admixture of Alfisol and lateritic combination, is it possible for the soil sampled in the natural forests lacking both organic carbon and nitrogen, though the nature of forest vegetation is quite normal in the sampling spot?
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That might be anomalous, I will repeat the analysis for the particular Sample.
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Hello !
I would like to extract gDNA for soil to do NGS. We have the QIAGEN Powersoil kit. I did it twice now. First, according the kit instruction : concentration = 10 ng/uL, 260/280 = 1.4, 260/230 = 0.7. And the second time, I changed the lysis step by vortexing for a longer period and I heated the elution buffer at 50C as ssen on other discussion but my results are still not that good : concentration = 10 ng/uL, 260/280 = 1.8, 260/230 = 0.8.
Do you maybe have an idea on how I can improve my ration to send the sample for NGS?
Thank you !!
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The 260/280 and 260/230 ratios are indicators of the quality of your DNA, but if they are lower than 1.8 it does not mean that your DNA is not suitable for PCR amplification or sequencing. I suggest to perform a PCR with bacteria or fungal universal primers to check if there are PCR inhibitors. If the PCR works you should be fine as the quality of the DNA is sufficient enough for downstream procedure.
If the PCR does not work try to dilute your DNA (e.g 1:10 or 1:20 or more) and then test it again via PCR. I had ratios similar to yours but after diluting the DNA template 1:20 my PCR worked fine.
You can also add beta-mercaptoethanol 1% or Polyvinylpyrrolidone (PVP) to the lysis buffer to remove polysaccharides and polyphenols. Use the lysis buffer together with bead-beating procedure.
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We have to determine easily-extractable glomalin (EEG) and total glomalin (TG) from soil samples, but we have found various contradicting methods and calculations. Is there a trusted method that can be used to yield more consistent and trusted results?
Thank you in advance for your kind assistance.
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@ Johan, the parameters of the NIRS calibration model (R = 0.90 for soils from arable land and grasslands and R = 0.94 for forest soils) proved that glomalin can be determined in air-dried soils by NIRS with adequate truthiness and precision.
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There are several methodologies and quality publications available regarding on soil quality index but they have not considered the soil biochemical properties.
Please let me know the scientific reason.
If we can consider the biochemical properties then what will be the criteria of indexing?
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Soil quality is measured by physical, chemical and biological indicators. Soil biological properties like microbial biomass carbon, microbial biomass nitrogen, soil respiration, mineralizable nitrogen and sulphur, soil microorganisms, etc. are import soil health indicators. Biological diversity is also considered in soil quality index computation.
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The radon concentrations in soil samples measured by registrant alpha-emitting radon (222Rn) by using (CR-39) track detector, The uranium concentrations in soil samples measured by using register at fission fragments tracks in (CR-39) track detector that caused by the bombardment of (U) with thermal neutrons from (241 Am-Be) neutron source that has flux of (5 ×103 n cm-2 s-1).
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you can measure it using gamma spectroscopy such as Germanium detector
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I am lay in this subject. Is DNA sequencing the best way to identify the different types of soil bacteria present in soil samples? Ideally, I'd like to find a technique that allows me to identify all different types of bacteria (from those that could be identified) present in a given soil sample. Thanks.
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Soil is a rich repository of microorganisms. Basic techniques include isolation by either pourplating or spreadplating on appropriate media. Identification can be done by laboratory procedures such as gram staining, motility test, spore staining and a battery of biochemical tests. Quicker results can be obtained by 16 S r RNA sequencing technique. Comparison with NCBI gives similarity of your organism with others.
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As soil quality represent it's "fitness to use" or "capacity of soil to function to sustain productivity maintaining environmental quality and improved health".
What are the basic components which must be included while developing the soil quality index?
Minimum set of data required for SQI ?
Is it necessary to rotate all the components ?
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The components for soil quality index from the measured soil properties of the mineral soil cores, may include sample weight, bulk density, water content, coarse fragment content, water and salt pH, carbon (total, organic, and inorganic C), total nitrogen (N), 1 M NH4Cl exchangeable cations (sodium [Na], potassium [K], magnesium [Mg], calcium [Ca], aluminum [Al]), 1 M NH4Cl extractable trace elements (manganese [Mn], iron [Fe], nickel [Ni], copper [Cu], zinc [Zn], cadmium [Cd], lead [Pb]), 1 M NH4Cl extractable sulfur (S), and Bray 1 or Olsen extractable phosphorus (P). e SQI
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There is a growing interest in developing means of early detection of crop nutrient deficiencies. It has held that by the time a deficiency shows up in a soil sample, the crop is already under stress. Does crop sap analysis help to resolve this information gap? If so, how can we expand the use of this from high margin specialty crops to commodity crops?
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Leaf and petiole analysis is an established tool. Protocol for perennial crops have been standardized for nutrient analysis.
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There are three primary areas of ground movement towards a pressurised TBM: at the face, along the shield skin and at the tail void -(In the attached figure).
Can the maximum surface Settelment of the tunnel Longitudinal Cross section due to the displacement of the tunnel face can be added with the Transverse cross-section surface Settelment and introduced as the final surface Settelment? in 2D model-numerical method.?
But in the transverse two-dimensional method, we cannot get Settlements dou to face pressure induced by tunnel advanc.
I was going to get the Settlements dou to face pressure from the longitudinal 2D model and add it to the other Settlements Caused by other factors
In the longitudinal section of the tunnel, details and geometries and conditions have been implemented so that only the displacement caused by the face pressure is created and that the shield cone and mortar injection and consolidation are not modeled.
so only max surface settelment in longitudinal cross cestion is occurred due to face pressure It is capable of adding with max surface settelment in transverse cross sestion due to injection pressure and shield cone?
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I simulated the shield driven-tunnel by FLAC 2D, in which step of numerical model must be applying the traffic loads of ground surface (20 Kpa)? the traffic loads of ground surface change along day and night
@steps:
1. elastic initial equilibrium.
2. elastic-plastic initial equilibrium.
3. Simultaneous with excavation and pre-installation lining.
*in which step influence the traffic loads is real? (interaction with ground above tunnel)
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I have found some tools which would be inserted to the soil, but I'm not sure about its accuracy. Can anybody suggest inexpensive, easy-to-use, accurate soil testing tools/kits?
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For NPK results, the nutrient level is indicated on a scale from 0 (depleted) to 4 (surplus). pH test results are indicated on a scale from 4.5 to 7.5. Make sure your soil contains the three main nutrients (NPK). The site below can help you.
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analysis of soil samples have shown that in addition to lead and zinc, manganese is also present
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Yes, these are the results of X-Ray Diffraction. I am investigating heavy metals contamination in an alluvial soil in Germany, I was expecting high values of Lead, since Lead and Zinc mining was historically carried out in the region, but I was not expecting the high Mn values. I am wondering if it had to do with the dissolution of siderite and thus the replacement of Fe by Mn ?
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How can we homemade measure the pH from a soil sample? I have two soil samples and I'm looking forward to knowing how can I measure the pH without technologies.
"pH is determined by measuring the hydrogen ion activity in an aqueous solution. A glass electrode, calibrated against a pH standard is used to do this. A sub-sample of soil is mixed with water or CaCl2 at a ratio of 1 part soil to 5 parts liquid and the pH of the suspension is measured after 1 hour shaking".
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@ Halley, you may very well measure your soil pH at home using pH strip by following the procedure: Dig for a Sample, Place 1 to 3 Teaspoons of Soil in a Clean Glass, Pour in Distilled Water, Agitate the Soil Vigorously by Stirring or Swirling, Pour Soil Sample Through a Coffee Filter and Into Another Clean Glass, Dip the pH Test Strip into the Liquid, Note the pH from colour change. You may also use pH tester if you have. Accuracy will depend on the range they cover, the number of colored spots, and the general quality of the product. Because the important pH range for soil is between 5.0 and 8.0, test strips covering this range are better than ones covering a wider range. A product with a range of 0.0 to 14.0 is quite useless for soil.
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Hi,
I am air drying soil samples of a number of soil types to be used to produce a soil moisture curve for the callibration of soil moisture sensors to the diffrent soil types. Once the soil is relativley dry I will rewet samples to produce a gradient of samples from dry to saturated to get a soil moisture curve for each of the soil types. Sensor readings will be compared to lab measurments of soil moisture content. To speed up theair drying process, I was thinking of drying the samples in an oven.
My question is , at what temperature should I dry the soil in the oven without causing the soil to develope hydrophobic properties?
Thanks in advance,
Asaf
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When in college many years ago, we oven dried soils. Then maybe 15 years ago, our soil scientist took volumetric samples, but then broke them up on bags for air drying, stating that air drying is the proper way as compared to oven drying. From what I can surmise, breaking up the soil is needed for air drying, and it might take weeks. When in college, we would saturate relatively undesturbed volumetric samples from the bottom, and then use pressure apparatus to push the water out at designated pressures, such as 1/3 bar and 15 bar. So I am not a professional soils scientist, but would suggest that going from saturated to various levels of moisture toward air dry is probably preferable. When you want to air dry, the sample is then disturbed so it can effectively dry. If you live in a humid climate, a dehumidifier may help it dry faster. But for research, consult the standard methods and stick with them. Air drying an undesturbed soil core may take a long time, so breaking it up is appropriate, but then rehydrating a disturbed soil and then taking it back through the drying cycle is likely somewhat different than using an undisturbed sample, and then measuring from saturated to air dry.
If I had to pick a temperature, for expediency, low humidity set at or approaching 100 degrees C (boiling point, but probably not hot enough to volatile organics). I think in my early college days, 105 degrees C was the typical setting.
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I am trying to understand if there is a relationship between the angle of internal friction of soils and the angle at which the stress is distributed within the soil if a vertical force (via a footing) is applied at the surface.
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The value of angle of load distribution β tends to increase with increasing angle of friction.
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I plan on adding chloramphenicol to PDA media with diluted soil samples to isolate fungi and suppress bacterial growth. My question is how exactly do i infuse the chloramaphenicol to the culture?
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Chloramphenicol can be added to media before autoclaving.
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I have been trying to isolate Bacillus from soil sample. I m not able to identify the Bacillus in the mass. I need suggestions to identify the Bacillus.