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Dear researchers,
I'm currently doing research related to the nitrogen cycle. But I am confused about the potential of the nitrogen/nitrate/nitrite reduction reaction relative to a standard hydrogen electrode (SHE).
Can anyone please provide some information for this question? I would be really thankful for your help.
Best regards
Yun
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Good feedback by Mohebul Ahsan. However, it should keep in mind that this equation gives the overpotential for any electrochemical reaction.
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N-fixation by various leguminous and non-leguminous plants is important and its quantification as function of nature of crop, crop growing condition, soil environment, soil N availability and N-addition needs to be evaluated. We wish to know from the experts colleagues on this kind of work done and like to share the publications by the group on this important aspect, as well some of the empirical technical coefficient generators in this regard.
regards.  
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Also check please the following very good link: https://ageconsearch.umn.edu/record/118041/files/11.pdf
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Hello,
I'm searching for some already published articles reporting GHG-Indexes for crops such as Wheat or leguminous forage crops. Possibly under rainfed and Mediterranean climate conditions.
Also, papers that do not directly report the GHG-Index but include both the annual cumulative CO2eq. emissions and crop yield would be OK (e.g., 60 t CO2 eq ha-1 y-1 and 10 t Dry matter ha-1 y-1)
Thank you very much!
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Kindly consult this article:
CARBON FOOTPRINT OF SELECTED CEREAL AND LEGUME CROPS CULTIVATED IN THE OLD BRAHMAPUTRA FLOODPLAIN SOIL
  • December 2014
  • DOI:
  • 10.13140/RG.2.2.31404.05766
  • Thesis for: MS in Soil Science
  • Advisor: Dr. Md Abdul Kader
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i have a test box which needs nitrogen environment, its size is about 1m^3.
Could i ask how much N2 flow (50slm or higher?) do we need to flow in the box to generate oxygen free environment? the pressure is standard atmosphere, ~760Torr.
Thanks!
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my original reply applies
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Most research on soil organic matter focus on how the addition of cover crop residue affect SOM and soil Carbon. But does the SOM content affect N release from cover crop residue at all? For example, comparing a soil with high SOM content, say 4%, to a low SOM content soil, say 1 %, can one expect differences in N release from cover crop residues planted in such soils at a temporal scale?
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Yes it's true because organic matter contents increase microbial population so that's why it takes part in mineral uptaken by plants
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Hi everyone,
I am doing an allantoin assay in urine and all the protocols seem pretty vague. I am currently using this website which seems to be the most helpful:
It mentions that I use 15 mL tubes, but since I am boiling the samples should I use glass tubes with a cap to prevent escape? Or can I just use plastic tubes like the ones here:
Thank you!
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Nice question
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I am working on the effect of pH on functional genes in the nitrogen cycle (amoA, nosZ..). Some of the papers i have read present results based on the ratio between functional gene (like nosZ) and 16S. Why do they compare the ratio between functional genes and 16S genes? Any assistance will be highly appreciated.
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In general, the gene number copies is expressed in relation to the suspension volume or sample mass (i.e. number of 16S gene copies per mL or number of 16S gene copies per gram of soil). The number of gene copies can also be expressed in Log10. While functional genes are expressed in relation to the total abundance of the community (16S rRNA). For example, number of nifH gene copies / number of 16S rRNA gene copies.
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I'm writing a chapter about the nitrogen cycle and discuss the different forms of reactive nitrogen such as NO3 and NH4. I also have some soil places where I discuss soil cations and others where I discuss plant nutrients such as "In a study with Sphagnum spp., Ca and Mg foliar content decreased as N deposition increased..." When should I show ionic charge? Thanks.
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Indeed, a good point. I see papers like:
Cole, J. C., Smith, M. W., Penn, C. J., Cheary, B. S., & Conaghan, K. J. (2016). Nitrogen, phosphorus, calcium, and magnesium applied individually or as a slow release or controlled release fertilizer increase growth and yield and affect macronutrient and micronutrient concentration and content of field-grown tomato plants. Scientia Horticulturae, 211, 420-430.
were the ‘formal’ notation is ‘loosely’ used. I think everybody understands that when talking about Mg content in these type of studies is actually Mg2+.
Personally, I would use Mg2+ as much as possible or talk about Mg ions, but I can imagine that in other disciplines other notations are tolerated or simply more costume.
Best regards.
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I am doing an in vitro research on the Nitrogen cycle in aquaculture pond water. For my experimental facilitation, I want to remove ammonia nitrogen from water without hampering the biomass of microbiota and other nitrogenous compounds. Can anyone please help me with possible solutions?
Thank you in advance.
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In the alternative, you may use Deep-Water-Culture technique of aquaponics to grow some useful vegetables which biologically utilize ammonia-nitrogen in form of nutrients. You may quantify the nutrients by running the proximate analysis of the vegetables after harvest. Read further. Thanks. @
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I am using the EDGAR v.5 database for worldwide NOx emission data from fossil fuel combustion. But I need to calculate only the contained N emitted. Is there a general ratio of NO2/NO emissions, so I can calculate N molar mass? Thank you!
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Plants usually uptake nitrogen in the form of ammonium and nitrate. If we supply 15N labelled nitrogen fertilizer in the form of ammonium which will eventually get nitrified. I am interested to know how can we differentiate how much ammonium and nitrate were consumed by plants. I will be thankful for any suggestion, guidance, advice or relevant literature.
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Plants those love to take nitrogen in aerobic condition they uptake nitrogen as ammonium, generally maximum vegetables uptake their nitrogen as nitrate form. Plants those growing in submersible /anaerobic condition as rice love to take up nitrogen as nitrate.
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I am looking for a cyanobacteria to be used in a toxicology assay on agricultural runoff. Preferably a single celled cyanobacteria with a large role in the nitrogen cycle that would survive in freshwater/ pond water and that would be easy to plate on solid media. I have a cultivation set up and plan to use BG-11 media and plates.  I have tried a few strains already but lately have been running into some issues and am looking to start over with something that may be a little closer to ideal.
Any and all suggestions would be appreciated.
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Good idea .
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Diazotrophs 'fix' atmospheric nitrogen into biologically available forms. In very general, non-technical terms, an over-abundance of these organic nitrogen forms within a soil beyond what biota in the soil metabolically require has been suggested to result in the increase of nitric acid in the soil. What I would be very interested in is if anyone has done work to help establish a rate of nitric acid production in response to this over abundance of organic nitrogen.
Cheers!
Eron
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I think yes...please do experiment
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Much thanks.
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IVL passive samplers may be used for collect of the nitrogen gas for air pollution measurement
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Is there any effects of air pollution (NO2 in this case) to water ecosystems through Nitrogen cycle. Has anyone researched in practice this type of associations? what people think is there direct link between these to parameters?
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When NO2 and NOx interact with water, oxygen and some other chemicals in atmosphere and form acid rain. ultimately acid rain harms ecosystems e.g. lakes and forests.
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Hello everyone,
For my research I need to know if Chlamydomonas reinhardtii cw15 arg- grows on nitrate or not, to see if I can do some tests changing the nitrogen source. However, I cannot try grow it myself because of the quarantine. Does anyone know if it does or where can I find this information?
Happy quarantine. Thank you!
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Please check the following PDF attachments.
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Please see photo of a typical field site ditch pool bubbling water. Photograph is of one of our larger study sites. The bubbling water would often occur in the small pools . You can see the larvicide spreader. Temperatures low 80s max 90s Celcius, pthis site pH 7.8, high in nitrate. I suspect a chemical reaction definitely not bacterial nitrogen cycling. Thank-you. Sharon Pratt Anzaldua
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Bubbling may occur due to aquatic plants or algae.
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Hi everyone,
I performed multiple regression and a nonmetric multidimensional scaling analyses in order to understand which environmental factors have the biggest impact on the abundance of several nitrogen cycling genes. From what I have been reading, the vectors fitted onto the ordination plot are calculated performing some kind of correlation analysis, so I was hoping to obtain similar results; however they seem to contradict each other.
Why is that?
Here are my multiple regression analysis results and the NMDS plot (colors represent the sampled stations and the shapes represent the sampled depth)
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In my opinion, from your table and figure, your two results are consistent instead of contradictory.
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1. There are several database containing nifH sequences like fungene (19500 seq), arb database (32,954 seq), zehr (72000 seq) and farnelid (5,00,000 seq). what is the difference between these databases ?
2. Can fungene pipeline be used for taxonomic classification of nifH functional gene ?
3. Any other pipeline/tool available for taxonomic classification of nifH gene ?
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In addition to the pipeline mentioned above ( ), you can also have a look at this one:
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I am processing a 16s RNA next gen sequencing data set and trying to compare between my samples the effects on organisms involved in the nitrogen cycle. I am just wondering if there is some sort of database or even a good paper that goes over all of the known organisms in the nitrogen cycle. The more detail the better but i would settle for just a simple list
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Thanks
Shan Thomas
i will check it out, looks like a more convenient solution than trolling through papers
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Calcium nitrate Ca(NO3)2 given same N use efficiency in all parts of plants which application in acid soil low pH. in comparison for NH4 sources, I appreciate all scientists comments, that could be explaining those reasons. thanks in advanced.
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The form of N and the fate of N in the soil-plant system is probably the major driver of changes in soil pH in agricultural systems.
Nitrogen can be added to soils in many forms, but the predominant forms of fertilizer N used are urea (CO(NH2)2), monoammonium phosphate (NH4H2PO4), diammonium phosphate ((NH4)2HPO4), ammonium nitrate (NH4NO3), calcium ammonium nitrate (CaCO3+NH4(NO3)) ammonium sulfate ((NH4)2SO4), urea ammonium nitrate (a mixture of urea and ammonium nitrate) and ammonium polyphosphate ([NH4PO3]n).
The key molecules of N in terms of changes in soil pH are the uncharged urea molecule ([CO(NH2)2]0), the cation ammonium (NH4+) and the anion nitrate (NO3-).
The conversion of N from one form to the other involves the generation or consumption of acidity, , and the uptake of urea, ammonium or nitrate by plants will also affect acidity of soil.
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Has anyone had any success using DAF FM diacetate, for Nitric Oxide detection, on bacterial or archaeal cells? I am seeing very little literature using this.
If so, are there any specific techniques I should know about for getting it through the cell membrane of various bacterial groups?
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I am trying to obtain plasmids containing functional genes from the N cycle, but lately I have been having some problems with my cloning and transformation experiments since I only obtain blue colonies in the blue-white screening. Any ideas of what could be happening?
This is what I do: I amplify the gene, then run an electroforesis gel of the products, I cut the gel and extract the DNA using the QIAEX II Gel Extraction Kit from QIAGEN, then I perform the subcloning reaction using the TOPO TA Cloning Kit by Invitrogen (with pCR 2.1 TOPO vector) and the transformation is done using chemically competent TOP10 cells. I use LB Agar + ampicillin and X-gal.
Thanks!
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Good for you. Ramiro, however, to whom your " You need to use both IPTG and X-Gal" advice was addressed, does.
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Industrial production of ammonia requires high temperature and pressure. But the natural fixation occurs in ambient environmental conditions.
I’d be interested to know the mechanisms employed (mediated by the enzyme) by the bacteria in achieving this?
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Yes, i agree with Dr. Rosa that Enzymes involved are key to understand this process in natural marine environments. So, better check literature on nitrogen species conversion processes.
Best!
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Dear All,
Nitrogen is on of the important gas element from the atmosphere.
Presently lot of study has been gone conducted in last 100 years in reference of many more things like specific ecosystem, lakes, forest, bio-gas system.
I want to know more about nitrogen cycle in reference of aerobic and anaerobic composting.
If some had known about this specific area or having any known literature. please share or guide the pathway of study.
Regards,
Dinesh joshi.
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Please have a look at these PDFs..
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I have followed NH4, NO2, NO3, ON, and TN dynamics in pilot scale- FWS treatment systems with and without FTW to get a mechanstic understanding of N-cycle with these systems.
I am trying to sddresing the complexity of the interacted removal processes within these systems using STELLA.
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Thank you very much Gustavo,
Really appreciate your comments.
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We are considering use new techniques to study the soil organic carbon and nitrogen cycle/availabity to plants in a biosolid application land. Does anyone have some kind of survey about new techniques/tools/methods to study soil N or C? Mainly N. 
Thank you for your time!
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There are many soil-based tests of N availability.  It's a case of finding one (or more!)  that makes sense in the context of what you wish to examine.  Soil extracts can used to localise different pools of N, e.g. by extracting with water (N in free solution), salt solution (free solution + adsorbed), CHCl3 + salt solution (free solution + adsorbed + microbial).  For each type of extract one could measure total pools of inorganic N or organic N, or even measure specific compounds or classes of organic N (e.g. amino acids).  There is also the option of measuring the rate at which inorganic forms of N are produced, i.e. various mineralisation assays.  There are suggestions that depolymerisation may be the limiting step in supplying plant-available forms of N, and thus it could be useful to measure rates of proteolysis as an indicator of N availability (see attached paper)
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Am interested with nitrogen cycling and nitrogen budget. Am looking for the current methods I can work on nitrogen budget. I will appreciate getting papers that can assist me.
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A nutrient budget takes into account all the nutrient inputs on a farm and all those removed from the land.
Abstract : The nutrient (P and N species) and chloride budgets were investigated in a representative floodplain in the seasonal wetlands of the Okavango Delta, Botswana. A variety of sources of nutrients in the surface water were considered, namely ion species coming with the floodwater, those generated from dry floodplain soils and those from water-soluble dust deposition (both local and long-range sources). Concentrations of total-nitrogen and chloride in surface water were below 1 mg l1 . Total-phosphorus concentrations were 0.05 mg l1 , reflecting the oligotrophic character of the system. Dust deposition rates were highest for chloride at 2.44 g m2 year1 followed by 0.79 g m2 year1 for total-N, 0.40 g m2 year1 for ammonia and only 0.02 g m2 year1 for total-P, respectively. Chloride was derived primarily from long-range transport, while N and P species were of more local origin. Dissolution rates for these ions combined were calculated to be 3.9 g m2 for the flooded area in the 1999 season and thus all dry deposits must be re-dissolved. The accumulation of dust deposits on dry surfaces and their subsequent dissolution causes 2–5 times higher concentrations of nitrogen, phosphorus and chloride with the onset of the flood, thus boosting the nutrient stock in the crucial phase of the onset of flooding. Chloride dissolved from dry soil surfaces and dust contributed approximately 40% to the overall floodplain budget. Although contributions from the soil surface and dust to the nitrogen and phosphorus pools of the floodplain are less prominent (with 10% of total), they nonetheless represent a significant source of nutrients in the entire system. Extrapolation to annually flooded swamps (10,000 km2 ) indicates a maximum contribution of 40% for total-nitrogen and 60% for total-phosphorus from dust deposition on wet or dry surfaces to the nutrient pool of the water body.Source :Wetlands Ecology and Management (2006) 14:253–267 Springer 2006,DOI: 10.1007/s11273-005-1115-0
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Even though we determine the net or gross organic nitrogen cycling microbes,  and microbial NUE, we cannot know who is taking charge in the process of organic nitrogen cycling.
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Dear Yinan , please find an interesting work entitled Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling  published in Nature Communications 5, Article number: 3694 (2014)
doi:10.1038/ncomms4694
Abstract
Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling. PDF enclosed for further reading...
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The hypothesis is that the protons formed during the nitrification react immediately in the denitrification reaction (in a combined system). In a separated system the protons formed during nitrification will react with bicarbonate forming CO2 + H2O leading to a higher decrease in TIC compared with the combined system.
NH4+ + 1,5 O2 -> NO2- + H2O + 2 H+ (nitrification)
NO2- + 0,5 O2 -> NO3- (nitrification)
CH2O + 0,8 NO3- + 0,8 H+  -> 0,4 N2 + 1,75 H2O +1,25 CO2 (denitrification)
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COretention or release from water or wastewater is pH dependant with pH<7 promoting CO2 release, hence nitrification can be expected to reduce inorganic-C via two pathways, (a) nitrifiers use CO2 as a C source to fix C and (b) CO2 release by acidity. However, inorganic-C dynamics may not be entirely influenced by nitrification. Aeration to promote nitrification can also promote CO2 release by oxidation of organic-C. If we ignore the above, continuous nitrification without denitrification could rate limit nitrification since nitrification rates are lower below pH<7 with high build-up of H+, thereby self-limiting the release of CO2 by high acidity. It could be argued that triggering denitrification by ceasing aeration at this point in a 'combined system' could promote alkalinity and when aeration commences again, there is greater potential for nitrification and release and use of CO2.
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Is the carbon atom recently found in the center of the M-cluster of nitrogenase ubiquitous in all nitrogenases (Mo, V, and Fe?
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thank you Bruce, I'm not crazy
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I encounter two questions during SI-ATRP. My experiment route is shown as follows.
First ATRP reaction, MSN-Br(100mg), GMA( Glycidyl methacrylate, 1.5mmol), PDMETA(Pentamethyldiethylenetriamine,0.1mmol),DMF(2 mL) mixed togather and degassed by three vacuum/nitrogen cycles. Then add CuBr(I) 0.05 mmol into mixture, degassed again. The polymerization was performed for 5 min at the room tempurature. This step can gain MSN-PGMA. After cleaved from MSN by HF, obtained PGMA can't dissolve in any solvent.Why??
First ATRP reaction, MSN-PGMA(100 mg), DMAEA(Dimethylaminoethyl acrylate, 5mmol),PDMETA(Pentamethyldiethylenetriamine,0.1mmol), Methanol(5mL) mixed together and degassed by three vacuum/nitrogen cycles. Then add CuBr(I) 0.05 mmol into mixture, degassed again. The polymerization was performed for 7 h at the room tempurature. This step can failed. The PDMAEA isn't grafted. Why??
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MSN-Br you mean ATRP initiator grafted Silica? If yes, see in that case you have sufficient initiator grafted on silica surface which can assist to graft (/hold) considerable number of chains on particles. I think in your case instead of surface initiated polymerization the cross-linking (both acrylate and ring opening of epoxide) may be giving you the insoluble polymer. OR it is also possible that during detachment HF mediated ring opening is leading to cross-linking which leads to insoluble polymer (less sure about this one but look for some ref.)
In the second case where you have PEGMA functionalized Si you can simply carry out free radical polymerization than ATRP it can also guarantee good polymer grafting.
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I'm working with recovery of soils that are damaged with physical structure, using cover crops.
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Dr. Souza, FTIR identifies and qualifies sensitivity to mineral and organic bonds that compose soil minerals and organic matter. To know the limitations and potential you may go through the attached file.
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Hi to all.
As you know there is a  big problm with gas wells as the pressure drops down the dew point. So condensate build up near the wellbore or in the well  blocks the gas flow. the most common solution is nitrogen cycling due to lift the condensate fluid and let the gas to flow again. another way is squeezing nitrogen into the formation to remove the condensate blockage.
Now, I'm working on a project to optimize the condition such as nitrogen flow rate, pumping pressure, pumping period and ... . Furthermore I want to know which job is more efficient.
So I would be appreciated if you can help me to know about the simulation program.
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Thank u so much Hector for your helpful and detailed answer.
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Denitrification-How is actual COD/NO3 determined for denitrification? Is it ok to take the difference of COD consumed/NO3 reduced for each day
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Dear Nasir,
COD/NO3 ratio in denitrification is a smart way  to ensure your bacteria gets a right dose of electron donor (i.e COD) for reducing your nitrates (electron acceptor).  You must calculate this ratio from your initial concentrations i.e how much COD is available for reduction of say X mg of nitrates.
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Can the analysis of Nitrogen 15 isotope in soil and plant samples be carried out using HPLC techniques?
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No, this is not possible. Neither by HPLC-IRMS because this technique is used for d13C analysis for now due to a lack of optimization of the instrumentation. None of the commercial enterprises dealing with IRMS is ready for that even if it is reallly interesting.
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I have read many studies which use anaerobic incubation method to determine PMN. My understanding is that when soils are flooded with water,  denitrification processes are enhanced because of lack or oxygen which result in some N lost as a gas and some leached. Are results from this method of incubation in determining PMN an accurate representation of the mineralization process? Does this method then encourage waterlogging in soils?
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Portia,
The objective of this test is to determine NH4-N production after a 7-day anaerobic incubation.  As incubation is done under anaerobic conditions, all NH4+ produced during the incubation remains as NH4+ since the nitrification is restricted by anaerobic conditions.  It is true that any already existing NO3- in the soil sample can be denitrified; but, it does not matter, since the aim of the test is to measure potentially mineralizable N.  It is the biological N availability index recommended by Keeney (1982) and the purpose and usefulness of the test is well explained in Keeney, D.R., 1982. (N availability indices.  Page 711-733, Methods of Soil Analysis Part 2.Agron. Monogr. 9 ASA & SSSA).
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I am using an invasive, saprotrophic lawn fungus (Amanita thiersii) as an integrator of carbon and nitrogen cycling in lawns.
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Hi Paul,
  Thank you very much for your reply. Amanita thiersii is mostly invading in the Midwest but I imagine that lawn care practices have mostly shifted similarly with time across the country. To give you more background, below I give the title and draft abstract of the study. Superscripts and subscripts were lost when I pasted.
Cheers,
Erik
The invasive fungus Amanita thiersii integrates site nitrogen and carbon dynamics across C3 and C4 lawns
Amanita thiersii is an invasive, saprotrophic fungus that is expanding its range rapidly in Midwestern lawns. Carbon isotope (δ13C) values from sporocarps collected between 1982 and 2009 correlated positively with mean annual temperature (MAT) and negatively with mean annual precipitation (MAP), reflecting presumably the relative use of C3 and C4 grasses in lawns. In addition, δ13C values correlated positively with the Suess effect, the drop in δ13C and increase in CO2 concentrations caused by anthropogenic fossil fuel combustion, with a coefficient of 4.9 rather than the expected value of 1. The apparent 13C discrimination accordingly increased by ~2.3‰ (check?) as CO2 concentrations rose by ~40 ppm over this time period. This enhanced 13C discrimination probably reflects increased assimilation by A. thiersii of C3-derived carbon, either resulting from management changes (increases in the planted proportion of C3 lawn grasses over time) or increased quantum yield and productivity of C3 grasses relative to C4 grasses with rising CO2 concentrations. Sporocarp nitrogen isotope (δ15N) values correlated positively with MAT and negatively with MAP, with a negative interaction of MAT with year. The negative correlation with MAP was three times stronger than in natural grasslands, suggesting that fertilization and watering of lawns in drier environments has enhanced 15N-depleted losses much more than in wetter environments. Isotopes in Amanita thiersii may integrate shifts over the last 50 years in lawn maintenance practices, soil nitrogen dynamics, and the physiological responses of turf grasses.
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i want to study the quantity of N and Water lost in different pathways following long term organic fertilization.
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One point which has not been covered is various  path ways  of N losses especially through denitrification (N2O and N2 gases),volatilization( losses of ammoniacal  N ) and leaching losses of nitrate N.From climate change point of view the  gaseous forms of N  emissions  especially through denitrification are important.
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In this case, I want to measure Nitrogen cycle including N fixed in soil, N uptake by plant, N leaching and N emission.  
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What is mentioned above is true, chamber based method provides a snapshot of gas emissions at the time of chamber deployment, while micro-met methods provide non-intrusive, area integrated continuous measurements.  Both methods have their advantages and disadvantages. 
As Brian already explained, chamber method is considerably less expensive, allows for the inclusion of many sampling sites in a small plot-scale field experiment, and can be adapted to wide range of research objectives, while micro-meteorological techniques require expensive instrumentation and demands more skillful operation.  For many who wish to measure soil surface greenhouse gas fluxes, micro-meteorological techniques are beyond the reach of their resource availability (especially in the developing countries).
However, that doesn’t mean that this area of research is out of reach.  If standard protocols related to chamber deployment and gas sampling frequency are followed properly, one can generate high quality data of soil surface gas fluxes (that are not second in quality to data obtained using micro-meteorological techniques).
Here is a link that provides a detailed protocol developed by USDA-ARS GRACEnet Project.  It explains standard guidelines for chamber construction, deployment, gas sampling and analysis and data interpretation.  If followed properly one can obtain a good data set.
Hope this will be useful.
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How is fix nitrogen in soil from atmosphere?
How much N fix in soil per mm rain? 
Which is the easy, accurate and low cost method to estimate the freshly fixed N from atmosphere?
How it is different from zone wise and region to region N fixation? When it is available to plants?
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Hi
You can find some interestin information on this  link:
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How can we manage nitrogen in wild rocket ?
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Hello Ramendra,
We have grown wild rocket (arugula) in our home garden and under home garden conditions it does not require any fertilizer.  All it needs is good quality compost and continuously moist soil conditions.
After seeing your question, I did a Google search and found the following paper that may be useful.  I am adding the abstract of the paper and the internet link for the full paper.  Hope that you would be able to get the full paper, otherwise, please let me know.  I can forward a copy.
Factors influencing tissue nitrate concentration in field-grown wild rocket (Diplotaxis tenuifolia) in southern England ( available at: http://www.tandfonline.com/doi/abs/10.1080/19440049.2012.696215?journalCode=tfac20)
Abstract
Wild rocket (Diplotaxis tenuifolia) is a leafy vegetable known for its high tissue nitrate concentration (TNC) which can exceed the limits set in the relevant European legislation designed to protect human health. The aim of this work was to understand the factors influencing TNC and to develop best practice guidelines to growers. Commercial crops of field-grown wild rocket were studied over two seasons. In 2010, ten separate crops were sampled representing a range of soil types and time periods during the summer. Two fields sampled using a ‘W’- or ‘X’-shaped sampling pattern demonstrated that 10 incremental samples bulked to make 1 kg of fresh material could be used to provide an adequate sample for determination of TNC in the wild rocket crop, as is the case for other leafy vegetables. Of eight commercial crops sampled in 2010 with an average nitrogen (N) fertiliser application of 104 kg N ha−1, two exceeded the limit of 6000 mg  kg−1 set in the legislation. In 2011, six N response experiments were carried out, and only two sites showed a significant yield response to N fertiliser. The reason for the lack of response at the other sites was principally due to high levels of soil mineral N prior to drilling, meaning the crops’ requirement for N was satisfied without additional fertiliser N. In the experimental situation at an N fertiliser application rate of 120 kg N ha−1, 50% of crops would have exceeded the 6000 mg  kg−1 limit. In both seasons, low radiation levels in the 5 days prior to harvest were shown to increase TNC, although the relationship was also influenced by N supply. Strategies for optimising N nutrition of field-grown wild rocket are discussed.
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How can the source be identified to have ANMMOX microorganisms in it? I want to prepare a lab-scale reactor for ANMMOX and hence I am looking for a natural source (other than pure cultures available in culture banks) of ANMMOX microorganisms.
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Annamox bacteria are autotrophic and oxidize ammonia anaerobically using nitrite as the electron acceptor.  They cannot tolerate oxygen and therefore can be found in reactors/conditions which  are anaerobic. For this you need to use NH3 and nitrite (from partial nitrification) at a ratio of ~1: 1.1 in the reactor feed in order to be able to conduct the above biochemical reaction. Further the carbon load (CBOD) should be very low for their enrichment. If you have high CBOD, annamox bac will not grow or activate in the reactor. Annamox bacteria are extremely slow growers and their doubling time is ~ 11 days. Therefore you need to maintain adequate SRT in your reactor in order to enrich these bacteria.  Enrichment can be done using conventional sludge may be granules/flocs from an anaerobic reactor.  
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I plan to quantify abundance and activity of anammox bacteria by quantitative PCR. Is there any functional gene (i.e. hzsA, hzsB, hzo ...?) that should be preferred in marine sediments? (I work in coastal muddy sediments)
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In my opinion, the paper "Quantification of anaerobic ammonium-oxidizing bacteria
in enrichment cultures by real-time PCR" in Water Research can give important information about the real-time PCR primers for Anammox bacteria. 
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I am confused. Both of these processes reduced nitrogen to ammonia. what's the difference then?
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It is true that both of these processes involve conversion to ammonia/ ammonium but the starting nitrogen form is different. Ammonification is the mineralization of organic nitrogen into ammonia. Dissimilatory nitrate/nitrite reduction to ammonia (aka DNRA) starts with inorganic nitrogen (nitrate/nitrite), not organic N. The nitrate/ nitrite is then reduced to ammonia/ ammonium. 
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I'm interested particularly in temporal variability of P, N, and C concentrations in organic sediments produced by macrophytes (particularly charophytes) in freshwater ecosystems.
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Dear Andrzej,
I am very familiar with organic matter and nutrient cycling in shallow marine sediments, but not so much with freshwater sediments. However, I did a brief search on the topic and I recommend you look at the following, that may also provide leads to other studies.
If you need information on marine systems, please let me know.
Best regards,
Angelos.
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These two processes are involved in the nitrogen cycle. I wonder why these two pathways need additional electrons !
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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.
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I want to describe a complex trophic web with primary and secondary consumers and different sources using carbon and nitrogen stables isotopes. Do I need to subtract the trophic fractionation for the secondary consumers, or I can just put in the model the raw data for both carbon and nitrogen isotopes?
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Dear Jean-Michel, 
Thank you to your opinion/suggestion. We will try to split the dataset and to use separate trophic enrichment factor for primary and secondary consumers, but how to deal with intermediate consumers?
And of course, I agree with you that a deep knowledge of the trophic web is necessary before to use mixing models.
Merci.
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B value represents the fractionation given by the nitrogenase and the 15N distribution in the plant. According to Höwberg (1997), the fractionation during N2-fixation is generally small. Besides, 15N distribution in the plant is not important when we harvest and analyze both above and below ground biomass. I think B value estimation is important when we harvest only above ground biomass, but if it is possible to harvest all biomass, can we assume B=0? What is your opinion about this?
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The B value basically refers to the fractionation that occurs for the two N isotopes. As a plant takes up nitrogen it preferentially uptakes the lighter isotope, 14N, by a small degree. This is something that would have to be determined experimentally, but there are also a range of generic values that you could use. I will paste a section below that discusses some of that. It is obviously important to know the δ15N of your soil...the larger the difference between the soil and the air then the less significant the B value is. You could do the experiment with the entire range of B values, and then say your results fall within that range of nitrogen fixation to be safe. Or to do your calculations with one "best guess" B value, and note that the B value may change. I will paste a couple sections below that may help.
Isotope fractionation constants are ex-
pressed as β in the expression 14k/15k = β, where
14k=first-order reaction rate constant of the conver-
sion of the 14N isotope substrate to product and 15k
the same constant for the 15N species. Shearer et al.
(1974) used a value of β of 1.005 for the incorpora-
tion of ammonium ion into microbial protoplasm and
1.025 for nitrification (Delwiche & Steyn, 1970). For
a similar model describing ammonification, microbial
assimilation of ammonium and nitrification, Herman
& Rundel (1989) used values of β of 1.0046, 1.0046
and 1.0176 for these three transformations, respect-
ively. Handley & Raven (1992) have cited values of
β for NH+ assimilation of between 1.012 to 1.020, 4
and for nitrification of between 1.015 and 1.035.
Good papers usmmarizing:
Use of the 15N natural abundance technique to quantify biological nitrogen fixation by woody perennials. Boddey et al 2000.
Measurement of Nitrogen Fixation by Soybean in the Field Using the Ureide and Natural 15N Abundance Methods' Herridge et al 1990.
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I am trying to do a comparison of soil microbe communities. I am only looking at the nitrogen cycle microbes. What plating medium should I use? I am looking for something that is inexpensive but will still give me a good look at what is in the community. Multiple media is okay. Thanks.
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One culture method will NOT capture the entire N cycle process. This is because not all components of N cycle are driven directly by microbes (for explanation sake I have highlighted different N cycling processes). For example ammonia volatilisation is driven by chemical conditions (e.g. soil pH) or enzymes (in case of urea the enzyme is urease).
As other colleagues suggested even if one is able to quantify microbes, the number of microorganisms may not to be directly proportional to the extent of any N cycling process. For example number of nitrifiers in soil (Nitrosomans spp and Nitrobacter spp) may not be directly related to the extent of soil nitrification. This is because there non-microbial factors that could dominate the nitrification process.
Biological N fixation by legumes can be quantified (plenty of literature available on this matter). On the other hand, N mineralisation of organic-N (or ammonification) process can be quantified by soil incubation methods (e.g. anaerobic incubation). Alternatively the ammonifiers (mainly heterotrophics) could be cultured.
Denitrification process (NO3 to N2O and N2) is driven by denitrifiers and these are heterotrophs and hence could be quantified. But since denitrification process is also driven by other factors such as level of nitrate, level of electron donor such as dissolved organic carbon and anaerobic/anoxic condition, the extent of denitrifcation will not be related to the amount of denitrifiers present.
Immobilisation of ammonium is driven by heterotrophs and hence could be quantified. But immobilisation will also rely on available C and ammonium hence microbial numbers may not relate to the extent of the immobilisation.
The other component of the N cycling involves plant uptake of N which is not related to microbial numbers. Also N input from fertilisers or animal excreta are also not related to microbes. Equally N leaching (NO3) from soil is not directly caused by microbes. So as ammonium fixation in soil is not driven by microbes (driven by clay mineral types).
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Say, targeting carbon/ nitrogen cycling at watershed/hillslope scales?
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I would like to look into the possibility of ammonium being nitrified in the forest canopy. I have searched for references on this topic but have come up empty handed so far. Can anybody offer any ideas or suggestions? Thank you.
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My problem is related to microbial nitrogen cycle.  
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I am also going to recommend a really good book on NItrification 
Ward, Bess B., Arp, Daniel J., and Klotz, Martin G., eds. Nitrification. Washington, DC, USA: ASM Press, 2011. ProQuest ebrary. Web. 12 September 2014.
But a short answer...
Nitrifying organisms obviously contain membrane bound enzymes to oxidize ammonia to nitrite, while other organisms will further oxidize nitrite to nitrate. The first step in the catabolic process is a protein super unit called the ammonia monooxygenase (AMO). This structure converts NH3 to NHOOH (hydroxylamine) and is substrate specific, in other words it can not process the Ammonium Ion (NH4+), this is one of the many reasons that soil pH has an effect on soil nitrogen cycles (with the caveat that there has been reported Archaea that are capable of utilizing NH4+ (although the mechanism is still unknown at least to my knowledge). But I would take at that book.
hope that helps a little 
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I'm working on nitrogen cycle and I want to quantify the potential rate of nitrification and denitrification through the quantification of functional genes. I want to known how many copies of these genes (nosZ, nirS, nirK and amoA genes) there are in a bacterial genome?
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Suppose I have over-fertilized soil ( festival area - places with the big  urine concentration) and I want to accumulate the nitrogen in plants to recycle it  further and make it available for other plants. What kind of plant could help me to bind the nitrogen from soil (in similar way as leguminosae fix and accumulate the nitrogen from atmosphere)? Is there any solution to make a use of this natural fertilizer (urine I mean ) which has a peak only two times a year?
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Dear Natalia,
First of all  study the local flora of the place where you are planning to work. As native plants need less effort to establish and have less impact of local climate on their growth. Make list of plants then we can make out which could be best according to the suitablity of your place. If you are planning to construct wetland then Eicchornia have great potential to accumulate nitrogen and after harvesting it can be used in biogas plant as well for the production of manure. In my native place people are using it in biogas plant and organic manure formed is being used by farmers. Cyperus and Typha  are also good options.
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Symbiotic N fixation has been shown to respond to N availability and is limited by high energy requirements. Plants appear to use symbiotic N fixation as a facultative strategy to overcome N limitation. However, in many ecosystems, N fixing plants are not present, and even in ecosystem where they are present, N fixation by free-living organisms appears to be an important additional source of N to the ecosystem. But, what controls this input on an ecosystem scale? Is there any observed variation across certain gradients? And how close is the interaction between plants and free-living fixers? Is there plant exudation of labile C as energy provision to free-living heterotrophs? - Thanks for any answers and references!
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Any newer synthesis would have cited this:
Cleveland, C. C. et al. 1999. Global patterns of terrestrial biological nitrogen (N2) fixation in natural ecosystems. Global Biogeochemical Cycles 13(2): 623-645
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A full scale MBR facility treating domestic WW has an effluent with a total N of 20 mg/L? However, [s] of NH4-N and NO3-N is 2 mg/L? NO2-N is not detectable. Hence, TKN analysis gave 1 mg N as NH4, the rest should be an organic content 17 mg/L? Amazingly TSS content is 2 mg/L, an indirect measure for biomass [VSS], don`t support loss of organic N assimilated into biomass? NO2-N is not detectable. Now, any similar experience with MBR effluent rich in organic N? What is the origin of that? EPS is responsible for that organic N? How measure EPS? Appreciate any feedback or citation of specific articles.
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I agree with the the first step being to make a complete Nitrogen balance in the reactor. But I don't understand how you can measure a TKN as 1 mg/l and a total N of 20? Normally, all organic N forms including bacterial by-products as EPS are taken in account by the TKN (Total Kjeldahl N method = strong boiling acid digestion with selenium as catalyser). So if you get such a high total N in the effluent of a MBR, this N must be a soluble form resilient to digestion - and such forms are very unlikely in an urban sewages... What are the methods you use for TKN and Total N?
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We got results of nitrogen fixation by unicellular cyanobacteria in an eutrophic estuary. In an eutrophic estuary they have enough nutrients available for their metabolism, so they do not have the need for nitrogen fixation. However, even under these circumstance they continue with nitrogen fixation. What is the reason for this?
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Well its a known fact that cyanobacteria can fix nitrogen. But in eutrophic waterbodies they have to compete with other algal species to bloom. At this stage, cyanobacteria can not risk to loose their energy in Nitrogen fixation, rather they use the available nitrogen source to increase their biomass rapidly.
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During fumigation-extraction method to determine microbial biomass N in soils, should I put the control soils into the vacuum drier without chloroform and exhaust air? Or put them elsewhere in room temperature? Or keep them in -20℃?
Thank you.
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Soil microbial biomass N (in form of organic N but not NO3 or NH4) is usually 1-2% of total soil N pool (the biggest one is soil organic N, contains above 90% of total N). But it has very high ecological value since the turnover rate is very fast. It is therefore very important to estimate not only the pool size but also turnover rate.
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Results of pre and post total C and N content analysis showed a marginal decrease in total N, some increases were also observed, whilst some remain unchanged. Most of the variation I have attributed to the instrument (CHN elemental analyser). I have used total N obtained pre HCl treatment for the calculation of C/N ratio.
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No, nothing happens. We did many tests and different concentrations of HCl and we found no effect on total N.
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See above
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You could determine the gene abundance of denitrifiers by Q-PCR, targeting either DNA or RNA. You can get information about Q-PCR of denitrifiers from estuarine sediments in this article:
Smith et al, (2007), Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, 73(11), 3612-3622.
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What is the mechanism?
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There are references that say probiotics can reduce the secretion of urea and ammonia in fish.
Lashkarbolouki, M., Jafaryan, H., Faramarzi, M., Zabihi, A. and Adineh, H. 2011. The effect of feeding with Saccharomyces cerevisiae extract (Amax) on ammonia and urea excretion in Persian sturgeon (Acipenser persicus) larvae by bioenrichment of Daphnia magna. Journal of research in Biology. 2: 110-115
Faramarzi, M., Jafaryan, H., Roozbehfar, R., Jafari, M. and Biria, M. 2012. Influences of probiotic bacilli on ammonia and urea excretion in two conditions of starvation and satiation in persian sturgeon (Acipenser persicus) larvae. Global Veterinaria. 8 (2): 185-189
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In extremely arid deserts, the soil nutrients, especially nitrogen, are always poor, but no significant effect was observed among the local desert plants. Therefore, I want to know your opinions on which are the key factors controlling nitrogen use efficiency in extremely arid environments?
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Bente's point is important - we can't neatly separate N availability from water availability. Another point of interaction is that Nitrate-N uptake is largely a function of mass flow, that is the movement of water through the soil toward the roots (driven by transpiration) carries NO3 to the roots. So in drier conditions N mobility may be more limiting.
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The impacts of reactive nitrogen addition has been largely studied, but mostly in the context of N-limited ecosystems such as North America, Europe and other high latitude areas. However, many tropical ecosystems are, in their natural state, N-saturated, probably as a result of high activity of symbiotic and a-symbiotic dinitrogen fixing organisms. I'm looking for research that can contribute to our understanding of how deforestation and conversion to agricultural land uses (fertilization, manure use) is affecting N dynamics within these systems and exports downstream.
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We are investigating C dynamics a false time series along a land use transect in Southern Amazonia (www.carbiocial.de). I wouldn't call tropical ecosystems N-rich. Usually, there is a limited amount of N in the game, and only the fast turn-over rates keep most consumers satisfied. As soon as forest is cleared and root uptake from larger depths is reduced because of missing trees, N starts to leach out of the system. If the land is turned into grassland, litter fall is almost comparable to a forest ecosystem. If turned into agriculture, C input is reduced and so the capability to store N in organic substances slowly decreases. Fertilised N rushes through, as most tropical soils have a limited CEC, and also anionic N fixation is limited due to the positive surface charge of the soils rich in sesqui-oxides. Tropical soils under agricultural land use are often high in SOM (~3%), but a large fraction of it is recalcitrant and does not release large amounts of N. N mineralisation of less than 100 kg N ha-1 are typical.
Hope that triggers a nice discussion.
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Our lab has been using the Holmes (1999; fluorescence-based using OPA) method of ammonia analysis to measure ammonia concentrations in oligotrophic seawater for its added sensitivity. However, our blanks are typically high and sometimes higher than samples we are measuring. Any advice on how to get "ammonia-free" water to use for this type of analysis? I know we could use a "low" seawater sample as a "blank", but I would prefer to try to get something more standardized, so I'm wondering if anyone has any experience with using HPLC-grade or some other high purity water they can order through a supply company.
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I agree, Milli-Q works best. When going on research cruises, we would take Milli-Q water with us in 10l carboys and then filter it again on board the research vessel using a bench top Milli-Q system (Millipore). Also, very important are thoroughly rinsed tubes for standards and samples. We soak 50ml Sarstedt/Falcon tubes in 1% HCL for at least 24h, then rinse the tubes with Milli-Q multiple times. You can reuse the tubes, they actually 'improve' over time. Only those in which you measure very high concentrations I recommend to discard. For the standard series always use the same tubes. Further, let the OPA age, at least 1-2 weeks. Always fix samples/standards immediately and wear gloves at all times.
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I am planning series of experiments in which I’d like to measure concentrations of N-15 labelled ammonia and urea in solution. I basically know that it is possible to measure concentrations of these compounds, and that it is possible to measure N-15 signature for all dissolved N-compounds. However, is it possible to measure this for each compound separately? If so, how do you do this? Could you recommend some literature?
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There is another diffusion method for 15N-NH3 where you buffer your sample with MgO to a pH of 9.5 to 10, which also converts the NH4+ to gaseous NH3 which can then be captured on a filter as ammonium sulfate. The filter is acidified beforehand with Sodium Bisulfate, and is made into a "filter packet" that floats on the aqueous phase. Diffusions last from 3 to 10 days depending on the concentration of ammonia, and the filters can then be dried and analyzed via EA-IRMS. Make sure to preserve your samples at pH2 with H2SO4 to prevent any loss of NH3 beforehand (although freezing also works). volatile organic nitrogen compounds can be a problem though
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While doing the culture DNA isolation and PCR amplification of 16s and nif H, got one band and nif H gene 2,3 bands respectively. What is the reason for getting nif H two to three bands
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Thank you Nityanand for the immediate reply.
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Conventional microscopic identification of nitrogen fixing cyanobacteria and heterotrophic bacteria (growing in nitrogen-free medium) is a difficult task. Does anyone work with a diversity of nitrogen fixing cyanobacteria and heterotrophic bacteria?
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Sorry - here's the other paper. Also anything by Jon Zehr will be worth your while looking at.
Cheers
Clare
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I'll try to find all chemical reactions related N - Cycle occurring in soil.
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Thank you very much Fulvio Rivano
I need more help in this area.
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I measured the δ13C and δ15N values of plant tissue and soil samples from a 13C and 15N pulse labeling experiment using MAT 253. The δ13C and δ15N values of the standard (UREA, add each 20 samples) exhibit some considerable variation and have no trend. How can I adjust the δ13C and δ15N values of these samples?
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You need to run 2 standards, 1 control, 6 to 10 samples, one control, 2 standards sequence. As previous authors noted, you need to chose the correct standard for your samples (“same” chemical composition) and you need also to have your isotope ratios between the two standards. Closer your standards are to your sample the better result you get. The second problem in IRMS (but generally in spectroscopy) is the memory effect. You can measure 10 times one sample and make a plot, having on X axis the sample sequence and on y axis the measured values. Then you can see how bad the memory effect is. Just as a caution. The memory effect depends on the value of the previous sample. Less memory effect you get if there are no big variations between samples.
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I am working with water quality data from a construction site, where elevated total nitrogen concentrations (> 20 mg/l) were observed. There might be several reasons behind the high nitrogen loads, such as illicit waste water discharges and the leaching of nitrogen from the soil after logging, but I would love to have some estimates about the impacts of blasting, which could be an important source.
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Just back from holiday... Thank you all for your new answers!
Nikos, do you know any publication about the nitrogen content of those mine waters you mentioned about? Can you say what is the estimated concentration or load of total nitrogen or nitrate resulting from those explosives?
Based on the answers I have gotten, I think that there is a very limited amount of research conducted on nitrogen loading from explosives and their impact on runoff quality.
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I worked on the influence of various levels of nitrogen applied to different cultivars of wheat and am looking for varietal response for good nitrogen use efficiency and aphid infestation at each level and variety.
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Total plant nitrogen analysis by near infra-red spectroscopy is a quicker and efficient method compared to Dumas method of estimation and it is inexpensive. An attached research papaer on Total plant nitrogen analysis by near infra-red spectroscopy is enclosed for ready reference