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Questions related to Soil Ecology
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Hi, I was hoping someone could recommend papers that discuss the impact of using averaged data in random forest analyses or in making regression models with large data sets for ecology.
For example, if I had 4,000 samples each from 40 sites and did a random forest analysis (looking at predictors of SOC, for example) using environmental metadata, how would that compare with doing a random forest of the averaged sample values from the 40 sites (so 40 rows of averaged data vs. 4,000 raw data points)?
I ask this because a lot of the 4,000 samples have missing sample-specific environmental data in the first place, but there are other samples within the same site that do have that data available.
I'm just a little confused on 1.) the appropriateness of interpolating average values based on missingness (best practices/warnings), 2.) the drawbacks of using smaller, averaged sample sizes to deal with missingness vs. using incomplete data sets vs. using significantly smaller sample sizes from only "complete" data, and 3.) the geospatial rules for linking environmental data with samples? (if 50% of plots in a site have soil texture data, and 50% of plots don't, yet they're all within the same site/area, what would be the best route for analysis?) (it could depend on variable, but I have ~50 soil chemical/physical variables?)
Thank you for any advice or paper or tutorial recommendations.
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Thank you!
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I am after some good reference on Soil Microbe Ecology and Biology. As a physicist I have approached this subject gently by reading things like "Life in the Soil" (James Nardi). Another book I have been recommended is "Soil Microorganisms and Higher Plants: The Classic Text on Living Soils" by Krasil'nikov. This I found very hard going due to the poor translation and somewhat outdated. I was wondering what folks consider a reliable modern reference on this.
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I could recommend you a Mycorrhizal interaction with plants book: "Mycorrhizal simbiosis" (Smith and Read, 2008).
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To be frank, I believe the answer is relative to this issue. Only textbooks that I am familiar with or have come across can be recommended. However, you are the only one who knows what study areas you are passionate about.
Rather than relying on a single textbook, I believe you can find knowledge by searching online databases, books, journals, and other serial blocks using keywords from your research objectives.
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Hi. I'm working with soil enzymes and I have an issue because i saw several papers that used "integrated biological response" or IBRv2 to integrate data from enzymes and build a hexagonal star plots (based on this paper from Beliaeff and Burgeot "Integrated biomarker response: A useful tool for ecological risk assessment"
See some examples:
Is a software (R package? specifical software? excel file?) available to calculate this index and build the hexagonal star plots? Or is only to calculate the data and after this, make the hexagonal star plot (radar chart) in SPSS?
I know the "Biomarker Integration Data Expert System", but this system is more appropriated for worm enzymes than soil enzymes.
Thank you in advance!!!
Andrés
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Hi Andrès,
I work regularly with the IBR and in general, I calculate it and make the graphs directly with excel.
I'm not sure that there is software available for the calculation.
The different steps are described in the articles. It seems complicated but once the formulas are understood, no worries. You just have to be careful to have all the necessary conditions.
I hope this will help you.
Good luck.
Eric
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I incubate the soil with earthworm and applied different concentrations of NMs. My pH data looks strange to me. Previously, literature documented that earthworms improve soil pH. Does anyone conduct the experiment to evaluate the pH response over combine exposure of earthworm and NMs? My weekly data is changing in a dose-dependent manner. pH should be increased or decreased with time and dose?
Please give me a clue regarding this issue. Your response is highly appreciated.
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Very nice question, following!
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Hello,
-So I have a set of bacterial communities extraced from rhizospheric soil in both saline and control environments for two different cultivars of plants, one is tolerant to salinity and the other is susceptible.
-I did ordination (N-MDS)and got the control and treated separated on first coordinate, but cultivars closer together in the second coordinate.
- I got p-value p=0.001, whic is good, indicating diffrence.
-However, i got R^2 values: axis1 = 0.9521, axis2= 0.0005229.
What does R^2 mean? what values indicate that my data is good. Is it a strong test for my data?
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The r-square value generally tells you the percent of the variation 'explained' by the axis. So this score tells you that Axis 1 'explains' approximately 95% of the variation in separation of the bacterial communities, whereas Axis 2 explains very little of the variation. Therefore, any environmental variable that aligns strongly with Axis 1 is likely to be a strong environmental influence on the bacterial communities. Conversely, an environmental variable that is strongly aligned with Axis 2 is much less likely to be influencing the communities, although they may be important in the absence of environmental variables that strongly align with Axis 1. For example, if Axis 1 is very strongly aligned with the salinity gradient, then it suggests that salinity is overriding most other environmental variables (and if you did a separate study with no salinity gradient, then other variables may become more important in separating the communities).
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Dear colleagues,
I want to destroy soil aggregate to investigate how the stability of soil aggregates affects soil functions. Is there any suggestion to completely destroy the soil aggregates? Ultrasonic? Ground? Or something else? Please also provide some important literature.
Thanks in advance.
Hui
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To completely destroy soil aggregates you should combine physical and chemical dispersion as used for granulometry analysis, but I think this is not you interest. Rather, you may want to grind the soil and sieved it to a certain size.
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Hi everybody,
I was looking for some decent company which supplies field material as kick nets, litter bags or emergence traps (aquatic biology bias, here). Does any one can recommend me some supplier within Europe?
Thanks for the help,
Best,
Raquel
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Thanks! Relly good ones!
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is there a reference number put to be used to say the obtained number of AMF spore per gram is low, medium or high? say for instance is 18 spore per gram of dry soil large or medium or small?
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Researchers based on the below reference classified AM root colonization based on categories:
very high (.80%),
high (60–79%),
medium (40–59%),
low (20–39%)
and very low (1–19%).
Arbuscular mycorrhizae of dominant plant species in Yungas forests, Argentina
Alejandra G. Becerra,Marta Cabello,Marcelo R. Zak &Norberto BartoloniPages
I also investigated by myself the rate infection of mycorrhizal fungi in the saline soil which has about EC 8. the results were different based on the tea materials (phenoles) added with mycorrhiza to support it to be more active and abundant.
the reference is :
Interactions between Mycorrhizal Fungi, Tea Wastes,
and Algal Biomass Affecting the Microbial
Community, Soil Structure, and Alleviating of
Salinity Stress in Corn Yield (Zea mays L.)
Salwan Al-Maliki * ID and Mugtaba AL-Masoudi
plants journal 2018
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I would like to know what is the significance of symbiotic relationships in plant nutrition.
Do we have evidences suggesting that symbioses have a significant potential to improve crop yields and quality ?
Especially about mycorrhizae, do you know to what extent they could contribute to plant nutrition? with examples for crops, or records in "nature".
Do we have an idea of the magnitude of the contribution ?
Could it play an important role with a little more selection and innovation?
Or is it just something that ecologists like to point out but have no interesting technical applications.
I guess the answer is somewhere in between ...
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Very good question. Surely the answer is in between.AMs have a huge role in improving plants ability both physiologically and biochemically through a series of enzymes to not only plant nutrition but add another dimension of antioxidants profile to offer much better resistance to plants under water stress or any other kind of stress including salt stress...
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Are there soil pore water screening values (for the protection of soil ecosystems) available for major ions and trace elements? Screening values seem to be solely based on total concentrations. However, I only have dissolved fraction data available. Thanks!
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You may have a look of the Ph.D. thesis by Di Bonito, Marcello (2005). Trace elements in soil pore water; a comparison of sampling methods. University of Nottingham.
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Please help me sharing some information on the identification keys of soil organisms in genera and species level
topics
Soil organisms, ants, termites, and earthworms in tropical soils 
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"The Soil Biology Guide" (Dindal 1990). This book is one of the
most important sources for soil fauna.
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Dear all. I am working on Earthworms and I am trying to recover their DNA from the soil and use the 16S and COI gene to prove that we can use the environmental DNA from the soil to identify different species of epigeic earthworms that are used in the vermicomposting processes. Bienert et al. (2012) forms the basis of my research since they proved that it is possible to track earthworms from the soil using their DNA.
My problem however, is that I am struggling with the PCR protocol to use in order to obtain positive results. Bienert et al. did not provide the protocol in their paper of these two genes and most of the literature has tissue DNA protocol for these genes instead of the eDNA. Please help the complete PCR protocol (reaction mix and PCR setup)
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you can use a temperature gradient PCR for adjusting the annealing temperature that will act with the primer and adjust denaturation at 94 degrees for 5 minutes and extension at 72 degrees for 3 minutes. the master mix will be adjusted either at 25 ul or 50 ul according to the type of the mix used and its protocol.
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Hello,
I would like to identify/detect what organic substrates (e.g. leaf litter remnants, frass, death canopy foragers, dissolved OC, etc.) are being used by soil microorganisms in the process of soil heterotrophic respiration by comparing the isotopic signature of the soil gas flux (i.e. collected in a soil flux chamber) and that of a potential substrate candidate. Is this possible at all? Does this make sense at all?  Are the isotopic signatures between substrates different enough to make this possible?
Thank you very much in advance for your replies!!
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A "representative" bulk sample will not be the solution because different organic matter sources are utilized differntly by microbes depending on e.g., degradability, N-content etc...
Fractionation is one problem because you cannot be sure if all organic matter will be 13C-discriminated equally (it likely will not). Second, how will you disentangle the sources in this mulit-pool-mixing-signal in respirated CO2? 
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In wetland situation pH of soil may approaches to neutrality. In this situation liming of soil may not have any effect. However, some researchers found positive effect of liming in wetland rice soil. Now the question is what is the mechanism or reason behind this findings?
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Thanks Anoop sir for nice response. Actually I am going to establish some experiments in northern part of Bangladesh (Rangpur and Dinajpur regions) in which I like to the effect of liming and different macro and micro nutrients  (NPKSZnBMo) on rice productivity and nutrient availability in soil. Soil of those areas are acidic (pH 5.1-5.3) and light to medium textured. Experiments will be started in next wet season (Monsoon/T. Aman season) and will be continued up to Boro season (dry season). Can I expect a positive response of liming. I shall be grateful if any one give some suggestion with different treatment combinations.
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I recently submitted my manuscript to a journal. the work done was related to soil ecology and plant pathology. Previous work related to my kind of work were carried out in foreign countries only and was not tried out in Indian conditions. In India except one investigation which was carried out very long back related to the aspect, I carried out the work after many years. However my article was rejected since the citations were old. there is no way of including new citations since previous works were carried out in countries outside India very long back. In India similar work was not carried out from long back since the plant disease which I am working upon affects the crop only in temperate hilly regions. I am in a helpless situation since the results of my work are very valuable to the farming community. I request scientific community/ scientists in area of plant pathology in relation to soil microbiology/soil ecology to help me in this regard. How can I convince journal editors to reconsider since i feel the similar problem may erupt when my manuscript goes for a peer review with other editors also. Please help me. I don't want my results to go in vain since I have taken a lot of pains and effort in my research work related to that. 
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Dear Krishnamoorthy,
First of all do not get disappointed and demoralized. You should have a lot of patience in research. If you have faith on your work, highlight your core findings and write in a nice manner so that, it could reflect the novelty and superiority of your research work over the earlier ones. Show very clearly, how your research contributes to the knowledge.
Then search a list of journals in relevant field and submit in a journal in which no such work has been published before. If rejected , no need to be disappointed. Submit to the other. Do not work according to the journal. Search the journal according to your work. Do not loose moral for a particular journal. It will definitely get published.
Good luck for your research.
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and the best way to identify variables which used in analysis?
Ecological data : physiochemical factors ( DO,pH,....etc...) ,Time (Months, seasons...) , Stations
Statistic : CCA, PCA , DCA....
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If you have a variety of variables (time, pH,... n var.). I would recommend using the NMDS multivariate statistical technique. Because you have multiple scales in your variables. However, the statistical technique that you need to use depends on the nature of your data and the question you want to answer.
Best regards
Cristian Martínez
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We think about transplant rare plant species from nurseries to the rehabilitated ecosystem. However soil pathogens (fungus, invertebrates and others) associated with the transplants have to be reduced to = 0.
Do you have any idea or protocole.
First, we plan to use substrat of destination.
Second, to isolate this substrat from the nursery land with elevated table.
Thanks for you advice 
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In California on imported nursery plants, we introduced a plant pathogen that we now call "Sudden Oak Death" and is killing our native oaks trees. Then in the Eastern USA there was the Chestnut blight and the Dutch Elm diseases of the 1800s.  
However, it was recently discovered that the California native plant nurseries are infested with 50 more plant pathogens that are related to Sudden Oak Death, that you can read about at http://paloaltoonline.com/print/story/2016/09/23/in-pursuit-of-a-plague 
Unfortunately the State officials that license and inspect nurseries are not interested in inspecting, testing and certifying for these 50 new pathogens, because it is going to cost the State tens of millions of dollars to clean up this mess.
 If anyone from the State of California is reading this, maybe they can explain why our native nurseries are not being inspected, tested and cleaned up?  
They have not even sent out any notices to the nurseries that a problem exists, or a flier to show what each nursery should look for with sick plants?  And once you spot a sick plant, what is the proper disposal and clean up procedure?
And the native plant nurseries are not spending the money either to clean up, the only action on a nursery-level is when a large-scale buyer insists that they clean up, then something is done, and that is only one nursery so far taking significant action.
So if California, one of the richest areas on the planet, does not invest in cleaning up their native plant nurseries because of costs, then that means that proper cleanup of nurseries elsewhere probably will never be done, and exotic plant pathogens may be a worse impact on native ecosystems around the planet, than global warming for example.
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I am working on the effect of Ti -salt as well as Ti -nano particle on soil ecology and soil microbial biomass, where how much bioavailable Ti is present in soil which might have an adverse effect on soil microbes is very important.
Thank you in advance for any help.
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Ti concentration of the aerial parts of plants is regarded by many as an index of particulate soil contamination on their surfaces
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I am interested in whether forest floor animal communities are spatially heterogeneous and have been following Colwell and Coddington (1994) and Gotelli and Colwell (2001) who say that the difference between the sample based and individual based rarefaction curves can be used as a measure of this patchiness. I have used Kolmogorov-Smirnov tests as well as looking at the 95% confidence limits of the individual based rarefaction to test the significance of the difference between these curves.  Are these tests the correct ones to use?
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Rarefaction allows the calculation of species richness for a given number of individual samples. This curve is a plot of the number of species as a function of number of individuals to compare species richness data among sets with different sample sizes, Species richness counts are highly sensitive to the number of individuals sampled, and to the number of size, and spatial arrangement of samples, Sensitivity to sampling effort cannot be accounted for by scalling species richness as a ratio of species counts to individuals, samples or any other measure of efforts. Sample-based and individual-based rarefaction methods allow for the meaningful comparison of diversity samples based on equivalent numbers of individuals and samples. I think, you can use Kalmogrov-Smirnov tests as well as looking at the 95% confidence limit of the individual based rarefaction to test the significance of difference between these curves.
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I collected some mites showing characters of Tetranychidae associated with stone from Syria.
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Did you locate any other stages? If it is a colony try them rearing. Usually plant associated spider mites like Petrobia are known to hibernate in soil near their host plants. Why dont you see any xerophytes near the stones. I will also search the literature and let you know.
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How to use a set of LIVE/DEAD BacLight Bacterial Viability Kits 13152 dyes for soil bacteria?
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Tatyana, I doubt you will get anything meaningful by applying BacLight protocol to soil. Sure, if you grow soil bacteria in liquid culture, then BacLight is fine, but for direct microscopic count of live vs dead cells in soil smears it does not work. Reasons: binding of stain to soil particles, heterogeneity of soil microorganisms, difficulty to differentiate cells from isometric soil particles. There are other ways to solve practically the issues associated with possible death of bacteria in soil (which is by the way, not significant factor for microbial ecology contrary to lab cultivation). There is NO build-up of microbial necromass in soil, more important are phenomena of dormancy, non-culturability and non-lethal stresses. But this is another issues... 
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Hi, I am currently running my very first Enchytraeid extraction :-) (O' Connor) and was wondering how long I can store the extract (water) before counting? I assume its easiest to count enchytraeids when they are still alive? Thanks for your advice!
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My own experience with enchytraeids from lowland soils in Slovakia was that they could survive in water few days, but only if it was kept in cool conditions. When left in room temeperature, they sometimes did not survive even one day.
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Dear All,
I'm looking for available literature data on concentrations of elements (in dry mass) in fresh and decomposed pine (P. sylvestris) litter, other litters, pine pollen (P. sylvestris), pollen of other anemophilous plants and organisms inhabiting forests floors (fungi, insects, molluscs, isopods, worms, millipedes, detritivores, various litter- and soil- dwellers, protozoans etc.). C concentration is of greatest importance for me, since it was rarely reported as % of C in dry matter (surprisingly, concentrations of other elements are easier to find). Also N and P are of great importance. Data on any other element would also be great. I've already found some literature but it is surprisingly scarce, so I will appreciate any additional data. If you know any paper related to the topic, please put a link below. Thank you in advance for your time and help!
Kind regards,
Michał Filipiak
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Hi,
I have data on Phragmites australis leave litter (green leaves and after litter fall). I am not sure if this could be of any help. The data are published in Flury and Gessner 2014 (Effects of experimental warming and nitrogen enrichment onleaf and litter chemistry of a wetland grass, Phragmitesaustralis). If they are of any help I could send you the raw data.
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The enigmatic role of soil microbes is gradually being de-codified towards better understanding of soil fertility transformations. We frequently talk of N-fixation , phosphate solubilisation , potassium solubilisation ..... but hardly debate about potential role of microbes including the AMF in improving the available indices of  micronutrients in soil with respect to micronutrients like Fe, Mn , Zn , Cu , Mo, B etc .The widespread deficiency  of these micronutrients is so ominous and of so far reaching consequences on both soil as well as plant health , in addition to quality of edible parts  . I invite the comments of our friends on the role microbes including the AMF in  transformation and availability of micronutrients across crops and soils.
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Thanks Dr Dabi  for your excellent response. Yes, on calcareous black soils  ( Vertisols) , occlusion of micronutrients is perhaps the most common phenomenon. We have experienced this in perennial crop like  citrus  where addition of organic manures in good quantity ( 10-20 kg/plant  , 3-6 tons/ha ) is a common feature , consistently over years ( 25-30 years on an average)  plus the litter fall as annual cycle . You just imagine , how much solubilisation would be a possibility. 
Microbes have the ability to diversify according to nature and properties of soil , soil pH is one of them , so microbes would be abundantly availalble , whether acidic or alkaline soil , or even saline soils. Thats  the beauty of the  soil microbial population ., otherwise where from micronutrients like Zn , B , Mo  etc will be available..?
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invertebrates are most complex organisms that are not much studied in functional role in the ecosystem in tropical countries. 
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Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging.
These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforest.
Diversity of Soil Fauna and Ecosystem Function :http://www.colby.edu/biology/BI131/Lab/Lavelle%201996.pdf
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Litter/soil dwellers (arthropods: detritivores and omnivores) feed on unbalanced food (mainly dead plant matter) that is scarce in some physiologically important nutrients. This food alone is insufficient as a source of needed biomass. It is known that fungi may supplement such a diet with nutrient needed by these animals. However it is very hard to find any specific data on how exactly this mechanisms works.
If an arthropod feeds on dead plant matter, what exact substances are scarce in its food? And how much of these substances may be given by fungi? Is it enough?
Do you know of any papers that give information on exact nutrients that are scarce in litter/soil and are given to the litter/soil dwellers by fungi in considerable amounts? 
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Thank you for your answer, Shilpa.
Energy (carbon-rich compounds are only source of energy, not biomass needed to grow tissues) is not the problem here, since it is relatively easily available for considered arthropods. The problem is matter needed for growth, development, body-building and maintenance (biomolecules rich in elements other than COH).
Excretion of specific substances by fungi is not the mechanism of diet supplementation. I meant that fungi themselves are diet supplements. They are eaten by arthropods and ‛give’ to the arthropods molecules composing fungal mycelia. They are so called ‛butter’ that covers ‛bread’ of carbon-rich, hardly digestible dead plant matter.
This is how it looks in theory. But how exactly this mechanisms works? What specific nutrients play main role here and what amounts of these nutrients must be eaten by the arthropods to make this mechanisms reasonable?
Kind regards! 
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Dear colleagues,
In our ongoing research of Siberian ice-wedge polygon mires (http://www.pimdeklerk-palynology.eu/html/polygon_mires_-e_siberia-.html) I am currently working on a rather clastic profile from the Lena Delta that shows clear signs of cryoturbation in various profile trajectories. 
Of course the pollen data does not provide much information on the local vegetation development because of considerable homogenisation of the material, but I hope that it reveals some insights in the effect of cryoturbation on the sediment and pollen record, since it is also an important process of ice-wedge polygon development.
So now I am searching for other pollen data of such disturbed soils, but I have not yet found much. 
Does anybody of you perhaps know of studies that I could use for comparison?
Thanks and best wishes from Karlsruhe,
Pim
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Dear Pim,
I am sure you will get polen from your samples, but most probably you have to try different methods for your samples. I guess your samples should be Quaternary, Holocene or even Late Holocene, then you have to follow the recent developed methods for pollen recovery of these ages through internet or contact Quaternary pollen experts.
Wish you all the best.
Habib.
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Hello everybody!
Could anyone help me with soil free inhabiting nematodes identification?
Would You recommend me some basic identification key at least to families and a checklist (article etc.) with common species in temperate agrosystems (fields of potatoes, corn and wheat).
Any cooperation is possible.
Thanks for your help!
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Hello,
there are several methods to identify soil nematodes.A very interesting method is well described in the following paper and in another paper in attachment.
Then, if you are looking for some interesting handbook describing easier identification methods you may have a look at 'Practical plant nematology: A field and laboratory guide' (http://www.uark.edu/ua/onta/info/2010%20Nematodes%20Manual%20ENGLISH.pdf ).
In addition, several people tried to classify nematode biodiversity around the world. Please see more papers in attachment.
I hope this helps.
Kind Regards
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During her Phd thesis under my direction Stéphanie Topoliantz obsrved that the peregrine pantropical earthworm Pontoscolex corehtrurus was the main component of the earthworm community in French Guianan slash-and-burn agricultural soils. She observed that it ingested charcoal particles which were mixed with mineral particles in its dark-coloured casts. She performed experiments on the ability of P. corehtrurus to ingest charcoal and mix it with the soil. She also demonstrated experimentally that P. corethrurus populations of slash-and-burn areas were differentially adapted to the consumption of charcoal. She also showed that charcoal could used in combination with manioc peels for improving soil fertility, rather than discarding them in the parcels to be cropped, as was common practice. Several papers were published:
In a short synthetic paper I suggested that P. corethrurus could well be the main agent of the formation of Amazonian Dark Earths, in which incorporation of black carbon (issued from charcoal) was considered as a main agent of durable soil fertility (see article and books by Bruno Glaser and Johannes Lehmann):
Since it has been shown that in Pre-Colombian times sedentary agriculture existed in Amazonia and charcoal was used as an amendment (originating in present-day Terra Preta), we may wonder whether this very common tropical earthworm could not be used to improve the application of Biochar, based on its ability to crush charcoal particles and finely mix them with the soil.
Catch as catch can...
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Very interesting. Who would the chemist then? Who would transform this charcoal into available nutrients for plants? 
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Respected all,
I would like to convert FAO soil types such as Regosols, Alisols, Acrisols etc. into texture units such as Sand, Loamy sand, Loam etc. Is there any information or document available for this??. Your kind help will be beneficial for me.
Thanks in advance..
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Dear Dharmendra,
soil texture class generally was not taken into consideration, when establishing FAO types (exception Arenosols) or their subunits,. Ut may be considered at lower levels WRB 2007 and especially  2014 as suffix qualifiers (WRB2007) or supplementary qualifiers (WRB 2014) but they are not, generally, considered on maps.
For this reason, such relation one to one does not exist (except Arenoslos and Vertisols), moreover, not only Arenosols may have texture of sand or loamy sand in upper layer, other soil types may have sand underlaid by loam (these may be especially Planosols and Stagnosols but not only).
If you want to derive soil texture from map, it would be more useful to see some geological maps, but only dose with upper layer of the earth cover . In Poland such a map is called lithological).
Best regards,
Michał Stępień
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I would like to study on spatial distribution of soil organic matter fractions [such as dissolved organic carbon (DOC), dissolved organic nitrogen (DON), particulate organic carbon (POC) and particulate organic nitrogen (PON)] and also microbial respiration, microbial biomass C and N in mono-species 20-year old plantations of alder (A. subcordata C. A. M.) and oak (Q. castaneifolia C. A. M.), planted at a spacing of 2×2 m, located in northern Iran. The stands were never fertilized. The study areas show very similar climatic conditions and management practices. The experimental plots were located at an altitude of 300 m above sea level. The area is on flat and uniform terrain with low slope (0–3%).
Unfortunately I didn’t find any reference about soil sampling design. I have two questions about this project:
Question 1: How many soil samples (the minimum) are enough for study on spatial distribution of soil organic matter fractions and microbial features for each of these stands?
Question 2: Which sampling design is the best for soil sampling?
May you please help me about these questions? Do you have any references about these to present?
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The number of samples depends on your experimental design and the heterogenity of your area. Usually the number of samples required is  if the carbon content is high and there is not a really good answer. 
We have been usually taken 10 samples per plot. This is too much if you have a well replicate experimental design (many blocks and plots) and might not be enough if you have a high carbon soil (not very probable in Iran I think). 
In sampling it might be good to go for a standard depth below the humus layer and take the humus and litter layer separately. The reason is that humus accumulates on the mineral soil and will falsify your samples.  Random sampling within a plot might be avisable. But you might also go for different distances from the trees.  
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Dear all,
I would like to know how to interpret the graph of Canoco. I have found a paper about Canoco and it's too complicated for me to understand. So, could someone help me or suggest me how to interpret the  graph of Canoco, I mean how can I know the relationships between environmental variables and species by arrow. I attached the graphs what I got. And, I would like to know what is the difference between CA and RDA.
Thanks in advance for your useful answers.
with best of regards
lynn
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CA is for a unimodal models and RDA not. You can use the book "Numerical ecology" (Chapter 9) to understand and interpret better the results of your ordination graphics. Also, in this book you can find other stadistics methods.
I suggest also that before to do the analysis you should know the correlation of your variables. If this variables have a correlation between them upper to 0.5 you should to delete one of them.
In your RDA you can see how the variables in the right side are relationed with the WL samples. In other words, in this WL samples these variables had high values. But WL samples have negative relation with Sand(%). The number of axes 1 is the % of variability explained by this axes. 
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One of the most interesting papers that I read about microbial transport (Dighton, John, et al. "The role of abiotic factors, cultivation practices and soil fauna in the dispersal of genetically modified microorganisms in soils." Applied Soil Ecology 5.2 (1997): 109-131.) talks about the role of soil fauna in the transport of bacteria, fungi and viruses.
I have dug a lot for info.
This kind of information is scarce and I hope you can help me to find some more, please let me know if your have seen some paper about it or are working with this.
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If I am not wrong there are more than thousands of references right from early 19th century on this subject Even a search engine like Google should be able to give more than your requirements.
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Hi,
Does someone have experience in using Hobo Pro v2 data loggers? - Are they robust enough to be placed directly in soil?
/Mathilde
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My cohort uses HOBO pendant sensors quite extensively to record soil temperature in our agricultural research plots.  They are smaller and less expensive that the pro v2.  First we make a electronic document that has a list of the serial numbers of all of the loggers, and which plot they will be placed in.  Secondly we put the loggers in a small plastic bag and label the bag with the plot number.  The bag protects the logger from getting scuffed and scratched during installation.  When instilling the sensors in the field we want to minimize soil disturbance. We install our sensor to a depth of 6 in, and we use a wooden stick to do so.  We press the stick into the ground 4 in deep, then place the sensor into the hole we just created.  Using the same stuck we force the sensor into the soil another 2 inches, and fill the hole back in.  The method is quite crude but has served us well.  Lastly, you need to mark the exact location of the sensor.  I cannot stress this enough.  I spent hours meticulouly digging through my plot like an archeologist looking for sensors because I did not mark the location well.  I suggest small flags.  I hope this help. 
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Dozens of papers and reports state that planting pits increase infiltration but none of them state by exactly how much or provide and figures whatsoever. Does anyone have any data in this regard?
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 Does anyone have figures for exactly how much zai/tassa/planting pits increase infiltration?
As pointed out the zai tassa or planting pit is way of harvesting and directing water.
In the arid region the retention and use of water can be dependent on the ability to add the stabilized organic material into the zai. On a sandy soil the increasing of the stabilized will depend of using organic clay complexes to amend the zai. 
The use of clay and/or silt to be included with organic waste will develop those complexes when composted. The mature compost is added in the area of the zai.
When amended the traansformation of the stabilized organoclay complex amounts more percolation of harvested water, more retention and use and facilitiates the mineral nutrition of the crop.
The soil of less than 1% soil organic matter can capture and retain less than 30 units for every 100 unites of the dry soil. On 5% soil organic matter the capture and retention is over 200 units of water in the same 100 units dry soil. The increase of conservation and retention is thus from less than 30 to over 200. 
The improved structure imparted from the organic amendment is able to increase not only the retention but also the percolation and feeds the soil microbial activity so important for high quality yield and health. 
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Is there any correlation of soil organic carbon, inorganic carbon, total carbon and total nitrogen concentration with leaf total carbon and total nitrogen concentration?
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Arshad your question is really articulative. Shall we take  it  this way , whether or not soil C:N ratio affect the leaf  C:N ratio ? . My answer will big affirmative. Any change in concentration of soil C will bring simultaneous change in N status , considering the C:N ratio   of  soil as a constant . Such  soil C:N ratio  will trigger  the better microbial diversity plus the higher buffering capacity of the soil , thereby , maintain the better nutrient supply to above ground plant parts  .
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What is the best method to determine only the amount of mineral nitrogen (NH4, NO3, NO2) but not of organic nitrogen in a soil sample? (or the other way around?)
I was thinking a reduced Kjeldahl might do the trick, but will I run into problems when omitting the digestion steps?
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As mentioned by Mr.Elephant and Dr.Wehr,the NO3,NO2 and NH4 can be estimated in 2M KCl extract of soil.As the amount of NO2 N is   less  in 2N KCI extract,usually NO3 and NH4 will  be estimated.The amounts of these ions can be estimated by distillation,autoanlyser/flow injection and colorimimetric methods.While NH4 is estimated by Indophenol blue colour method,NO3 can be estimated by several methods like cadmium reduction,nitrate specific ion electrode and phenoldisulphonic acid method.Nitrite is estimated by sulphanilic acid method.Over time these methods have been modified by several workers.
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what are the soil fertility requirements (pH, P, K,Mn,Cu,Bo,Ca,Mg levels ) and nutrient removal figures for pyrethrum?
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Start by studying its Cation Exchange Capacity then evaluate the level of saturation of the exchange bases and the elements present in parts per million .. therefore you may assess the amount of nutritive cations available for uptake (K, Mg, Ca, etc).. build relations between uptake tables and pH requirements of different species and whats available in the soil.. etc
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 Hi,eyeryone.In  the  process of  fungal  denitrification,nitrite  reductase(nir) and  nitric oxide  reductase(P450nor) participate in it. And the  nirk  gene  encodes  the nitrite reductase,cyp55 gene  encodes  nitric  oxide reductase.now  I  have find  the  primer  of  nirk  for  PCR   of  soil  samples,but  the  question is  that  cyp55 is  a super family,different  strain  has  different  primer  of  cyp55,for  example,  primer      of Fusarium oxysporum's cyp55A1 gene has  been fund,now  my  sample from the  rice paddy  soil ,so  I  want  to  find  the  universal primer   target  cyp55 gene,do  you  konw  this  primer?I hope  anything  you  know  could  tell  me.thanks  very  much.I  need  your  help.
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Hi again, sorry for not answering earlier, I was on vacation. The problem with these genes in fungi as their variability. There are some quite degenerate primers for cyp55 genes which can be considered as universal, but from my experiences they produce more than one band after PCR of pure cultures of N2O producing fungi and after sequencing, there is no homology with known cyp55 genes. Other cyp55 primers were designed just for one or a few species so they are not universal at all.
I think it is this reference* but I am not sure if you will be able to read it. I will try to find some other later today, ok?
*Zhang and Shoun 2008. Purification and Functional analysis of fungal nitric oxide reductase cytochrome P450nor. In Poole RK (ed): Methods in Enzymology, vol 437, Globins and other Nitric oxide-reactive proteins, part B. pp 117-134
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 I am working Lyallpur soil series ( aridisol-fine-silty, mixed, hyperthermic Ustalfic, Haplagrid ) and Haplic Yermosols in the FAO classification. Since the new World Reference Base for Soil Resources does not include the Yermosols any longer. What is the right classification of the soil used in any experimental study then
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Hello,
according to FAO 1974 soil classification key Yermosols are " Other soils having a very weak ochric A horizon and an aridic moisture regime; lacking permafrost within 200 cm of the surface."
As in WRB the moisture regime is not diagnostic, an Haplic Yermosol correspond to a Regosol.
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For microbial community structure and function using molecular fingerprinting techniques
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Everything is depended on soil type and conditions, Noa is right. If you did not removed soil you have the same results from soil and from rhizosfere. 
1 shake off the soil
2 place roots into 50 ml falcon tube add 25 ml of physiologic solution cca 0.85% NaCl
3 shake it on shaker, at least 200rpm but depends on shaker, best in 4°C for at least 20 min
4 remove roots 
you can use this solution for plating methods or so
if you need DNA, then 
5 centifuge solution 5000g for 20min, 4°C
6 remove supernatant
7 pelet can be use for DNA isolation. Simply resuspend pelet in extraction buffer and use isolation procedures  for soil microbes
When DNA is main aim, you can use benzylchloride extraction from plant roots - it seems to be very effective
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I am currently setting up an experiment using fine meshes to exclude soil fauna from soils. For one of the treatments I will use a 20 micrometer mesh to exclude microarthropods. I assume it will also exclude soil enchytraeids, however I can only find values for body length of enchytraeids but not 'thickness'.. Would for example juvenile enchytraeids be able to pass this mesh? Thanks for your answers!
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But the need of Eva is to exclude fauna, not to allow them to pass through a mesh !!
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I was planning to conduct an experiment involving extraction of microarthropods from soil samples using berlese funnels. These funnels best capture mobile organisms that don't easily dry up thus causing bias on immobile and moisture-dependent microorgs. Is there a way to address this problem?
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Yes there is! Instead of using a heat source above the funnel (such as a lamp) which, as you imply, will roast most organisms of low motility, simply allow the soil sample to dry out naturally and over a longer period (up to ten or twelve days - sometimes eight is enough). If you replace the collection vessel at the bottom of the funnel each day, or every couple of days, you will be able to determine how the assemblage of organisms being extracted changes over time. You will also be able to observe a decline in individuals extracted over time and determine the duration over which most of the organisms in the sample have been extracted. If the soil is particularly moist, and/or has a  high clay content, you many need to crumble it after a day or two of drying. I place my crumbled soil cores on a double layer of nylon gauze on a coarse steel or zinc mesh at the top of the funnel. Ideally the humidity of the air surrounding the funnel should be low and the temperature relatively warm (ca. 18-25 C). My funnels are set up in a greenhouse. I have used this technique successfully for over 20 years and it has a high extraction efficiency (ca. 85-95%) of a wide range of organisms of different motilities. Hope this helps.
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Subtropics sites identified lack of phosphorus available, show that the years after clearcutting of a plantation, the sum of the phosphorus content increases. Year 2 to 4 shows a sharp increase in the undergrowth. 4 to 6 year increases the phosphorus content in the biomass of the plantation. In both periods the content of available soil phosphorus is stable. Then, the rate of replacement of phosphorus is sufficient to meet the demand of the strata above the ground?
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 Phosphorus is finite and limited resource in any soil.   It is good if our soils have sufficient native  mineral P which can be mobilized during the tree growth over years.If the native P in soil is low and if we are not supplying P from external source like fertilizer or any other source ,then the rate of mobilization from soil P or addition from fallen leaves will be limited .As forest system is more or less a  closed system, only soil and the vegetation have to exchange the nutrients.whatever nutrients are mobilized ,they will come from the action of roots , root exudates ,organic acids and enzymes produced in the rhizhosphere on soil P and P present in fallen leaves and other debris So the replenishment depends on the  reserve P present in the soil..Even before planting forest plant saplings, one has  to test  the soil profile for P status and take necessary remedial measure in the beginning it self.If the demand for P increases in the growing tree ,we have to see how can it be supplemented.
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The Idea of soil sampling is the assumption that it is randomly taken.
If you want to follow the distribution of the elements AFTER band placement than accurate position of each amling volume relative to the band must be taken and analysed separately.
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You need to define exactly what it is you want to learn then design the sampling to deliver what you need
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Hi All:
I am working on some alkaline soils which have high inorganic carbonates. Yet I need to analyze the soil C content, microbial biomass C, and the 13C isotopic signature of both. Are there any classical methods for removing those inorganic carbonates? In doing so I can get clear results after the carbonate removal.
Thanks very much.
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Hi Allen,
The paper available at the link below explains a simple and convenient method to remove Carbonates from soil samples prior to analysis of δ 13 C of soil organic carbon. It involves HCl-fumigation of finely ground soil samples for 48 to 72 h period and the method can be easily adoptable if you have access to a fume hood equipped with a vacuum system.
Good luck.
-SJ
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There are different kind of substrates used in soilless culture. Organic and inorganic substrates are used in substrate based soilless culture. Inorganic substrates are creating problem to the environment while disposing into the nature. For reducing environmental pollution, organic substrates can be used for soilless culture. Availability of organic substrates is a problem. 
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Sphagnum peat moss is by far the most widely used substrate for containerized cultivation. It is very often mixed with perlite and vermiculite or pine bark. There is a push to replace the peat market with coco coir because it is more readily available. In turf, sand and gravel are often used. For my soilless lettuce project, I am using Hydroton expanded clay aggregate exclusively, but we have conducted studies on charcoal, coconut croutons, and perlite as well.
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I would like to find a simple method other than the one outlined in "Methods in Soil Biology" by F. Schinner, R. Oehlinger, E. Kandeler, and R. Margesin to determine soil nitrifier and denitrifier populations.
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Dear Maren
Dettermination nitrifiers and denitrrifiers  usingthe most probably numbers (MPN) technique, (Cochrane 1950)
Nitrifiers:
Determined using the Stephenson’s medium for autotrophic nitrifiers
(Stephenson, 1950):
Ammonium sulphate         2.00 g
K2Hpo4                                               0.75 g
FeSo4.7H2o                        0.01 g
KH2 PO4                            0.25 g
MnSO4.4H2O                     0.01 g
MgSO4.7H2O                     0.03 g
CaCl2                                  0.002 g
Distilled water                   1000 ml.
After sterilization, a knife tip of sterile CaCO3 was added to each tube.
Incubation temperature was 30 +0.5 CO for 21 days. Diphenylamine in
concentrated sulphuric acid was used for detection of the produced nitrate.
 Denitrifiers:
Were counted using the yeast – extract– peptone- nitrate medium (El-
Saify, 1976):
Peptone             10.0 g
Yeast extract     0.5 g
KNO3                1.0 g
K2HPO4             0.5 g
Agar agar           2.0 g
Distilled water  1000 ml.
pH                     7 – 7.2
The determination tubes were equipped by inverted Durham tubes. Incubation was for 10 days at 28 + 0.5 OC. Replicates showing gas in the
Durham tubes after addition of a strong NaOH solution were considered to be denitrifiers positive.
Cochrane, W.G.(1950). Estimation of bacterial densities by means of the       «most probable number». Biometrics 6, 105-116.
Stephenson, M. (1950). Bacterial metabolism, 3rd ed., Longmans, Green&Co. London.
El-Saify,N.A. (1976).Nitrate reduction and denitrification in soils. M. Sc. Dept. Fac. of Agric. Ain. Shams univ. A.R.E.
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I have been reading in the literature that fungi could reduce nitrate but I haven't see any specific study on that yet.
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Hi Roberta,
Your question is interesting. I'm working on denitrifying woodchip bioreactor. Here denitrification is primarily mediated by bacterial community. Fungi colonizing in the woodchips play an indirect role for the denitrification process by making organic substrates from the woodchips more accessible to bacteria.
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I am trying to lyophilize small volumes of whole extracted soil organisms (nematodes and smaller). I don't have any experience with this...but I do know that it is a benchtop unit that is generally used with larger volumes ~10mL or more. Does anyone have any suggestions for how to maybe use this unit with smaller volumes without purchasing a smaller flask? The lab I will be working in has 600mL flasks and generally use them with 50mL conicals tubes (falcon and the like). If you have any ideas, please do let me know! Especially if you have done this before-- we are thinking of cutting the lids from the 1.5mL eppendorf tubes and placing them just so-- but it's very possible that this is a bad idea! Thanks in advance. 
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Don't cut the lids off your eppendorfs as you risk contamination when returning the pressure to atmospheric in your lyophilisor. Poke holes in the lid (with a syringe needle or a scalpel). They will dry fine. Just make sure you freeze your samples well (ideally in -80C) and then place in the lyophilisor. If the sample bubbles out of the holes, you need to freeze your samples for longer as it suggests the sample is boiling and not subliming. 
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Hi All,
Can some one confirm (in basic terms):
1.The reasoning behind the addition of BaCl2.
2.Why its more desirable to record the HCL titrated btw pH 8.3 & 3.7
My understanding is:
-Bacl2 precipitates Carbonate  therefore enabling the amount of NAOH consumed during the adsorption of CO2 to be determined 
-After the addition of Bacl carbonate is locked away and Biocarbonate is more prevalent bwt ph 8.3&3.7 
Any help would be much appreciated
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Michael,
I can't help you on the BaCl2 question, but the chemistry behind the pH titration is explained in this paper, if you can get hold of a copy:
Tinsley, J., Taylor, T.J. and Moore, J.H. (1951) The determination of carbon dioxide derived from carbonates in agricultural and biological materials.  Analyst 76, 300-310.
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Does such a correlation always exist between these two?
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 thanks for the info. It was much helpful
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I am developing a habitat suitability model for endangered lizard at the local scale (20-50 m resolution). One of my hypotheses considers shallow ravines being more suitable habitat for the lizard, compared to flat hill tops. Soil crust of sandy slopes in ravines is more friable than that on flat surfaces, so lizards have better survival rates because of being more efficient in digging burrows and finding refuges. My soil data coverage however is not nearly as detailed as the topographic data coverage, so I want to find a topographic variable that will indirectly reflect differences in soil quality in the final model. So far I tried Ravine shapes manually delineated from elevation isolines; Aspect, Slope, Surface Ratio, Fragmentation Index, and Topographic Position Index. Manually delineated ravine shapes worked well when I was comparing average numbers of lizards collected in ravines, with average numbers of lizards encountered outside of ravines using Mann Whitney test during the initial exploration. However because  (1). Ravines were delineated manually (subjectively) (2), sample sizes were small (comparisons were made between small groups of ravines and hill tops), I decided to search for more advanced alternatives. Fragmentation Index (FI) was useful in delineating the habitat along with land cover variables, but was not sensitive enough to reflect relief details.  So did slope and Surface Ratio. Since all thee were highly co-linear I have chosen to use FI alone, as it was gaining the highest score in the model. Topographic Position Index contributed little since it was continuous throughout the study site, irrelevant of the suitability of the habitat. However, the visual image represented by this variable suggested that if I brake it down into categories that will primarily reflect values within the suitable habitat, I may be able to produce a variable that will reflect the ravine effect, for the suitable variable primarily. I tried it and few categories produced get higher contributing scores in the model. Moreover, surprisingly, in the final predictive map I am even getting marginal patches supported by field observations of lizard presences, ans maps produced using soil sample data., which were not identified by models calibrated without these derivates of TPI. Which I like a lot. On the other hand I understand I am applying a subjective choice into the model, which may be sub-optimal. What would be the most serious critique to be applied to this kind of the data-manipulation?
P.S. By the way in general I am seeking a collaborator (preferably a statistician with interest and experience in habitat suitability modeling) that may be interested in brainstorming around this study and co-authorship. I do this on my free time and have no current financial support for this project.
Thanks in advance
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The topographic position index (TPI) is scale dependent, so finding the analysis scale for TPI that contributes the best to your model may be a matter of adjusting the area over which the TPI is calculated (neighborhood). Although similar analysis scales won't differ from each other very much, the larger the difference between analysis scales, the more the results will differ. In other words, it is beneficial not to view TPI as only one potential covariate, rather treat each analysis neighborhood size (or step in size) for TPI as separate potential covariates.
Your idea of segmenting the landscape may also be fruitful. I would recommend taking a look at the TPI classifications used by Weiss (2001) or those used by Deumlich et al. (2010). They combined multiple analysis scales of TPI to create useful classifications of slope position and landforms. You may need to adjust the analysis scales to better fit your landscape, but at least those examples may provide some ideas on how to use multi-scale analysis to differentiate important areas.
Because you mentioned slope may also be informative for your purpose, you may want to consider trying hillslope position. The digital classification of hillslope position (Miller and Schaetzl, 2015) uses relative elevation (similar to TPI), but also takes into account slope gradient and profile curvature.
I've put together an ArcGIS toolbox that can process a DEM for all of the analyses mentioned here, and it can be found at the last link included below.
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I am interested in developing  a mathematical model for biopolymer coated fertilizers using a multiscale modelling approach. I would be greatful if anybody could guide me more on this.
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Hello, I have real soil samples from which I need to isolate thermophilic actinomycetes. I cultivated the soil at 58 °C and then pipetted extracted solution of soil on agar with biodegradable polymer suspension. Then again cultivation of plates at 58 °C. It seems that actinomycetes are responsible for the degradation of polymer, but they are inseparable from Geobacillus sp. I need to obtain the pure culture of actinomycetes. I have tried various selective media (R8, GYM, media 7) or antibiotics (nystatin, cycloheximide), but nothing helped. When I identify the samples (16s rRNA) there is only Geobacillus sp. (even when I used DGGE to separate DNA). Can anybody tell me how to separate those 2 organisms? Or some media which will support thermophylic actinomycetes growth? Do you think that for example HVA agar would eliminate Geobacillus? Hope my question makes sense...
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Hi, you can try to heat the suspension content actinomycetes in 80 oC for 3 minutes, add 25 ml of glycerol/liter and antibiotics(cycloheximid and nalidixic).
You can also try to use glycerol sol extract medium.
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Earthworms are known to modify the physical and chemical characteristics of soils and, through ingestion, produce nutrient-rich casts. These casts often have greater concentrations of exchangeable cations (notably K+, which I am currently focusing on). Although there appears to be considerable research on the availability of exchangeable K+ ions to plants, I am wondering whether these are bioavailable to organisms through ingestion or bioturbation.
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There was great hope 50 years ago that cation uptake by plants could be predicted from exchangeable cations but the situation is far more complex that that.  That is not to deny that the exchangeable pools are those plants draw upon, far from it!
I know nothing about your question, but if one makes the simplifying assumption that the worms are not growing, or that their absorption efficiency for minerals is low, then the 'permanent' components of their organic rich diet will be concentrated in the casts,   This happens with cattle.  So since K is present at relatively high concentrations in plants, one would expect the concentrations in casts to also be high. 
I imagine that there is literature on bioturbation and worms.
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I am interested in interactions among soil invertebrates and I would like to have some opinions whereas the localization of soil organisms in the different soil layers may constrain their interactions. Does anyone have some references about this?
Thank you very much!
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Hi, thank you very much for your contribution. As I can see, not much has been done yet, particularly in relation to trophic interactions among species as constraint by vertical distribution. I think that combined methods of soil stratified sampling and stable isotope analyses will provide additional insights in the future.
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I want to choose some commercially manufactured biochars as soil amendment to immobilized heavy metal. The biochars are already characterized but I want to know the features to be considered in choosing the biochars. I understand that a good biochars for metal adsorption must have large surface area and high phosphate content/phosphorus. What are other features to considered aside the feedstock choice?
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Hi, 
Apart from surface area and nutrient content of biochars, you can consider oxygen-containing functional groups, aromaticity, CEC, surface pH, porosity of your selected biochar. 
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How to you tell a enchytraeid from a lumbricidae: the pot worm vs earthworm dilemma? I probably only need to separate out invasive Dendrobaena octaedra. from a native enchytraeid, any suggestions? Is there anything I could see in a alcohol preserved specimen? Both are small usually less than 2cm in length
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Pot worms are tiny unpigmented worms (except some rare cases) earthworms are more robust and e.g. D. octaedra is dark red-violet.  Enchytraeids (when they are adult) possess clitellum on/around segment 12, lumbricids have longer clitellum and positioned more tailward  (from segment 20 or more back).
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AOA has similar role with AOB in soil ecosystem. AOA were proved to generate N2O in pure isolate and enrichments in recent years. How to distinguish microbial source of nitrification-N2O emission in complex soil environments?
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Ammonia-oxidizing Archaea (AOA) can be distinguished in soil samples from Ammonia-oxidizing Bacteria (AOB) through analysis of the DNA in the soil. The gene for ammonium monooxygenase (amoA) is closely related but not identical between AOA and AOB, so various techniques that quantify this gene can be used. For example, DNA-microarrays have been constructed that target the known diversity of amoA sequences from both AOA and AOB - look for papers by Dr. Guy Abell and colleagues in Australia.
If you analyze a soil sample and find a high abundance of AOA but low abundance of AOB, you can hypothesize that the N2O produced from this soil is coming from AOA. Follow-up experiments are needed, of course, and you'd need to show that denitrification is not the main source of N2O in that system. There are inhibitors for various parts of the denitrification pathway, but the use of inhibitors requires some careful controls in your experimental design.
There are other methods, this is just one example of how to distinguish between AOA and AOB in soils.
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I would like to contribute some kind of ecological assessment of soil, and ecological analysis of creatures from a soil sounds good, but I am not sure, does it possible to create some conclusion based of analysis of mentioned organisms? If you have some similar articles, please, recommend them to me! I would like to hear your opinion.
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Yes, there is a close relationship between the soil biota and the ecological condition (or biological state) of the soil. However, it is very difficult and not very helpful to analyze all organisms that constitute a soil community (often some thousand species per square meter). More reasonable is the use of proxies to characterize the ecological condition of a soil. Biological assessments of soils have been successfully performed with earthworms as indicator group. Enchytraeids (microannelids) or microarthropods can be additionally analyzed to get a more differentiated picture. Please take a look at this
Best regards,
Ulfert
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I'm imagining some form of isomorphic substitution of oxygen from silicate lattices that involves a biological (enzymatic?) step that could substitute the O2- with something else, and then perhaps an additional step that converts (oxidation?) O2- atoms to O2?
Please let me know if I am missing something or am not clear. I would imagine that there is a lot about this seemingly really complex series of reactions that I am not understanding properly.
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I believe what is being questioned is whether isotope exchange is likely on quartz or in other silicates; the chemical mode is known for phyllosilicates that involves H2O but generally higher temperatures and  either high or low pH ( acid or base catalysis). This doesn't preclude a biochemical approach, but higher plants are the ones usually associated with Silicic acid and silica uptake and deposition ( phytoliths). Quartz is much more resistant obviously- it is evident in the definition of the ultisol soils. 
One place that would be worth investigating for quartz, would be the gut of earthworms, as these would be microenvironments drastic enough to perhaps enhance such an isotope exchange. I would suspect it only of scrambling , and not a detectable isotope enrichment.
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I would like to obtain information about the biodiversity and know which specific organisms are in a soil. What are my options for sequencing the genetics or otherwise understanding the microbial diversity?
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http://www.earthmicrobiome.org/emp-standard-protocols , check this out. Other than SSU profiling, Geochip  is always a good way to go with the aim of  understanding the functional communities in soil 
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I am going to study the diversity of soil microbe in rubber tree plantation.
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You may find the solution of your query in following article..good luck
  1. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
  2. Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community
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I am assisting with a student research project in which they are trying to identify antibiotic producing bacteria in soil.  They are growing isolated colonies of the bacteria on TSA plates and then trying to extract DNA for use in PCR of the 16S region for eventual sequencing.  The bacteria are both Gram positive and Gram negative mostly bacillus shaped. 
They have tried several different methods for DNA extraction:  Chelex, Chelex with ethanol precipitation, Chelex with Proteinase K, and freeze/thaw with Proteinase K.  Regardless of the DNA extraction method, the 260/280 ratio (song a NanoDrop Lite) of the soil bacteria is around 1.2-1.3; the best has been 1.43 using the freeze/thaw/Proteinase K method.  The lab strain of E.coli that we use as a positive control consistently yields a ratio of 1.7.  I am not sure why there is such a difference between the soil bacteria and the lab strain E. coli when they are extracted at the same time using the same method. 
Any suggestions that I can give to the instructor in charge would be greatly appreciated.
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Dear Kendra Kimberley,
I think that the low 260/280 ratio of soil bacteria might be influenced by the Gram positive spore forming bacteria present in your cultures (Firmicutes such as Bacillus and Clostridium species, etc.). Spore-forming bacteria are more dificult to extract and to purify. So, it is not surprizing that the freeze/thaw/Proteinase K method lead the best results. It may help to: add a Lysozyme treatment  for the lysis step, increase the incubation time for proteinase K; add another phenol/chloroform step for cleaning; add another 2 cleaning steps only with cloroform; 2 steps with ethanol and increase the drying time of your matrix before elution.
Since the abnormal 260/280 ratios indicate that the sample is either contaminated by protein or a reagent such as phenol, repeated cleaning steps might really work. Although purity ratios and spectral profiles are important indicators of sample quality, the best indicator of DNA quality is functionality in the downstream application of interest such as PCR. So, abnormal 260/280 ratios might still lead to good PCR amplificatios.
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Traditionally people use 15N fertilizers to trace the N in soil. For lab incubation without plants, priming means extra or less mineralization of soil native N (organic matter) within N treated soils compared to N mineralization in no-N soils. However, when plants present, the priming is the difference of the amount of N taken up by plants and the control (no-N) plants. This priming with plants, however, is not a real priming effect but a estimate of priming, as plants cannot take up all N mineralized in soil, so the remains of mineralized N may get lost via leaching, denitrification, etc. We know they are different but classical papers ( such asJenkinson, et al, 1985 SBB) always use plant N uptake as a proxy for priming or mineralization of soil native N (or organic matter). Can we compare the N priming results derived from plant N uptake and soil net N mineralization? 
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Hi Allen,
Did you mean soil net N mineralization in the absence of plants? If that is the case, N priming results derived from plant N uptake can not be compared with soil net N mineralization, because the presence of plant roots (by their addition of extra C by rhizodeposition) can change the immobilization-mineralization turnover in soil appreciably.  Let me know if I am correct.
Another point:  Jenkinson et al (1985) used the term 'added N interaction' (ANI).  I think this is the term they used for 'N priming'.  ANI can be 'apparent' (resulted from pool substitution) or 'real' (resulting from plant roots exploring larger native soil N pool due to their larger root system in fertilized treatment compared with unfertilized treatment). Again, please let me know if I am correct.
Susantha
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Soil serves us many goods and services while soil erosion affects these economic and ecological services. I am interested to know how these impacts can be quantified in terms of PES, if conservation measures is used to check soil erosion?
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I agree with the view of Dr. Firoz Khan on relating emergy concept with PES. It is not always possible to convert ecosystem service into emergy; then what is the option? I also appreciate the view expressed by Wendy Peterman. In fact he had attached a paper which is really dealing the topic. Thank you guys for the response.
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I have been reading many papers about adding glucose, sugar or other complex substates (cellulose, litter, crop residues) to soil to analyze soil organic matter decomposition and soil respiration. The confusing issue I ran into was: how to express the amount of C from substates added to soil? For example, some report the ug or mg C per g soil, and some simply use the percentage of C based on the soils used. For the respiration, some use the ug CO2-C per g per h, some ug CO2-C per g per day or week, and some even use mg CO2-C per g per h/day/week.
Other than the inconsistent report of the amount of substrate, different papers have different experiments periods or lengths. I am wondering if it is better to express the amount of C from substrates using a time scale? For instance, two papers report the same amount of 1000 ug C per g soil, but they have different duration, let's say 10 days and 100 days. By using the time scale, we see the C addition is completely different: 10 ug C/g soil/day vs 100 ug C/g soil/day. But I don't know which way is best for respiration.
Does anyone agree or disagree that we should propose a common way to specify the expression of substrate input and respiration? Feel free to leave your comments and suggestions below. Thank you.
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The respiration rate must be expressed as amount of CO2 (ug or mg or g of CO2-C or mmol of CO2) per amount of soil (g, kg) per unit time (min, hr, day or even week/month/year).
If you see the published data with the missed time units, then it is qualified as error made by authors and editors.
What is better, mg of CO2-C or mmol of CO2? In a C-balance studies mass units of carbon are better. In the studies of metabolic pathways (e.g. degradation of PCB in soil), the molar concentration is preferable.
What is better, ug, mg or g of CO2? g or kg of soil? hr or day? No strict rules, just make your numbers easy to read. There was a tendency to unify the units to international standard but it is not always justified.
Finally, per g of soil or per m^2 of soil surface? Depends on technique you use, whether you measure a flux of CO2 by chambers or incubate few g of soil in a vessel.
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Thanks all for the comments, the paper has been published in Applied Soil Ecology ( ). Here also attached the file for your reference.
Add inorganic fertilizers to soils without plants showed no native soil N mineralization, but applying organic fertilizers (soybean, corn residue, clover, or other green manure) caused less soil native N mineralized, indicating increase of immobilization of soil N. However, applying both inorganic and organic fertilizers to soils with plants caused more soil native N mineralization. Does this mean plants control the soil N mineralization regardless of fertilizer types, while without plants, organic fertilizer CN ratios switch soil N mineralization to immobilization? If yes, what is the critical or threshold value for CN ratio, like 5, 10, 15, 20? 
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It is also important to remember that the C/N ratio is usually measured as total carbon to total nitrogen. Not all organic molecules are easily degraded, particularly some of the carbon rich ones. So the quality of the organic material is important. The C/N is more a qualitative rather than quantitative measure of substrate quality and the relative availability of C and N.
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Extracted from soil samples.
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Order Entomobryomorpha
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Me and a collegue are thinking of starting a small, side-project, study on earthworm (Dendrobaena veneta) growth. Neither of us have worked with live earthworms before though. We would like to feed them some kind of "standardized" feed and were thinking of oat flakes as a potential choice. Does anyone know if this is a good choice, or do you have any better suggestion?
Other tips regarding rearing of worms are of course welcome as well.
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Refer to our published articles in RG
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Does anyone who works with hydroponics ever faced the appearance of fungus in the roots??If so, how do you dealt with it? I tried to sterilize everything in 4% bleach, but it appears to come back after a week or so.
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Dear Dr. Pereira,
The solution given by Dr. Weiland is the same I was about to advice you with. Since you're running hydroponics so it's not an organic system. It will depend on the system it self whether it's closed of open hydroponics. The first option sends you back to the solutions given by Dr Weiland, but the second option of open hydroponics in addition to UV and H2O2 treatments of incoming water, you may add ozone sterilization with O3 generator that start to be cheaper than before. The gas generated is toxic rather for plant and microbes but it's stable in water till 15 min after injection in the water, then it will go to O2 (2 O3--> 3 O2) and you have enriched your hydroponic solution with oxygen. I would recommend you to use aromatic and medicinal plant extract but I don't want to turn your chemical solution to an organic one!
Good luck
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Im going to start my pHD studying the biodiversity of the soil. I have done my first extraction of DNA, but it was a total failure. I used the KIt ZR Soil Microbe DNA MiniPrep, and I want to now if anyone else has used this, or what other protocol you recommend to try.
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DNA extraction protocol should be carefully chosen in relation to the soil type you study and what you want to do with the DNA. There is no perfect protocol. Even if lots of people use PowerSoil from Mobio (me included), this protocol can also present some problem for metagenomic. PowerSoil was shown to be less efficient when the soil pH is below 7. So my advice would be to try different protocols. You have also the ISO standard DNA extraction protocol which was developed in Europe few years ago, FastDNA SPIN kit for Soil (MpBio), Griffiths et al (2000), Zhou et al (1996)…
Please, have a look on this question on RG about DNA extraction of soil for which I gave a more detail answer, and where people gave some protocols:
Hope that helps
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Roundworms are small, but have a potential role in recycling of nutrient and minerals in soil along with other micro-fauna they form the large base of soil ecosystem and helps in sustainability of soil health and by studying these nematode fauna one can suggest the status and health of soil ecosystem through community analysis means they are really good bio-indicators. But I want to know what are the characteristic of good bioindicators?
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thank you Pierre
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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.