Soil Ecology - Science topic

I discovered this Cunaxid in a soil core sample and tried to key it. I came down to Scutopalus, which if correct is the first record for the genus in North America. Since I'm new to this I would like expert confirmation. I attached photos below of all the relevant features for identification.

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.

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 This I found very hard going due to the poor translation and somewhat outdated.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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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:

https://doi.org/10.1016/j.scitotenv.2020.139453

https://doi.org/10.1016/j.scitotenv.2020.138849

https://doi.org/10.3389/fphys.2018.01173

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

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.

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?

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

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

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?

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 ...

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!

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 

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)

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!!

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?

soil ecology

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. 

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....

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 

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.

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?

I collected some mites showing characters of Tetranychidae associated with stone from Syria.

How to use a set of LIVE/DEAD BacLight Bacterial Viability Kits 13152 dyes for soil bacteria?

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!

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

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.

invertebrates are most complex organisms that are not much studied in functional role in the ecosystem in tropical countries. 

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? 

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

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!

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...

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..

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?

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

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.

Hi,

Does someone have experience in using Hobo Pro v2 data loggers? - Are they robust enough to be placed directly in soil?

/Mathilde

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?

Is there any correlation of soil organic carbon, inorganic carbon, total carbon and total nitrogen concentration with leaf total carbon and total nitrogen concentration?

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?

what are the soil fertility requirements (pH, P, K,Mn,Cu,Bo,Ca,Mg levels ) and nutrient removal figures for pyrethrum?

 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.

 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

For microbial community structure and function using molecular fingerprinting techniques

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!

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?

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?

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.

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.

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. 

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.

I have been reading in the literature that fungi could reduce nitrate but I haven't see any specific study on that yet.

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. 

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

Does such a correlation always exist between these two?

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

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.

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...

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.

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!

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?

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

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.

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.

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?

I am going to study the diversity of soil microbe in rubber tree plantation.

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.

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? 

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?

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.

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? 

Extracted from soil samples.

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.

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.