Soil Microbiology - Science topic

The geoform or relief of the soil, associated with the taxonomic nature of the soil (tropical and temperate soils) and its climatic conditions (tropical in the case of Paraguay) influence the availability of nutrients and these influence the microbiological quality and quantity of the soil. An interesting area of ​​research would be to relate these conditions to the sustainability of agricultural systems, seeking management associations that allow strengthening ecosystem services, as management tools that compensate actions to combat neutral land degradation.

Nand Ram I agree to your point of view but however Qasim Ali has answered in a little brief way

Paul Reed Hepperly I agree to your 5% soil organic matter make the soil not supportive for many pathogenic soil microbes and yes this depends on the locations too

Qasim Ali your answer sums about the main microflora found in soil and its functions too thank you

Hi

The composition and diversity of soil microflora—comprising bacteria, fungi, archaea, protozoa, and other microorganisms—are influenced by a complex interplay of factors that vary across different ecosystems. These factors include environmental conditions, soil properties, plant communities, and human activities, each playing a critical role in shaping the microbial communities present in the soil.

1. Environmental Conditions:

2. Soil Properties:

3. Plant Communities:

4. Human Activities:

5. Biotic Interactions:

Prem Baboo Thanks for adding your expert views on Soil Micoflora interaction however I felt that Dr Sakshi Balyan point of view is in line with my question and thanks for both the experts for your comments and supporting my research

Abdelhak Maghchiche Thanks and yes this would be of help for my present research on Soil Micoflora at a particular location in India where there are climate disturbances and yes I am trying this with and without biogas slurry to understand in a better way and at the same time I can have two researches with me

In substrate-induced respiration (SIR) assays, the measurement of microbial activity through the quantification of produced CO2 is a common practice. These assays often involve the absorption of CO2 in a base, such as NaOH, and subsequent titration with an acid, like HCl, to determine the amount of CO2 produced. The lack of observed difference between a blank (control without substrate) and a sample (with substrate) after titration against HCl could be attributed to several factors, each of which must be considered systematically to troubleshoot and address the underlying issue.

1. Inadequate Substrate Concentration

2. Microbial Activity

3. Experimental Setup and Titration Accuracy

4. CO2 Absorption Efficiency

5. Interference or Contamination

6. Analytical Sensitivity

Conclusion

A lack of difference between the blank and sample in a substrate-induced respiration assay after titration against HCl suggests issues with either the experimental setup, microbial activity, substrate concentration, or analytical sensitivity. By methodically examining and addressing these potential factors, one can identify the root cause and take appropriate measures to rectify the problem, ensuring accurate and reliable measurement of microbial respiration in response to the substrate.

With this protocol list, we might find more ways to solve this problem.

What do you mean by "healing"?

Go to the Rodale Institute website Douds and the collaborators have formulated the method for on farm mycorrhizae production.

The on farm propagation gives an adaptive mixture of species with ability to be effective under your conditions.

can anyonne suggest me how to adjust WHC for my rice to its full in pots?

I just needed basic steps

You can use H2O2 by concentration range 10 - 20 mM

i will send you results it thats ok

@ Shreya, I advise you to go through the below reference:

Methods for Root Exudate Collection and Analysis by Hugo A. Pantigoso, Yanhui He, Michael J. DiLegge & Jorge M. Vivanco , The Plant Microbiome (2020) pp 291–303.

@ Asela, the attached manuscript may be helpful for you.

I am totally agree with @ J.C. Tarafdar Sir. Apparently soil Respiration and dehydrogenase activity measures the microbial activity in soil. For soil Respiration we can go for either alkali trap that has been discussed or we can go for rapid techniques by comprehensive analysis of soil health by Cornell University.

I found these links, hope they are useful:

Oxidation and microbial proliferation leads to SOM loss. So as long as it is safe from oxidation and microbes there will be no loss of SOM. But still if tillage is done in soil and exposure of surface soil to sunlight is happen then it will take very less time for SOM to loss.

This is a good question.

Jose Risomar Sousa I am not sure how that helps answer my question. Could you please elaborate?

Dear Laith

As a Proportion, its the same 1:10

You can classify your bacteria up to a certain level by various microbial and biochemical techniques. But to identify the bacteria to the genus and species level, you need to do 16S rRNA gene sequencing. You can try sanger dideoxy sequencing method. If you are using applied bio-systems sequencer, You will get 2 trace files .abi1 and .abi2(fwd and reverse) files. You may use DNA baser software to assemble both the forward and reverse trace files. After assembly you will get the contigs sequence in fasta format and then perform a nucleic acid blastn against 16S ribosomal RNA sequences(Bacteria and Archea). You can identify your bacteria.

Hi Bjorn Tytgat,

bit of an old thread, but would you maybe have some updates, e.g., resulting publications that describe how you eventually proceed?

TIA

Cedric

A special issue "Applications of Plant Pathology in Horticultural and Floricultural Crops" has been recently issued in Journal of agronomy MDPI (IF: 2.603). Submit your manuscript in this journal and you will get published your paper in a short period of time. Good luck 👌👌👌

I could recommend you a Mycorrhizal interaction with plants book: "Mycorrhizal simbiosis" (Smith and Read, 2008).

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.

Hi Albert

I think this article:

"Extracellular Microbial Metabolomics: The State of the Art"

Good Luck

When you amplify the ITS region for fungi or bacteria, it is normal to obtain multiple bands from environmental samples such as soil. The ITS region is variable in length between different taxa. So, having 2 bands is normal and I would expect that both bands being different fungi. The ITS vary in length between 200 bp - 1000 bp and more. I usually get many more bands (not just 2) from ITS amplification out of soil, I would 2 bands is not many with the ITS.

There is a "old school" fingerprinting methods called ARISA that use the variation in length of the ITS amplicon to assess the bacterial or fungal community composition.

Regarding Illumina sequencing for the ITS, you will not have much overlap of the forward and reverse reads. You will have to run your analysis just for the forward reads. Worth trying to merge the reads, but if you have complex samples such as soil, most forwards and reverse reads should not merged. You can also run the analysis on the reverse reads and compare the results with the forward.

definetly same....the specie was reclassified.....this reclassification in itself if a vast subject and years of research on the specie leads to the same...

Czapek Dox Agar is a solid medium for the general cultivation of fungi, yeasts and soil bacteria. It contains:

Agar: 15 (g/lit)

di-Potassium hydrogen phosphate: 1 (g/lit)

Iron sulphate heptahydrate: 0.01 (g/lit)

Hanuman Singh Jatav

Dear Jatav,

In the last decade or so, there have been remarkable advances in our knowledge of various topics in soil science. It is not possible to list all of them, so I will try to recall some based on what has been discussed in conferences, and what has been published in soil science journals. These include the fate and effects of antibiotics in soils, 4 per mile initiative, clay-organic matter interactions, soil change due to anthropogenic impact, biological soil health indicators, biochar effects on soil properties, soil variability at the aggregate and soil profile scales, use of non-invasive techniques for soil research, nano-fertilizers, temporal and spatial variability of soil properties, factors controlling nutrient availability in soils, the role of dust deposition on soil development, silicon dynamics in soils and ecosystems, pedometrics, pesticide transport in soil, indicators of soil development, the genesis of technosols, fate of heavy metals in soils, new methods of soil analysis, and many others.

Keep safe,

Victor Asio

Dear Colleagues

These are papers in Russian. Maybe it will help. Regards, Sergey Viktorovich Pushkin Shumao Wang

1) By adding organic matter humus can form phosphohumic complexes which is easily assimilated by plants, humate ion can replace phosphate ions and humus can form coating around the Fe and Al ions so that coating prevent P from fixation....

2) There are P - solubilizing organisms a) Bacteria - Pseudomonas and Bacillus

b) Fungi - Aspergillus and Pencillium

3) VAM Fungi can increase the absorption of P from soil by extension of root system

4) Placement (Band placement) of fertilizers (Placing the fertilizer below the seed can reduce the fixation of P by reducing the contact between the soil and fertilizer)

5) Liming of acid soils also release fixed P from Fe and Al compounds

@ Chandra, the agar use to prepare microbial media is a jelly like substance, obtained from red algae. Agar is a mixture of two components such as linear polysaccharide agarose and a heterogenous mixture of smaller molecule called agaropectin. Therefore, agar as such does not have any phosphorus content.

K solubilization is done by a wide range of saprophytic bacteria, fungal strains and actinomycetes . There are strong evidences that soil bacteria are capable of transforming soil K to the forms available to plant effectively. There is considerable population of KSB in soil and in plant rhizosphere. These include both aerobic and anaerobic isolates that the most frequently KSB in soil are aerobic. These include both aerobic and anaerobic isolates that the most frequently KSB in soil are aerobic. A considerably higher concentration of KSB is commonly found in the rhizosphere in comparison with non-rhizosphere soil

We worked on Pseudomonas aeruginosa but not on Pseudomonas fluorescens .

Thank you

Hello,

You need to determine a few things before starting to isolate rhizosphere bacteria: 1- Why do you want to isolate rhizobacteria?               to select PGPR, or biocontrol agents? Remember only 1 to 5% of rhizobacteria are PGPR so you need to test a very large number of isolates to find a few intereting ones. 2- To study  their diversity? For this aim you can use molecular methods, pyrosequencing combined with bioinformatics can give you very interesting results. Let me remind you a few definitions: a) the surface of roots is what we call therhizoplane (some authors include very very strongly attached particle of soils. b) soil sticking to the roots when you shake them vigourously is what we refer to as the rhizosphere. But an important point frequently neglected is to check if your plant is colonized with mycorhizae or not. If your plant is mycorrhizal then you should talk about the mycorrhizosphere, so most reports refering to the rhizosphere are indeed studying the mycorrhizosphere. You also need to determine which crop you want to study and the area or region targeted. Now the protocole for isolation is relatively simple and unfortunately their is no standard method: For PGPR or biocontrol isolates you will have to visit many fields growing the same crops and to talk with the farmers to obtain permission and  to know the cropping  history (previous crops, crop rotation etc...) and fertilization history, and you need to sample 3 plants with their roots, and you should choose those that are vigourous. Any information you have on the sampled field and the cultivars planted will be very helpful. Note that for ecological study your sampling should be representative to the field sample and should be done according to an experimental design. The plant roots with attached soils (you can take many subsamples, and don't forget to take roots to color and observe if there is a mycorrhizal colonization) are transferred to the lab on ice in sterile bags. All tools used should be desinfected. Once in the lab transfer to a fridge and process as soon as possible (1-3 days max). Some of my students separate bulk soil from the roots by vigourously shaking the roots in the field, you need to collect the soil for chemical analyses (pH, org. matter, N,P,K, Ca, Mg K). The rest is like any plate count of microbes in soil, but for the first dilution you can put the roots with the attached soil in a fisrt bottle containg 90 ml saline, and then you shake mechanically on a reciprocal or orbital shaker for 15-20 min) In this bottle you will have the rhizospheric or mycorhizospheric microorganisms. If you transfer the roots to another dilution bottle and shake for a longer period of time  you will have the rhizoplane bacteria. If you want to enumerate bacteria you need to collect the soil in the first dilution bottle and determine if dry weight (after drying at 1050C). If you want the endophytes you need to surface desinfect  root surface before homogenizing with a mortar and pestle. The dilution used should give you single colonies on agar media, for a first isolation you can use 10% Tryptic soy agar with any fungicide to inhibit fungal growth. Now for identification and characterization purpose you need first  to indicate what is exactly your aim? Hope this is helpful, wishing you all the best. http://femsec.oxfordjournals.org/content/48/1/1.full http://aem.asm.org/content/64/12/5004.short

We use this and get quiet good yields. We have just replaced the bead beating step and use TriZol for this step.

Megha Kaviraj

Thanks

MiSeq is a platform that sequencing all of microorganims' DNA. I meant e.g. for detection of one unknown bacterium! among the million microogranims in a sample how the technology is able to detect one single bacterium, fungus, or archaea? It is my question.

By studying the TIME FACTOR of soil genesis. There are factors that accelerate and those that retard soil profile development. Investigation of resistant and non-resistant parent materials can also give insights on past pedogenic activities.

Excessive use of nitrogenous fertilizers leads to an increase in incidence of pests, while the application of phosphate and potassium fertilizers reduces the incidence of pests.

Thanks all for your comments. Haitao Wang I agree with your suggestion but I guess the 515F/806R are shown to be biased against both the Crenarchaeota/Thaumarchaeota (https://msystems.asm.org/content/1/1/e00009-15) so after going through some articles I found that the V4-V5 primers 515F/926R performs well and can reduce bias and can detect more environmentally important taxa including archaea. I just posted here as I thought it might be helpful.

Best,

Sandipan

Dear Mengying Ni,

I think that you could do some basic drying-rewetting experiments on soil cores that have been frozen at -80°C, but you will need to be careful about your expectations and the caveats you will need to state.

It is most likely that the freeze-thawing process will differentially kill microbes already present in your soil cores. Depending on your post-thaw incubation conditions, some microbes may recover, grow and produce compounds which may effect the following drying-rewetting experiments.

If your soil cores initially had a high water content, humus and clays, the thawing might result in significant changes in core pore structure, especially at the micro-metre scale. This in turn might effect the drying-rewetting experiments.

If you have enough soil cores to play with, you could see what the drying-rewetting characteristics are like (you could measure the water content / matrix potential, or total weight of water uptake, and then look at the drying profile over time at a set temperature), and use replicate cores to produce you own, new, packed sieved-soil aggregate cores (i.e. thaw them, sieve them to 2-3 mm or whatever is appropriate, and then repack them to the original soil density). (You would also need to decide whether it is better to sterilise the soil or use it as it is.)

We have previously looked at packed double-autoclaved sieved-soli aggregates as part of some work to establish whether bacterially-produced surfactants effect water distributions in partially-saturated soil pore networks. This was rather fun to do as it is not normally what we do, but it is important to do the soil biophysical measurements properly and in a way that the soil biophysics community expects (rather than what a microbiologist, such as myself, might think is reasonable).

Good luck, Andrew.

Proteinase K is used during DNA extraction to digest many contaminating proteins present. It also degrades nucleases that may be present in DNA extraction and protects thee nucleic acid from nuclease attack. Can be added to extraction procedure to optimize RNA yields. For isolating cytoplasmic RNA , centrifuge the cell lysate, remove the supernatant and add 200ug/ml proteinase K and SDS to 2% (w/w) then incubate for 30 minutes at 37oC. For more details consult https://agscientific .com --- 2019/04

I agree with answers above. Basically the dose depends upon purpose why biochar is used. For example de Oliveira Mendes et al. (2014), Appl.Environ.Microbiol. 80(10):3081-3085 employed biochar concentration of 3 g.L^-1 in culture medium to enhance rock phosphate solubilization by Aspergillus niger.

Best regards

Vit

@ Indrani, I think you may use X-ray Diffraction Software by Malvern Panaltycal.

following

Really interesting question.Thats the most challenging issue to deal with , simply because of enormous variation in nutrient ratios partitioned across different crop phenophases, so much conditioned by the inherent supply of plant variable nutrients versus changed under added fertilization practices.In that context , I would suggest to first work out the nutrient ratio of particular medicinal plant species which remain either static or follow certain definite pattern throughout its growth period.

Coming back to second issue , adjusting nutrient requirement in certain ratio wiĺ largely depend upon nutrient ratio of recycled biodegradable plant residues .Such residues most often change so much their nutrient ratio that makes almost impossible to tailor nutrient ratio of plant vis- a- vis recycle plant residues as nutrient supply system. But surely it's a real task in hand , keeping all these mind , I can wish you all the best...And in the process , if something worth comes out , it will be worth appreciating....

Following

I think that better option is sterilization by high temperature in dry environment

Soil is abundant with millions of microbes but all of them were not helpful or sometimes they do not show their impact at right time for various reasons. Perhaps you can start screening your bacteria for various plant growth promoting properties like IAA, Gibberellic acid, cytokinins, phosphate solubilization, siderophore and HCN etc., For possible protocols and inoculation methods you can refer to Zulfikar Ali Shaik papers.

Please use S₁V₁=S₂V₂ formula for calculation.

S₁=concentration of pure sample (known); V₁= volume of pure sample to be taken for your desired concentration (you need to know); S₂=Concentration you need (known, like 1 ppm, % or mM etc.); V₂= volume you need (you have to decide; working volume).

Dear Mengying Ni,

It depends on what the purpose of these measurements are.

If you for instance want to compare it with fractions obtained after sieving, you are more interested in the minimum diameter.

If you want to describe how spherical/ellipsoid your aggregates are, you can think of taking the longest diameter trough the centroid and use the ratio between the minor and major axis (https://en.wikipedia.org/wiki/Ellipse).

You can also think of importing your image in for example qgis, draw a polygon over the aggregate and calculate different size/statistics with the Geometry tool.

You only need a scale in your picture to be able to convert the results.

As you will do a more precise volume analysis later, I would recommend to keep it simple. As long as you're working with 2D images, it will be anyway an estimation.

When you measure mean weight diameter of aggregates, it does not mean that you physically measure the length, width, etc of the aggregates in centimeter or millimeter. Rather, us you a set of sieve with different but known mesh sizes (diameter).

Then you assume those aggregates remaining on a specific sieve have diameters equal to the diameter of the sieve.

Then, you multiply the mass proportions of soil aggregates left on the ith sized sieve with mesh size (diameter) of the sieve.

Thank you for all answers to this question, I will seriously consider it! Thank you all.

Dear Earl,

I never mentioned that I am not in any way connected with SciNote. I have however been using it for quite a while now, even before I joined the team, for my own research work and hence the recommendation. So, I'm not ashamed as you are suggesting, on the contrary, I'm flattered you too are seeing the great potential scinote has. Have a nice evening and enjoy the summer! 

This paper will probably be helpful

Kouno, K., Tuchiya, Y., & Ando, T. (1995). Measurement of soil microbial biomass phosphorus by an anion exchange membrane method. Soil Biology and Biochemistry, 27(10), 1353-1357.

Dhanushka N. Wanasinghe

Thank you for the information

Hi Samuel,

Before you culture the fungus on petri dish, put a sterile sheet of cellophane on the selected medium surface, in order to seprate the mycelium from the medium. Then culture your fungus on the cellophane. Don't worry about that, because the transability of celluphane is good, so fungus can grow normally. Once you got a full growth, you could scratch fungal mycelium easily using steril spatula. I have used this technic to collect the mycelium for DNA extraction. Please find out this links:

DOI: 10.1093/femsle/fnw089

DOI: 10.1016/S0168-1656(99)00154-6

Good luck

Afra

@ Wong, CFU /g soil = Count per Plate/ dilution factor

For example, if 30 colonies are present on 10 ^-6 dilution plate, the calculation will be:

CFU = 30/ 10 ^-6 = 3x 10 ⁷ colonies per gram soil.

Dear Raheleh

Tri calcium phosphate is always an water insoluble compound under normal pH conditions. That is why you should sterilize it separately as dry powder in the same autoclave when you sterilize the agar or liquid medium. Then just before pouring plates (in case of agar medium) or inoculation of the liquid medium add the powder tri-calcium phosphate in the well cooled medium, shake well to disperse as evenly as possible and proceed.

One of the reasons is that, solid PVK media, consist on testing a single fixed bacterial colony, while in liquid media, the bacterial densities are much higher with better access to the nutients, which makes the solubilization more efficient and important.

The amount and distribution of rainfall directly affected soil moisture, which determined the survival and proliferation of rhizobia as well as growth of the host legume.

you can read the attached research about the ecological Indicators of Native Rhizobia in Tropical Soils

Ref.10 = Assessing the Biocontrol Potential

Try to handle the soil samples after their transportation as early as possible for culturing microbial strains.

Hi Diego,

If you use anything that can be cut for the column (tygon?) you can cut off cross sections (going from top to bottom) to get material for the independent layers.

Good luck

I believe that natural fertilizers are more effective than synthetic ones.

Dear Dr. SK,

Please try our method and see whether you could get high molecular weight DNA.

Shaik Yazdani Basha and P. Palanivelu

Two simple non-enzymatic procedures to isolate high molecular weight DNA from fungi, Current Science, 68, 587-588 (1995)

Mr. Sarkar,

You can spike the pesticide in soil and also compare natural the soil respiration activity or autoclave soil and add spike PGRs and measure same. You can refer Thesis chapter 5, in following link, where instead of phytate you can add pesticide.

http://hdl.handle.net/10603/72057

this has detailed information regarding your query

You can follow the Gerdemann and Nicolson (1963) method, see the

Baccharis incarum and fungus Arbuscular Mycorrhizal symbiotic relationship for land fallow in the Bolivian highland article (CienciAgro (2014) 3(1): 51- 58)

The best media for cultivating bacteria from soil are 10% tryptic soy agar or R2A agar, the soil extract is optional. They support growth of a wide range of bacteria and fungi, so it would be difficult to find those decomposing a particular pesticide. The best thing to do is search the literature for a minimal salts medium and appropriate pesticide concentrations. You can inoculate agar directly with soil suspension or enrich the bacteria on a liquid medium with the pesticide and then spread plate it.