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Structural equation modelling is key to understanding the internal workings of an ecosystem. I wanted to know if it's possible to build a SEM utilising data such as
1. Soil physical and chemical properties
2. Fungal diversity
3. Agronomic trait.
I have some experiences with AMOS for building simple models. However I don't know if this technique or steps are in the right order.
My work plan is
1. PCA to sort the variables (is it alright to combine all the variables?)
2. CFA to reduce redundancy.
3. Pathway analysis.
One factor that I am worried about is the fact that soil data are quantitative in nature, so different parameters will have different values. Will this effect the model? Or do I have to use the assign a score range. Eg
pH: 0-2(assigned a value of 1)
pH: 2-4 (assigned a value of 2)
And so on.
I would be interested in knowing if there are any suggestions or comments on both techniques and steps. Regards.
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Hello Wati,
you should try to take a look into
Shipley, B. (2004). Cause and correlation in biology. A user's guide to path analysis, structural equations and causal inference. Cambridge UK: Cambridge University Press.
Shipley, B. (1997). Exploratory path analysis with applications in ecology and evolution. The American naturalist, 149(6), 1113-1138. doi:10.1086/286041
Furthermore, you are mixing two different approaches how to connect measures with concepts--the reflective / common factor model which is the relevant measurement model underlying EFA and CFA and the composite model which refers to PCA.
In this thread, I posted some relevant key concepts and further papers
HTH
Holger
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Under semi-hydroponic conditions certain genotypes repeatedly showed specific fungal growth, while others not. Is it because of variability at endophytic fungi level?
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Are these fungal growths present in the dormant seed prior to hydroponic growth? What is the relative abundance of the sequences from the fungal growth relative to other sequences present in the dormant seed? What is the species of these fungal growths, are they endophytes?
My thought would be that the semi-hydroponic environment would be creating perhaps a greater selective pressure for some fungal species over others, this pressure maybe greater than that created by the host plant species genotype?
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I have attached a photoplate and it was found on leaves.
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You need to have molecular data. I dentification based on morphology is not correct very often.
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Hello,
I did an analysis with MrBayes version 3.2.6 (Ronquist et al., 2012) with the GTR + G + I model with these commands
;
END;Begin mrbayes;
outgroup polyzona;
lset   nst = 6   rates = invgamma; prset statefreqpr=fixed(equal);
mcmc samplefreq=100 printfreq=100
nchains=4   Starttree=random  savebrlens=yes  filename=Antrodia-sl(complet).nex   ngen=8000000;
sumt filename=Antrodia-sl(complet).nex  nruns=2   ntrees=1  burnin=20000;
I want to know if I have all the commands for the GTR + G + I model and also if I get the majority rule consensus tree as a result?
To finish, I took MrBayes version 3.2.6 (Ronquist et al., 2012) and I wondered if I have the same thing as: Bayesian inference was calculated with MrBayes 3.1.2 with a general time reversible (GTR) model of DNA substitution and a gamma distribution rate variation across sites (Ronquist and Huelsenbeck 2003). 
I relied on the article Han et al. 2016 attached.
Thank you in advance.
Serge Audet
LITERATURE CITED
A. Rambaut, FigTree v1.4.2, A Graphical Viewer of Phylogenetic Trees. Available from 〈http://tree.bio.ed.ac.uk/software/figtree/〉,2014.
Han, ML; Chen, YY; Shen, LL; Song, J; Vlasák, J; Dai, YC; Cui, BK. 2016. Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera. Fungal Diversity. 80:343-373.
Nicholas KB, Nicholas HB Jr (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the authors. http://www.psc.edu/ biomed/genedoc.
Ronquist, Fredrik & Teslenko, Maxim & Mark, Paul & Ayres, Daniel & Darling, Aaron & Höhna, Sebastian & Larget, Bret & Liu, Liang & Suchard, Marc & Huelsenbeck, John. (2012). MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic biology. 61. 539-42. 10.1093/sysbio/sys029.
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" Bayesian inference was calculated with MrBayes 3.1.2 with a general time reversible (GTR) model of DNA substitution and a gamma distribution rate variation across sites " means GTR+G, i.e. lset nst=6 rates=gamma.
Both G and I accomoate the rate variation across sites. So use G+I together appears redundant (somewhere in manual of RAxML).
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Can anyone help us find Labs, researchers or Collections (particularly private) which have isolates of the aquatic hyphomycete genus Dendrospora?
Any help will be deeply appreciated. :)
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Yes, we have isolates of the genus Anguillospora. Please send me a private message or email me to isabelrodriguesfernandes@bio.uminho.pt to talk about this.
Best regards,
Isabel
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Dear colleagues;
I am fairly awestruck by one of the samples I've collected from my main study site in Saskatchewan for next field season. Other experts in the field weren't even sure that the specimen was biotic, but I was finally able to borrow a proper compound scope yesterday and demonstrate that it is indeed a fungus - I believe a lichenized ascomycete. It has a clearly defined layer of an algae or cyanobacterium within the fruiting bodies, and I believe I've even been able to see the ascospores, which are simply pill-shaped and 1-septate.
I apologize for the poor quality of the photos, I had to take photos with my cell phone through the eyepiece because apparently the U of Regina doesn't have the ability to take photos, or I haven't found it yet. I'm working on getting local experts interested enough to allow me to use their scopes with cameras - your professional excitement, if any, would help.
This ascomycete makes a brain-like raised pattern upon the surface of a limestone rock face, and has tiny blue fruiting structures near the center of the vegetative tissue. These are very small, only about 1-2mm across. I was finally able to section one of them yesterday and it was immediately clear that they are not a random mineral accretion but the fruiting body, complete with an algal or cyanobacterial photobiont.
I am looking for collaboration with experts in the Ascomycota as I have a sneaking suspicion that this is an unusual member of this diverse and enthralling group. Because of the nature of the vegetative growth form in and over the rock face, and the very conspicuous and three dimensional structure of that vegetative growth, I am keenly interested in identifying this organism.
All input and guidance or direction toward appropriate experts is deeply appreciated.
See the iNaturalist observation here: https://www.inaturalist.org/observations/36873951
Michael.
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I have now added more photos to this comment of the photobiont, ascii, paraphyses, and the ascospores, which are much clearer than I was able to attain before. The ascospores are 1-4 septate, and appear to either come in two types/maturities (one of which seems to have very distinct jigsaw-puzzle shaped septa, as shown in the photos), or the ascocarp I squashed may have had another species present. Average spore sizes of the two types (n=8 each) are 15.7 x 3.8 μm (jigsaw septa) and 17.9 x 4.4 μm (opaque spores) for the two types.
I still don't have access to Iodine to stain the ascus tips, but I am working on it!
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I need know if Dicranidion is reported from America -mainly México.
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Please have a look at the following RG link.
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I want to examinate intraspecific variation in Phellinus sp. and its relationship with other members of the Hymenochaetaceae family.
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The ITS region is generally a good marker for differentiating species. However, the intraspecific variation might not be enough and it is not phylogenetically conserved.
If you plan to do any phylogeny at family level as you mention, I wouldn't recommend it, at least not by itself. The D1-D2 or D1-D3 sections of the LSU have been used more and more in the last years for being more variable than the SSU, but unlike the ITS is more phylogenetically consistent. Otherwise, the EF or alpha-tubulin might do, but I have no experience with them so I can't tell you for sure.
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Could it be useful to determine the size of a fungal organism?
Image for illustrative purposes only (Source: Webster & Weber 2007).
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Hola Cristian
VCG is a classification at the subspecies level. You are not going to be sure if two isolates, belonging to the same VCG, are the same, albeit they are more closely related than two isolates of two different VCGs. However, it is a well-known (and relatively easy) tool that is going to give you useful ecologic information about your population; for example, in general, and depending on your species, you population could sexually reproduce if you have isolates of different MAT within a given VCG.
Un saludo
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Dear colleagues, herein some points that I would like some discussion and, if possible, some answers in regards to global fungal richness estimates:
The question of how many species of Fungi there are has occasioned much speculation, as said Dr. D. Hawksworth and Dr. R. Lücking, but the estimatives, in many cases are too big!
Do we have any estimates of the species richness of all fungi for the neotropical region?
And what is the most up-to-date estimate for fungal species richness globally?
Is it possible to determine how much of this corresponds to soil mycobiota?
How sensitive are the methods of estimating fungal richness?
Attached, some useful papers:
HAWKSWORTH (2012) and HAWKSWORTH & LÜCKING (2017)
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Dear Francisco, thank you for the information provided. The attached files may provide you some more information.
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Dear all, please, I would like to know, if someone could to define it to me, why, thinking in molecular sense, was choosen the internal transcribed spacer (ITS) and 18S rRNA to access fungal diversity?
And why ITS-region is best to access total fungi (for example in soil) and 18S rRNA is most suitable to access arbuscular mycorrhizal fungi?
Thank you for your response!
Best regards,
F. Calaça
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The ITS loci, specially ITS1 – ITS2 and ITS can provide very accurate data about the specific identification of the fungal species. The reason behind that may be lies on the nature of these loci in terms of their very high consensus sequences among fungal genera. Furthermore, some ITS loci provide more accurate data to the species level. The detective ability of ITS regions extend beyond fungal species to include other micro- as long as macro-organisms.
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Background:
First, I want to sequence fungal DNA collected from samples of over 100 individual trees. Each PCR sample was amplified with an unique barcoded combination of forward and reverse primers. This was done with the intent of pooling all samples together into one library, and later separating them via their respective barcode combinations.
Second, I am having trouble eliminating primer dimers from my PCRs. One solution is to E-gel or BluePippin to isolate the desired bands without the dimers. However, such approaches is too expensive and lengthy for this many samples.
Third, I'd like to be able to pool them together for one run, but running several samples under a bioanalyzer implied concentrations of dimers as well as the wanted sequences differed among all samples. The Bioanalyzer, and regular electrophoresis-gels also indicated species richness may also vary among all samples.
I've been told that equal molar dilutions are necessary to prevent erroneous estimations of fungal species-diversity among samples.
Questions:
1) I am separating each tree sample by an unique barcode combination to group their respective fungal community composition using said unique barcode. Instead of dilutions, is it reasonable to expect that I can analyze each individual sample's approximate fungal diversity for comparisons with other samples to develop general trends of species diversity among all samples?
2) According to the Qubit, my samples dsDNA concentrations range from 2 ng/ul to 14 ng/ul (includes primer dimers). What biases or confounding factors may be introduced with dilutions to equal molar dsDNA concentrations? Or in respect to inconsistent species diversity among all samples?
Thank you.
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As per my understanding from your complete details given above.
You are planning to do Metagenomics of Fungal species isolated from different/plant.
You have amplified with the given 96 adapters by the manufacturer.
As per the manual, they says, you have to dilute all the samples in an equimolar concentration, otherwise, if u dont follow the same.
You may endup in a wrong image of fungal species among your samples.
Its better to do with Equimolar concentration, its like Reverse transcriptase PCR, you need a control. without that how could you say this fungal species is predominant or less prediminant among the test samples.
Hence, You try to take a qubit for the amplified products, and do dilution with calculations in excel sheet given by the manufacturer.
Primer dimer, need not to worry, it will be removed during size selection and other washing steps, even if it goes upto upstream process, it can be removed during bioinformatic analyses.
All the best.
Murugan N
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Dear fellow scientists,
I am looking for a collection (can be a private one... your own catalogued images, etc.) of micro fungi optical microscope images, i need different images for each genus / species...
Do you know of any site/repository (preferably curated) that has links for different species and corresponding images / image sets ? 
Would appreciate some help here ;)
Cheers!
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You are welcome
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I suppose it belongs to Microphysidae family, Myrmedobia genus. I would be very thankful for any suggestion of identification key for this group? I found a lot of specimens of this species in the litter of coniferous forest.
Thanking in anticipation
Vytautas
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Dear Thomas,
thank you very much for your help. 
Best wishes
Vytautas
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I got a funal strains sequences from the amplicon using ITS1 and ITS4, which shown 100% similarity with two species of Aspergillus!! Is it possible? If yes, How to differentiate?
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Yes its possible. Unfortunately there is the possibility that one of the barcode was attributed to Aspergillus but comes from a different species, basically a mistake by th eperson that entered the sequence. Try the the Bar Code of life it is well curated: http://www.boldsystems.org/index.php/IDS_OpenIdEngine
The second possibility is that the two aspergillus species cannot be separated at the species level using their  bar code, however 100% is surprising, I would go for the above mentionned option.
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How can i find relative fungal diversity in soil by culturing techniques? Can i use colony count method??? Is there any software to find relative fungal diversity. Kindly suggest me.
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I suggest that culture technique is not especially useful in this application.  Many fungi will not be readily culturable and recovery will be driven by sporulating fungi that are readily culturable.  Note Dr. Tarafdar 's linked paper.
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I wanna to extract RNA in best way from Panonychus citri by trizol
please say me what is the best way for good result?
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Hi Elahe
Just you need to monitor few steps  carefully of Trizol manual method  to get good result
First, crush that creature (mature 3-5 will be enough) with trizol either with a micropestle or by a homogenizer. The volume of trizol will be 750-1000uL.
All the centrifugation should be done @ 4 degrees.
Then centrifuge (10000 rpm for 10 min) to pellet the debris, supernatant will be separated. Wait for 5 min @ RT.
Add 200-250uL of chloroform shake vigorously for 20 sec (Red color of trizol will be turned pinkish ) wait for 5 min @ RT.
Centrifuge @ 12000 rpm for 15 min to separate transparent sup. in a new vial.
Then add ice child (-20, 500uL) Isoprop dropwise by pipette wait to react for 5 min @ rt and incubated for overnight @ -80.
Centrifuge @ 12000 rpm for 15 min, a white pellet will be observed and then clean by 70% chilled ethanol, air dried and dissolved in 50 uL RNase-free water.
During RNA extraction each and every accessory should be RNase free and try to use a dust free enviornment for better result.
Hope will help.
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 I want to identify ochratoxingenic strains——Aspergillus carbonarius. Does it enough for Aspergillus carbonarius just use the species-specific CARBO1/CARBO2 primers? Do I also need to do the ITS or the beta-tubulin simultaneously?
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Thank you dear  Barkat and Dhurgham for responding me!
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Which fungus is in these pics ??
Kindly identify...
thanks
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The pictures are paired. 1&2, 3&4 and so on, Thank you very much.
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239
Hi Yifan Ooi
The culture is old and Pic. 1 is chlamydospores
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Hello everybody,
I have sequenced 4 plant taxa belonging to the same genus. I sequenced the trnH-psbA and ITS markers. Could anyone give me a detailed procedure of how I could confirm the idintification of those taxa using available sequences? i.e I need the instructions of the DNA barcoding technique used for authentication of a plant species.
Thank you all
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I think using trnH-psbA  as chloroplast region is not enough because it's too short to match the sequence. Therefore it needs another region, I recommend adding rbcL or matK to make the results stronger. The useful program is TaxonDNA .
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Hi....I am working on ipomoviruses infecting vegetables in Iraq and I wonder if there is any primer set specific for detection of the genus Ipomovirus? As the only available option for the genus detection is Potyvirididae specific primer set.
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Dear Prof.  Gibbs, I really appreciate your time and efforts dedicated  to get me the answer, your data is so valuable , I am going to test the potivirid primers to detect ipomoviruses....
Many thanks
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I have identified the genus of my fungus morphologically but for species level identification,I did PCR with ITS1 and ITS4 primers but when coming to the blast hits I am getting 100% and 99% similarity to most of the strains.So while constructing phylogenetic tree it is difficult to identify as to which clade my organism belong to?Please give me a solution to clear this
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Penicillium and Aspergillus genus only
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The fungal ITS region varies roughly, with some exceptions, between approximately 450 and 750 base pairs (bp) in length. This feature makes it hard to compute the phylogenetic diversity.  I used the tranditional method to align sequences and builded phylogenetic tree, but the bootstrap value was very low (most branches < 50%). So I suspect the tree is not robust to evaluate the fungal phylogenetic diversity. I wonder are there any  feasible method to evaluate the fungal phylogenetic diveristy by ITS2 sequencing?Thank you for your kind reply.
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Hi Laith,
Thanks for your suggestion, I know how to construct ITS2 phylogenetic tree, but I don't know how to find the secondary structures by MFOLD and generate consensus structure by 4SALE. Could you give me an example if you know how to do? Thank you!
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Can you help identify this red sac fungi from the Philippines.
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This is for sure a member of Sarcoscyphaceae. It is likely a species of Sarcoscypha if it is collected during the winter and no hairs. If it is from tropic area with some hairs, it would be species of Cookeina.
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Can you help us identify this mushroom from the Philippines. Please help identify the genus. Thanks
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Agree with Prakash
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Please help us identify this reddish polypore mushroom from the Philippines. This was from a decaying log in the forest.
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Dear Ourlad,
In my opinion this one can be Hexagonia sp., but additional checking od the specimen is needed. Besides you can obtain some information and look through pictures from an Indian paper at http://threatenedtaxa.org/index.php/JoTT/article/view/2553/3763
With best regards,
Elena
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I am trying to identify some wild fungal species using ITS and D1-D2 regions, but in the hits from NCBI getting even different genera in both regions (ITS&D1/D2) for the same species.
Any helpful suggestion ?  
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Dear Farrukh Baig
Even though NCBI is a great database collecting a lot of information useful for scientists, it has the problem that too many data are registered with wrong species determination, bad sequence quality etc.
Therefore we use some other databases for the molecular idenfication of taxa, which are managed by curators. That means curators ensure the quality of (i) DNA sequences and of (ii) species determination.
First we check databases with curators, then we compare with NCBI...
- UNITE: https://unite.ut.ee/ (go to "run analysis", use field "blastn"). Check the taxon/taxa with the best score bits. Below the list of taxa you will find the nucleotide sequences displayed and they are linked to the corresponding NCBI entry. If your sequence has gaps or differs in some nucleotide, check your raw data. Are you sure your sequence quality is "good"?
- BOLD: http://www.boldsystems.org/index.php/IDS_OpenIdEngine (go to "ITS", use "all barcodes"). You can check the best match on the right column: press on "published". If sequences are depostited in BOLD but still not published, you will not be able to open this file ("early release").
I hope this helps you!
Carolina
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Dear, Ourlad,
The fungus is Amauroderma sp. Microscopical analysis is needful for more precise identification.
Best regards,
Elena
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Dear Oadi,
This is Ganoderma applanatum, a conk growing on deciduous tree species, known as artists` fungus for its pore surface bruising brown and retains as that. The species is saprotrophic. You can see http://www.mushroomexpert.com/ganoderma_applanatum.html for further details.
Best regards,
Elena
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Dear colleagues!
Can anyone help with the identification of a stipitate fleshy poroid fungus? The problem is in lacking of spores - fruitbodies were immature. Molecular analysis will be carried out, but maybe anyone has suggestions based on fruitbody habitus? The habitus was tricholomatoid, fruitbodies firm-fleshy, as in some agaricoid species. Appearance Tricholoma-like, but there was a white tube layer under a cap. My proposal was Boletopsis, but all Boletopsis species I know have another cap-stipe size ratio and are considerably larger.
The specimen was collected at Moscow Region (hemiboreal zone) on damp naked soil near a pond (probably, some buried wood was under the fruitbodies). Trees nearby were alder, spruce, birch, linden and bird cherry.
Photos (unfortunately, of not-so-high quality) are attached.
With thanks and regards,
Elena
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Hallo Elena, it could be perhaps Polyporus ciliatus Fr. The growth on the ground (even if probably linked to wood residuals) could have masked the typical white - felty stipe base. In the web there are some collections that could look like to your collection. 
Regards, 
Giampaolo
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I would request my scientific brethren to provide taxonomic descriptions and photograph, if possible of Lentinus anthocephalus Peg.?
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Hi
Here is the protologue of Agaricus anthocephalus (=Lentinus anthocephalus):
 A good description and plate is on Pegler´s 1971 monograph on Lentinus
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Please suggest a low cost non-sophisticated method of generating ascocarp artificially from the sclerotia of sclerotinia sclerotiorum under in vitro conditions. A method consuming the least number of days would be desirable
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Thank you sir
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As supporting document I have attached two microscopic images of that fungus. So can somebody help me to identify this fungi?
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Shuvrah,
 They are synonims:
Drechslera oryzae (Breda de Haan) Subram. & B.L. Jain, Current Science 35 (14): 354 (1966)  
Synonymy:
≡Helminthosporium oryzae Breda de Haan, Bulletin de I'lnstitut Botanique de Buitenzorg 6: 11 (1900)
≡Bipolaris oryzae (Breda de Haan) Shoemaker, Canadian Journal of Botany 37 (5): 883 (1959) ]
≡Luttrellia oryzae (Breda de Haan) Gornostai, Vodorosli, Griby i Mkhi Dal'nego Vostoka: 81 (1978)
=Helminthosporium macrocarpum Grev., Scott. crypt. fl. (Edinburgh): pl. 148 (1825)
Alex
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ok
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Dear Pulak,
near all the variants you've mentioned are possible. Majority of plants have only one type of mycorrhiza, but some species can combine both AM and EM strategies. For example, Eucalyptus is a tree which can have both mycorrhizal types in one root system and proportion of ecto- and arbuscular root tips depends on a range of biotic and abiotic factors (e.g., the age of the plant or N or P lack dominating under certain conditions). Details you can see in
Jones M.D., Durall D.M., Tinker P.B. 1998. A comparison of arbuscular and ectomycorrhizal Eucalyptus coccifera: growth response, phosphorus uptake effi ciency and external hyphal production // New Phytologist. Vol.140. P.125–134.
Lapeyrie F.F., Chilvers G.A. 1985. An endomycorrhiza-ectomycorrhizal succession associated with enhanced growth by Eucalyptus dumosa seedlings planted in a calcarious soil // New Phytologist. Vol.100. P.93–104
Reddell P., Malajczuk N. 1984. Formation of mycorrhizae by jarrah (Eucalyptus marginata Donn ex Smith) in litter and soil // Australian Journal of Botany. Vol.32. P.511–520.
Pagano M.C., Scotti M.R. 2008. Arbuscular and ectomycorrhizal colonization of two Eucalyptus species in semiarid Brazil // Mycoscience. Vol. 49. P.379 http://link.springer.com/article/10.1007%2Fs10267-008-0435-3
Adams F., Reddell P., Webb M.J., shipton W.A. 2006. Arbuscular mycorrhizas and ectomycorrhizas on Eucalyptus grandis (Myrtaceae) trees and seedlings in native forests of tropical north-eastern Australia // Australian Journal of Botany. Vol.54. P.271–281. http://www.publish.csiro.au/paper/BT05028.htm
As for natural ecosystems, as a rule they contain many plant species with diverse mycorrhizal types. Boreal and temperate forests have  ectomycorrhizal tree layer along with predominantly arbuscular mycorrhizal herb layer. For basics on mycorrhizas and its role in broader contexts you can see Smith S.E., Read D.J. 2008.  Mycorrhizal Symbiosis (Third Edition). ISBN: 978-0-12-370526-6 http://www.sciencedirect.com/science/book/9780123705266.
At any case, mycorrhizal types combinations depend on plant species involved.
Best regards,
Elena
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I am analysing my sponge meta-transcripts data obtained from GeoChip. According to my data, at least over 1000 fungal genes showed transcriptional activity, most of them are assigned to filamentous fungi. However, I couldn't find any mycelium in my TEM/SEM pictures. Also there's no convincing picture that shows the fungal mycelium in sponge tissue. Yet, people can isolate filamentous fungi from marine sponges and amplify fungal 18S rRNA/ITS genes from sponge metagenome. I am thinking the paradox is due to the genes related to mycelium development are somehow transcriptionally inactive. But I don't know much about fungal genomics. Can someone give me some guidance? Thanks.
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You are right Chris. According to my RNA-seq data, sponge transcripts resembled way higher similarities with fungal transcripts than I expected. In the end I used GhostKOALA instead of blast to distinguish if it's fungal transcript or sponge transcript. But I did recover ~20,000 fungal transcripts, including several house-keeping genes like actin.
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I will be determining the fungal diversity in soils using PGM Ion Torrent and barcoded primers.
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Hi Caitlin,
It depends of your barcode. If you target rDNA genes, several pipelines can be used to manage and treat efficiently your results, e.g. QIIME, Mothur, or other ones such as Frogs or GnS-PIPE.
If your target is the ITS, you'll need to use some other pipelines dedicated to the ITS analysis, as some steps of treatment are different.
If you need more information, just ask, I'll be pleased to help
Best regards.
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Can anyone please help me identify this crustose lichen?
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it's also within my concern this species belongs to genus Chapsa...right now i'm doing the analysis...tq for the enlightenment mr Adam Flakus...
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The enormous geographic extent and the scarcity of mycologists in the region presently limit the comprehension of the Amazonian mycota, but are there solutions we can figure out collectively to increase our knowledge?
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Dear Ricardo most hot spots in poor countries without taxonomist face sort of same issues. Of course the Amazon is bigger, so the challenge is bigger. In my experience in Mexico where most mushrooms are unknown and few taxonomist available (particularly in tropical regions) a good approach is to do good voucher specimens and sequence (ITS region) all your collections. Even in the species is not in public databases, the sequences most of the time give you the genus an closer species.  They also give good clues on new potential taxa and help in focusing on groups of interesting taxa. They also allow you to know many things you have even if you dont have names for them.
sequencing is not very expensive, we expend doing every thing in mexico like 12 american dollars per sample, from DNA extraction to double strand sequencing.
Given, the hot, moisture, insects and molds, I would say your biggest challenge is not collecting or identifying but keeping the materials in good shape por the near future. You may think having DNA collections also.
my best
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Kindly  suggest,,
I am using a few stains, I would like to know current usage of different stains in the terrestrial fungal diversity.
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If you mean bitunicate asci, lactophenol blue or Congo red are good choices, but if you want to see a differential stain to characterize the apical ring, Lugol can give amyloid, dextrinoid or hemiamyloid reactions in fresh ascomycetes.
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or is it a chance that these intermediates are just chucked and by chance these are active against particular organisms. Can someone enlight me in this case with some publications. Thank you
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In marine and terrestrial environments it is an interesting aspect about how this competition evolves and is regulated for the fitness of the producer:  http://mmbr.asm.org/content/71/2/295.short https://femsre.oxfordjournals.org/content/35/5/957 http://science.sciencemag.org/content/337/6098/1107 http://www.nature.com/ismej/journal/v9/n1/abs/ismej2014106a.html  
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I just wonder why the diversity of fungal community is higher when they closer to root surface? Thank you for your consideration!
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Zhang Apple,
Elena makes some really useful points above. The interaction is a two way process and the plant wants to encourage the right microbiology around it's outer surfaces.
You will I guess already be aware of fungal mycorrhizal associations with plant roots, these associations are truly beneficial to both parties. Many edible fungi are Ceps are associated with trees.
The rhizosphere is a very interesting aspect of modern microbiology. The whole subject of microbial interactions with other living surfaces is part of the paradigm shift is looking for help from the beneficial microbes rather than trying to fight the bad guys.
This is receiving lots of research effort from many companies who see it's potential in improving nutrient uptake, reduced pesticide usage etc
I found the two attached papers very interesting with this regard.
I think you are working in a very inciting area of research, good luck with your studies.
Andrew Goddard
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To understand individuality in the fungi is a difficult proposition, and except when using molecular tools, one cannot be sure about individuality of a fungal species. In this situation, which methods could be utilized to ascertain the structure of abundance in the case of macrofungi?
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Dear Prakash,
This problem is difficult to resolve indeed. Macrofungi are usually treated the same way as clonal plants or colonial invertebrates are and they are commonly assessed by artificial units (modules) such as fruitbodies. This approach is not perfect but it allows to compare your data with data other researchers obtained and to get relative results for comparison within your research. Besides, the protocols are strongly depending on fungal ecology - soil fungi are different to wood inhabitants and so on. For more details you can see Foster M., Mueller G., Bills G. (2004) Biodiversity of fungi. Inventory and monitoring methods. Boston. Elsevier Academic Press and the manual in attachment.
With best regards,
Elena
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Is there any taxon specific "chytridiomycota" fungal primer available?
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Dear Milind Mutnale,
Yes, it does. You should have a look at these 2 papers:
Cheers,
Vincent Hervé
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I'm studying soil microbial communities response to nutrient addition and cattle grazing (cows) in the Pampean Region, Argentina. I'm doing DNA amplicon sequence analysis for bacterial and fungal diversity, but I'd also like to do bacterial RNA analysis to see changes in this group's functioning in soil.
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You can always do a PyCrust functional prediction based on which taxa were identified from the amplicon sequencing to get an idea of what to expect from your RNA sequencing. You could remove rRNA sequences from your dataset by using a database-based filtering approach. If you want to avoid sequencing the rRNA genes altogether, you could consider doing a rRNA subtraction with probes (see attached paper).
Hope this at least points you in the right direction!
Kind regards,
Riegardt Johnson
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I'm studying soil microbial communities response to nutrient addition and cattle grazing (cows) in the Pampean Region, Argentina. I'm doing DNA amplicon sequence analysis for bacterial and fungal diversity, but I'd also like to do bacterial RNA analysis to see changes in this group's functioning in soil.
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Your preservation could be as simple as snap freezing in liquid nitrogen and then storing on dry ice until you get the samples back to the lab. You don't want them to thaw until you do the extraction, however. You could also test out Lifeguard or RNAlater for nucleic acid preservation. You would still want to freeze the samples or at least keep them on ice.
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Fruit body dimension height 4 cm, cap diameter 3 cm, stipe with a prominant ring, cap surface warty/spiny. Is it a species of Amanita?
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Hello, Girish Gogoi.
To demonstrate that an agaricoid collection belongs to the Amanitaceae, it is necessary to do two things:   (1) Make a transverse section of a gill and observe that the lamella trama is bilateral and divergent and (2) make a thin longitudinal section of the flesh of the stem (not in an area of central pith and not near the external surface) and demonstrate that the tissue is "longitudinally acrophysalidic."  These terms will be found defined on a set of pages of the "Studies in the Amanitaceae" website starting with this page:
Many of the generalizations about macroscopic characters of amanitas in the literature are not true.  The above method is definitive for agaricoid mushrooms.
The above two microcharacters (note that no measurements are required) are the precise way to determine a member of the Amanitaceae.  To separate Amanita and Lepidella within the Amanitaceae, there are many useful characters that are also treated on the same web site.  For example, Amanita gill edges are sterile while Limacella edges are fertile.  This is because of the radically different ontogenies of the organisms in the two genera.  This is also treated in the pages mentioned above.
If the material you photographed is an Amanita, then it is very likely that it belongs to Amanita section Lepidella sensu Bas.  This would require its spores to be amyloid and the margin of its cap to be appendiculate with relatively fine universal veil material and its stipe's base not to be enclosed in a saccate volva. 
Within section Lepidella, the structure of the volva, the pallid colorations, and the rooting bulb on the stem base suggest that the species might belong (you will have to demonstrate this) to Amanita subsection Solitariae. 
It appears from your researchgate page that you are collecting in Assam.  I don't think that any European Amanita name will apply; nor will any name from the Americas. 
I would suggest your reviewing the literature of Colonial times in the Himalayan region.  For species of section Lepidella, the 1969 thesis of the late Dr. Cornelis Bas is a very good place to start.
  Also the recent extensive work done by the group in Dr. Z. L. Yang's laboratory in Kunming, Yunnan, PRC will be very relevant to your study of the mushroom.
The list of amanitas for India published by R. P. Bhatt et al. [Bhatt, R. P., R. E. Tulloss, K. C. Semwal, V. K. Bhatt, J.-M. Moncalvo and S. L. Stephenson. 2003. Amanitaceae reported from India. A critically annotated checklist. Mycotaxon 88: 249-270.] may be of some use.  However, it is just a beginning and cannot serve to help you with details of determination.
Very best,
Rod Tulloss
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I'm going to send some soil samples to analyse the fungal community by Illumina MiSeq. I can choose between two pairs of primers: ITS1F-ITS2aR and ITS3F-ITS4R. I've been reading about this and I've found some studies that use ITS3 / ITS4. I have to use the region that I can amplify by PCR but I don't know if I have to consider anything else before choosing one or another pair with the aim to get the best results.
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Hi Tatiana,
a lot of studies proposed fungal primer pairs to NGS approaches (Ihrmark et al., 2012; Toju et al., 2012; Blaalid et al., 2013). Our latest results confirmed that the primers ITS1F / ITS2 (Gardes & Bruns, 1993) are the most convincing, using mock fungal communities. The Toju’s primers seem also valid. The primers developed by Ihrmark are good also (better covering for Ascomycetes), but they also amplify the plants (eg oak). Pay attention to the environmental matrix you use ...
Be careful, if you include your bacterial 16S amplicons in the same run as your fungal ITS amplicons, because Miseq technology requires that your amplification products are fairly similar sizes ...
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113–118.
Toju, H., Tanabe, A. S., Yamamoto, S., & Sato, H. (2012). High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.
Ihrmark, K., Bödeker, I. T., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., ... & Lindahl, B. D. (2012). New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS microbiology ecology, 82(3), 666-677.
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Dear colleagues,
I would be very grateful if you could give me any information about the distribution of Harmoniella chrysocephala. I have found only 1 publication about it, the original paper where it was described from pine needles in Ukraine. Do you have any literature reporting this fungus from a different country?
Thanks in advance,
Hugo
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Dear colleague
Harmoniella chrysocephalus V.N. Boriss.is located in Ucrania, and Crimea also, asociated to Pinus spp. please check: http://www.cybertruffle.org.uk
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I recommend Our book: East Asian Polypores (Nunez & Ryvarden 2001, vol. 1-2). Fungiflora, Oslo. Macro-and microscopical descriptions, but not Pictures. There is a good Japanese polypore flora with pictures that can be useful for many of your species. Dr. Tsutomu Hattori from FFPRI in Tsukuba is a very goog polypore taxonomist.
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Can anyone help me to identify this Entoloma species? I found it in Hungary, in a fire ring, on carbon pieces.
Cap: 1-3 cm in diameter, omphalinoid, surface with fine radial fibrils. 
Stem: 2-4 cm, cylindrical, smooth.
Lamellae: moderately distant, broadly adnate, with a subdecurrent tooth, edge concolorous.
Odor and taste: none (non farinaceous)
Spore: 7-8 micrometer in diam., isodiametric, predominantly 6-angled.
Cheilocystidia: none
Is there anthracophilous species in this genera?
Thank You for the help!
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Dear Attila,
nice photographs ! The squamulose pileus and the growth on burnt ground (see Noordelos, Fungi Europaei 5, pag. 627) are quite typical for E. flocculosum (Bres) Pacioni whose holotypus was picked up in northern Italy (not far from Hungary) by Giacomo Bresadola.
Other characters fit quite well (isodiametrical spores, lack of cheilocystidia, odourless basidiomes and so on)
Please let me know what you think about it.because I could be wrong, of course.
I am always at your disposal.
All the best.
Eliseo
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I have drawn the tree of my fungal population Rep-PCR, and I want to know how to read the results and what it means, I have use three primers Rep, ERIC, and BOX , and I am looking for genetic diversity. Any suggestions?
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Dear Oadi
Trees only tell you how diversity is partitioned. From your graph, I would say you have two single outliers and the rest forms one group without any further clear structuring. Anyhow, it is good practice to estimate how many times the branching at each node is supported, which is usually done by bootstrapping (for a genetic distance matrix you could use "seqboot" from the Philip suite)
Hope this helps
Pablo
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What deduction can be made?
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Fungal isolate is defined as race when it is specifically virulent on a particular crop variety. This particular race may be avirulent on the second , third or 4th or 5th crop variety. This doesn't mean this particular race has five avirulent genes. This phenomenon can only be determined through differential set inoculation experiment, supplemented by molecular analysis. A fungal isolate may possesses one, two, three, four, hundreds or thousands virulent genes, this is counted only when this particular isolate appears as a virulent pathogen on a particular crop variety, avirulent genes are never counted.
It is established  fact an avirulent race may be used as an antagonist against the virulent race of the same pathogen- the technique is called local or systemic acquired resistance.
If a host variety allows the growth of an aviruelnt isolate, the crop variety is susceptible. However, if this isolate cannot grow on that particular crop variety, it is no way be wise to call it a resistant variety.
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I am looking for publications with identification keys to chanterelles, to help me identify samples collected in Iran. Is there anyone who can possibly aid me to have access to some key literature? I would appreciate.
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Thanks to all of you
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some of the  isolation methods like Single spore isolation , direct transfer, particle filtration can be followed . 
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If the fungus won't sporulate, there are alternatives to single sporing and morphological identification. 
Using a dissecting microscope or magnifying lens you can cut out a hyphal tip from the agar and plate that. It should only be a few cells which will be the one species and reproduce clonally. You can also use the ITS region, elongation factor1 and beta tubulin sequences to identify the fungus. 
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During spring April-June 2015 I had collected many microfungal specimens (over 200), some smut and rust fungi and downy mildews from Rostov region (Southern European Russia). Also my colleague had given me about 100 analogical specimens from Arkhangelsk region (Nothern European Russia, White sea coast of Russia) and Krasnodar region (Caucasus, Black sea coast of Russia) some days ago.
If you or your colleagues are interested in these microfungal specimens, we are ready to send them (gratuitously) to you for any scientific research in systematic mycology or any close field of science.
Excuse me, but for some reason I did not have time now to make a detailed check-list and to identify all specimens (especially because some of them maybe new species or needed in eutypification). Here are just basic taxa. Perhaps I accept new taxa in the list. You can ask me about anything, to clarify the information.
Please, see Attachment.
Some photo of infected plants (the specimens collected by my colleague Gennady Okatov) from Russia you can find here
Are anybody interested?
Preliminary taxa check-list of fresh specimens from Russia collected in 2015 (Archangelsk region – conifer forest zone, Rostov region – steppe zone, Krasnodar region – subtropical forest zone)
Also I have large private collection with old microfungal specimens (2005-2014) from Southern European Russia (include plant pathogens and saprobic species). I can send them also if you need.
General check-list is here (book)
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Dear Timur, for sure I would be interested
 in smut specimens. If there are specimens of which the data is interesting for a publication we usually work like that: Marcin Piatek works on morphology (LM + SEM), I work on molecular phylogeny and you will be included as author, too. Could you provide a list of host plants on which you have smut specimens available?
Would be nice to cooperate with you!
Cheers
Matthias
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I have collected this material in the Paderu region of Eastern Ghat of India.Andhra Pradesh, India.
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This is either Parmeliaceae or Physciaceae because of the distinct lobes. If you collected it, can you make another picture?
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grow in PDA at 25⁰C
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Fungi are identified by their cultural and  morphological characters on natural and synthetic media, Potao carrot agar, Czapek agar etc. which are easily available and cheap. Visit some lab where mycological studies are done. and learn the techniques  which are simple. Alternately , use practical guide to study fungi.  If you want identification send it to ITCC, iNDIAN AGRICULTURAL  RESEARCH INSTITUTE, NEW DELHI.
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Adults and eggs of killifish kept in a small modular recirculation system, showed fungal disease (cotton like appearance) on the anal fin and around the egg corion.
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Use acriflavine hydrochlorid, dosage 0.45 per 100 ml in vehicle q. s. p. Treatment of adult fish: two drops of 3 liters. Eggs: diluting a water drop in a 10ml container and collected with a pipette content of the diluted and pour just a drop in the containers containing the eggs.
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My friend has bred under controlled conditions on a tree bark Myxomycetes species that has not been recorded in this area before - Central Europe. I wonder whether it is possible that the spores brought by the wind from another climate will be at the cortex, but not because of the favorable conditions do not develop. Only better microclimate created artificially stimulated to grow them?
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I think: if you use distilled water for soaking the bark samples and sterile vessels for the collecting and Transport, it is reliable: the species you get were on the sample and are not introduced. Surely you could object: two spores would be enough that have been on the sample - and they can have been wind-blown to the sample from far away. Likely? No.
If you use dirty vessels and tap water for soaking, the species you obtain can be foreign.
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homo and heterobsidium
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The basidium of the homobasidiomycetes is a usually more or less clavate undivided cell (= without septae), whereas the basidium of a heterobasidiomycete is a cell divided longitudinal or transverse in (usually) four parts by three septae
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I would like to select a molecular marker to compare about 100 strains of Trichoderma harzianum. I think these isolates be too similar, so an appropriate  maker need to differentiate them.  
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Since you have one species of Trichoderma only. The best marker will be SSRs. Don't do simple diversity but see the population structure which will help you in indentifying the various evolutionary forces shaping the fungus tragteroies
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I am presently working on the diversity study of Fusarium verticilliodes isolated from maize in southwest Nigeria. I would like to know the different combinations of AFLP primers that can be used for this study.
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It would be nice that Maria Marta Reynoso from Universidad de Río Cuarto (Argentina) answers this question!!
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How does NaCl affects the metabolism of a fungi? NaCl up to a certain concentration promotes fungal growth whereas at higher concentration inhibits it. Can anybody elaborate on the mechanism responsible for both the cases?
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Well its a normal phenomenon, any metabolically acceptable mineral in low or adequate amount will be useful and its excess amount will be bad e.g. hypercalcemia in our body etc. Same is the case for fungi too.
Well about higher (filamentous) fungi, people have not studied the affect of NaCl much, but to the level of yeast, especially on halophilic yeast there are publications available particularly on Hortaea werneckii, Saccharomyces cerevisiae, etc. Mostly the high salt creates the low water activity in the cells of fungi which slows down the flow of transportation in and outside fungal cells. In halophilic yeast some bio-compatible solutes helps to maintain the balance of materials inside and outside yeasts. 
I am working on obligate halophilic fungi, which cant grow without NaCl, and quite a high concentration helps their metabolic machinery such as enzymes. These come out to be more interesting case than normal halophilic organisms. We are still working to see how they do so.
I hope I have answered a bit of your query.
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hello everyone 
please help me to find out good published record about the morphology and pathogenic characters of Colletotrichum citri. one isolate of my Colletotrichum  collection provides 98% identity with 99% query coverage to Colletotrichum citri in Blastn search for ITS. It's CAL, GAPDH and TUB2 sequences are also matching with C. citri. But I couldn't found any detailed record to confirm it. Thank you.....
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Hi,
% similarity doesn't help to much. Colletotrichum citri, as far as I know, belongs to the C. acutatum species complex and it has been firstly described by Huang et al. 2013 in "Colletotrichum species associated with cultivated citrus in China" (http://link.springer.com/article/10.1007%2Fs13225-013-0232-y). If there are info around they should be in this paper. If you need any help let me know.
Good luck
Riccardo