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Fungal Taxonomy - Science topic

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the difference:genus of fungi and symptoms and how can Differentiate between two in field 
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agree with Dr. Ajay gautam garu regarding symptomatology. microscopic view of late leaf spot and early leaf spot structures are little confusing.
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sterile control of a mineral substrat for plants
grow medium: sabouraud agar
sample 2
tia
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In the picture above, the grayish brown mycelium represents the fungus Rhizopus. While the white and greenish blue colonies represent the fungus Penicillium.
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steril control of a mineral substrats for plants
grow medium: sabouraud agar
sample 8
tia
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The above micrograph shows penicillium spp.
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sterile control of a mineral substrate for plants
grow medium: sabouraud agar
tia
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The colony which limited with yellow marker with white mycelium may be belong to the fungus Beauveria bassiana, but not exactly. It needs more images to clearly identified.
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I am no expert in fungi. However I need to identify few fungal growth on sabouraud agars. Are there any easy to read and recommended book that has both the culture growth images and the microscopic images? Thank you.
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I have been reading various articles concerning fungi and Fusarium classification in particular. The more I read the more I get to know less of what the future of Fusarium classification shall be. I have now landed these two very interesting articles that could form a very concrete basis for this discussion:-
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Even complicating everything more
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(Modern taxonomy = considering Morphology, Multi-gene sequencing and phylogeny)
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This is very interesting question. I really do not understand the reason to "the morphological and the microscopic method will not give a good result" since morphological has being (together with molecular phylogeny) a very useful and powerful tool to describe and characterize distinct ranking of taxa. There are distinct situation about family ranking in fungi. Families based in several genera (and species) and monospecific genus, generally strongly based on molecular (phylogenetic) distance. Description of a new family should be based on strong phylogenetic (with independent genes) and morphological data set at least.
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I need the type of mycorrhiza of all fungal species? Or a list containing this information? Does anyone know if this exists?
Thanks!
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Dear, Franz-Sebastian Krah...
Kindly see the following attachments:
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The attached images are of endosymbiontic actinobacteria from a marine sponge. It shows long rods as well as short rods with spore like structures within hyphae. I am confused why does is show such a morphology. The gram stain and the colony development photos are of 3 days old colony while the streak is of >7 days old.
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Hi! Do you know if the spores of actinobacteria can be stained with Gram? I have two different morphologirs but I dont know for sure if the little are spores or anotjer type of bacteria.
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Dear All,
The forward and reverse sequences obtained from the PCR products are not identical at all.
Can I still make the contigs for doing BLASTn?
Individually both sequences are showing the same species in BLASTn.
Together, by placing one sequence after another they are showing a different species.
Kindly suggest a way to identify the organism by using both forward and reverse sequences.
Best regards
Arush
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Matthew B Paddock is correct but I will add one more thing. If your amplimer has a small insert or deletion ( CA repeat or poly A or similar) near to one end then the sequence will look good from the other end but will be weak signalled and messy after the indel when sequenced from the indel end. You may have to trim off poorly sequenced bases at the ends of each sequence to get a good Blast result but if you are looking at gene coding sequences then genes are highly conserved through species and it may just be that your search finds many identical sequences and the one that you are interested in is way down a list of nearly identical sequences. You may have to increase the number of matches shown
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I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases contain species not assigned to a species level?
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Not familiar with taxonomy databases, but I can always recommend SDL Multiterm. It is a customisable type of database that is used for storing terms and their explanations, create 'fields' between them etc. Hopefully the program can be of help for you, or at least point you in the right direction.
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So far I have not been able to find a camera lucida that fits a low range microscope.
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here are my suggestions
Graphics tablet
In theory, the component is optional, since you can draw with the mouse. Practically necessary. You can choose a tablet based on your requirements or budget. The better the tablet, the more comfortable it will be to draw and the more accurate the drawing will be.
The equipment we used:
Jenaval microscope
ScopeTec DCM 500 USB camera
Wacom Intuos 4M graphics tablet and stylus
Computer configuration:
Intel Core 2 Duo Processor E7500 2.93 GHz
4GB memory
500GB hard drive
ATI Radeon HD 4550 512M Graphics Card
and a laptop (Dell Inspiron 600m), which also worked, but with an effort:
Intel Pentium M processor 1.6GHz
512 MB memory
HDD 200 GB
ATI Mobility Radeon 9000 Graphics
The general rule is that the higher the picture resolution will be given by the video camera, the more powerful the computer is required. For low resolutions (up to 1280x900) and 15 frames per second, our laptop was quite enough. A large RAM will be useful if you want to draw a large poster in a graphics editor.
and programs:
Apart from the operating system, everything is distributed under a free license.
Here are our picks for today:
Windows XP SP2 Home Edition Rus http://www.microsoft.com/
VLC media player http://www.videolan.org/
for bitmaps InkScape http://www.inkscape.org/
for vector drawings
Tried, but liked it less. It is possible that in your hands it will work as it should:
picked up the video camera every other time
no full support for Wacom tablet under Windows XP
ArtWeaver (v. 1.0) http://www.artweaver.de/
tends to give almost all processor resources to the video player, and as a result, they are not enough for drawing
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can anyone help me in identifying this fungi?
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Dear all, any guesses about this? Its a creamy-white round colony on PDA.
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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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In some papers of microbial ecology, I found that all the microbial names from phylum to species are italic, but there were also some papers just presenting the genus or species names in italic. So, what's the standard rules of names' writing of taxonomic names? Should all be in italic from phylum to species or just parts of them?
Thank you
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"Italics are used for bacterial and viral taxa at the level of family and below. All bacterial and many viral genes are italicized. Serovars of Salmonella enterica are not italicized.
For organisms other than bacteria, fungi, and viruses, scientific names of taxa above the genus level (families, orders, etc.) should be in roman type."
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Hi,
i have a fluid sample of a plant extract that over the weekend grew a massive contamination (lab bench - room temperature).
So to find out which of the used ingredients (dry substances or water) might have caused this it would be great to know what genera this could be - as this info may be used to track back the origin.
I am aware of the difficulties of specie identification from macroscopic pictures only, but this is unfortunately all we have.
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It might be of Cladosporium or penicillium sp by the gross morphology. If you attach a microscopic view, i will definitely let you know.
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Is it possible to separate (distinguish) different AMF morphotypes which may possibly represent different taxa just by looking spores under a stereo microscope of say, 60x?
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The spores may be separated based on colour ,shape and size under stereomicroscope. After separation of the spores , they have to be observed under 100 x research microscope. Genus level is possible in some cases.
Species level can be identified by molecular techniques .
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In my project, I am inoculating seeds with AMF fungi and I am interested in to see how AMF colonisation could alter rhizosphere communities, bacteria and fungi. I am bit confused in selection of fungal region. So I would like to ask which region is best for this analysis ITS or 18S rRNA.
Thanks in advance
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can any one help by identifying this fungi which was isolated from contaminated workspace
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you need to conform  by molecular
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Please identify this mushroom which is found in Casuarina equisetifolia stem cuttings. 
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I recommend joinging Mushroom Observer for ID: https://mushroomobserver.org/
It's an outstanding resource.
Also, good quality photos, close-up, in focus, and pictures of the top and bottom of the fruiting body area big help.
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The polymerase chain reaction (PCR) technique has created new ways of revealing DNA polymorphisms among closely related genotypes.Molecular markers which have been applied to Colletotrichum sp. diversity studies include internal transcribed spacer (ITS) regions, restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers.
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Check out this paper: Liu, F. et al. Unravelling Colletotrichum species associated with Camellia: employing ApMat and GS loci to resolve species in the C. gloeosporioides complex. Persoonia 35, 63–86 (2015).
These authors combine two gene regions, Apn2-Mat1-2 intergenic spacer and partial mating type (Mat1-2) gene (ApMat) and glutamine synthetase (GS), as "secondary" barcodes, with higher delimiting power compared to ITS.
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I have isolated some fungi from infected Tomato leaves. I am in doubt is that Mucor or Rhizopus. In media PDA it producing some-how colourless mycelial growth with black dot on the tip.
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'Unseptate mycelium' does not mean that the organism never develops septae. I is rather typical for zygomycetes to produce septae below reproductive structures, in this case below mitosporangia.
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DNA extraction protocol using Chelex-100 is cheap and very useful technique. However, the protocol varies between lab to lab, or people to people.
My lab is fungal taxonomy lab, so DNA is frequently from lab-grown fungal colony.
Currently in my lab, the protocol is:
1. Prepare 10% of Chelex-100 solution with ddH2O, stored at 10'C convective fridge.
2. aliquote 300λ of Chelex sol. to 1.5mL tube, harvest fungal colony (about (0.5mm)^3), from media, mix it by inverting or vortex mildly.
3. Pre-heat samples 56'C with Heating block for 15 min.
4. Load the tubes into floater, boil at 100'C for 10 min.
5. Vortex tube vigorously.
6. Again, Boil the tubes at 100'C for 8 min.
7. Centrifuge at 101g, 4'C, for 10 min.
So far there were no problems yet, but I'm looking for ways to improve yield or purity of the DNA.
Would this protocol be changed or fixed?
Waiting for the Answers from the best :)
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you can test both of Chelex and Te buffer as:
mix chelex 100 150 ml and 50 ml TE buffer
add sample and squelch and crush it in mix of two liquids for 30 second
after put in PCR in 95 c for 5 min
after take 4 ml for PCR reaction
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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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Dear all,
I have found a pretty cute contamination in a colleague flask. We think it is a fungus, does anyone know which species it is (round, white and hairy)
Have a nice fluffy day!
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Are there any fungal genetics near by - one of the old-timer favorites is Neurospora? 
Neurospora grows as a white colony in the dark with a medium containing greater than 1% Sorbose (Arabinose?)  looks identical.  Put the flask into some strong of sunlight if the colony turns orange - (carotenoid pigments) it's likely to be Neurospora. 
Oadi above is correct  too - however, you have to jump through some serious hoops to  sporulate an ascomyetes.  Now a days a skill left to the equivalent of a Jedi Knight.
Have a great day - Let me know if it turns orange - implies the  presence of a Jedi Knight.
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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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I am carrying identification of fungi by using microscopic examination, and i need more explanation about differentiation between species.
Many thanks
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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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Pictures are paired. Microscopic and morphology on cellulose basal agar.
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Increase the power plz
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I would like to ask for help in identifying a mold culture I recently isolated from a sample in the lab. Would like to get alternative opinions regarding this matter.
Briefly, I was able to culture this unknown mold in PDA with rose bengal and streptomycin. The mold grows as black compact fibrous colonies which could be tough and crusty and embeds well in the agar plate.  From this plate, I did slide culture on a PDA agar block to check for fruiting bodies and vegetative structures.
I narrowed down my putative ID's to either Stachybortys or Sporothrix but I would like to getalternative perspectives on this. Since I'm only depending on microscopy data for preliminary identification.
I am attaching some photos of the colony from the plate as well as some microscopic images. I hope someone can give insights.
Thank you so much!
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When still in doubt identify the species by a gun-shot gene-analysis. It costs but it give a clear answer.
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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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I only can observe its conidia, that is not enough.
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I can not pen the reference 1, DOI Not found,What should I do the next?
My good friend Laith Al-Ani !
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May be you can suggest the genus name for this fungus. 
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You need to give us more information. Where was the fungus isolated? What media does it grow on? Have you tested which carbon sources it can utilise? Please provide more information to aid the identification. 
Most importantly, provide microscope photos, preferably both unstained and stained with methylene blue at 400x magnification. Photos of the conidia/spores are the most important. 
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Some fungus-like materials were found in the deep dermal inflammation tissue from a 76-year-old lady's right hand. She presented with soft tissue swelling with redness on her right hand after antibiotic treatment failure. She said she has high blood sugar when she tested herself with a blood glucose test kit. But she was not properly diagnosed or treated for that.
What kind of fungus should I include in the differential diagnosis?
(phaeohyphomycosis?) Is this definitely fungal infection? if not, what this would be?
Any ideas are welcome!
Attached pics are PAS stained slide taken at x1K
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Dear Yosep,
Not because I work on protist pathogens, but to me looks like trophozoites of some amoeba. Try to grow the swab assisted wound material on sabouraud's medium to rule out fungus. Could be Acanthamoebal trophozoites, deep eosinophilic cells??
Best,
Mannan
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I am a PhD candidate in mycology. I need the key to identify cunninghamella species. Could anybody help me?
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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 black polypore mushroom from Philippines. Thank you
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Dear Ourlad,
The pictures look like Amauroderma rugosum, but microscopic analysis is needed.
With best regards,
Elena
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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 isolated this fungus from a marine sample. Can anyone help me in its identification?.
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Sporothrix spp.
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isolated from skin of some patients by mycology lab researcher so to any species it may belong ?figure 1 from plate show in picture  2 , figure 4 ,5 and 8 from plate show in picture  6
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Dear Ali,
The second slide exhibits the microconidia of Fusarium sp.
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Please advice me about identity of this fungus produced spores on SDA media.
Regards
Shuvrah Rehman
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Hi Shuvrah,
You can also see this book "Seifert K, Morgan-Jones G, Gams W, Kendrick B. 2011. The Genera of Hyphomycetes. CBS Biodiversity Series no. 9: 1–997. CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands ".
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These fungi are recovered from a Neogene wood of North-east India
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its not clear .
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Please help to identify the attachments.
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you need to see the book contain key of taxonomy .
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I isolated this fungus from fruit can any one identify this fungus?
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Dear , Maliha Fatima . I agree with Anisetti Thammayya. It  belongs to Aspergillus niger group ( Section Nigri ) . As I see in the picture it may be Aspergillus carbonareus which belongs  to this group and gave a black colonies like carbon . You also must check phialides weather they were biseriate or uniseriate , conidia size and shape and conidial margins weather they were smooth or roughened , the color of colony reverse on MEA or CYA media . You also can return  to the References ( The genus Aspergillus by Raper and Fennel , 1973 ) ; Al-Musallam , 1980 ; Pitt and Hocking , 1985 .
I hope you have a good luck.
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I enclosed Microscopic photos for this fungus, Thank you
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Dear Liqaa,
Looking at the pics, it looks like you have Fusarium sp., definitely not T. rubrum.
Regards
Mohammed
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Has anybody got an idea what are the filaments in the attached photo?
I mean, a distinction between bacteria and fungi is far enough.
This is an aqueous sample stained with hematoxylin. No other photo is possible.
Thank you very much in advance,
Aleksandra
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Thank you Maria and Nicolas for answering and Nicolas, I must have misunderstood you, thank you for clarifying this point.
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I got this fungal isolate from termite insects when I was trying to isolate entomopathogens.  Dear colleagues please let me know what is the identity of this fungi.
Regards
Shuvrah
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Dear Yehya A. Salih
No I did not test pathogenicity on termites. Till now I am completing isolation protocol. Yes I will upload plate culture.
Thanks.
Shuvrah
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We have found this fungus on the twigs of blackcurrent (Ribes nigrum). Clavate asci, formed in cleistothecium, ascospores with one septum. 
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surely a Mycosphaerella sp., or these days, one of the Mycosphaerella-like genera within the Mycosphaerellaceae. To identify these reliably to genus level requires either the asexual stage or a DNA sequence.
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Hello all,
i going to work on alternaria and i need to key of identification species of it . who can help me?
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Dear Djamel , 
In order to identify Alternaria solani and Alternaria alternata , you have to observe first of all  the conidia , there are some differences such as : seize of conidia and formation of conidia (in chain or not ) , and you have to check by molecular methods , because morphological characters are not enough to distinguish beteween them.
You should read this article :  Biodiversity and taxonomy of the pleomorphic genus Alternaria 
Best regards.
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Recently, some novel or interesting helminthosporioid fungi and black yeast-like taxa were isolated from soil and plants of the Atacama desert. Among the latter group, one species genetically close to Knufia peltigerae was identified. I would like to compare the morphology of the Chilean fungus with that species in order to assess its identity. Thanks in advance!.
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Dear Hugo,
I attached a recent paper in which we described a related species (Knufia petricola). I hope this helps.
As already mentioned I believe the work of de Hoog and Untereiner are strong references.
Best regards,
Corrado
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In morphology, Macrocystidia is supposed to be a close relative genus of Lactocollybia (Singer 1986) as both have gloeocystidia in the context of pileus, stipe, lamellae, etc., but blast searched results of the nrLSU/ITS sequences of Lactocollybia/Macrocystidia did not find each other as the closest genus (within first 100 matched species). Thanks for your attention.
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Thanks Iqbal!
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Can my fellow brethren researchers share with me the number of species under the taxon Lentinus along with description of each taxon? If possible, with an image or a diagram
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Dear Ankur,
I think the attached publications might bring some generous knowledge for your topic.However, you can also search the Wikipedia, in this concern. The cross references in the enclosed publications might be helpful for you.
Wish you Good luck !
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can somebody help me to identify this fungus?
Thank you
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Why don't you use molecular identification?
It's quite easy to extract DNA, amplify taxonomycal relevant target such as ITS (ITS1-ITS4 primers) and sequence it. Than you'll have a strong indication about your strain. Also EFT-1alpha, calmodulin and beta-tubulin are good marker to test for the identification.
Cheers
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The picture needs more magnification
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I believe I have  isolated a fungus and need to identify it before moving forward with my research. When cultured in SDA it's white, but in the special agar I am using it's mostly green. It grows slowly, taking about a week to cover  a petri dish. In the special agar the growing edge is white, then green, then the other coloured growths appear ON the green after three or four days. Microscopic analysis show that all coloured types are part of the same fungus (only about 90% sure)
I have attached pictures of both cultures, as well as microscope shots. I lost the more detailed microscope shots and can't redo them now. I hope these will be sufficient.
I really need this and would be grateful for any and all assistance.
 Thank you
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I'm thinking also that it might be Trichoderma. One of the interesting things is that the two cultures above were subcultures innoculated at the same time, from the same parent growth (which by the way was a pure culture). The white one is on SDA and the green is on specially formulated agar. I'm not a microbiologist. That's why I'm so confused...