Fungal Taxonomy - Science topic

This has been proposed and discussed: see

(093–096) Proposals to permit nuclear DNA sequences as nomenclatural types when preservation of specimens is not feasible Susanne S. Renner Washington University, Department of Biology, Saint Louis, Missouri 63130, U.S.A. Address for correspondence: Susanne S. Renner, srenner@wustl.edu DOI https://doi.org/10.1002/tax.12607

and respective decissions....however, over time things might change - evolve!

A lot of people like the Olympus Tough TG-6 or TG-7. It’s very tough, small, takes good micro pictures and is able to photo stack which means every part of the image is in focus. It’s particularly good with smaller fungi

In contrast to a true binding hypha, which typically has tapering side branches growing from a main stalk, skeletal hyphae typically have an even diameter along most of their length. The family Ganoderma contains arboriform skeletal hyphae. They are unbranched for the first 200 metres before developing tree-like limbs.

It is chlamydospore

Plate No 4 contains Penicillium (blueish colony, Aspergillus paraciticus (dark green colonies), Fusarium (whitish colony), and Alternaira blackish colony)

Hello Rakhe Tepin , I provide figure 7c from the bilingual book of Eugene Yurchenko on corticioid fungi of Belarus https://rep.polessu.by/handle/123456789/21094. Check the layer marked as 'co'. It is a layer between the regular trama and hairs. If present, it is recognised with a naked eye or via stereomicroscope as something denser and darker colored that the trama.

agree with Dr. Ajay gautam garu regarding symptomatology. microscopic view of late leaf spot and early leaf spot structures are little confusing.

Ajay Kumar Gautam

In the picture above, the grayish brown mycelium represents the fungus Rhizopus. While the white and greenish blue colonies represent the fungus Penicillium.

The above micrograph shows penicillium spp.

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.

Look at the books listed here, they might be of help

Even complicating everything more

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.

Dear, Franz-Sebastian Krah...

Kindly see the following attachments:

The sequences should be the reverse complement to each other, so you will need to convert one of your sequences to a reverse complement so you can combine them to form a consensus sequence.

If you did the above and it was still a problem, it is possible the sequence is long and there was a breakdown towards the end of sequencing, meaning there may be no clear sections of overlap. If this is the problem, you can rerun the PCR and sequencing using primers closer together to crease a shorter contig.

That being said, since both the forward and reverse sequences agree, you probably have identified the organism.

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.

All the markers may be effective but use combination of different marker systems. Like u can use about three different markers to get more reliable results.

DearCristian Riquelme

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/

GIMP http://www.gimp.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:

Media Player Classic (MPC) http://sourceforge.net/projects/guliverkli/

picked up the video camera every other time

Paint.NET (v. 3.36) http://www.getpaint.net/

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

Regards, Sergey Viktorovich Pushkin

Dear all, any guesses about this? Its a creamy-white round colony on PDA.

Dear Jingjing Du ,

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

"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."

https://wwwnc.cdc.gov/eid/page/scientific-nomenclature

It might be of Cladosporium or penicillium sp by the gross morphology. If you attach a microscopic view, i will definitely let you know.

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 .

Targeted the 18S rRNA gene

Check paper:

"https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&cad=rja&uact=8&ved=2ahUKEwiI_6eKv6zlAhWL6qQKHTmHD644ChAWMAB6BAgGEAI&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%2Fdownload%3Fdoi%3D10.1.1.261.2152%26rep%3Drep1%26type%3Dpdf&usg=AOvVaw1puUNW4puyD0JEm5oYfTjn"

you need to conform  by molecular

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.

I agree with Hero Mohammad Ismae

'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.

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

 

You are welcome

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.

Dear Thomas,

thank you very much for your help. 

Best wishes

Vytautas

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.

This paper may help with visual identification: https://www.researchgate.net/publication/275335972_A_review_of_fungal_contamination_in_pharmaceutical_products_and_phenotypic_identification_of_contaminants_by_conventional_methods

Thank you dear  Barkat and Dhurgham for responding me!

 

Increase the power plz

When still in doubt identify the species by a gun-shot gene-analysis. It costs but it give a clear answer.

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 .

I can not pen the reference 1, DOI Not found,What should I do the next?

My good friend Laith Al-Ani !

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. 

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

Dear , Esmaeil Rahkhodaei

You can see the following links :

With best regards 

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.

Agree with Prakash

Dear Ourlad,

The pictures look like Amauroderma rugosum, but microscopic analysis is needed.

With best regards,

Elena

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

Sporothrix spp.

Dear Ali,

The second slide exhibits the microconidia of Fusarium sp.

118

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 ".

its not clear .

you need to see the book contain key of taxonomy .

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.

Dear Liqaa,

Looking at the pics, it looks like you have Fusarium sp., definitely not T. rubrum.

Regards

Mohammed

Thank you Maria and Nicolas for answering and Nicolas, I must have misunderstood you, thank you for clarifying this point.

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

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.

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.

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