I'm working with soil fungi and I observed its morphology and spore structures under a scanning electron microscope up to the genus level. I think they are rhizopus genus but how can I know which particular species they belong to? Could anyone recommend a biochemical test for identification?
I assume that you are working on fungi that you cultured from the soil.
If morphology is not discriminant enough you cans use the ID32C strips. You'll find a link to the PDF of a nice paper describing "Carbon Assimilation Profiles as a Tool for Identification of Zygomycetes".
Otherwise you can use DNA sequence analysis, and now we use MALDI-TOF mass spectra to identify colonies from cultures.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865868/
Dear Dr Ratna sri. The best way for identification of Zygomycetous fungi is using molecular tools. I recommend you this text. http://books.google.com.co/books?id=t1iEGCciqckC&pg=PA485&lpg=PA485&dq=rhizopus+genetic+identification&source=bl&ots=vB8tqWPJS7&sig=JE3EgcA0XpuD428_TZ7o6u1ddtY&hl=en#v=onepage&q=rhizopus%20genetic%20identification&f=false
With best regards
Juan Bueno
Even there are biochemical tests for identification, you will finally need molecular methods for an optimal identification. For that, sequencing the ITS regions of the rDNA is well recommanded for fungi.
Good luck
You can use Endoterol and B-D-glucan as biomarkers for detecting fungi but you will need molecular biology tools (essentially sequence ITS-NL regions) to get identification.
Best,
JP
For identification of fungi you can use MALDI - TOF mass spectra, but the best option is PCR assays. I think that biochemical test for identification of Fungi is mainly for identification for medical Fungi
Biochemical tools is not the authetic way for the identification of fungi, Several kits for identification of fungi and bacteria are availble in the markets, if u find difficulty for the idntification of fungi by Molecular bioassay then u should used that kit
You can use biochemical tests only for yeast identification. Filamentous fungi should be identified by morphological methods. The identification should be made by observing at first the colony morphology, color and appearance, then observing by microscope the asexual and/or sexual reproductive structures (conidia, spores, hyphae, etc.). Molecular techniques may be used to confirm or support the morphological identification, but they are too expensive and in many cases are not accurate.
Identification of fungi by other then morphological methods does not give accuracy and is only recommended by those who have no practical or grass root experience / expertise in morphological identification . They are also not aware the huge morphological variation in fungi on the bases of large number of fungi have been nomenclatured. Molecular or biochemical attempts leads to more confusion in correct identification at species or genus level- P.N.Chowdhry
Dear Dr. Chowdhury, you are absolutely right. In some of the cases molecular identification creates problem to identify the genera as well as species. In some of the cases, it has also been observed that Amanita and Agaricus are same by their molecular diagnosis. Where as these two are completely different by their morphological features i.e presence or abscence of volva. Molecular diagnosis is necessary, but only based upon those molecular data we hesitate to identify and confirm the species. Morphological features are also very much necessary for proper identification of fungal genera as well as species.
As Stephane Ranque have mentioned, you can have some help using carbon profile assimilation or MALDI-TOF technique (better). Also, you can perform termotolerance tests. Last years have brought substantial modifications of the zygomycetes taxonomy, so you have to use a molecular technique for an accurate identification on species level.
you go for "Carbon Assimilation Profiles as a Tool for Identification of Zygomycetes"
Identification of zygomycetes have gone molecular with the aid of PCR system. This is now a suitable mean, with the aid of kits, for rapid, automated and throughput analysis. However, cultural morphological methods should still be in place for some physiological identifications differences of organisms (like Aspergillius flavus and Aspergillius parasiticus) with almost same biomolecular similarities.
"Identification of fungi by other then morphological methods does not give accuracy and is only recommended by those who have no practical or grass root experience / expertise in morphological identification" .
If the above statement is from a taxonomic end-user, it is understandable. But if this view is of a fungal taxonomy "expert", I would say you haven't tried much in terms of using different gene markers and developing a set of curated reference sequences for sequence comparison. It demands hard-work and a deep understanding of fungal groups you are interested in. Please have a look at recent developments in taxonomy of Fusarium, Colletotrichum, Trichoderma etc.
cheers,
shenoy
You can generate ITS sequence-data and compare it against the type strain sequences. To separate R. oryzae from R. delemar you can use GAPDH gene marker.
In ours labs, we can do identification of fungi by morphological feature or by using molecular sequence.
Biochemical analysis or identification of the fungal spores or hyphae is rather difficult. the best way to identify the fungal spores is to culture them and with the help of available literature and micrometry methods, the spores can be identified up to the species level
The cost of sequencing has gone down sharply (now currently in 2020) and more informative molecular markers for fungal identification like tef-1-alpha and beta-tubulin are being used as per the suitability of the species studied.
The better way for identification would be molecular method such as using the ITS regions. That will give you an accurate identification of fungal species!
Identification of a fungal species is usually done by their morphology by observing them under research microscope rather than carrying out chemical test.
Maximum growth temperature can help differentiate R.oryzae (which grows to a maximum temp of 46C) from R.microsporus (which can grow up to 52C). R stolonifer only grows up to 32C
Speciation can also be accomplished by mass spectrometry such that used in MALDI TOF given that you have database that have enough entries of each species. Molecular methods such as D1/D2 amplification and sequencing would be your gold standard method in identification
Fungal identification at species level is only authentic with taxonomic characters through microscope
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