Morphological Identification of Species
The identification of one or more species from either soils or preserved specimens is a difficult and often time-consuming task, regardless of the experience of the person doing the work.
- For species common to the collection, an identification takes a minimum of one hour to complete (involving extraction from sample, preparation of a permanently mounted slide, microscopic examination, comparison with reference voucher specimens).
- For other species in which reference cultures are available, the time increases to 1-2 days to accommodate more extensive comparative analysis.
- For species not present in the collection, the time requirement is a minimum of 4 months because the germ plasm source must be passed through one culture cycle in our facility to obtain abundant healthy spores for examination and comparative study.
Identification of the dominant (or only) fungal species in a deposited accessions will be provided free of charge to the contributor upon request. This request can be submitted at any time after the culture has gone through at least one propagation cycle and produced enough spores for a thorough evaluation. Identification of associated species will depend on amount of material and level of difficulty. Characterization and comparative analysis of undescribed species will be left to the discretion of the contributor. Any unique characteristics or biological properties discovered during the culture and examination of these species also will be available to the contributor. INVAM will not be involved in publication of new species descriptions unless specific written arrangements are made with the contributor.
Requests for identification of non-INVAM isolates will be honored if time permits, provided that the spores originated from pot/root cultures or are healthy spores from field-collected samples. Moreover, the spores must be submitted in the medium from which they originated. Extracted spores or slides will not be accepted because they rarely arrive in a condition suitable for analysis. Fees will be waived only if an identification is not possible or the fungus/fungi present in the sample can be successfully deposited as an accession in the collection.
Molecular Identification of Species
As of mid-2013, we have almost 400 LSU sequences of 76 species in a maximum likelihood phylogenetic tree and there is remarkable congruence with clades defined by morphological characters. With this extensive library, we can position an unknown within a genus clade most of the time, and almost always in clades at the family level. If the unknown sequences match closely with sequences in our library, the species ID can be made with relatively high confidence.
Our typical approach is to extract and amplify DNA from three typical healthy spores, obtain at least 20-30 transformant clones from each spore, and then retrieve at least 1-2 random sequence from each spore. The contributor can decide, based on results, whether to sequence more clones for one or more of these spores. The cost to us for each sequence (Davis Sequencing, California) is $8. Adding labor and materials for the DNA preps, as well as shipping and sequence editing (accompanied by raw chromatograms), the final cost is estimated to be $75 per fungus. If the result is inconclusive or spurious, no charge will be assessed.We cannot offer this type of service at this time, as the collection is on a no-cost extension and thus has a very limited budget and cannot fill the position of the person who would do this work. When it is possible, ONLY fungal material produced in pot or root organ culture will be acceptable.