I dont know the type of primer that you can use for but it is more easy to identify the species with morphological analyses of the spore 

If you just want to identify the species that are presente in the inoculum, primers addressed at LSU should work fine (e.g. LR1-FLR4 - see:

van Tuinen, D., E. Jacquot, B. Zhao, A. Gollotte, and V. Gianinazzi-Pearson.

1998. Characterization of root colonization profiles by a microcosm community

of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR.

Mol. Ecol. 7:879–887.

Gollotte, A., D. van Tuinen, and D. Atkinson. 2004. Diversity of arbuscular

mycorrhizal fungi colonising roots of the grass species Agrostis capillaris and

Lolium perenne in a field experiment. Mycorrhiza 14:111–117.).

Of course, you could also design primers specific for each fungal species declared on the label, but then you would loose all the undeclared species.

I do not agree that morphological identification is easier. It take a lot of experience and I don't know many people who are reliably able to do that.

There is no need to use any  primer..simplest way is to identify the species with morphological analyses of the spore...you can send me the pics if you want......

I know many people will have disagree with me..because they want easier way for identification.... problem is many people beleive machine are more reliable....

Many a times we just want to do molecular analyses...because it become habit for us to rely on the tools...no one wants to learn basic and fundamental ways ..... instead of identifying by using primer.it will be better to see wheather the given AM fungal species is functioning well in that particular commercial inoculum....,,it is neccesaary o study more about the sproulation pattern ,rate of sporulation etc...we can study that by naming at A or B species..and not neccessarlily go for Molecular identification.....without checking the potential of given AM fungal species...

HI James,

Inaki asked for primers and primers I suggested. Concerning the use of PCR, the thermal cycler is a machine as much as the microscope... it requires interpretation and understanding after you collect your data.

I do not think that machines are more reliable, but the results by pcr can practically and coneniently re-examined once there are novelties in the classification (something very frequently occurring, in this field...).

Furthermore, if Inaki is familiare with molecular biology, he can set up his protocols and be independent in his future work (which doesn't mean that looking for a collaboration is bad). Morphological identification can be used as well, but I insist that (in spite of the relative low number of species) it takes longer to learn and relies on very little details and it requires a large experience in order to be reliable.

Finally, there is a debate in the mycorrhizal community about the attribution of some names (SEE the following paper:

Mycorrhiza

October 2013, Volume 23, Issue 7, pp 515-531

Date: 05 Apr 2013

An evidence-based consensus for the classification of arbuscular mycorrhizal fungi (Glomeromycota)

Dirk Redecker,  Arthur Schüßler, Herbert Stockinger, Sidney L. Stürmer, Joseph B. Morton, Christopher Walker), if you rely on morphology alone you should be ready to deal with this problems.

This said, I am not saying (and I did not say before)  that learning basic and fundamental ways is wrong. On the contrary is very good.  But please let's not mix up things.

  Dear Guido Lingua,

Thanks for the information...

Molecular techniques are of huge importance in AM fungal research  .....

 i never criticized the molecular technology nor any primers ..my point of disscusion was  before identify the particular AM species..through more advanced techniques we first  need to  study their potential or check  functional aspect , their performance with different host,they germination and sporulation potential, their role in promoting growth of  of various host (including commercial important crops) of AM fungal species.and if we went for identification  of AM species through more advanced techniques and it turns out to be non performing AM species With Most of host plant  .. than what??

i agree it takes longer time to  learn and but more details are can be also noted... only if one trust Traditional methods... and than  confirmed that by using molecular  tools ....

more studies are needed where in we can check more functional aspect of AM fungal species and depending on their potential  and  and grouped them  different groups.....with best performing one at the top of the table... and than takke aid of molecular techniques to substantiate it... otherwise we will keep on revising the classification   may 100 times more  overlooking the functional aspect of Am species...

Dear All,

Many thanks to Guido and James for the expertise you both have contributed.

Molecular analysis does help with confirmation, after morphological identification, however it also has its drawbacks especially when trying to extract spore DNA or conduct a PCR using a spore. Could someone please suggest the best optimised method for using single spores in PCR for identification?

Hi Sumaiya,

I am not an expert but I found this information that I think could help you. http://invam.wvu.edu/methods/dna-extraction-amplification/spore-selectioncleaning

Regards,

If you really want to know which species are present, then I would both look at the spores (ideally with DIC --differential interference contrast, after mounting in PVLG and separately in 1:1 PVLG/Melzer's reagent; Brundrett's protocol for isolating spores is excellent) and also by PCR. For species-level detection you should probably use ITS primers (although you will get some intraspecific differences).  I don't like any of the supposedly AMF-specific primers particularly well at this point, so why not use fungal primers for the ITS (consult Vilgalys Lab website for a list), sort by PCR product length (and maybe RFLP) and sequence the ones of the right length for AMF (much shorter reads than most basidiomycetes and ascomycetes and longer reads than most yeasts from these groups)? And last but not least, you (unlike the vast majority of researchers these days) will actually be able to link the morphology of the spores to the sequences. Of course, high-throughput is getting cheap enough that you could just sequence everything in the inoculum for almost the same cost as traditional cloning and sequencing (but you still wouldn't know which spore generates which sequences).

Thank you everybody! Even if I agree that morphological characterization should not be forgotten and completely replaced by molecular analysis, you have to take into account that nowadays there are some ways to produce mycorrhiza (consider in-vitro root-organ cultures for instance) where the morphology of the spores changes dramatically compared to "natural" spores, so the morphological identification is sometimes impossible.