You may use DDGE cloning method. Sequential amplification of 18SrDNA fragments by nested PCR using primer pairs AM1-NS31 and Glo1-NS31GC follwed by DDGE analysis yielded a high resolution band of profiles from that you may count the clone number.
I think it highly depends on the sample you have (i.e., how diverse you expect it to be).
My colleagues and I published a paper where we did clone libraries from potato roots. We usually analyzed 48 clones per sample, using RFLPs to select clones and Sanger-sequence them. For most samples this was enough in terms of clones, looking at the rarefaction curves.
But be aware that with a clone library and Sanger sequencing approach you may not cover the diversity of environmental samples. We discuss this in the paper:
Senés-Guerrero C, Torres-Cortés G, Pfeiffer S, Rojas M, Schüßler A (2014) Potato-associated arbuscular mycorrhizal fungal communities in the Peruvian Andes. Mycorrhiza 24: 405-417. DOI: 10.1007/s00572-013-0549-0.
I would also suggest that you use primers for the AMF Barcode published in:
Krüger, M., Stockinger, H., Krüger, C. and Schüßler, A., 2009. DNA‐based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytologist, 183(1), pp.212-223.
THANK you for your reply Mr. Laith Al-Ani, there is something that affects the appearance of different bands, my bands exceeds the target, so I can not take the clone