Hello Srđan G.

Maybe if you put a good picture of the macroscopic appearance of colonies , and the images you have of the microscopic characteristics ,be easier approach to identification.

Arbuscular mycorrhizal fungi (AMF) have been symbionts of land plants for at least 450 Myr. It is known that some AMF host in their cytoplasm Gram-positive endobacteria called bacterium-like organisms (BLOs), of unknown phylogenetic origin. In this study, an extensive inventory of 28 cultured AMF, from diverse evolutionary lineages and four continents, indicated that most of the AMF species investigated possess BLOs. Analyzing the 16S ribosomal DNA (rDNA) as a phylogenetic marker revealed that BLO sequences from divergent lineages all clustered in a well-supported monophyletic clade. Unexpectedly, the cell-walled BLOs were shown to likely represent a sister clade of the Mycoplasmatales and Entomoplasmatales, within the Mollicutes, whose members are lacking cell walls and show symbiotic or parasitic lifestyles.

http://www.nature.com/ismej/journal/v4/n7/full/ismej201021a.html

Picture is not clear to resolve

I uploaded now several new images below and instead of the original image (they are as attachment links below the visible images). Macro- and microscopic images of the ball-like structures and the mycelium structures, respectively. Let me know is this better now - I cannot magnify more the mycelium since my microscope only goes to 400x. And I wanted to tell you that the fuzzy balls and mycelium both repel water. Thank you all.

It looks like to be a soil born fungi. Because arbuscular mycorrhizal fungi should be colonized in root and rhizosphere soil. I have never seen AMF growing up on the soil surface. Why don't you pick up some of mycelium and put it on the PDA plate. It possible to grow on there, and then check by microscope again or directly observe its morphology under microscope.  

Already transferred it to PDA. Grows slowly.

I think it may be soil born fungi since it could grow on PDA. In case of arbuscular mycorrhizal fungi, it can not be cultivated on PDA, normally use plant (corn, sorghum grass) as host for multiplication of spore. 

I support Shawn Kenaley that root anatomy is important and from which axenic culture may be obtained, but still seedling experiments are required to prove its ectomycorrhizal nature. 

These structures look like sclerotia of Rhizoctonia anamorphs

Thank you for the hints and guidelines. Soilborne fungi are not my specialty. I will check more of the morphology once I get the clean culture.

Did you check where the substrat (the soil) came from, or the smell of the substrate? To me, the small white boddies look like primordia of Agarycus bisporus (white bottom mushroom) and other fungi that are usually present in mushroom farms as parasites or competitors. Does it make a sence? 

It makes sense. There is no specific odor except the pit moss-like scent. The fruiting bodies are forming only on the bottom of the soil root-ball near the contact surface with the pot bottom and on the surface of the soil. The substrate source is the largest supplier of retail soil mixes for nurseries. 

Have you observed any connection between the fungus and root of the dracena plant...... if so, then upload the photograph or picture of root section with hypahe of the same fungus. Then it could possible to differentiate the fungus whether is a pathogen or mutualistic.

The dracena in the pot from where these structures were collected is not dying or showing any disease symptoms. It is growing quite great. So it is not a pathogen. And I think it is growing only on soil substrate.

It could be a mixture of bacterial and fungal infection. Off course you have not seen any pathogenic symptom but what is the reasons of this kind of overgrowth. Definitely it is saprophytic bacteria and fungi. Bacteria may be some strains of Agrobacterium  rhizogenes. On what basis you are telling the fungus as Botrytis spp. As per your information basipetal condidiogenesis is too rapid and luxurious at top giving the appreance of bunch. Pl follow the book of Alexopolus and Mims to characterize it.

Could you upload new pictures showing the growth of the fungus on the substrate. Is there any change? Did you get a pure culture?

Here are maccros of the pure cultures I isolated on PDA full strength. Still, I will probably send all three for ITS seq.

A picture of conidiophores and conidia would help, esspecially for the first colony. But, you are right, ITS seq. will give the answer

Do you have the answer? I think this is a very important species. It grows very fast.

It looks like fungal sclerotium.

This species may be Leucocoprinus birnbaumii