probably Sclerotium roufsi . you need to culture it and then identify.

Go for surface sterilisation of the infected tissue and put in the media. Then identify the pathogen based on mycelial growth if it is fungal or bacterial colony identification if it is Bacteria. I have also attached the onion diseases compendium which extensively covers the various disease infecting the onion. Compare them with the disease symtpoms you are observing . If after culturing the fungus, if you could observe chlamydospores or sickle shaped conidia, it is Fusarium which causes basal rot. In the field itself, if you could identify whitish cottony growth of mycelium on the infected tissue and mustard seed shaped sclerotial bodies, it is Southern blight caused by Sclerotium rolfsii.

Could this be Stem and Bulb nematode (Ditylenchus dipsaci) symptom? Try to check for information of this nematode. It could just be what you are looking for. Cut out a piece of the onion skin from the infected area on a petri dish and add some drops of water to it. After some time, view under a dissecting microscope. If you see some tiny 'worms' upon viewing, then it could be a nematode infection.

it is hardly bacterial - only as secondary infection after nematode or fungi. Looks more like Sclerotium sp. 

It is difficult to know. The picture is not very clear, and also even with very good pictures it is very difficult to distinguish a certain pathogen. Due to the white mycelia could be Sclerotium spp. If small sclerotia (1 mm diameter) formation occur could be S. cepivorum. In any case other pathogens like Fusarium spp. or Pyrenochaeta setosa could also induce similar root rot symptoms, but in this later case reddish-pink colored roots should be observed. The white mycelium could be saprophytic growth form secondary organisms.

I agree with the opinion of Mr Konstantinos. In my opinion it is rather for fungus F. oxysporum. Mycelium of S. cerpivorum is more abundant and white.

Dear Andreas,

It is hard to tell from just a single picture. The best thing you can do is to take samples to the closest plant pathology lab you had. Since you are in Ambato, the Plant Pathology Lab in Santa Catalina Agricultural Research Station of the INIAP is the closest to you. There you will be able to obtain help in the identification of the pathogen (the lab where I work is located near Guayaquil in the Agricultural Research Station Litoral Sur of INIAP). The usual procedure includes humid chambers and/or pathogen isolation from the diseased tissue, and identification of pathogen structures. I hope this info had been helpful to you.

Regards,

Ricardo

Dear Andreas, could you publish a better and sharper macro photography of infected onion bulb?

Best regards, Franci

Thanks for all the excellent advice and suggestions !!

I was able to prepare various media now to start cultivating the pathogen(s). I followed the suggestions and isolated the fungi (?) according to standard protocols from the infected plant tissue.

I can include a picture from an infected onion, made from the same place I took infected tissue for isolation

http://andreasb.net46.net/responsive/zwiebel2.jpg

The picture is a cross section showing infection at the bulb neck, such as seen before.

Andreas, did you make also isolation from tissue on the bottom of the onion (disc)?? Symptoms are similar to infection with Fusarium oxysporum.

Hi Franci,

Yes,  I also isolated from tissue on the bottom of the onion. And yes, on the growth plates it looks like it could be Fusarium, I hope I will soon have access to a a microscope.

Good luck :-) Open link, picture of F. oxysporum f.sp cepae on agar plate.

http://www.insectimages.org/browse/detail.cfm?imgnum=5364062

Fusarium Oxysporum or Botrytis alli. can go for cultivation and identification.