I just sliced an onion and found that there is a large section of one of the layers that's black. What is the black substance? Is it safe to eat? If not, is the rest of the onion safe to eat?

The onion in question:

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This is either mold or bacteria-caused rot. Don't eat it - the microorganisms which feed on raw plants are rarely pathogenic for humans, but will frequently create toxic metabolic byproducts. I would throw out the whole onion, molds can be toxic in very low doses, just from contamination between layers.

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    What if it's on the outside layer? That happens all the time. – Cascabel May 26 '14 at 22:02
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    @Jefromi I normally eat the onion when it's only on the outside - the yellow papery skin is quite dense, and besides, if there are no signs on the inside, I figure it probably wasn't feeding on that particular onion spreading invisible colonies within it, but came to stick on the outside only. I am not sure this is not risky though. – rumtscho May 26 '14 at 22:37
  • @rumtscho Do you have a link available? I would like to read more about it – Dr. belisarius May 27 '14 at 19:14
  • @belisarius no, no link. I don't even remember where I got this information from - years of reading books, I guess. – rumtscho May 27 '14 at 21:34
  • @rumtscho OK! no problem, I'll search for it. Thanks! – Dr. belisarius May 27 '14 at 22:16

Quoting from Can you use onions with black mold?:

Black mold on onion is caused by aspergillus niger, a common fungus in soil. To discourage mold growth, store onions in the refrigerator up to two months. Rinse off small amounts of the black mold on the outer scales of the onion under cool, running tap water or cut off the affected layers. The unaffected part can be used. Persons known to be allergic to Aspergillus niger should not use onions with black mold.

But if the mold penetrates the inner shell of the onion, I recommend throwing it away. Only use the above mentioned advice if the black mold is on the outside.

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