I don't know the full details, but part of it:

• In the store you can walk between the books. This takes loads of room. In the Amazon warehouse, this can be veeery cramped.
• The land value of the store is probably mich higher than the Amazon warehouse land.
• They sell much more, so all costs can be shared across a million orders, instead of across just 10 books sold.

All the solid answers posted plus they're now a massive store - they can live on, say, $0.10 profit on a book because they made plenty more on the backpack and tire patch kit and deodorant you also added to your cart because convenience.

Plus no retail rent, no retail staff to pay.

It's like gas stations barely breaking even on gas, but making bank on snacks. Bookstores usually won't have those other product categories to fall back on like Amazon does.

Not in Germany.

At a guess:

• Volume discount: Amazon will buy a hell of a lot more books than a single mom and pop store
• Retail rule of thirds: (very loosely) a third of the price you it goes to manufacturing, a third to distribution/logistics, and a third to the retailer. Amazon vertically integrates the second two.
• Online only: website capacity costs a lot less than running a brick and mortar store
• Margin: amazon will make less per book but sells more books because people prefer to buy them cheaper. There’s a separate discussion here about anti competitive practices (eg undercutting competition to put them out of business, then raising prices later) but that is a whole other debate