Chains’ inventories are diverse as well, especially compared to big discount merchandisers like Wal-Mart, because of the size of their stores allow them to keep books on shelves for longer if they don’t sell initially. But independents can do this even better, McNally said, because they stock books by more obscure authors.

“In my buying, I try and remember there’s someone out there who will love something weird and wonderful so I often will remember to include weird and wonderful choices,” she said.

But the trick to staying afloat for bookstores in New York City isn’t just about what books they sell; it is also involves the sale of prominent display space.

Last week, the Wall Street Journal reported that Borders will be displaying more books on shelves with the covers face-out. When books are displayed this way, fewer of them can fit on the shelves, reducing the diversity of titles in the stores.

This method also increases the price publishers may pay to get their books displayed prominently, said Andie Laties, author of “Rebel Bookseller,” a guidebook on how to set up an independent bookstore.

With this practice, known as the cooperative advertising agreement, publishing companies play a role in determining which books will be displayed in which part of the store by paying for the placement of their books. They may pay $18,000 for the right to have a new book placed on a table for one month, Laties said.

This pay-for-view system is somewhat controversial and has been seen as a betrayal of bookstore owners’ editorial independence and accountability to customers, because it can be confused with "hand selling," a practice whereby bookstores prominently display staff recommendations.

The cooperative is an agreement between the publisher and the bookseller. Sales representatives of publishers recommend books to place in the store’s front, for example, and pay the owner money to follow through with the agreement, said Carrie Kania, senior vice president of Harper Perennial and a faculty member of New York University's Center for Publishing. It’s not just up for grabs to the highest bidder, because bookstores won’t waste that space if they don’t think the book will sell.

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