Now the earth was formless and empty, darkness was over the surface of the deep.
1 or 2?
1 resting on the surface of somebody/ something and partly or completely covering them/ it
2 in or to a position higher than but not touching somebody/ something; above somebody/ something
(Oxford Advanced Learner’s Dictionary)
I apologize for the confusion, but the answer can be either 1 or 2.
Physically, darkness is the absence of light, and therefore must "fill" (or affect) a three-dimensional space such as a room. Therefore, it can be thought of as either above the floor or covering the floor.
However, Biblical verses are often poetic (especially when reading the older translations) and so you should expect to encounter words used in unusual ways. Poetically (and Biblically), darkness is like a blanket hiding the body from the light of truth. When the body is "uncovered," it is bathed in the light. And a blanket can be thought of as either resting on the surface of the body or laying above the body.
However, if I were forced to choose only one of the two definitions, I would choose #1 for this example.
Both 1 and 2 refer to material objects. Regarding your sentence,however, both are equally OK in the abstract senses.
