A. At the depths of the earth's oceans lie habitats teeming with creatures, plants and containing microbes that have yet to be discovered by science
-in "teeming with creatures, plants and containing microbes that have yet to be discovered" meaning is kind of distorted as seems like only microbes are to be discovered. sounds fishy

let's keep it for a while
B. Lying at the depths of the earth's oceans are habitats teeming with creatures, plants and microbes that have yet to be discovered by science
seems good
C. Lying at the depths of the earth's oceans is habitats teeming with creatures, plants and microbes yet to be discovered by science
SVA error "is" should be "are"
D. At the depths of the earth's oceans lie habitats teeming with and containing creatures, plants and microbes that have yet to be discovered by science
use of "and containing" is redundant
E. At the depths of the earth's oceans lies habitats that are teeming with creatures, plants and microbes that have yet to be discovered by science
SVA error "lies" doesn't agree with plural subject habitats
between A nd B ,B is better choice.IMO B