The moon doesn't have a direct effect on metabolism. Nor does it affect menstruation (an archaic theory existed which claimed so!!). The lunar effects are due to its gravitational field which is known to affect tides (Spring tides and neap tides). Even on a daily basis if you might have observed the sea advances into the beach in the night and recedes in the day. This effect is also because of the lunar gravity.
The abstract of the article, that you mentioned, says that moonlight may have some effect on certain organisms; I am highly skeptical about that.
I think it is just the tidal patterns that might affect the behavior of marine/coastal organisms. I am also slightly skeptical about whether the currents produced by lunar gravitation would be deep enough to affect benthic life. In that case even the heating effect of the sun can produce sea currents. Perhaps it can also produce an upward current because of differential heating.