I didn't realize that you were planning on setting up a tank with a temperature in the high 50's...
If you're worried about the metabolism of the bacteria that would break down the waste at that temperature, I'd just make your remoted deep sand beds a little bigger. If there is enough food and habitat to support them, the bacteria populations will grow until either of the two isn't available anymore (if that makes sense).
As far as plankton goes, I'd be carefull to select species that would thrive in those temperatures if you were going to cultivate them yourself. Fortunately Nannochloropsis oculata (the strain that is used the most in aquaculture and in plankton food supplements) will thrive between 60 and 86 degrees (according to the article linked below):
http://www.advancedaquarist.com/issues/aug2002/breeder.htm
I don't have the link on my home computer, but at work I found a university that sells samples of live planktons from all over the world and they have quite an extensive and searchable catalog. If I remember to do so, I'll post the link tomorrow when I'm at work. So, if you were looking to recreate the environment off the coast of Oregon, then you'd be able to purchase the strains of plankton that are present in that environment. They sort the strains by location and even tell you which strains are bioluminescent - which would make your tank look freaky in the dark!! Do a google immage search for bioluminescent plankton for some ideas. After looking at the pictures, I don't think thats what I'd do with my aquarium...
Going through some of the links I've come up with an saved over the years, below is a link for an aquaculture supply company. They have quite a large selection of large and inexspensive holding containers which you might find useful for your sumps or various storage containers.
http://www.aquaticeco.com/