bio-neural circuitry

It's ironic that 2 prominent shows in my childhood, Space Cases and Star Trek Voyager both had 2 common themes- a living ship. Space Cases left the statement relatively undefined and mechanics are left up to the imagination; Star Trek Voyager expanded on this idea through bio-neural circuitry, which was composed of "gel packs" full of unicellular organisms, all of whom generated energy which was subsequently somehow collected and utilized (think "magic technology" as coined by Ray Kurzweil). Kind of like humans as a power source depicted in the Matrix, only unicellular organisms as the batteries. This alludes to the analogy of a large floating garden. This seems efficient, and more importantly balanced. It seems as though there are multiple ways to produce this energy source.

Starting with an immortal germ cell line,
1. genetically engineer bacteria with multiple metabolic pathways
2. generate superhardy nitrogen fixing bacteria (I recently coined the term superhardiness)

These microbes could be kept in some sort of suspension medium, I doubt the matrix would be the difficult aspect to this experiment.

Remaining concerns:
1. How to collect the energy and transform it (if necessary) to be used to power a star ship?
2. Plus the potential problems that this technology could generate- especially if the microbes got "sick" with something that could be potentially virulent to humans- leaving the ship stranded, powerless, with 100% mortality rate...

And what about a huge "garden" bio-dome self sustaining ecosystem at the bottom of the ocean...