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How well do tardigrades withstand outgassing? Because you could also make sure that any gasses in the manure containers get vented into space. Unless you harvest them and sell them as methane, on the side.

One way to treat human waste is heated heavily pressurized water. Get water hot enough and under enough pressure and no organic material is going to survive for very long. You also have the thermal depolymerization process to think about. As for Phosphates....waste not want no. A super huge hive...

Actually why not have the planet grow some of it's own food as part of the water and air recycling bit? Simply use strains of algae and yeast that are edible. Cull off the excess and viola. I mean they are cleaning your water and air have them pull double duty. Because if a ship is a closed...