Compost with Earthworms
All settlements generate waste biomass as a direct result of their biological population. Waste biomass recycling and recycling of water is a vital part of any colonization strategy.
A settlement's initial supply of bone will be low, as the majority of farming will be plant-based.
Bone ash is the result of burning bone. It is used in the manufacture of fertilizer and ceramics.
Bone char is created by charring bone. It is useful in filters, where it acts similarly to charcoal. It captures metals such as fluorine, copper, and zinc. Bone char is also used as a pigment.
Crushed bone is used as a fertilizer.
Collagen and Gelatin
The bones and connective tissue of animals contain collagen, which can be extracted. The collagen can by hydrolyzed into gelatin, used in many foods and other products.
Most terrestrial animals flush waste from their bodies with water, producing urine.
Urine contains ammonia and urea, both useful in industry. Saltpeter is harvested from stale urine.
Urine contains high levels of nitrogen and phosphorus.
Urine can be filtered or distilled to provide water. This method of water reclamation is used on the ISS.
In extreme emergencies, urine can be used as an antiseptic.
Plants grown primarily for food and life support can provide several side benefits.
The cell walls of plants contain cellulose, the main component of paper.
From grass mats to fine linen, humans have been using plant fibers to make textiles.
Corn husks, wheat stalks, and vines can be made into a variety of goods.
Biomass has been used in construction since the beginning of human history. Wood is often used by itself to construct large structures. Dead plants can be mixed with cob or brick, adding strength.
Many types of biomass are well suited to Hydrocarbon synthesis. Methane and other small hydrocarbons are produced naturally by certain types of microbes and cows as they feed on biomass.
Compost and Feed
Much of the waste biomass of a settlement can be used to feed the organisms in the greenhouses. Mushroom, certain fish and insects feed directly on waste biomass, assimilating its chemical energy into their own metabolism. A compost heap is easy to maintain, even in a Martian settlement. Decayed plant remnants and feces, combined with charcoal and lactic acid fermentation, mixed with regolith, gives a high value humus, called Terra Preta. This would be an excellent soil for the greenhouse.
Trickle Filter C.R.O.P.
A glass cylinder, filled with spongy lava stones, can decompose most organic wastes, including urine, feces, leftover food and plant parts. It uses bacteria, that are normally living in terrestrial soil. The columns are trickled with a steady stream of water. The DLR (Jens Hauslage) is working on the optimization of this principle for space stations and planetary missions.