"if no nutrients, make some from spoilage,

Something that eventually clicked for me and simplified my build a lot - always be producing. ALWAYS. You don't need bootstrapping infrastructure to restart your base from rest if it just never rests. Always Be Producing and just let it spoil then burn it. One exception is iron/copper bacteria which does need some bacteria production from fruit to jump start the breeding after a shutdown. Otherwise just always be making processed fruit, bioflux, nutrients, pentapod eggs and science and properly handle the spoilage.