What we don't do - monoculture
There is no one place in nature where you can locate a single thing with no other thing next to it. This applies to plants and animals. You would never see a prairie that only had bison on it without also having rabbits, birds, mice, horses, and various other critters. For plants you would never see a field of flowers that doesn't also have weeds of some sort or another, a few bushes, and probably a tree or two!
A monoculture is the exact opposite of what you might find in nature. A monoculture is the practice of producing or growing a single crop or plant species over a wide area and for a large number of consecutive years. This effectively means that you are trying to support the needs of one thing. What ever that one thing consumes out of the environment is eventually depleted. This leads the farmer to attempt to replenish the necessary required bits either in the form of external inputs such as compost or in the form of chemical sprays.
In addition to the drain of required bits out of the support system, a monoculture also has a down side in the form of various outputs that must be dealt with. In the case of an industrial cow or hog farm the output is a large amount of excrement (pee and poop). Many of these large monoculture meat farms have a raw sewage output that is larger than medium sized cities! EGAD.
What we do - permaculture
At our farm we attempt to grow all of our plants and animals in a manner that they can achieve a natural harmony with one another.
As an example (a simplified one), we run our sheep on large fields of grass. They love this! They hang out in the sun. They move about in their flock socializing as necessary. They mow down the grass. And they poop and pee all over the place. After our sheep have moved on to a new paddock we turn out our pigs. The sheep enjoy the grasses in our fields where as the pigs enjoy nuts, clovers, and other legumes (perhaps an occasional grass). They also root around turning over our soil as they feel is needed. Again they are happy. They are removing extra bits and adding extra bits. Once the pigs move on we turn out our puoltry and rabbits. Poultry like to scratch up the soil. They also remove various bugs and larvae that is either found in the field or the fecal matter of the larger animals. Then we let our grass recover a bit before starting all over. This means that the grass is mowed. And fertilized. And aerated. Just about everything it needs from a nature based approach to farming. No extra inputs or outputs in this system.
For our produce products (not grass, not clover, or other feed based produce) we strive to not farm in the dirt. There are many more technologically advanced ways to do small scale produce farming these days. These ways are much easier on the environment, the soil, use less energy, and waste less water. The way I am speaking of is aquaponics.
For this reason we look to aquaponics for our food production. Since we covered animals above this is sort of a mixed bag. Aquaponics produces a high yield of vegetables AND FISH! Aquaponics is a three part system. Water, plants, and fish. Aquaponics is a fine example of how nature does it. If you look at any stream you will see a happy ecosystem between the fish in the water and the plants surrounding the water. Remove any one of these parts of this system and you have a faulty system!
The plant/water problem: The plants consume oxygen and nutrients from the water and media they are planted in. In a hydroponics system then you have two inputs that you must provide: nutrients and oxygen. The oxygen can be introduced into the system with an air pump. The nutrients are introduced into the system in the form of fertilizers, solutions, or other chemical form (yuck). And over time your water can become out of balance and you will need to flush it (dump half the water and add new water). While this works, (many large growers use this type of system) there is a lot of waste in the system as well as the need for external inputs.
The fish/water problem: The other side of the plant problem is the fish. Growing fish in a water based system without plants is called aquaculture. In this type of system you also have external inputs. You must feed the fish and again provide oxygen. Once fed, the fish poop and pee. Both of these build up amonia in the system and in general create waste. There are many sub-systems that can be put into an aquaculture system to deal with these issues. And while the fish can withstand that build up for a while, eventually the water must be changed out. Once you put new water in the fish are happy again and the subsystems will attempt to do their job. But what do you do with that toxic water? And what about all the fish poop?
In an aquaponics system the fish feed the plants and the plants and bacteria clean out the toxic amonia build up in the water. While you still need to feed your fish and provide oxygen to both the fish and the plants, you don't need to dump off any toxic water. You also don't need to deal with fish sludge. And there are many clever ways for having this system generate food for your fish so that the system becomes completely self contained.