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Organic gardening relies on the principles of organic agriculture when it comes to soil building and conservation, pest management, and plant cultivation. This is a green form of gardening, and is designed to work with natural ecological systems. 

When it comes to agriculture, organic farming involves crop rotation, green manure, compost and biological pest control. Fertilizers and pest controls are used, but limits the use of synthetic pesticides and fertilizers. This also includes hormone additives and antibiotics. The International Federation of Organic Agriculture describes this as "Organic agriculture is a production system that sustains the health of soils, ecosystems and people. It relies on ecological processes, biodiversity and cycles adapted to local conditions, rather than the use of inputs with adverse effects. Organic agriculture combines tradition, innovation and science to benefit the shared environment and promote fair relationships and a good quality of life for all involved..."

When it comes to methodology there are many aspects that fall into this like soil management,  weed management, controlling other organisms, and genetic modification. Soil modification involves the use of plowing crop residue back into the soil, as well as using animal manure to fertilize the soil. Plants need nitrogen, phosphorous, and potassium to flourish. Farms with both livestock and crops allow the land to gather nutrients through both the livestock and crops. Farms without livestock will have a harder time with fertility, and may rely on imported manure, as well as legume and grain manure. Biological research on soil has been beneficial to organic farming. Fields with active manure produced healthier and more bountiful yields of crops. Weed management is done to control weed growth, for organic farming it is about suppression and not elimination. Organic farmers work to manage weeds without using synthetic herbicides. Crop rotation is important for organic farming, and therefore weed cover crops are often used as well. This helps to discourage weeds that are particular to certain crops. Organic farming has the goal of increasing soil organic matter content, which can support microorganisms that destroy common weed seeds.

There are organisms that affect crops besides weeds. These include organisms like mites, insects, nematodes, fungus, and bacteria. Crop rotation helps with preventing pests, nutrition management, sanitation, and pest-resistant crops, and provided a beneficial habitat for beneficial organisms. If these means do not work, and organic farmer may use a pesticide. However the pesticide will be organic, and not synthetic. Pesticides will need rotated as well, as pesticide resistance can occur. Organic farming includes the rejection of genetically engineered plants and animals. In fact, IFOAM actually voted to exclude the use of genetically modified organisms in food production and agriculture. There is some debate however, as some researchers feel that including transgenic technology in organic farming will allow for sustainable agriculture. There is also a concern that the GMO’s are pollinating the organic and heirloom seed stocks. Therefore, it is kind of impossible to completely remove the threat.

Organic Agriculture is still highly debated over other forms of agriculture, and research continues to be done to determine if this methodology is actually better and more productive. Although many researchers feel that organic farming is better for replenishing the soil nutrients. Research continues to look at the economic viability, energy usage, and human health of organic farming.