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Agroecology is the study of agriculture through an ecological lens; that is, by treating agricultural systems as ecosystems managed by humans for food, fiber, and fuel production. Ecosystems have both biotic and abiotic components: They are composed both of organisms and the elements of the environment in which they live. Agroecosystems include organisms such as crop plants, livestock, weeds, vertebrate and invertebrate pests, bacteria, viruses, and fungi, as well as inorganic components such as water, minerals, air, light, energy, and the nonliving soil matrix. Each agroecosystem also has a specific geographical, economic, and social context; that is, it is located in a particular landscape, economy, and set of communities ranging from local to global. To underscore the importance of these nonagronomic features and the breadth of scope, some agroecologists define their field as the ecology of the food system.

The field of agroecology stems from the disciplines of ecology and agronomy. It is similar to other types of applied ecology, such as restoration ecology, in its work to use ecological principles to improve managed ecosystems, as well as to use managed ecosystems as experimental sites to test ecological principles. This focus on application may make it seem to closely resemble its agronomic roots; however, agroecology differs from agronomy in at least two ways. First, it more purposefully includes the human component of agroecosystems, reaching across disciplinary boundaries to include sociological, anthropological, and economic analysis of agricultural problems and potential solutions. Second, where agronomy tends toward reductionism, agroecology approaches farming systems from a holistic perspective. Instead of confronting a particular management challenge, such as a weed, an insect pest, or the need for a particular nutrient concentration in the soil to support a potential maximum yield, with a single mechanistic solution, such as an herbicide, insecticide, or fertilizer, and then trying to minimize the solution's negative effects, agroecologists look for strategies that treat the problem as part of the system. Such strategies might imitate natural ecosystems in some way or draw on knowledge from or approaches used in traditional agroecosystems. They also might be multifaceted, trying to meet multiple goals such as improving soil fertility while disrupting several pest cycles. For some agroecologists, the ultimate goal is to create agricultural systems that have cycles and processes that imitate natural systems with reduced human intervention. This might include systemic regulation of pest populations or of nutrient cycling.

There is no single group of agroecological production methods. Agroecology is not synonymous with organic, biodynamic, or other specific sets of codified or culturally defined practices but is a way to evaluate one or more practices within a given agricultural system. For example, there are several interacting components to consider when evaluating shade-grown coffee production from an agroecological perspective. Researchers have found that growing coffee in shade can minimize disease and support noncrop biodiversity, including species richness of birds, ants, and native trees. Increased abundance and richness of bird and ant species can in turn provide ecosystem services such as a reduction in invertebrate pest damage or outbreaks. Reduced pest damage can increase the yield of saleable fruits, and sales of noncoffee products from the shade vegetation, such as fuel wood and construction materials, can provide additional farm income. However, certification costs (e.g., for marketing under a bird-friendly or organic production label) can reduce the final net income, and certification schemes themselves may be susceptible to market forces. There are also questions as to whether certification programs directed to geographically distant consumers can fundamentally transform the relationships with and vulnerability of farmers and thus the biodiversity associated with the shade production system. Agroecologists may examine both these natural and social factors of shade-coffee agroeco-systems and work with people along the commodity chain, from farmers to consumers, to look beyond short-term yield and economics and to develop more sustainable systems appropriate to each location.

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