Diversity of species: Arable land and grassland are ecosystems itself, with several species nesting, thriving and foraging on them. Many of them are already endangered and can be found on the IUCN Red List, e.g. the lapwing (Kiebitz).
There is difference between the number of species and abundance of wildlife.
Genetical diversity: By using regional species of crop plants and livestock, agriculture can maintain regional identity and diversity. Regional species are usually adapted to the climatic and geographical conditions in the area.
An example from Switzerland: 90% of pear cultivation areas are growing only four of the 600 pear varieties, that exist in Switzerland.
Habitat diversity: Each land has its own characteristics that have to be maintained and used in favour of nature and agriculture. Habitats (mountainous, flat), structures (shrubs & forests) and soil types (clay, sand) differ from region to region.
Many species we preserve are pollinators and can control pests. Earthworms and other organism in the soil are maintaining soil fertility. A lot of medicinal plants can grow on low-fertility meadows and flower strips. Low-fertility meadows possess a deeper root system than high-fertility meadows and can protect the soil from erosion. Regional species that are adapted to local conditions are the key to new breeds and resistance. At last, beautiful landscape, due to species and habitat diversity, can possess touristic and economic value.
Positive: Organic agriculture can increase the species richness of plants, birds, mammals (bats), arthropods (beetles, spiders, earthworms). Even endangered species (lapwing) are increasing again on organic farms. Some species increase their activity rate and population (passerines, earthworms). Field margins (flower strips) increase biodiversity as well, but is not strictly an organic phenomenon.
Negative/Neutral: Beetles simultaneously showed increase and decrease of species, due to competition between one another. Aphid (pests) abundance is increased in conventional agriculture, probably because of the faster growing (chemically fertilised) crops. So are their predators (e.g. ladybugs). Soil microbes (bacteria, fungi & nematodes) show little differences and many inconsistencies.
Difficulties: Time: long-term data record & recovering time of biodiversity (after conversion from conventional to organic, lack of studies in the megadiverse tropics, no understanding of the processes behind biodiversity increase/loss.
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