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Aquatic nuisance species are non-native plants or animals that threaten the diversity or abundance of native species; the ecological stability of infested waters; or the commercial, agricultural or recreational activities that depend on such waters. In recent years, the Puget Sound has seen an increase of invasive species, specifically from Japan, as early as 1971. In recent decades, society and how it relates to the ocean has become increasingly globalized. Invasive species have come to the Puget Sound via several factors, including aquaculture, importation of live seafood, shipping (attached to ship hulls and through ballast water), research and academic institutions, deliberate introductions, pet stores and public aquaria, and natural dispersal. The European green crabCarcinus maenus and the marine grass Spartina are currently two of the most damaging species. In response to such trends, ocean species have migrated to places they shouldn't. The Puget Sound has the most introduced invasive species. Nationwide, about 400 of the 958 (42 percent) species listed as threatened or endangered under the ESA are considered to be at risk, primarily due to competition with and predation by non-native species.

The WDFW is now attempting to combat its exotic species problem with the Washington State Aquatic Nuisance Species Management Plan. Under this plan, Washington State Patrol Commercial Vehicle Inspectors search incoming vessels for harmful invasive species, such as the zebra mussel, and decontaminate the vessels before they can spread the organism. The plan also established an Aquatic Nuisance Species committee to find other ways to protect Washingtonians from the harm done by invasive species. The committee coordinates responses to threats at the federal, state, local and tribal, as well as private, levels, and presents a biennial report to the Governor's office to ensure that the situation is always under control.

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