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African Penguins are faced with multiple pressures that are cumulatively contributing to their decline.
These include:

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Image credit: Steven Benjamin

Reduced availability of fish

The recent population decline of African penguins has been attributed to food shortages caused by shifts in the distributions of their prey species; namely, declining small pelagic fish stocks and competition with commercial purse-seine fisheries for food. The island closure experiment, conducted over 10 years ago, revealed the value of closing fishing in some of the areas in proximity to breeding African Penguin colonies. However, despite many years of negotiation, no long-term decisions have been implemented.

Oil and noise pollution

Many African penguin colonies occur in areas that are near existing or planned major shipping routes or ports. A growing threat is the expansion of harbours and an increase in ship traffic. Another emerging threat for the African penguin is ship-to-ship bunkering, which started in Algoa Bay and is planned to expand to the West Coast. A large oil spill could destroy the remaining population. For example, four oil spills have already occurred in Algoa Bay since 2016, when bunkering started. In some areas, marine noise pollution is an emerging threat to African penguins, with evidence suggesting the scale of this impact could be large. The maritime industry, including exploration for oil and gas reserves using seismic surveys, is a further looming threat.  

Changes in breeding habitat

In the past, penguins made their nests in the burrows of guano. Harvesting guano removed the penguin nest material. Although guano harvesting is no longer allowed, a lack of nesting habitat is a concern. This is being addressed through revegetation efforts at some colonies, and deployment of artificial nests is currently being tested at several colonies. 
Other threats include disease, is currently being tested at several colonies. All these threats require carefully implemented management plans for each penguin colony.
For more information on current threats to penguins: The Biodiversity Management Plan for the African Penguin (Spheniscus demersus) Department of Forestry, Fisheries and the Environment.

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