Coral reefs next to a major conurbation: a study of temporal change (1985-2011) in coral cover and composition in the reefs of Jakarta, Indonesia

Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturbations, such as pollution and overfishing, and widespread phenomena, such as bleaching. Here, we report on the history of the Jakarta Bay-Thousand Islands reef system from 1985 to 2011. Over this period, we recorded significant shifts in coral generic composition and an overall decline in coral cover with widely different trajectories between in-, mid- and offshore zones. In 1985, coral cover exhibited a clear on-to-offshore gradient with low coral cover inshore (10%), moderate cover midshore (49%) and high cover offshore (74%). The low coral cover inshore contrasts strongly with reports of high coral cover for inshore reefs in 1929. Inshore, coral cover declined from 10% in 1985 to <5% in 1995. The greatest change in coral cover and composition, however, occurred in offshore reefs, where mean cover declined from 74 to <20% between 1985 and 1995. Acropora species were particularly affected and declined from 36 to just 5% cover offshore. Recovery of coral cover occurred offshore between 1995 and 2005. From 2005 to 2011, however, a less severe loss in coral cover was observed. With the exception of inshore reefs, which appear to be on an ongoing trajectory of decline that started before the 1985 surveys, the reefs of the Jakarta Bay- Thousand Islands system have shown a propensity to recover.