Very few coral reefs are located close enough to metropolitan cities to study the influence of large urban populations on reef communities. Here, we compare the impact of a large-scale disturbance gradient with local-scale disturbance on coral richness, cover, and composition in the Jakarta Bay and Pulau Seribu reef complex off Jakarta, Indonesia. We found no effect of local land-use type of coral reef islands on richness, composition or cover, nor did taxon richness differ among zones at the large-scale. There was, however, a pronounced difference in composition and coral cover among zones. Cover was very low and composition differed markedly in the near-shore zone 1 (Jakarta Bay) where human-induced disturbance is most intense. Cover was highest in the outlying reefs of zone 3. The highly perturbed zone 1 reefs were, furthermore, distinguished by the virtual absence of otherwise abundant coral taxa such as Acropora hyacinthus and Porites rus and the prevalence of taxa such as Oulastrea crispata and Favia maxima. Almost 60% of the spatial variation in composition was related to variation in shelf depth and island size. The importance of shelf depth was related to the prevalence of a strong environmental gradient in reef depth, pollution, and mechanical reef disturbance and salinity from Jakarta Bay to the outlying reefs. Although there was a significant univariate relationship between spatial variation in composition and distance, this did not enter into the multivariate model, except when presence-absence data was used, indicating that environmental processes are the primary structuring forces in determining local coral assemblage composition across the Pulau Seribu complex.
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