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The 1997–1998 El Niño Southern Oscillation (ENSO) event, which elevated Sea Surface Temperatures (SSTs) of tropical oceans by more than 3°C, was one of the most extreme ENSO events in recent history. Such increases in SSTs above the seasonal average can trigger widespread bleaching in coral reefs. This study examined bleaching in three Indian coral reef regions in relation to SSTs using quantitative rapid assessment methods between April and July, 1998. The Gulf of Kutch reefs showed an average of 11% bleached coral with no apparent bleaching-related mortality. In contrast, bleached coral comprised 82% of the coral cover in lagoon reefs of Lakshadweep and 89% of the coral cover in the Gulf of Mannar reefs. Bleaching-related mortality was high – 26% in Lakshadweep and 23% in Mannar. The coral mass mortality may have profound ecological and socio-economic implications and highlights the need for sustained monitoring for coral reef conservation in India.