Pari Island is one island in the middle of the Thousand Islands cluster. Nitrate is a nutrient as a determining factor for the preservation of marine productivity, nutrients becomes an important factor. The problem is, whether the support is derived from the availability of nitrate in the water or in the coral polyps. Related to the above, this research will study the nitrate support in coral polyps and their effects on the presence of zooxanthellae. The purpose of this study is to determine the diversity of coral species, environmental factors affecting the coral, nitrate content and the density of zooxanthellae in some types of coral on the Pari Island Reef Flat in Thousand Islands Jakarta. This study was conducted in March to April 2016, with descriptive method. The results obtained are the the dominant coral species Acropora sp., Porites sp., and Montipora sp., With live coral cover in the station I (pier) of 36,4% medium category, station II (residential) of 22.4% poor category and station III (away from the population activity) of 67,2% good category.The coefficient of R2 determination between nitrate with a density of zooxanthellae in each the dominant coral species have different values R² is Acropora palifera obtained R²= 0.787 means that the independent variable X has the effect of a contribution of 78,7% to 21,3% Y variables, the coral species Acropora divaricata obtained R²= 0.989 has the effect of a contribution for 98,9% to 1,1% Y variables and coral species Porites cylindrica R²= 0.955 has the effect of a contribution of 95,5% to other variable Y 4,5% influenced other than the variable X of the results showed that the value of R² above 0,5 which means that the closer the relationship between the variables X and Y. the higher the nitrate content in coral polyps, the higher the density of zooxanthellae contains.
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