One of the most useful water streams in Egypt is the Ismailia Canal. However, despite its significance, numerous factories discharge their waste into the canal, causing a drastic decrease in its water quality and fauna. In this respect, this study aims to evaluate the negative impact of fertilizer discharge on community structure, zooplankton biodiversity, and water quality in the Ismailia Canal. Four stations were selected, where the Canadian Water Quality Index and the Metal Indexwere used to determine the point source of contamination at each station. As revealed in the Canadian WQI results, Stations (3) and (4) have marginal water quality, but no metal pollution was shown in the Metal Index results of the study area. The Canonical Correspondence Analysis (CCA) was also applied. The zooplankton community structure and biodiversity were examined, where their total density recorded an average of 598,854 ind./m3. Nineteen zooplankton species—belonging to the groups: Rotifera, Cladocera, Copepoda, and Nematoda—were identified. Rotifera was predominant, representing 97.05% of the total zooplankton density. Although Station (3) had the highest diversity index, there was a special abundance of organic matter bio-indicators. That is why mandatory laws and management plans had to be enforced to mitigate the canal deterioration.
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