Molecular identification and environmental characterization of Gracilaria firma in Lapindo-affected aquaculture ponds

The continuous discharge of Lapindo mud into the Porong River since 2006 has altered the ecological conditions of coastal aquaculture ponds in Kedungpandan Village, Sidoarjo. Resultant changes in water quality, organic loading, and heavy metal variability may influence the performance of cultivated Gracilaria species. This study aimed to molecularly identify local Gracilaria using the p23SrV genetic marker and characterize pond water quality under the influence of Lapindo sedimentation. Molecular identification was conducted on seaweed samples collected from a single sampling site (station TD2), while environmental conditions were evaluated through water quality assessments at nine sampling stations. DNA analysis involved extraction, PCR amplification, and Sanger sequencing, followed by BLASTn analysis and phylogenetic reconstruction. The sampled specimen exhibited 100% sequence identity with Gracilaria firma, supported by 100% query coverage and an E-value of 0, supporting species-level identification. Environmental parameters across stations ranged as follows: temperature 29.7-34.1 °C, salinity 19-24 ppt, pH 7.19-8.91, dissolved oxygen 7.7-9.9 mg L⁻¹, nitrate 0-12.1 mg L⁻¹, and total organic matter (TOM) 22.12-91.64 mg L⁻¹. Lead (Pb) was detected at very low concentrations 0.001-0.0037 mg L⁻¹, while cadmium (Cd) remained below the detection limit. In contrast, copper (Cu) and zinc (Zn) were present at concentrations ranging from 0.25 to 3.42 mg L⁻¹ and 0 to 0.07 mg L⁻¹, respectively. Principal Component Analysis (PCA) identified TOM, Cu, and nitrate as the principal drivers of spatial variability in pond conditions. This study provides the first molecular-based identification of Gracilaria firma in this region based on the analyzed specimen and presents an integrated analytical approach that contributes to environmental assessment in coastal aquaculture systems.