Quantification of host-associated fecal markers in the Seven Crater Lakes of San Pablo, Laguna, Philippines through library-independent microbial source tracking

Freshwater lakes in tropical regions are increasingly threatened by fecal contamination from agricultural and domestic sources, necessitating precise tools for source identification and water quality management. This study evaluated and applied three host-associated microbial source tracking (MST) markers, Pig-2-Bac (swine), Cow-Bac2 (cattle), and Ckmito1 (chicken), to assess fecal pollution in the Seven Crater Lakes of San Pablo, Laguna, Philippines. Marker performance was evaluated using fecal samples from known sources and showed high accuracy ( ≥ 0.94 ), sensitivity ( ≥ 0.85 ), and specificity ( ≥ 0.97 ). Quantitative PCR (qPCR) analysis revealed widespread multisource fecal contamination, with Cow-Bac2 exhibiting the highest concentrations ( 4.38 × 10 6 gene copies/100 mL) and detection frequency ( 92.68 % ), indicating cattle as the dominant source among the evaluated livestock hosts. Marker concentrations varied significantly between seasons, with higher levels observed during the dry season ( p < 0.001 ). Although no significant differences were detected among lakes ( p = 0.792 ), within-lake variations suggested localized pollution dynamics. Significant correlations were observed between MST markers and water-quality parameters, including biological oxygen demand (BOD), total suspended solids (TSS), and fecal coliforms (FCs), underscoring the contribution of livestock waste to organic and microbial pollution. The study provides preliminary evidence supporting the application of host-associated MST approaches for identifying livestock-associated fecal contamination in tropical lake systems and establishes baseline data to support evidence-based water-quality management and regulatory monitoring in similarly hydrologically constrained environments.