Comparative Evaluation of Hollow-Fiber Ultrafiltration and Syringe Microfiltration As Efficient Concentration Methods for Targeted and Comprehensive Detection of Bacterial, Viral, and Animal DNA in Water

Environmental waters contain diverse microbial and macrobial DNA, necessitating methods capable of efficiently concentrating various organisms, cells, and free DNA. This study compared hollow fiber ultrafiltration (HFUF) and syringe microfiltration (MF) for recovering microbial and macrobial cells and DNA from surface water and stormwater runoff. Performance was assessed by quantifying a spiked virus (phiX174), naturally occurring E. coli, bacterial 16S rRNA genes, and crAssphage, along with metabarcoding of mitochondrial DNA and full-length 16S rRNA genes. The syringe MF method showed higher recovery and quantitative accuracy for bacterial and viral targets but suffered from membrane clogging, reducing DNA extraction efficiency. HFUF had higher sensitivity for low-abundance targets, particularly E. coli, due to its greater concentration factor. However, it was more prone to PCR inhibition, especially for long-fragment targets. Metabarcoding demonstrated that both methods captured microbial and macrobial community composition, although HFUF detected more fish DNA and a slightly greater number of bacterial genera. Overall, syringe MF is more suitable for accurate quantification, while HFUF is better for detecting low-abundance and small targets. The choice of method should be based on study objectives, target organisms, and trade-offs among recovery efficiency, DNA extraction, and PCR performance.