Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing.

Area of Science:

• Environmental microbiology
• Molecular biology
• Water quality assessment

Background:

• Traditional microbial source tracking (MST) methods have limitations in identifying fecal pollution sources.
• Next-generation sequencing (NGS) technologies provide new molecular tools for environmental monitoring.

Purpose of the Study:

• To review and discuss two novel NGS-based MST approaches for identifying fecal pollution sources in recreational waters.
• To highlight the advantages and challenges of NGS-based MST compared to traditional methods.

Main Methods:

• Review of two NGS-based MST approaches: OTU-based source identification and SourceTracker Bayesian analysis.
• Discussion of sequence processing requirements, including quality filtering, clustering, and primer selection.
• Consideration of traditional MST limitations such as differential decay and spatiotemporal variations.

Main Results:

• NGS-based MST methods enable rapid characterization of fecal source contributions at a broader scale.
• These methods define source-specific or shared operational taxonomic units (OTUs) and quantify contributions using Bayesian algorithms.
• Challenges include the need for optimized processing and understanding of environmental factors affecting accuracy.

Conclusions:

• NGS-based MST tools offer a promising, efficient approach for water quality monitoring and remediation.
• Further development and validation, including expanding fecal taxon libraries, are crucial for improving accuracy.
• Careful data interpretation is necessary due to inherent method limitations and environmental complexities.