HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in...

Area of Science:

• Microbiology
• Ecology
• Genomics

Background:

• Aquatic ecosystems harbor diverse life forms, but understanding inter-kingdom interactions is challenging due to limited detection methods.
• Current DNA-based methods struggle with comprehensive species identification across all six life kingdoms.

Purpose of the Study:

• To develop a high-fidelity (HiFi) metagenomic barcoding approach for accurate transkingdom species detection in environmental DNA.
• To investigate stable interaction networks and their molecular mechanisms within aquatic microbial communities.

Main Methods:

• Developed HiMBar, a method utilizing long, accurate reads to extract multiple full-length marker genes directly from eDNA.
• Clustered extracted genes into operational taxonomic units (OTUs) for species identification without PCR amplification or assembly.
• Compared HiMBar's performance against existing DNA-based methods for accuracy, recall, and consistency.

Main Results:

• HiMBar demonstrated superior accuracy, recall, and consistency compared to existing methods.
• Identified a stable interaction network involving Cyanobacteria, Planctomycetota, Verrucomicrobiota, and Fungi.
• Discovered the crucial role of glucose metabolism in sustaining these transkingdom interactions.

Conclusions:

• HiMBar provides a powerful new tool for transkingdom species monitoring in environmental samples.
• The study elucidates key molecular mechanisms, particularly glucose metabolism, underlying complex ecological interactions.
• Advances the understanding of microbial community structure and function in aquatic ecosystems.