Unveiling the overlooked small-sized microbiome in river ecosystems.

Area of Science:

• Environmental microbiology
• Metagenomics
• River ecosystems

Background:

• Standard river microbiome studies often use 0.22-μm pore size filters for pretreatment.
• The impact of this pore size on microbiome diversity and information loss is not fully understood.

Purpose of the Study:

• To compare the microbiome diversity and characteristics of large-sized (>0.22 μm) and small-sized (0.1–0.22 μm) microbial fractions in a subtropical river.
• To assess the extent of microbiome information lost by using the standard 0.22-μm filtration method.

Main Methods:

• Comparative metagenomics analysis of large-sized and small-sized microbial communities from river water.
• Bioinformatic analysis to assess microbial diversity, community composition, viral communities, and antimicrobial resistance genes (ARGs).

Main Results:

• The small-sized microbiome, though less abundant, significantly contributes to overall microbial diversity.
• 347 microbial genera, diverse viral communities, and distinct antimicrobial resistance risks, including pathogen genomes, were exclusively found in the small-sized fraction.
• Filtration using only 0.22-μm pores leads to substantial loss of river microbiome data.

Conclusions:

• The 0.1–0.22 μm microbial fraction is critical for a comprehensive understanding of river ecosystems.
• Current standard filtration methods in river microbiome research overlook vital microbial diversity and functions.
• Future research should consider including the small-sized microbiome for accurate ecological and health risk assessments.