Unveiling the overlooked small-sized microbiome in river ecosystems

• Published in: Water research (Oxford) 2024-11, Vol.265, p.122302, Article 122302
• Main Authors: Gao, Fang-Zhou, Hu, Li-Xin, Liu, You-Sheng, Qiao, Lu-Kai, Chen, Zi-Yin, Su, Jian-Qiang, He, Liang-Ying, Bai, Hong, Zhu, Yong-Guan, Ying, Guang-Guo
• Format: Article
• Language: English
• Subjects: Bacteria - genetics; Ecosystem; Metagenomics; Microbial ecology; Microbiota; Risk assessment; River microbiome; Rivers - microbiology; Size gradient filtration
• ISSN: 0043-1354; 1879-2448; 1879-2448
• DOI: 10.1016/j.watres.2024.122302

•Small- and large-sized microbiome was comparatively studied in the river ecosystem.•Small-sized fraction had diverse microbiome despite with lower DNA biomass.•The viral community in small-sized fraction was two-folds more than that in large-sized fraction.•Small-sized fraction had distinct AMR risks in relation to resistome profiles and high risk ARGs.•The genomes of five resistant pathogens were only assembled in small-sized microbiome. Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment. [Display omitted]