SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical, Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
Water Res. 2024 Nov 1;265:122302. doi: 10.1016/j.watres.2024.122302. Epub 2024 Aug 18.
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.
用 0.22μm 孔径的滤膜富集微生物是河流微生物组研究中的一种常规预处理方法。然而，这种方法会丢失多少微生物组信息尚不清楚。在这里，我们对亚热带河流中大于 0.22μm（大尺寸）和在 0.22μm 和 0.1μm 之间的微生物组（小尺寸）进行了基于宏基因组学的比较研究。尽管小尺寸微生物组的绝对浓度约为大尺寸微生物组的两个数量级，但仅对大尺寸微生物组进行测序会导致微生物组多样性显著丧失。具体来说，两种尺寸的微生物群落不同，并且仅在小尺寸微生物组中检测到 347 个属。小尺寸微生物组的病毒群落比大尺寸微生物组更加多样。这些病毒具有丰富的生态功能，由 169 个科的 825 个种所携带，包括与病原体相关的科。小尺寸微生物组具有与大尺寸微生物组不同的抗生素耐药风险，表现出 8 种抗生素耐药基因（ARG）类型的富集以及 140 种独特的 ARG 亚型和 5 种富集风险等级 I 的 ARG 的检测。具有多种生态和污染物降解功能的五种主要耐药病原体的基因组草图仅在小尺寸微生物组中组装。这些发现为河流生态系统提供了新的见解，并强调了环境中被忽视的小尺寸微生物组。
