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Unveiling the overlooked small-sized microbiome in river ecosystems
•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 ris...
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Published in: | Water research (Oxford) 2024-11, Vol.265, p.122302, Article 122302 |
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creator | 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 |
description | •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.
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doi_str_mv | 10.1016/j.watres.2024.122302 |
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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.
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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]</description><subject>Bacteria - genetics</subject><subject>Ecosystem</subject><subject>Metagenomics</subject><subject>Microbial ecology</subject><subject>Microbiota</subject><subject>Risk assessment</subject><subject>River microbiome</subject><subject>Rivers - microbiology</subject><subject>Size gradient filtration</subject><issn>0043-1354</issn><issn>1879-2448</issn><issn>1879-2448</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNp9kLtOwzAUhi0EoqXwBghlZEnwLXG8IKGKm1SJhc6WY5-ASxIXOy0qT0-qFEamc4bvP5cPoUuCM4JJcbPKvnQfIGYUU54RShmmR2hKSiFTynl5jKYYc5YSlvMJOotxhTEeKHmKJkwSUeaSTNF82W3BNa57S_p3SPwWQuP9B9gktrpp0ui-h751JvjK-RYS1yXBDVQCxsdd7KGN5-ik1k2Ei0OdoeXD_ev8KV28PD7P7xapoZz0qZHARcW1LGSZ6zw3lgIjklshREmAg8krTTAGQakVIGvMiwpyw6StNDY1m6Hrce46-M8NxF61LhpoGt2B30TFsCyKghe5GFA-osPdMQao1Tq4VoedIljt9amVGvWpvT416htiV4cNm6oF-xf69TUAtyMAw59bB0FF46AzYF0A0yvr3f8bfgDBhIN2</recordid><startdate>20241101</startdate><enddate>20241101</enddate><creator>Gao, Fang-Zhou</creator><creator>Hu, Li-Xin</creator><creator>Liu, You-Sheng</creator><creator>Qiao, Lu-Kai</creator><creator>Chen, Zi-Yin</creator><creator>Su, Jian-Qiang</creator><creator>He, Liang-Ying</creator><creator>Bai, Hong</creator><creator>Zhu, Yong-Guan</creator><creator>Ying, Guang-Guo</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20241101</creationdate><title>Unveiling the overlooked small-sized microbiome in river ecosystems</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c241t-c9e47b4a96985a55cd2e3194d77781e4ec5ba100e722d7e9f046be5c39dba0cf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bacteria - genetics</topic><topic>Ecosystem</topic><topic>Metagenomics</topic><topic>Microbial ecology</topic><topic>Microbiota</topic><topic>Risk assessment</topic><topic>River microbiome</topic><topic>Rivers - microbiology</topic><topic>Size gradient filtration</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gao, Fang-Zhou</creatorcontrib><creatorcontrib>Hu, Li-Xin</creatorcontrib><creatorcontrib>Liu, You-Sheng</creatorcontrib><creatorcontrib>Qiao, Lu-Kai</creatorcontrib><creatorcontrib>Chen, Zi-Yin</creatorcontrib><creatorcontrib>Su, Jian-Qiang</creatorcontrib><creatorcontrib>He, Liang-Ying</creatorcontrib><creatorcontrib>Bai, Hong</creatorcontrib><creatorcontrib>Zhu, Yong-Guan</creatorcontrib><creatorcontrib>Ying, Guang-Guo</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Water research (Oxford)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gao, Fang-Zhou</au><au>Hu, Li-Xin</au><au>Liu, You-Sheng</au><au>Qiao, Lu-Kai</au><au>Chen, Zi-Yin</au><au>Su, Jian-Qiang</au><au>He, Liang-Ying</au><au>Bai, Hong</au><au>Zhu, Yong-Guan</au><au>Ying, Guang-Guo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Unveiling the overlooked small-sized microbiome in river ecosystems</atitle><jtitle>Water research (Oxford)</jtitle><addtitle>Water Res</addtitle><date>2024-11-01</date><risdate>2024</risdate><volume>265</volume><spage>122302</spage><pages>122302-</pages><artnum>122302</artnum><issn>0043-1354</issn><issn>1879-2448</issn><eissn>1879-2448</eissn><abstract>•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.
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subjects | Bacteria - genetics Ecosystem Metagenomics Microbial ecology Microbiota Risk assessment River microbiome Rivers - microbiology Size gradient filtration |
title | Unveiling the overlooked small-sized microbiome in river ecosystems |
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