Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary
Antibiotic resistance is an increasingly concerned hotspot of human health. Microbial determinants that may affect the profiles of antibiotic resistance genes (ARGs) in the environments need be explored. Here, sediment cores in the Pearl River Estuary (PRE) were analyzed using metagenomic approaches...
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| Veröffentlicht in: | Environmental pollution (1987) 2024-12, Vol.363 (Pt 1), p.125176, Article 125176 |
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| container_title | Environmental pollution (1987) |
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| creator | Li, Zhaohong Lin, Lan Xie, Xiuqin Ming, Lili Li, Songzhang Liu, Lan Yuan, Ke Lin, Li Hu, Ligang Luan, Tiangang Chen, Baowei |
| description | Antibiotic resistance is an increasingly concerned hotspot of human health. Microbial determinants that may affect the profiles of antibiotic resistance genes (ARGs) in the environments need be explored. Here, sediment cores in the Pearl River Estuary (PRE) were analyzed using metagenomic approaches. ARGs were vertically stratified in the PRE sediment cores in terms of both diversity and absolute levels. Multidrug resistance genes could account for approximately 65.0% of the total ARGs, followed by sulfonamides (19.1%), aminoglycosides (5.9%), beta-lactams (4.5%), etc. ARGs related to aminoglycosides, lincosamides, macrolides, sulfonamides and tetracyclines were preferentially enriched in the surface layers of sediment cores. Sulfate-reducing microbes (SRMs) (e.g., Desulfocapsa and Desulfobulbus) and iron-reducing microbes (IRMs) (e.g., Pseudomonas and Sulfurospirillum) were consistently popular and dominant in the PRE sediment cores. The total levels of both SRMs and IRMs were significantly correlated with those of ARGs in the PRE sediment cores (p |
| doi_str_mv | 10.1016/j.envpol.2024.125176 |
| format | Article |
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[Display omitted]
•ARG profiles were vertically stratified in the PRE sediment cores.•Desulfocapsa and Desulfobulbus (SRMs) were dominant in the PRE sediment cores.•Pseudomonas and Sulfurospirillum were main IRM genera in the PRE sediment cores.•SRMs and IRMs were significantly correlated with ARGs in the PRE sediment cores.•Pseudomonas, mexF, and mexK were identified as the ‘hubs’ of the generated network.</description><identifier>ISSN: 0269-7491</identifier><identifier>ISSN: 1873-6424</identifier><identifier>EISSN: 1873-6424</identifier><identifier>DOI: 10.1016/j.envpol.2024.125176</identifier><identifier>PMID: 39442608</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>aminoglycosides ; Anaerobic microbes ; antibiotic resistance ; Antibiotic resistance genes ; beta-lactams ; Desulfobulbus ; Desulfocapsa ; Desulfovibrio ; estuaries ; human health ; macrolides ; metagenomics ; multiple drug resistance ; Pearl River Estuary ; pollution ; Pseudomonas ; rivers ; Sediment cores ; sediments ; Shewanella ; Sulfurospirillum ; Vertical distribution</subject><ispartof>Environmental pollution (1987), 2024-12, Vol.363 (Pt 1), p.125176, Article 125176</ispartof><rights>2024 Elsevier Ltd</rights><rights>Copyright © 2024 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c274t-406197fb6b333b53100456d7e06cf33e555b77ffbeed067d9d88f3256f182e373</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.envpol.2024.125176$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,777,781,3537,27905,27906,45976</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39442608$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Zhaohong</creatorcontrib><creatorcontrib>Lin, Lan</creatorcontrib><creatorcontrib>Xie, Xiuqin</creatorcontrib><creatorcontrib>Ming, Lili</creatorcontrib><creatorcontrib>Li, Songzhang</creatorcontrib><creatorcontrib>Liu, Lan</creatorcontrib><creatorcontrib>Yuan, Ke</creatorcontrib><creatorcontrib>Lin, Li</creatorcontrib><creatorcontrib>Hu, Ligang</creatorcontrib><creatorcontrib>Luan, Tiangang</creatorcontrib><creatorcontrib>Chen, Baowei</creatorcontrib><title>Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary</title><title>Environmental pollution (1987)</title><addtitle>Environ Pollut</addtitle><description>Antibiotic resistance is an increasingly concerned hotspot of human health. Microbial determinants that may affect the profiles of antibiotic resistance genes (ARGs) in the environments need be explored. Here, sediment cores in the Pearl River Estuary (PRE) were analyzed using metagenomic approaches. ARGs were vertically stratified in the PRE sediment cores in terms of both diversity and absolute levels. Multidrug resistance genes could account for approximately 65.0% of the total ARGs, followed by sulfonamides (19.1%), aminoglycosides (5.9%), beta-lactams (4.5%), etc. ARGs related to aminoglycosides, lincosamides, macrolides, sulfonamides and tetracyclines were preferentially enriched in the surface layers of sediment cores. Sulfate-reducing microbes (SRMs) (e.g., Desulfocapsa and Desulfobulbus) and iron-reducing microbes (IRMs) (e.g., Pseudomonas and Sulfurospirillum) were consistently popular and dominant in the PRE sediment cores. The total levels of both SRMs and IRMs were significantly correlated with those of ARGs in the PRE sediment cores (p < 0.01). Network analysis showed that SRM and IRM genera (i.e., Pseudomonas, Shewanella, and Desulfovibrio) had the high co-occurrence with multiple ARG subtypes in the PRE sediment cores such as rsmA, mexK, and mexF. This study highlighted that anaerobic microbes could play significant roles in shaping vertical ARG distribution in the sediments of aquatic environments.
[Display omitted]
•ARG profiles were vertically stratified in the PRE sediment cores.•Desulfocapsa and Desulfobulbus (SRMs) were dominant in the PRE sediment cores.•Pseudomonas and Sulfurospirillum were main IRM genera in the PRE sediment cores.•SRMs and IRMs were significantly correlated with ARGs in the PRE sediment cores.•Pseudomonas, mexF, and mexK were identified as the ‘hubs’ of the generated network.</description><subject>aminoglycosides</subject><subject>Anaerobic microbes</subject><subject>antibiotic resistance</subject><subject>Antibiotic resistance genes</subject><subject>beta-lactams</subject><subject>Desulfobulbus</subject><subject>Desulfocapsa</subject><subject>Desulfovibrio</subject><subject>estuaries</subject><subject>human health</subject><subject>macrolides</subject><subject>metagenomics</subject><subject>multiple drug resistance</subject><subject>Pearl River Estuary</subject><subject>pollution</subject><subject>Pseudomonas</subject><subject>rivers</subject><subject>Sediment cores</subject><subject>sediments</subject><subject>Shewanella</subject><subject>Sulfurospirillum</subject><subject>Vertical distribution</subject><issn>0269-7491</issn><issn>1873-6424</issn><issn>1873-6424</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqNUd1qFDEYDaLYbfUNRHLpzaz5z86NIKVqoaKIXofM5EvNMpOsSWalT-Urmu1UL8WrEL7zwzkHoReUbCmh6vV-C_F4SNOWESa2lEmq1SO0oTvNOyWYeIw2hKm-06KnZ-i8lD0hRHDOn6Iz3gvBFNlt0K-PUO0txDSHEdtop7sSCp5tDB5KDfEWh1hziKWdM0y2gotQCh6g_gSIjVLDEFK9PzdqtXEE3AShtJvDZZl8I3X3n5BT7DK4ZTwJN8echoYLERdwYYZY8ZiaDE4e1--AP4PNE_4SjpDxVamLzXfP0BNvpwLPH94L9O3d1dfLD93Np_fXl29vupFpUTtBFO21H9TQAg-S0xZdKqeBqNFzDlLKQWvvBwBHlHa92-08Z1J5umPANb9Ar1bdQ04_llaFmUMZYZpshLQUw6kUVLY-1X9AGSFS9VQ2qFihLXkpGbw55DC3WIYSc1rV7M26qjmtatZVG-3lg8MyzOD-kv7M2ABvVgC0So4BsiljgLaECxnGalwK_3b4DToLuOs</recordid><startdate>20241215</startdate><enddate>20241215</enddate><creator>Li, Zhaohong</creator><creator>Lin, Lan</creator><creator>Xie, Xiuqin</creator><creator>Ming, Lili</creator><creator>Li, Songzhang</creator><creator>Liu, Lan</creator><creator>Yuan, Ke</creator><creator>Lin, Li</creator><creator>Hu, Ligang</creator><creator>Luan, Tiangang</creator><creator>Chen, Baowei</creator><general>Elsevier Ltd</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope></search><sort><creationdate>20241215</creationdate><title>Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary</title><author>Li, Zhaohong ; Lin, Lan ; Xie, Xiuqin ; Ming, Lili ; Li, Songzhang ; Liu, Lan ; Yuan, Ke ; Lin, Li ; Hu, Ligang ; Luan, Tiangang ; Chen, Baowei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c274t-406197fb6b333b53100456d7e06cf33e555b77ffbeed067d9d88f3256f182e373</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>aminoglycosides</topic><topic>Anaerobic microbes</topic><topic>antibiotic resistance</topic><topic>Antibiotic resistance genes</topic><topic>beta-lactams</topic><topic>Desulfobulbus</topic><topic>Desulfocapsa</topic><topic>Desulfovibrio</topic><topic>estuaries</topic><topic>human health</topic><topic>macrolides</topic><topic>metagenomics</topic><topic>multiple drug resistance</topic><topic>Pearl River Estuary</topic><topic>pollution</topic><topic>Pseudomonas</topic><topic>rivers</topic><topic>Sediment cores</topic><topic>sediments</topic><topic>Shewanella</topic><topic>Sulfurospirillum</topic><topic>Vertical distribution</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Zhaohong</creatorcontrib><creatorcontrib>Lin, Lan</creatorcontrib><creatorcontrib>Xie, Xiuqin</creatorcontrib><creatorcontrib>Ming, Lili</creatorcontrib><creatorcontrib>Li, Songzhang</creatorcontrib><creatorcontrib>Liu, Lan</creatorcontrib><creatorcontrib>Yuan, Ke</creatorcontrib><creatorcontrib>Lin, Li</creatorcontrib><creatorcontrib>Hu, Ligang</creatorcontrib><creatorcontrib>Luan, Tiangang</creatorcontrib><creatorcontrib>Chen, Baowei</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Environmental pollution (1987)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Zhaohong</au><au>Lin, Lan</au><au>Xie, Xiuqin</au><au>Ming, Lili</au><au>Li, Songzhang</au><au>Liu, Lan</au><au>Yuan, Ke</au><au>Lin, Li</au><au>Hu, Ligang</au><au>Luan, Tiangang</au><au>Chen, Baowei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary</atitle><jtitle>Environmental pollution (1987)</jtitle><addtitle>Environ Pollut</addtitle><date>2024-12-15</date><risdate>2024</risdate><volume>363</volume><issue>Pt 1</issue><spage>125176</spage><pages>125176-</pages><artnum>125176</artnum><issn>0269-7491</issn><issn>1873-6424</issn><eissn>1873-6424</eissn><abstract>Antibiotic resistance is an increasingly concerned hotspot of human health. Microbial determinants that may affect the profiles of antibiotic resistance genes (ARGs) in the environments need be explored. Here, sediment cores in the Pearl River Estuary (PRE) were analyzed using metagenomic approaches. ARGs were vertically stratified in the PRE sediment cores in terms of both diversity and absolute levels. Multidrug resistance genes could account for approximately 65.0% of the total ARGs, followed by sulfonamides (19.1%), aminoglycosides (5.9%), beta-lactams (4.5%), etc. ARGs related to aminoglycosides, lincosamides, macrolides, sulfonamides and tetracyclines were preferentially enriched in the surface layers of sediment cores. Sulfate-reducing microbes (SRMs) (e.g., Desulfocapsa and Desulfobulbus) and iron-reducing microbes (IRMs) (e.g., Pseudomonas and Sulfurospirillum) were consistently popular and dominant in the PRE sediment cores. The total levels of both SRMs and IRMs were significantly correlated with those of ARGs in the PRE sediment cores (p < 0.01). Network analysis showed that SRM and IRM genera (i.e., Pseudomonas, Shewanella, and Desulfovibrio) had the high co-occurrence with multiple ARG subtypes in the PRE sediment cores such as rsmA, mexK, and mexF. This study highlighted that anaerobic microbes could play significant roles in shaping vertical ARG distribution in the sediments of aquatic environments.
[Display omitted]
•ARG profiles were vertically stratified in the PRE sediment cores.•Desulfocapsa and Desulfobulbus (SRMs) were dominant in the PRE sediment cores.•Pseudomonas and Sulfurospirillum were main IRM genera in the PRE sediment cores.•SRMs and IRMs were significantly correlated with ARGs in the PRE sediment cores.•Pseudomonas, mexF, and mexK were identified as the ‘hubs’ of the generated network.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>39442608</pmid><doi>10.1016/j.envpol.2024.125176</doi></addata></record> |
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| identifier | ISSN: 0269-7491 |
| ispartof | Environmental pollution (1987), 2024-12, Vol.363 (Pt 1), p.125176, Article 125176 |
| issn | 0269-7491 1873-6424 1873-6424 |
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| source | Elsevier ScienceDirect Journals |
| subjects | aminoglycosides Anaerobic microbes antibiotic resistance Antibiotic resistance genes beta-lactams Desulfobulbus Desulfocapsa Desulfovibrio estuaries human health macrolides metagenomics multiple drug resistance Pearl River Estuary pollution Pseudomonas rivers Sediment cores sediments Shewanella Sulfurospirillum Vertical distribution |
| title | Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary |
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