Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

Yuyi Yang, Zan Li, Wenjuan Song, Linna Du, Chen Ye, Bo Zhao, Wenzhi Liu (Lead / Corresponding author), Danli Deng, Yongtai Pan, Hui Lin, Xinhua Cao

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Abstract

A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)–1.34 × 10 0 and 1.22 × 10 −3 –1.98 × 10 −1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.

Original languageEnglish
Pages (from-to)371-380
Number of pages10
JournalEnvironment International
Volume127
Early online date4 Apr 2019
DOIs
Publication statusPublished - Jun 2019

Fingerprint

aquatic environment
stratification
gene
antibiotic resistance
metal
seawater
relative abundance
geography
multivariate analysis
variance analysis
lake water
epilimnion
bioinformatics
hypolimnion
lake
ocean
diversity index

Keywords

  • Bacitracin resistance genes
  • Mercury resistance genes
  • Metagenomic analysis
  • Principal coordinates analysis
  • Stratification

Cite this

Yang, Yuyi ; Li, Zan ; Song, Wenjuan ; Du, Linna ; Ye, Chen ; Zhao, Bo ; Liu, Wenzhi ; Deng, Danli ; Pan, Yongtai ; Lin, Hui ; Cao, Xinhua. / Metagenomic insights into the abundance and composition of resistance genes in aquatic environments : Influence of stratification and geography. In: Environment International. 2019 ; Vol. 127. pp. 371-380.
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abstract = "A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)–1.34 × 10 0 and 1.22 × 10 −3 –1.98 × 10 −1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.",
keywords = "Bacitracin resistance genes, Mercury resistance genes, Metagenomic analysis, Principal coordinates analysis, Stratification",
author = "Yuyi Yang and Zan Li and Wenjuan Song and Linna Du and Chen Ye and Bo Zhao and Wenzhi Liu and Danli Deng and Yongtai Pan and Hui Lin and Xinhua Cao",
note = "This work was supported by the National Natural Science Foundation of China [grant number 41673127], the Youth Innovation Promotion Association of the Chinese Academy of Sciences [grant numbers 2015282 and 2017388], the Wenzhou Science and Technology Major Project [ZS2017001], and Basic Public Welfare Research Projects in Zhejiang Province [LGF18E090007].",
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Metagenomic insights into the abundance and composition of resistance genes in aquatic environments : Influence of stratification and geography. / Yang, Yuyi; Li, Zan; Song, Wenjuan; Du, Linna; Ye, Chen; Zhao, Bo; Liu, Wenzhi (Lead / Corresponding author); Deng, Danli; Pan, Yongtai; Lin, Hui; Cao, Xinhua.

In: Environment International, Vol. 127, 06.2019, p. 371-380.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Metagenomic insights into the abundance and composition of resistance genes in aquatic environments

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AU - Yang, Yuyi

AU - Li, Zan

AU - Song, Wenjuan

AU - Du, Linna

AU - Ye, Chen

AU - Zhao, Bo

AU - Liu, Wenzhi

AU - Deng, Danli

AU - Pan, Yongtai

AU - Lin, Hui

AU - Cao, Xinhua

N1 - This work was supported by the National Natural Science Foundation of China [grant number 41673127], the Youth Innovation Promotion Association of the Chinese Academy of Sciences [grant numbers 2015282 and 2017388], the Wenzhou Science and Technology Major Project [ZS2017001], and Basic Public Welfare Research Projects in Zhejiang Province [LGF18E090007].

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N2 - A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)–1.34 × 10 0 and 1.22 × 10 −3 –1.98 × 10 −1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.

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