Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation

Mao, Daqing; Luo, Yi; Mathieu, Jacques; Wang, Qing; Ling, Feng; Mu, Quanhua; Chen, Feng; Alvarez, Pedro J. J.

doi:10.1021/es404280v

Cited by 395 publications

(221 citation statements)

References 48 publications

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“…not using commercial kits) were used in the majority of studies (e.g. Callejas et al 2011;Barberan & Casamayor 2014;Mao et al 2014) DNA in a number of studies, but only twice since 2014 (Merlin et al 2014;Wasaki et al 2015).…”

Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

“…To date, studies on environmental DNA have most commonly been conducted on samples collected from freshwater environments, with research on water column samples (Thomsen et al 2012b;Bradford et al 2013;Mao et al 2014) far outnumbering studies based on freshwater sediments (e.g. Pansu et al 2015b) or biofilm samples (Callejas et al 2011;Zimmermann et al 2015; see Table S3 in Supplementary Material).…”

Section: Study Environmentsmentioning

confidence: 99%

“…These water column studies targeted a broad range of taxa including prokaryotes (e.g. Barberan & Casamayor 2014;Mao et al 2014), fish (e.g. Jerde et al 2013;Takahara & Minimoto 2013), amphibians (e.g.…”

Section: Study Environmentsmentioning

confidence: 99%

“…Regions of the prokaryote 16S rRNA gene were used in almost all studies targeting the DNA of Bacteria and Archaea (e.g. Barberan & Casamayor 2014;Mao et al 2014;Dong et al 2015), unless primers were designed to detect individual species and genera (e.g. Aeromonas hydrophilia strain Vah; Griffin et al 2013).…”

Section: Summary Of Gene Regions Used In Prior Analyses Of Environmenmentioning

confidence: 99%

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Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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Section: Summary Of Dna Extraction Methodsmentioning

confidence: 99%

Section: Study Environmentsmentioning

confidence: 99%

Section: Study Environmentsmentioning

confidence: 99%

Section: Summary Of Gene Regions Used In Prior Analyses Of Environmenmentioning

confidence: 99%

See 2 more Smart Citations

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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show abstract

“…As we are aware, the prevalence of antibiotic-resistant bacteria in hospital, industrial [8], as well as domestic wastewater [9] environment is not uncommon; nevertheless, increasing use of antimicrobial compounds leads to similar problem of resistance in bacteria from sewage and surface water, drinking water, etc. [10][11][12]. Bacterial resistance for PCPs such as parabens in aquatic system is a growing environmental problem [11].…”

Section: Introductionmentioning

confidence: 99%

Environmental Risk Assessment of Personal Care Products

Ramaswamy

2014

The Handbook of Environmental Chemistry

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Extensive usage and continuous release of personal care products (PCPs) lead to ubiquitous contamination of aquatic environment. As PCPs are mainly intended for external use on the human body, they are not subjected to metabolic alterations; therefore, large quantities enter the environment as such. Being biologically active and persistent, they are expected to pose a wide range of risks to aquatic habitat. Although studies on environmental concentration and toxicity endpoints are available for many PCPs, environmental risk assessment (ERA) was scantily reported. It was observed that most of the ERAs were based on hazard/risk quotient approach and not following three-tier approach due to lack of sufficient toxicological data (i.e., long-term toxicity at environmentally relevant (ppt-ppb) concentrations). From the ERA reports, it was understood that disinfectants, triclosan and triclocarban, cause high risk to aquatic organisms. In case of preservatives (parabens), the risk was low. Some fragrances (synthetic musks) and UV filters were also shown to be toxic in the aquatic habitat; however, majority of them are categorized as less risky. Other than the risk to macro forms, the antibacterial PCPs are likely to affect the community structure of nontarget (nonpathogenic) bacteria and may aid in developing (multidrug) resistance among pathogenic and nonpathogenic species. Therefore, for better risk assessment, environmentally relevant studies on nontarget organisms are to be given due importance, and it may include interactions of chemical mixture, degradation products, and bioavailability criterion as well.

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Examining the behavior of crop‐derived antibiotic resistance genes in anaerobic sludge batch reactors under thermophilic conditions

Gardner

Volkoff

Gunsch

2019

Biotech & Bioengineering

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The consumption of transgenic crops and their by‐products has become increasingly common in the United States. Yet, uncertainty remains regarding the fate and behavior of DNA within food matrices once it exits the digestive track and enters into wastewater treatment plants (WWTPs). Because many transgenic crops have historically contained antibiotic resistance genes as selection markers, understanding the behavior and uptake of these transgenes by environmental microbes is of critical importance. To investigate the behavior of free transgenic crop DNA, thermophilic anaerobic batch reactors were amended with varying concentrations of transgenic crop genes (i.e., LUG, nptII, and bla) and the persistence of those genes was monitored over 60 days using quantitative PCR. Significant levels of nptII and bla were detected in extracellular DNA (eDNA). Furthermore, LUG maize marker genes were also detected in the control reactors, suggesting that other crop‐derived transgenes contained within digested transgenic foods may also enter WWTPs. Possible bacterial transformation events were detected within the highest dose treatments at Days 30 and 60 of incubation. These findings suggest that within the average conventional digester residence times in the United States (30 days), there is a potential for bacterial transformation events to occur with crop‐derived transgenes found in eDNA.

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Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation

Cited by 395 publications

References 48 publications

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Environmental Risk Assessment of Personal Care Products

Examining the behavior of crop‐derived antibiotic resistance genes in anaerobic sludge batch reactors under thermophilic conditions

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