Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR)

Zhu, Bin

doi:10.1016/j.watres.2006.06.040

Cited by 90 publications

(49 citation statements)

References 32 publications

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“…Phages persist better in aquatic environments than their bacterial hosts (3,18) and, due to their structural characteristics, better than free DNA (37). This higher survival and the abundance of phages carrying ARGs in animal and human wastewater (10,28) support the notion that phages are a Slurries were from a farm with fecal loads from diverse animal origins.…”

mentioning

confidence: 74%

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

Colomer-Lluch

Imamovic

Jofre

et al. 2011

Antimicrob Agents Chemother

134

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This study evaluates the occurrence of bacteriophages carrying antibiotic resistance genes in animal environments. bla TEM , bla CTX-M (clusters 1 and 9), and mecA were quantified by quantitative PCR in 71 phage DNA samples from pigs, poultry, and cattle fecal wastes. Densities of 3 to 4 log 10 gene copies (GC) of bla TEM , 2 to 3 log 10 GC of bla CTX-M , and 1 to 3 log 10 GC of mecA per milliliter or gram of sample were detected, suggesting that bacteriophages can be environmental vectors for the horizontal transfer of antibiotic resistance genes.

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mentioning

confidence: 74%

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

Colomer-Lluch

Imamovic

Jofre

et al. 2011

Antimicrob Agents Chemother

134

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“…As was the case with eDNA transport, much of study of eDNA persistence has been motivated by concern over the release of transgenes from genetically modified organisms. Such studies have examined persistence of genes from transgenic crops in terrestrial soils (Widmer et al 1996(Widmer et al , 1997Hay et al 2002;Gebhard and Smalla 2006) and nearby groundwater and riverine environments (Matsui et al 2001;Zhu 2006). Across these studies, transgenic material remained detectable for long periods of time (days to years) in terrestrial soils, but much shorter periods of detection (hours to days) occurred in aquatic environments (Table 1).…”

Section: Fate: What Factors Influence Edna Persistence?mentioning

confidence: 99%

“…Most recently, research on this frontier has begun to address the substantial uncertainties and artifacts inherent to using PCR and HTS on eDNA, which often exists in trace quantities within the environment (Nguyen et al 2015). These include falsepositives and false-negatives (Ficetola et al 2014), PCR and sequencing errors (Schnell et al 2015), marker Zhu (2006) selection bias (Deagle et al 2014), and bioinformatic processing artifacts (Rossberg et al 2014). When uncertainty is handled transparently and rigorously, HTS can obtain robust biodiversity information from eDNA and provide reliable inferences for conservation.…”

Section: Description Of Whole Communitiesmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

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Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

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“…It has been shown that fragments within a range of 300-400bp can persist in the aquatic environment for at least a week in controlled conditions (Alvarez, Yumet, Santiago, & Torantos, 1996;Zhu, 2006). In contrast, shorter fragments of DNA (100bp or less) have been known to remain stable after several weeks and even years depending on environmental conditions (Willlerslev et al, 2003(Willlerslev et al, , 2007Taberlet et al, 2012a).…”

Section: Edna Persistencementioning

confidence: 99%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA d...

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Degradation of plasmid and plant DNA in water microcosms monitored by natural transformation and real-time polymerase chain reaction (PCR)

Cited by 90 publications

References 32 publications

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

The ecology of environmental DNA and implications for conservation genetics

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

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