The use of extracellular DNA as a proxy for specific microbial activity

Nagler, Magdalena; Podmirseg, Sabine Marie; Griffith, Gareth; Insam, Heribert; Ascher‐Jenull, Judith

doi:10.1007/s00253-018-8786-y

Cited by 59 publications

(81 citation statements)

References 50 publications

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“…Applying such a sequential extraction, next to providing exDNA, increases the total amount of not only extractable soil DNA but also that of iDNA (e.g. Ascher et al 2009b; Nagler et al 2018; Wagner et al 2008). …”

Section: Methodological Considerations With Exdna Extractionmentioning

confidence: 99%

“…Consequently, a ratio of both DNA fractions (exDNA:iDNA) might provide a reliable approximate measure for microbial activity in soils and other environments (Gómez-Brandón et al 2017a, b; Nagler et al 2018). Surprisingly, the activity of different microbes was found to not correlate perfectly with the ratio of exDNA:iDNA but could best be tracked measuring exDNA amounts without relation to iDNA (Nagler et al 2018). These results suggested that exDNA is released by microorganisms proportional to their activity.…”

Section: Applicationsmentioning

confidence: 99%

“…Extracellular DNA has also been investigated within dead wood (Gómez-Brandón et al 2017a), cattle rumen and manure (Chroňáková et al 2013; Fliegerová et al 2014; Nagler et al 2018), aerobic and anammox granules (Cheng et al 2011; Xiong and Liu 2012; Dominiak et al 2011) and human epithelial cells used in forensics (Wang et al 2017). In addition, exDNA was found to act as a trap for infectious organisms in mammalians (reviewed by Ciesluk et al 2017) and during root tip growth of plants (Hawes et al 2012; Pietramellara et al 2013).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Extracellular DNA in natural environments: features, relevance and applications

Nagler

Insam

Pietramellara

et al. 2018

Appl Microbiol Biotechnol

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192

151

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Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.

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Section: Methodological Considerations With Exdna Extractionmentioning

confidence: 99%

Section: Applicationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Extracellular DNA in natural environments: features, relevance and applications

Nagler

Insam

Pietramellara

et al. 2018

Appl Microbiol Biotechnol

Self Cite

192

151

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show abstract

“…The pellet and filter were combined and processed for genomic DNA using a MoBio PowerWater DNA Isolate Kit (MoBio, Vancouver, CA) modified by adding a heating step during cell lysis. Total genomic DNA was fluorometrically measured (Quant-iT dsDNA Assay Kit, ThermoScientific, Waltham, MA), and used as proxy for total microbial biomass (Baas et al 2015, Nagler et al 2018). The samples were amplified, targeting the V4 hypervariable region of the bacterial 16S rRNA gene (515-F/806-R, Caporaso et al 2011), and sequenced with Illumina MiSeq (PE 150bp; V2 chemistry) at the Environmental Sample Preparation and Sequencing Facility (ESPSF) at Argonne National Laboratory.…”

Section: Methodsmentioning

confidence: 99%

Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion

Rocca

Simonin

Wright

et al. 2019

Preprint

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Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events allow us to address a central question in ecology – what processes shape community assembly. We used a reciprocal transplant and mixing experiment to directly and independently unravel the effects of environmental filtering and biotic interactions on microbiome success when freshwater and marine communities coalesce. The brackish treatment and community mixing resulted in strong convergence of microbiome structure and function toward the marine. Brackish exposure imposed a 96% taxa loss from freshwater and 66% loss from marine microbiomes, which was somewhat counterbalanced by the emergence of tolerant rare taxa. Community mixing further resulted in 29% and 49% loss from biotic interactions between freshwater and marine microbiomes, offset somewhat by mutualistically-assisted rare microbial taxa. Our study emphasizes the importance of the rare biosphere as a critical component of community resilience.

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“…In this study, specific microbial activities have not been taken into consideration. As an estimate, the ratio of intra-/extra-cellular DNA might be used (Nagler et al 2018), as DNA is considered to be a major component of the extracellular polymeric substances (EPS) in biofilms (Flemming and Wingender 2010). This information might strengthen the allocation of main TEA degradation to the biofilms in the CLC and should be considered in future experiments.…”

Section: Resultsmentioning

confidence: 99%

Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation

2018

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Cooling and lubrication agents like triethanolamine (TEA) are essential for many purposes in industry. Due to biodegradation, they need continuous replacement, and byproducts of degradation may be toxic. This study investigates an industrial (1,200 m³) cooling-lubrication circuit (CLC) that has been in operation for 20 years and is supposedly in an ecological equilibrium, thus offering a unique habitat. Next-generation (Illumina Miseq 16S rRNA amplicon) sequencing was used to profile the CLC-based microbiota and relate it to TEA and bicine dynamics at the sampling sites, influent, machine rooms, biofilms and effluent. Pseudomonas pseudoalcaligenes dominated the effluent and influent sites, while Alcaligenes faecalis dominated biofilms, and both species were identified as the major TEA degrading bacteria. It was shown that a 15 min heat treatment at 50°C was able to slow down the growth of both species, a promising option to control TEA degradation at large scale.

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The use of extracellular DNA as a proxy for specific microbial activity

Cited by 59 publications

References 50 publications

Extracellular DNA in natural environments: features, relevance and applications

Extracellular DNA in natural environments: features, relevance and applications

Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion

Microbiota in a cooling-lubrication circuit and an option for controlling triethanolamine biodegradation

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