Strong adsorption of DNA molecules on humic acids

Saeki, Kazutoshi; Ihyo, Yasutaka; Sakai, Masao; Kunito, Takashi

doi:10.1007/s10311-011-0310-x

Cited by 63 publications

(47 citation statements)

References 23 publications

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“…This fraction of aqueous macrobial eDNA is likely to remain in suspension indefinitely until the DNA molecules degrade (Isao et al 1990). Water could advect eDNA in this state over long distances, especially in lotic systems, strong currents, and when extracellular/extraorganellar eDNA is protected via adsorption to other submicron particles (Saeki et al 2011). For example, transgenes from genetically modified corn were detected in river water up to 82 km downstream of a corn cultivation plot (Douville et al 2007), and plant DNA fragments as long as 1000 bp are detectable in groundwater (Pot e et al 2009).…”

Section: S T a T E A N D F A T E O F A Q U E O U S M A C R O B I A L mentioning

confidence: 99%

Particle size distribution and optimal capture of aqueous macrobial eDNA

et al. 2014

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Summary1. Using environmental DNA (eDNA) to detect aquatic macroorganisms is a new survey method with broad applicability. However, the origin, state and fate of aqueous macrobial eDNA -which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified and assayed -are poorly understood. 2. The size of aquatic particles provides clues about their origin, state and fate. We used sequential filtration size fractionation to measure the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry and SPM with gravimetric analysis. 3. In a lake and a pond, we found Carp eDNA in particles from >180 to <0Á2 lm, but it was most abundant from 1 to 10 lm. Total eDNA was most abundant below 0Á2 lm, and SPM was most abundant above 100 lm. SPM consisted of ≤0Á1% total eDNA, and total eDNA consisted of ≤0Á0004% Carp eDNA. 0Á2 lm filtration maximized Carp eDNA capture (85% AE 6%) while minimizing total (i.e. non-target) eDNA capture (48% AE 3%), but filter clogging limited this pore size to a sample volume <250 mL. To mitigate this limitation, we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA. 4. Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling may therefore play an important role in its fate. For optimal eDNA capture, we recommend 0Á2 lm filtration or a combination of larger pore size and water volume that exceeds the 0Á2 lm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms. Our method for eDNA particle size analysis enables future research to compare the PSDs of eDNA from other organisms and environments, and to easily apply them for ecological monitoring.

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Section: S T a T E A N D F A T E O F A Q U E O U S M A C R O B I A L mentioning

confidence: 99%

Particle size distribution and optimal capture of aqueous macrobial eDNA

et al. 2014

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“…This fraction of aqueous macrobial eDNA is likely to remain in suspension indefinitely until the DNA molecules degrade (Isao et al 1990). Water could advect eDNA in this state over long distances, especially in lotic systems, strong currents, and when free eDNA is protected via adsorption to other submicron particles (Saeki et al 2011). For example, transgenes from genetically modified corn were detected in river water up to 82 km downstream of a corn cultivation plot (Douville et al 2007), and plant DNA fragments as long as 1000 bp are detectable in groundwater (Poté et al 2009).…”

Section: State and Fate Of Aqueous Macrobial Ednamentioning

confidence: 99%

Particle size distribution and optimal capture of aqueous macrobial eDNA

Turner

Barnes

et al. 2014

Preprint

170

299

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ABSTRACT1. Detecting aquatic macroorganisms with environmental DNA (eDNA) is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNAwhich collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified, and assayed -are poorly understood. 2.The size of aquatic particles provides clues about their origin, state, and fate. We used sequential filtration size fractionation to measure, for the first time, the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry, and SPM with gravimetric analysis. 3.In a lake and a pond, we found Carp eDNA in particles from >180 to <0.2 !m, but it was most abundant from 1-10 !m. Total eDNA was most abundant below 0.2 !m and SPM was most abundant above 100 !m. SPM was "0.1% total eDNA, and total eDNA was "0.0004% Carp eDNA. 0.2 !m filtration maximized Carp eDNA capture (85%±6%) while minimizing total (i.e., non-target) eDNA capture (48%±3%), but filter clogging limited this pore size to a volume <250 mL. To mitigate this limitation we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA. 4.Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling plays an important role in its fate. For optimal eDNA capture, we recommend 0.2 !m filtration or a combination of larger pore size and water volume that exceeds the 0.2 !m isocline. In situ filtration of large volumes could maximize detection probability . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx

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“…SOM is expected to increase the negative charge on minerals (Equation 1), leading to a mutual exclusion between SOM-rich allophane and negativelycharged phosphate groups of DNA. In contrast to Cai et al (2006b), Saeki et al (2011) showed that humic acid had a high affinity for DNA, hence the influence of SOM on DNA (and potentially aDNA) adsorption in Andisol is still debatable.…”

Section: Dna Adsorption On Allophanementioning

confidence: 86%

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

et al. 2014

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Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmonsperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosols.

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Strong adsorption of DNA molecules on humic acids

Cited by 63 publications

References 23 publications

Particle size distribution and optimal capture of aqueous macrobial eDNA

Particle size distribution and optimal capture of aqueous macrobial eDNA

Particle size distribution and optimal capture of aqueous macrobial eDNA

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

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