Particle size influences decay rates of environmental DNA in aquatic systems

Brandão-Dias, Pedro F P; Hallack, Daniel M C; Snyder, Elise; Tank, Jennifer L.; Bolster, Diogo; Volponi, None Sabrina N.; Shogren, Arial J.; Lamberti, Gary A.; Bibby, Kyle; Egan, Scott P.

doi:10.1111/1755-0998.13751

Cited by 9 publications

(16 citation statements)

References 68 publications

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“…Aggregation of smaller particles transitioning to larger ones is also a possibility, such that what we are measuring as slower removal of large particles could actually be the replenishment of large particles by the aggregation of small particles. 44 Water Column Removal Rates Varied by Target. For larger particles (>10 μm), tetW had higher water column removal rates than all targets across all treatments, while for smaller particles (>0.45 μm but <10 μm), removal rates for tetW and ermB were similar and typically higher than bla TEM .…”

Section: ■ Resultsmentioning

confidence: 99%

“…In general, we see higher removal rates of ARGs associated with small particles compared to large particles, which could simply be a surface area phenomena, with more “sticky” surface area, or biofilm, associated with smaller particles. Aggregation of smaller particles transitioning to larger ones is also a possibility, such that what we are measuring as slower removal of large particles could actually be the replenishment of large particles by the aggregation of small particles …”

Section: Discussionmentioning

confidence: 99%

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Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Ginn,

Tank,

Badilla-Aguilar

et al. 2023

Environ. Sci. Technol.

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Antibiotic resistance (AR) determinants are enriched in animal manures, a significant portion of which is land-applied as a soil amendment or as fertilizer, leading to potential AR runoff and microbial pollution in adjacent surface waters. To effectively inform AR monitoring and mitigation efforts, a thorough understanding and description of the persistence and transport of manure-derived AR in flowing waters are needed. We used experimental recirculating mesocosms to assess water-column removal rates of antibiotic resistance genes (ARGs) originating from a cow manure slurry collected from a dairy farm. We quantified the effect of three benthic (i.e., bottom) substrate variations and particle sizes of manure slurry on water column removal rates. Overall, we observed variation in ARG behavior across substrate treatments and particle sizes. For ARGs associated with small particles, removal rates were higher in mesocosms with a substrate. tetW was typically removed at the highest rates across particle size and treatment, followed by ermB and bla TEM . Our data suggests that both substrate character and particle size exert control on the fate and transport of ARGs in surface waters, laying the foundation for future research in this area to establish a predictive framework for AR persistence and fate in flowing waters.

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Section: ■ Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Ginn,

Tank,

Badilla-Aguilar

et al. 2023

Environ. Sci. Technol.

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“…This difference in mechanisms of removal between large and smaller eDNA components is an important and novel finding that may help explain spatial–temporal changes in the eDNA composition observed in the field. The longitudinally variable eDNA composition hypothesis predicts that eDNA components will change predictably in their relative proportions over time and space, thus enabling prediction of target organism location and abundance with eDNA size data. Accordingly, the variation of eDNA particle and fragment size with decay has been previously observed in a small number of studies. – Therefore, linking removal rates of different eDNA components to variation in environmental factors is fundamental for future modeling of eDNA transport and removal associated with downstream transport in flowing waters.…”

Section: Discussionmentioning

confidence: 99%

“…The longitudinally variable eDNA composition hypothesis predicts that eDNA components will change predictably in their relative proportions over time and space, thus enabling prediction of target organism location and abundance with eDNA size data. Accordingly, the variation of eDNA particle and fragment size with decay has been previously observed in a small number of studies. – Therefore, linking removal rates of different eDNA components to variation in environmental factors is fundamental for future modeling of eDNA transport and removal associated with downstream transport in flowing waters. For example, in a rapid-flowing, low-nutrient environment (e.g., a mountain stream), we may expect large eDNA particles to persist longer in the water column, whereas in a slow moving, high-nutrient environment (e.g., a wetland), large eDNA particles will be removed more rapidly than small particles, and the presence of large particles will be a stronger sign of a proximal eDNA source.…”

Section: Discussionmentioning

confidence: 99%

“…But because different eDNA components in the water column change differently over time and space, 7−10 their relative proportions may be the key to tease apart abundance and location of target organisms. 7 Therefore, if environmental drivers predictably influence the various eDNA components, we can potentially use these data to make informed methodological decisions to optimize the resolution and probabilities of detection of target organisms in different aquatic environments. 11−13 A relevant component of the eDNA mixture is DNA that is either loosely or strongly adsorbed to suspended particles and benthic substrate.…”

Section: ■ Introductionmentioning

confidence: 99%

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Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters

Brandão-Dias,

Tank,

Snyder

et al. 2023

Environ. Sci. Technol.

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Environmental DNA (eDNA) in aquatic systems is a complex mixture that includes dissolved DNA, intracellular DNA, and particle-adsorbed DNA. Information about the various components of eDNA and their relative proportions could be used to discern target organism abundance and location. However, a limited knowledge of eDNA adsorption dynamics and interactions with other materials hinders these applications. To address this gap, we used recirculating stream mesocosms to investigate the impact of suspended materials (fine particulate organic matter, plankton, clay, and titanium dioxide) on the eDNA concentration and particle size distribution (PSD) from two fish species in flowing water. Our findings revealed that eDNA rapidly adsorbs to other materials in the water column, affecting its concentration and PSD. Nonetheless, only particulate organic matter affected eDNA removal rate after 30 h. Moreover, we observed that the removal of larger eDNA components (≥10 μm) was more strongly influenced by physical processes, whereas the removal of smaller eDNA components was driven by biological degradation. This disparity in removal mechanisms between larger and smaller eDNA components could explain changes in eDNA composition over time and space, which have implications for modeling the spatial distribution and abundance of target species and optimizing eDNA detection in high turbidity systems.

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Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study

Vanderpool,

Wilcox,

Young

et al. 2024

Ecology and Evolution

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Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non‐destructive and suitable for the detection of endangered species where “no take” restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.

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Particle size influences decay rates of environmental DNA in aquatic systems

Abstract: Detecting macro-organisms using environmental DNA (eDNA), especially in aquatic ecosystems, is quickly becoming one of the most prevalent environmental monitoring methods for the detection of single target-species (e.g.,

Cited by 9 publications

References 68 publications

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Persistence of Antibiotic Resistance Genes Varies with Particle Size and Substrate Conditions in Recirculating Streams

Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters

Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study

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