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A nitrifier‐enriched microbial community contributes to the degradation of environmental DNA

Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism‐specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve de...

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Published in:Environmental DNA (Hoboken, N.J.) N.J.), 2023-11, Vol.5 (6), p.1473-1483
Main Authors: Beattie, Rachelle E., Helbing, Caren C., Imbery, Jacob J., Klymus, Katy E., Lopez Duran, Jonathan, Richter, Catherine A., Thambirajah, Anita A., Thompson, Nathan, Edwards, Thea M.
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creator Beattie, Rachelle E.
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description Environmental DNA (eDNA) surveys are a promising alternative to traditional monitoring of invasive species, rare species, and biodiversity. Detecting organism‐specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with species abundance can be difficult due to the many abiotic and biotic factors that influence eDNA persistence and degradation. Here, we assessed the impact of a nitrifier‐enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt eDNA using experimental aquatic mesocosms and a quantitative PCR approach. The NEM community was cultured from combined sediment and water samples collected from a golf course pond in Columbia, Missouri (USA), and experiments were conducted in the dark at 22°C. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, both in the presence and absence of ammonia nitrogen. Additionally, regardless of ammonia availability, milt eDNA followed a one‐phase exponential decay pattern after an initial 24‐h plateau in the presence of the NEM community. However, milt eDNA had a shorter half‐life (12.5 h) in the absence of exogenous ammonia compared to when ammonia was present (15 h). In sterile mesocosms, eDNA was stable during the 72‐h experiment. Together, these results suggest that the presence of microorganisms is necessary for short‐term degradation of eDNA. Furthermore, nitrifying microbial communities, which are ubiquitous in most soil and water environments, could limit eDNA persistence in the environment. Understanding the contributions of environmental microbial communities will allow more confidence in sampling design and eDNA result interpretations for biodiversity management applications. We assessed the impact of a nitrifier‐enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt environmental DNA (eDNA) using experimental aquatic mesocosms and a quantitative PCR approach. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, but in sterile mesocosms, eDNA was stable during the 72‐h experiment. Together, these results suggest that the presence of microorganisms is necessary for short‐term degradati
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Detecting organism‐specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with species abundance can be difficult due to the many abiotic and biotic factors that influence eDNA persistence and degradation. Here, we assessed the impact of a nitrifier‐enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt eDNA using experimental aquatic mesocosms and a quantitative PCR approach. The NEM community was cultured from combined sediment and water samples collected from a golf course pond in Columbia, Missouri (USA), and experiments were conducted in the dark at 22°C. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, both in the presence and absence of ammonia nitrogen. Additionally, regardless of ammonia availability, milt eDNA followed a one‐phase exponential decay pattern after an initial 24‐h plateau in the presence of the NEM community. However, milt eDNA had a shorter half‐life (12.5 h) in the absence of exogenous ammonia compared to when ammonia was present (15 h). In sterile mesocosms, eDNA was stable during the 72‐h experiment. Together, these results suggest that the presence of microorganisms is necessary for short‐term degradation of eDNA. Furthermore, nitrifying microbial communities, which are ubiquitous in most soil and water environments, could limit eDNA persistence in the environment. Understanding the contributions of environmental microbial communities will allow more confidence in sampling design and eDNA result interpretations for biodiversity management applications. We assessed the impact of a nitrifier‐enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt environmental DNA (eDNA) using experimental aquatic mesocosms and a quantitative PCR approach. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, but in sterile mesocosms, eDNA was stable during the 72‐h experiment. 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Detecting organism‐specific eDNA reduces the need to collect physical specimens for population estimates, and the high sensitivity of eDNA assays may improve detection of rare or cryptic species. However, correlating estimated concentrations of eDNA with species abundance can be difficult due to the many abiotic and biotic factors that influence eDNA persistence and degradation. Here, we assessed the impact of a nitrifier‐enriched microbial (NEM) community on the persistence and degradation of Hypophthalmichthys molitrix (silver carp) milt eDNA using experimental aquatic mesocosms and a quantitative PCR approach. The NEM community was cultured from combined sediment and water samples collected from a golf course pond in Columbia, Missouri (USA), and experiments were conducted in the dark at 22°C. We found that the NEM community transformed organic nitrogen from silver carp milt to measurable amounts of nitrate, both in the presence and absence of ammonia nitrogen. 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subjects Ammonia
Biodegradation
Biodiversity
Biotic factors
Carp
Cryptic species
Degradation
Ecosystems
Environmental degradation
Environmental DNA
environmental DNA degradation
Experiments
fish
Glycerol
Hypophthalmichthys molitrix
Introduced species
Invasive species
Mesocosms
Metabolism
Microbial activity
Microbiomes
microorganism
Microorganisms
Mitochondrial DNA
Nitrates
nitrification
Nitrogen
Nonnative species
Organic nitrogen
Population statistics
Rare species
Sampling designs
Sediments
Soil environment
Soil water
Temperature
Water analysis
Water sampling
title A nitrifier‐enriched microbial community contributes to the degradation of environmental DNA
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