USGS Science⌕ Search
Home/Archive/USGS

USGS · 70248078

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

Rachelle Elaine Beattie·Caren C. Helbing·Jacob J. Imbery·Katy E. Klymus·Jonathan Lopez Duran·Cathy A. Richter·Anita A. Thambirajah·Nathan Thompson·Thea M. Edwards
View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

Environmental DNAArticle

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Rachelle Elaine Beattie, Caren C. Helbing, Jacob J. Imbery, Katy E. Klymus, Jonathan Lopez Duran, Cathy A. Richter, Anita A. Thambirajah, Nathan Thompson, Thea M. Edwards. 2023-08-28. A nitrifier-enriched microbial community contributes to the degradation of environmental DNA. https://doi.org/10.1002/edn3.469

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

USGS2026

Temporal replication and sampling efficiency in high-frequency autonomous and manual eDNA sampling

Environmental DNA (eDNA) sampling is a valuable tool for ecological research, but its reliability as a quantitative approach can be improved by accounting for unexplained spatiotemporal variability and autocorrelation in eDNA concentrations. Sampling designs with temporal replication can separate sampling variation from temporal variation, but obtaining true temporal replicates is difficult when samples are collected sequentially. Autosamplers may facilitate high-frequency eDNA sampling, but their sequential sampling structure raises questions about when closely spaced samples can reasonably be treated as temporal replicates. This 19.5-day study evaluated temporal variation in invasive Round Goby ( Neogobius melanostomus ) eDNA concentration at a single large-river site with short-term hydrologic variability. We used two synchronized autosamplers and a backpack sampler to collect samples as frequently as every 15 min using polyethersulfone (PES) or mixed cellulose ester (MCE) filters. We fit hierarchical temporal models that decomposed sampling and temporal variation, evaluated evidence for residual temporal correlation under alternative priors for the effective range, and used simulation to assess bias when closely spaced sequential samples were treated as simultaneous temporal replicates. We found evidence of residual temporal correlation at short lag scales, but the effective range of temporal correlation was weakly identified and sensitive to prior assumptions. Hydrologic covariates had limited explanatory support once temporal structure was accounted for. Simulations showed that treating sequential samples collected over 15–60 min windows as simultaneous temporal replicates can bias estimates of sampling and temporal variation, especially when temporal correlation is relatively weak. MCE filters produced higher expected recovered copy numbers than PES filters, while evidence for systematic differences among sampler types was weaker. These results emphasize that eDNA temporal replication should be collected as close together in time as possible, and that uncertainty in temporal correlation should be explicitly considered when designing and analyzing high-frequency eDNA surveys.

New York↗
USGS2026

Bright spot in eDNA monitoring: Early detection of invasive New Zealand mudsnails (Potamopyrgus antipodarum) prompted effective rapid response for fish hatchery

The New Zealand mudsnail (NZMS; Potamopyrgus antipodarum ) is a widespread aquatic invasive species that is parthenogenic, requiring only a single individual to initiate an infestation. Fish hatcheries–which are critical infrastructure that raise fish to support conservation, recreation, and subsistence fisheries–frequently use local water sources to provide cool water and are especially vulnerable to NZMS invasion from the contamination of water supplies. If an invasion proceeds undetected, hatcheries pose a risk for compounding the spread of NZMS because their operations transfer live organisms and associated water between hatchery facilities and, when stocking, to rivers and lakes. The U.S. Fish and Wildlife Service's Alchesay National Fish Hatchery, located on the Fort Apache Indian Reservation in Whiteriver, Arizona, produces trout to stock in Tribal reservoirs, lakes, and rivers across the southwestern U.S. New Zealand mudsnails were first documented in Arizona in 1995, are now widespread in this region, and occur at the confluence of the hatchery's outflow with the North Fork White River. Contamination of water supplies is the principal pathway for NZMS invasion into the hatchery. Here, we describe early detection environmental DNA (eDNA) surveillance efforts for NZMS at Alchesay National Fish Hatchery. Positive eDNA detections initiated a chain of events that ultimately led to four NZMS individuals being discovered and a rapid response eradication effort. Follow-up eDNA sampling and visual observation efforts after the eradication effort have yielded no detections of NZMS eDNA. We credit the success of this case with four key elements: rapid turnaround times, a robust quality assurance scheme, a proactive eDNA sampling design, and established partnerships. To our knowledge, this is the first published case of eDNA monitoring being used for early detection and successful rapid response for complete removal of an invasive species in a fish hatchery.

Arizona↗
USGS2026

DNA retention in sea lamprey digestive tracts: Insights from controlled feeding experiments

The sea lamprey ( Petromyzon marinus ), a non-native species in the Laurentian Great Lakes, has significantly impacted native fish communities and commercial fisheries, requiring population suppression efforts. While traditional control methods such as lampricides and barriers have reduced sea lamprey population abundance, questions remain regarding sea lamprey dietary composition given the focus of current damage assessments on economically and ecologically important host species. Recent advances in molecular technology offer promising methods of sea lamprey dietary assessment. Specifically, DNA metabarcoding enables species-specific identification of taxonomically diverse prey items from gut and fecal samples, and has proven effective in many taxa, including hematophagous species such as Arctic lamprey ( Lethenteron camtschaticum ) and sea lamprey. However, studies on DNA retention within digestive tracts are limited, particularly given the potential effects of environmental and dietary factors among hematophagous species. We used controlled feeding experiments to understand the effects these factors may have on DNA retention and host detectability within sea lamprey digestive tracts. Additionally, we evaluated the utility of metabarcoding for identifying multiple host species from consecutive feedings. Results indicate that host DNA can be detected up to 30 days post-feeding, with detection probability decreasing with increasing time following feeding. Temperature effects were dependent upon fasting periods, and host-switching trials indicated multiple previous host species could be detected from a single lamprey. Findings provide valuable insights for refining dietary analysis protocols for wild-caught sea lamprey within native and introduced ranges.

Environmental DNA↗