Selective collection of long fragments of environmental DNA using larger pore size filter

DNA State Influences the Uptake and Persistence of Environmental DNA by Marine Sponge Natural Samplers

Marine sponges as natural samplers of environmental DNA (eDNA) are receiving growing attention as an untapped source of biodiversity data. However, little is known about the state of DNA (e.g., cellular or extracellular) that is captured by these samples and how this compares to conventional aquatic eDNA samples. Here, we present an artificial spiking experiment where DNA in cellular and extracellular states was added into tanks containing two sponge species. Aquatic eDNA samples and sponge natural sampler DNA (nsDNA) samples were collected over 7 days and DNA from the two states was quantified in each sample using quantitative real-time PCR (qPCR). We found that there was a significant interaction between DNA state and sample type (eDNA and nsDNA), with lower detection and concentration of extracellular DNA, compared to cellular DNA, found in nsDNA samples. We also found that detection rate and concentration of DNA were significantly lower in nsDNA than in eDNA overall. During methodological testing, PCR inhibition was observed in both sponge species; this was prohibitive in one of the species. Further work to investigate the degree of PCR inhibition during nsDNA metabarcoding is important to understand its impact on the communities resolved using nsDNA methods. Synthesis and applications. We show that nsDNA may originate from a subset of the DNA present in environmental media, potentially providing a more stable picture of local communities. Natural samplers provide a promising option for hard-to-reach environments and for retrieving biodiversity data from archived samples; however, further work and optimization are required to understand what is and is not well represented by this sample type compared to widely applied aquatic eDNA approaches.

Biodiversity monitoring in remote marine environments: Advancing environmental DNA/RNA sampling workflows

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 12 sites in three fiords within Fiordland National Park, Aotearoa-New Zealand. For filtration comparison, a modified cruising speed net was used to concentrate eDNA/eRNA onto 20 μm nylon filters, while water from the net's cod-end was filtered through a 5 μm Smith-Root self-preserving filter using the eDNA Citizen Scientist Sampler. To compare preservation methods, Smith-Root filters were cut in half, with one half preserved in the self-preserving unit and the other in DNA/RNA Shield™ buffer. Biodiversity screening was performed by sequencing the 18S rRNA gene for eukaryotes and two mitochondrial 16S rRNA genes for fish and marine vertebrates. Comparable amplicon sequence variant (ASVs) richness was observed between methods, yet samples preserved with buffer showed higher richness of fish and marine vertebrate taxa and higher PCR amplification success. There was little variation in community composition, except for 16S rRNA targeting fish, where distinct patterns emerged based on preservation methods. Overall, sampling workflows showed similar community composition and alpha diversity across both nucleic acids. These results confirm that enhancing eDNA/eRNA yields for sparse taxa requires consideration of collection and preservation methods. However, abundant taxa biodiversity is captured consistently, allowing for adjustments without compromising robustness. These insights support streamlined eDNA/eRNA sampling, emphasizing adaptive strategies based on targeted taxa.

Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga

Early detection of nuisance species is crucial for managing threatened ecosystems and preventing widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity of biomonitoring programs, often at minimal cost and effort. However, eDNA analyses are prone to errors that can complicate their use in management frameworks. To address this, eDNA studies must consider imperfect detections and estimate error rates. Detecting nuisance species at low abundances with minimal uncertainty is vital for successful containment and eradication. We developed a novel eDNA assay to detect a nuisance marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one of the world's largest marine reserves. Chondria tumulosa is a cryptogenic red alga with invasive traits, forming dense mats that overgrow coral reefs and smother native flora and fauna in PMNM. We verified the eDNA assay using site-occupancy detection modeling from quantitative polymerase chain reaction (qPCR) data, calibrated with visual estimates of benthic cover of C. tumulosa that ranged from < 1% to 95%. Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. Overall, the probability of detecting C. tumulosa at occupied sites was at least 92% when multiple qPCR replicates were positive. False-positive rates were 3% or less and false-negative errors were 11% or less. The assay proved effective for routine monitoring at shallow sites (less than 10 m), even when C. tumulosa abundance was below 1%. Successful implementation of eDNA tools in conservation decision-making requires balancing uncertainties in both visual and molecular detection methods. Our results and modeling demonstrated the assay's high sensitivity to C. tumulosa, and we outline steps to infer ecological presence-absence from molecular data. This reliable, cost-effective tool enhances the detection of low-abundance species, and supports timely management interventions.

Impact of Surface Adsorption on DNA Structure and Stability: Implications for Environmental DNA Interactions with Iron Oxide Surfaces

Environmental DNA (eDNA), i.e., DNA found in the environment, can interact with various geochemical surfaces, yet little is known about these interactions. Mineral surfaces may alter the structure, stability, and reactivity of eDNA, impacting the cycling of genetic information and the reliability of eDNA-based detection tools. Understanding how eDNA interacts with surfaces is crucial for predicting its fate in the environment. In this study, we examined the surface interaction and stability of herring testes DNA, a model system for eDNA, on two common iron oxide phases present in the environment: α-FeOOH (goethite) and α-Fe2O3 (hematite). Utilizing spectroscopic probes, including attenuated total reflection Fourier-transform infrared (ATR-FTIR) and UV-vis spectroscopy, we quantified the DNA adsorption capacity at pH 5 and determined its secondary structure. DNA adsorbed irreversibly at pH 5 and 25 °C, primarily through its phosphate groups, and retained the solution-phase B-form structure. However, the infrared data also indicated some distortion of the B-form likely due to additional interactions between nitrogenous bases when adsorbed on the α-Fe2O3 particle surfaces. The distortion in the double helical structure of adsorbed DNA on α-Fe2O3 led to a lower melting temperature (Tm) of 60 °C compared to 70 °C for DNA in solution. In contrast, DNA adsorbed on α-FeOOH melted at higher temperatures relative to solution-phase DNA and in two distinct phases. Upon testing adsorbed DNA stability at higher pH values, there were distinct differences between the two iron oxide phases. For α-FeOOH, nearly 50% of the DNA desorbed from the surface when the solution pH changed from 5 to 8, while less than 5% desorbed from α-Fe2O3 under the same conditions. Overall, these findings underscore the importance of mineral-specific eDNA-surface interactions and their role in adsorbed eDNA stability, in terms of DNA melting and the impact of solution-phase pH changes.

The forensic potential of environmental DNA (eDNA) in freshwater wildlife crime investigations: From research to application

Environmental DNA (eDNA) is widely used in biodiversity, conservation, and ecological studies but despite its successes, similar approaches have not yet been regularly applied to assist in wildlife crime investigations. The purpose of this paper is to review current eDNA methods and assess their potential forensic application in freshwater environments considering collection, transport and persistence, analysis, and interpretation, while identifying additional research required to present eDNA evidence in court. An extensive review of the literature suggests that commonly used collection methods can be easily adapted for forensic frameworks providing they address the appropriate investigative questions and take into consideration the uniqueness of the target species, its habitat, and the requirements of the end user. The use of eDNA methods to inform conservationists, monitor biodiversity and impacts of climate change, and detect invasive species and pathogens shows confidence within the scientific community, making the acceptance of these methods by the criminal justice system highly possible. To contextualise the potential application of eDNA on forensic investigations, two test cases are explored involving i) species detection and ii) species localisation. Recommendations for future work within the forensic eDNA discipline include development of suitable standardised collection methods, considered collection strategies, forensically validated assays and publication of procedures and empirical research studies to support implementation within the legal system.

Enhancing the DNA yield intended for microbial sequencing from a low-biomass chlorinated drinking water

DNA extraction yield from drinking water distribution systems and premise plumbing is a key metric for any downstream analysis such as 16S amplicon or metagenomics sequencing. This research aimed to optimize DNA yield from low-biomass (chlorinated) reverse osmosis-produced tap water by evaluating the impact of different factors during the DNA extraction procedure. The factors examined are (1) the impact of membrane materials and their pore sizes; (2) the impact of different cell densities; and (3) an alternative method for enhancing DNA yield via incubation (no nutrient spiking). DNA from a one-liter sampling volume of RO tap water with varying bacterial cell densities was extracted with five different filter membranes (mixed ester cellulose 0.2 μm, polycarbonate 0.2 μm, polyethersulfone 0.2 and 0.1 μm, polyvinylidene fluoride 0.1 μm) for biomass filtration. Our results show that (i) smaller membrane pore size solely did not increase the DNA yield of low-biomass RO tap water; (ii) the DNA yield was proportional to the cell density and substantially dependent on the filter membrane properties (i.e., the membrane materials and their pore sizes); (iii) by using our optimized DNA extraction protocol, we found that polycarbonate filter membrane with 0.2 μm pore size markedly outperformed in terms of quantity (DNA yield) and quality (background level of 16S gene copy number) of recovered microbial DNA; and finally, (iv) for one-liter sampling volume, incubation strategy enhanced the DNA yield and enabled accurate identification of the core members (i.e., Porphyrobacter and Blastomonas as the most abundant indicator taxa) of the bacterial community in low-biomass RO tap water. Importantly, incorporating multiple controls is crucial to distinguish between contaminant/artefactual and true taxa in amplicon sequencing studies of low-biomass RO tap water.

Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums

Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.

Methodological considerations for aqueous environmental RNA collection, preservation, and extraction

Environmental RNA (eRNA) analysis is expected to infer species' physiological information (health status, developmental stage, and environmental stress response) and their distribution and composition more correctly than environmental DNA (eDNA) analysis. With the prospect of such eRNA applications, there is an increasing need for technological development for efficient eRNA detection because of its physicochemical instability. The present study conducted a series of aquarium experiments using zebrafish (Danio rerio) and validated the methodologies for capture, preservation, and extraction of eRNA in a water sample. In the eRNA extraction experiment, an approximately 1.5-fold increase in lysis buffer volume resulted in a more than sixfold increase in target eRNA concentration. In the eRNA capture experiment, although GF/F and GF/A filters yielded similar eRNA concentrations, a GF/A filter may be capable of passing through more volume of water samples and consequently collecting more eRNA particles, given the time required for water filtration. In the eRNA preservation experiment, the use of RNA stabilization reagent (RNAlater) allowed for stably preserving target eRNA on a filter sample at - 20 and even 4 °C for 6 days at least. Altogether, the findings enable the improvement of eRNA availability from the field and easily preserve eRNA samples without deep-freezing, which will contribute to the refinement of eRNA analysis for biological and physiological monitoring in aquatic ecosystems.

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.

Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses

Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states of eDNA on its persistence is not completely understood. Here, we performed meta-analyses including 26 previously published papers on the estimation of first-order eDNA decay rate constants, and assessed the effects of filter pore size, DNA fragment size, target gene, and environmental conditions on eDNA decay rates. Almost all supported models included the interactions between the filter pore size and water temperature, between the target gene and water temperature, and between the target gene and water source, implying the influence of complex interactions between the eDNA state and environmental conditions on eDNA persistence. These findings were generally consistent with the results of a reanalysis of a previous tank experiment which measured the time-series changes in marine fish eDNA concentrations in multiple size fractions after fish removal. Our results suggest that the mechanism of eDNA persistence and degradation cannot be fully understood without knowing not only environmental factors but also cellular and molecular states of eDNA in water. Further verification of the relationship between eDNA state and persistence is required by obtaining more information on eDNA persistence in various experimental and environmental conditions, which will enhance our knowledge on eDNA persistence and support our findings.