Science AI Journal
Environmental Science · Research topic

Open research questions in Environmental DNA in Biodiversity Studies

114 unresolved questions extracted from the limitations and future-work sections of 382 Environmental DNA in Biodiversity Studies papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • The quantitative accuracy and bias of DNA metabarcoding in reconstructing dietary composition remain a limitation across taxa and sample types. Differential digestion biases can affect DNA metabarcoding results. The study faced challenges in detecting and proportionally representing a target species, Medicago sativa, when added to the diet in varying amounts.

    Evaluating the Quantitative Accuracy and Application of DNA Metabarcoding for Dietary Reconstruction in Ruminants · 2026 · DOI

  • multi‐marker approaches should be explored, - calibration controls should be developed, - further studies on differential digestion biases are needed, - research on low-digestibility conditions is required

    Evaluating the Quantitative Accuracy and Application of DNA Metabarcoding for Dietary Reconstruction in Ruminants · 2026 · DOI

  • The complexity of eDNA workflows and technical language can create a barrier to understanding for non-molecular ecologists. The need for a simple and memorable way to communicate complex eDNA workflows. The importance of understanding false negatives and occupancy modeling in eDNA metabarcoding.

    Making eDNA more digestible: A pizza analogy for understanding false negatives and occupancy modeling · 2026 · DOI

  • While the influence of individual environmental properties on the presence of target eDNA has been widely studied, it remains unclear how variables like temperature, pH, flow rate and conductivity correlate collectively with site electrofishing counts and eDNA concentrations.

    Mining association rules for targeted spatiotemporal aquatic environmental DNA (eDNA) sampling · 2026 · DOI

  • Dormant taxa exhibited a broader taxonomic distribution than previously recognized, underscoring the need for further research on microbial ecophysiology, function, and biogeography across temporal and spatial scales.

    Seasonally and niche-differentiated diversity of active, dormant and dead microbes in coastal waters and surface sediments · 2025 · DOI

  • Overall, small-bodied fish dominate the mainstem of the Jialing River, and the species preferring flowing habitats are relatively scarce.

    Environmental DNA Insights into the Spatial Status of Fish Diversity in the Mainstem of the Jialing River · 2025 · DOI

  • Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity.

    eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities · 2024 · DOI

  • , DNA found in the environment, can interact with various geochemical surfaces, yet little is known about these interactions.

    Impact of Surface Adsorption on DNA Structure and Stability: Implications for Environmental DNA Interactions with Iron Oxide Surfaces · 2024 · DOI

  • The study was conducted in controlled indoor tanks and outdoor ponds, which may not reflect all environmental conditions. The sample size was limited, with 6 indoor tanks and 3 outdoor ponds. The study did not consider samples from ponds in qPCR analysis.

    Passive eDNA sampling as a method for freshwater crayfish monitoring · 2026 · DOI

  • There is a lack of systematic evaluations of passive eDNA sampling for monitoring freshwater crayfish. Prior work has focused on active filtration, but passive eDNA sampling has the potential to be a more efficient and cost-effective method.

    Passive eDNA sampling as a method for freshwater crayfish monitoring · 2026 · DOI

  • Biomonitoring in the Arctic is challenging and time-consuming - Current approaches are limited by effort and expertise - Climate change is inducing rapid changes in Arctic ecosystems

    Tracking biodiversity in changing Arctic waters: insights from eDNA metabarcoding in Svalbard · 2026 · DOI

  • Current approaches for monitoring biodiversity in Arctic coastal ecosystems are limited - There is a need for effective methods to study species composition in Arctic waters

    Tracking biodiversity in changing Arctic waters: insights from eDNA metabarcoding in Svalbard · 2026 · DOI

  • There is a lack of understanding of the species distribution characteristics of H. bleekeri. The study aims to address this gap using metagenomic and amplicon sequencing.

    Metagenomic and amplicon sequencing reveal the species distribution characteristics of the critically endangered Hucho bleekeri in wild and farmed environments · 2026 · DOI

  • The study was limited to 16 sites and 31 seawater samples. The study did not include a comprehensive analysis of the impacts of climate change on marine vertebrate diversity.

    Winter is leaving: an eDNA-based assessment of marine vertebrate diversity in Svalbard coastal waters · 2026 · DOI

  • There is a lack of biodiversity assessments in the Arctic due to logistical constraints and protection regulations. The study addresses this gap by using eDNA metabarcoding to assess marine vertebrate diversity in Svalbard coastal waters.

    Winter is leaving: an eDNA-based assessment of marine vertebrate diversity in Svalbard coastal waters · 2026 · DOI

  • The challenge of quantifying abundance from eDNA surveys. Secondary DNA transfer, where DNA from organisms not present on site can be detected. Limited geographical certainty on the location of each eDNA detection, with a chance of it having come from anywhere within an 80 km radius.

    Gone with the Wind: Airborne Environmental DNA for Avian Biomonitoring · 2026 · DOI

  • Standardization of field protocols for aeDNA surveys. Development of detection probability databases and shedding rate databases. Repurposing air quality systems for aeDNA surveys. Citizen science projects to distribute DIY filter kits and compare aeDNA results with citizen-observed eBird lists.

    Gone with the Wind: Airborne Environmental DNA for Avian Biomonitoring · 2026 · DOI

  • Metabarcoding suffers from primer bias, which can lead to uneven amplification of species. Metagenomics has not been commonly used for fish communities and eDNA. There is a need to compare fish species detection between metabarcoding and metagenomics.

    Comparative analysis of eDNA metabarcoding and eDNA metagenomics for fish biodiversity estimates using standard and novel filtration methods · 2026 · DOI

  • Sampling methods differed between Guatemala and south Texas, - Outdoor mosquito collections may not reflect indoor feeding patterns, - Forage ratios depend on household-based host availability estimates, - Wild host communities were not surveyed, - Studies had limited sample sizes and sampling designs

    Bloodmeal metabarcoding reveals host feeding patterns for Aedes aegypti and Culex quinquefasciatus in Jutiapa, Guatemala and Texas, USA · 2026 · DOI

  • Investigate Ae. aegypti feeding patterns with more standardized sampling designs, - Interrogate differences in indoor and outdoor environments, - Examine the impact of household infrastructure on mosquito-human contact patterns, - Conduct further research on mixed feeding patterns and their implications for arbovirus transmission

    Bloodmeal metabarcoding reveals host feeding patterns for Aedes aegypti and Culex quinquefasciatus in Jutiapa, Guatemala and Texas, USA · 2026 · DOI

  • These results suggest that current DFO methods are insufficient to classify drains and, hence, adequately protect sensitive fishes and fish habitat within them.

    Protecting fishes in agricultural drains: evaluating Canadian policy using environmental DNA · 2026 · DOI

  • Future research could explore the use of coprolites as a source of ancient environmental DNA in other contexts. The study suggests that the use of metagenomic classification and authentication controls could be applied to other types of ancient DNA samples.

    Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years · 2026 · DOI

  • The gap is the lack of understanding of the preservation of ancient DNA in coprolites. The study identifies a need for new sources of ancient environmental DNA to study Quaternary ecosystems.

    Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years · 2026 · DOI

  • Reliable species identification from highly degraded DNA remains a critical methodological challenge. Standard reference-based and metagenomic classification approaches may generate false-positive assignments.

    A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA · 2026 · DOI

  • Several limitations should be acknowledged. While the pre- sent study focuses on collagen-based materials, the work- flow is designed to be adaptable to other types of degraded samples. Its application to different matrices may therefore be feasible, although further validation across diverse sub- strates would be required to fully assess its transferability. The accuracy of species attribution depends on the com- pleteness and phylogenetic coverage of the reference panel. S. Morelli et al. Reads originating from unrepresented or closely related taxa may be preferentially assigned to the most similar available genome or classified as shared, potentially leading to biased or ambiguous taxonomic signals. This reflects a fundamen- tal trade-off between sensitivity and specificity: a restricted reference panel improves interpretability and reduces spuri- ous assignments but may limit the detection of unexpected or unrepresented species, whereas broader panels increase sensitivity at the cost of higher ambiguity. In this study, the reference panel was intentionally restricted to species relevant to collagen-based glue produc- tion, enabling a controlled and application-specific compari- son while prioritizing interpretability over exhaustive taxo- nomic coverage. More generally, reference databases should be carefully curated and tailored to the expected taxonomic composition of the samples. Importantly, the read-ubiquity classifier does not force unambiguous assignment when evidence is insufficient, as reads mapping across multiple genomes are explicitly clas- sified as shared. However, when the true source species is absent from the panel, species-specific assignments should be interpreted with caution. Controlled mixtures with known species proportions would provide a more systematic framework to evaluate performance under varying levels of mixture complexity and cross-mapping and represent an important direction for future work. Although the dataset includes closely related taxa (e.g. bovine, ovine, and caprine species), further valida- tion using controlled mixtures would be necessary to sys- tematically assess the discriminatory power of the workflow. The performance of the workflow may be influenced by fragment length, sequencing depth, and library complex- ity. While fragment length distributions are provided in this study, a systematic evaluation of detection thresholds across varying fragment sizes and coverage levels would represent an important direction for future work. Additionally, uneven sequencing depth or pooling imbalance may influence the absolute number of species-specific reads, although relative patterns remained stable across treatments in this study. Tar- geted capture strategies could enhance sensitivity in some contexts, but their effectiveness depends on prior knowledge of expected taxa and may be less suitable for unknown or heterogeneous samples.

    A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA · 2026 · DOI

Most-cited papers in Environmental DNA in Biodiversity Studies

Most recent work

Find a gap in your own Environmental DNA in Biodiversity Studies sub-topic

This page shows what the Environmental DNA in Biodiversity Studies literature already flags as unresolved. To narrow it to your specific question, run the guided finder — it searches the gap library on demand and checks candidates against 250M+ OpenAlex works.

Open the Research Gap Finder →

Related topics in Environmental Science

Environmental Education and Sustainability
814 open questions
Microplastics and Plastic Pollution
446 open questions
Climate variability and models
410 open questions
Urban Green Space and Health
407 open questions
Research studies in Vietnam
406 open questions
Remote Sensing in Agriculture
384 open questions
Sustainability and Climate Change Governance
376 open questions
Land Use and Ecosystem Services
371 open questions
114 open questions have been extracted from the limitations and future-work passages of 382 Environmental DNA in Biodiversity Studies papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

Tools for your next paper

Gaps & Literature SearchFind open questions in any field — 120,000+ open gaps mined from our own library.Pre-CheckIs your paper ready? A Tier 1–5 acceptance probability in seconds.Journal FinderA ranked shortlist of target journals from a 17,500-venue index.Duplicate Publication CheckerCheck prior-publication & salami-slicing risk across 8 sources.Citation GeneratorFreeA DOI or title → APA, MLA, Vancouver, Chicago, BibTeX, RIS. No signup.Graphical Abstract MakerFreeTurn your findings into a colorblind-safe graphical abstract.

Compare the category — Honest roundups of the AI research tools, ours listed alongside the alternatives.

Command palette

Jump anywhere, run any action.