Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

Abstract

Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

When conventional methods fall short: identification of invasive cryptic Golden Apple Snails (Pomacea canaliculata; P. maculata) using environmental DNA

“…(Matsukura & Wada, 2017). Furthermore, the use of Environmental DNA or "eDNA" has provided a promising non-invasive/ non-destructive approach for quick monitoring (Taberlet et al, 2012;Banerjee et al, 2021). In fact, monitoring approaches using eDNA based methods have gained popularity amongst ecologists, conservation biologists, and wildlife managers as it generally: (i) does not require direct observation or handling of organisms (Taberlet et al, 2012).…”

“…In fact, monitoring approaches using eDNA based methods have gained popularity amongst ecologists, conservation biologists, and wildlife managers as it generally: (i) does not require direct observation or handling of organisms (Taberlet et al, 2012). This approach thus provides detection (presence/absence), relative abundance, distribution, and even species interaction data in a fast, cheap, and non-invasive manner (Qu & Stewart, 2019;Banerjee et al, 2021); (ii) is found to be equally (or more) accurate as compared to conventional methods for various species (Kuzmina et al, 2018)-especially in circumstances of low abundance, extreme habitats, phenotypic plasticity, juvenile stages, and during the early stages of invasion; and (iii) records a higher diversity of taxa in a single sampling than morphological and DNA-based (tissue samples) methods (McElroy et al, 2020;Fediajevaite et al, 2021). In fact, eDNA-based methods are well known for detecting invasive species early during colonization (Ficetola et al, 2008), and recent optimization/standardization practices have improved their accuracy for more reliable detection of targeted species, reinforcing eDNA's trustworthiness for field applications (Deiner et al, 2021).…”

Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords

“…An additional cause to such patterns could also be explained due to amplification efficiency. Sequence abundance output is subjected to amplification biases due to primer efficiency (Kelly et al, 2019), especially when using universal primers, where selected taxa have a higher match with the primer than others (Banerjee et al, 2021). Such biases influence the commonness of the species, which can lead to divergence from the true species as drivers of differences between ecosystems (since low amplification species will be encouraged to be the species indicators).…”

Evaluating eDNA for Use within Marine Environmental Impact Assessments

“…In addition to the large number of unknowns about the fate of DNA, other authors have noted that there is not yet enough methodological validation of sample processing steps (i.e., filtration, preservation, amplification and sequencing) before sequences are read and aligned [4,35]. Presently, frequently cited problematic issues in eDNA studies are the lack of standardization of the methods, incompleteness of referenced sequence database, and lack of appropriate contamination controls, or sensitivity measures [36,56,57]. Together these create many theoretical and analytical challenges for the interpretation of eDNA results within EIA.…”