Why eDNA fractions need consideration in biomonitoring

Multicellular species environmental DNA (eDNA) research constrained by overfocus on mitochondrial DNA

Environmental DNA (eDNA) is becoming an established tool across the biological and medical sciences. Despite the evident successes and wide adoption of eDNA approaches, some fundamental questions remain. For instance, there is almost a dogma in the field around the superiority of mitochondrial DNA for use in eDNA studies, however robust comparison with nuclear eDNA is widely lacking. The dominance of mitochondrial-based eDNA for animal and plant studies appears to be largely settled, despite a widespread lack of rigorous nuclear eDNA testing. Outside of the source organism the protections conferred on eDNA by the cell, mitochondrial and nuclear membranes are poorly understood, including the contribution of each to eDNA persistence and degradation. Utilizing shotgun sequencing to unbiasedly assess the level of nuclear and mitochondrial eDNA across samples, we reveal stark differences in nuclear versus mitochondrial eDNA persistence and abundance. By focusing too heavily on mitochondrial DNA alone the field is underutilizing eDNA's full potential.

New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review

Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.

Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6-18 h for open mesocosms versus 18-48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0-0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.

Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review

MAIN CONCLUSION

Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.

Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters

Environmental DNA (eDNA) in aquatic systems is a complex mixture that includes dissolved DNA, intracellular DNA, and particle-adsorbed DNA. Information about the various components of eDNA and their relative proportions could be used to discern target organism abundance and location. However, a limited knowledge of eDNA adsorption dynamics and interactions with other materials hinders these applications. To address this gap, we used recirculating stream mesocosms to investigate the impact of suspended materials (fine particulate organic matter, plankton, clay, and titanium dioxide) on the eDNA concentration and particle size distribution (PSD) from two fish species in flowing water. Our findings revealed that eDNA rapidly adsorbs to other materials in the water column, affecting its concentration and PSD. Nonetheless, only particulate organic matter affected eDNA removal rate after 30 h. Moreover, we observed that the removal of larger eDNA components (≥10 μm) was more strongly influenced by physical processes, whereas the removal of smaller eDNA components was driven by biological degradation. This disparity in removal mechanisms between larger and smaller eDNA components could explain changes in eDNA composition over time and space, which have implications for modeling the spatial distribution and abundance of target species and optimizing eDNA detection in high turbidity systems.

An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization

Background

Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity.

Methods

A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis.

Results

The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.

Pooling of intra-site measurements inflates variability of the correlation between environmental DNA concentration and organism abundance

Environmental DNA (eDNA) analysis can promote efficient ecosystem monitoring and resource management. However, limited knowledge of the factors affecting the relationship between eDNA concentration and organism abundance causes uncertainty in relative abundance estimates based on eDNA concentration. Pooling of data points obtained from multiple locations within a site has been used to mitigate intra-site variation in eDNA and abundance estimates, but decreases the sample size used for estimating the relationship. I here assessed how the pooling of intra-site measurements of eDNA concentration and organism abundance impacted the reliability of the correlative relationship between eDNA concentration and organism abundance. Mathematical models were developed to simulate measurements of eDNA concentrations and organism abundances from multiple locations in a given survey site, and the CVs (coefficient of variability) of the correlations were compared depending on whether data points from different locations were individually treated or pooled. Although the mean and median values of the correlation coefficients were similar between the scenarios, the CVs of the simulated correlations were substantially higher under the pooled scenario than the individual scenario. Additionally, I re-analyzed two empirical studies conducted in lakes, both showing higher CVs of the correlations by pooling intra-site measurements. This study suggests that it would make eDNA-based abundance estimation more reliable and reproducible to individually analyze target eDNA concentrations and organism abundance estimates.

Special Issue on ‘Hide and Seek of Soil Microbes—Who Is Where with Whom and Why?’

Our question posed for and used as title of the special issue ‘Hide and Seek of Soil Microbes’–Who is Where with Whom and Why [...]