Environmental DNA
[9] On 7 December 2022 a study in Nature reported the recovery of two-million year old eDNA in sediments from Greenland, which is currently considered the oldest DNA sequenced so far.
[6] eDNA can come from skin, mucous, saliva, sperm, secretions, eggs, feces, urine, blood, roots, leaves, fruit, pollen, and rotting bodies of larger organisms, while microorganisms may be obtained in their entirety.
[20] Additionally, eDNA is capable of detecting rare species,[21][17] but not of determining population quality information such as sex ratios and body conditions, so it is ideal for supplementing traditional studies.
Additionally, the varying lengths of time to degradation based on environmental conditions and the potential of DNA to travel throughout media such as water can affect inference of fine-scale spatiotemporal trends of species and communities.
[17][22][16][23][18][20][19] Despite these drawbacks, eDNA still has the potential to determine relative or rank abundance as some studies have found it to correspond with biomass, though the variation inherent in environmental samples makes it difficult to quantify.
The selfDNA phenomenon has been postulated to drive ecological interactions and to be mechanistically mediated by damage-associated molecular patterns (DAMPs)[29][30] and to have potential for the development of biocidal applications.
[32][22][25][20] Ecosystem-wide applications of eDNA metabarcoding have the potential to not only describe communities and biodiversity, but also to detect interactions and functional ecology over large spatial scales,[33] though it may be limited by false readings due to contamination or other errors.
[32][7][34][25][19] Altogether, eDNA metabarcoding increases speed, accuracy, and identification over traditional barcoding and decreases cost, but needs to be standardized and unified, integrating taxonomy and molecular methods for full ecological study.
[40] Various possible functions have been proposed for eDNA: it may be involved in horizontal gene transfer;[41] it may provide nutrients;[42] and it may act as a buffer to recruit or titrate ions or antibiotics.
[46] Under the name of environmental DNA, eDNA has seen increased use in the natural sciences as a survey tool for ecology, monitoring the movements and presence of species in water, air, or on land, and assessing an area's biodiversity.
[74] Terrestrial arthropods are experiencing massive decline in Europe as well as globally,[75][76][77][78] although only a fraction of the species have been assessed and the majority of insects are still undescribed to science.
[82] For instance, pollinators like bees and butterflies represent an important ecological group that has undergone severe decline in Europe, indicating a dramatic loss of grassland biodiversity.
In some instances, these techniques fall short of performing efficient and standardized surveys, due to, for example, phenotypic plasticity, closely related species, and difficulties in identifying juvenile stages.
DNA from snow track samples has been used to confirm the presence of such elusive and rare species as polar bears, arctic fox, lynx, wolverines, and fishers.
[115][116][117][118] In 2023, scientists developed a specialized sampling probe and aircraft surveys to assess biodiversity of multiple taxa, including mammals, using air eDNA.
Atlantic cod (Gadus morhua) is an iconic example that demonstrates how poorly constrained data and uninformed decision making can result in catastrophic stock decline and ensuing economic and social problems.
[121] Traditional stock assessments of demersal fish species have relied primarily on trawl surveys, which have provided a valuable stream of information to decision makers.
[122] However, there are some notable drawbacks of demersal trawl surveys including cost,[123] gear selectivity/catchability,[124] habitat destruction[125] and restricted coverage (e.g. hard-substrate bottom environments, marine protected areas).
The constant loss and shedding of genetic material from macroorganisms imparts a molecular footprint in environmental samples that can be analysed to determine either the presence of specific target species [13][127] or characterise biodiversity.
[128][129] The combination of next generation sequencing and eDNA sampling has been successfully applied in aquatic systems to document spatial and temporal patterns in the diversity of fish fauna.
Furthermore, in oceanic systems, large habitat volumes and strong currents are likely to result in physical dispersal of DNA fragments away from target organisms.
[149][150][151][152] Previous studies provided evidence that an important fraction of extracellular DNA can escape degradation processes, remaining preserved in the sediments.
[155][156][157] In particular, extracellular DNA has been used to reconstruct past prokaryotic and eukaryotic diversity in benthic ecosystems characterized by low temperatures and/or permanently anoxic conditions.
[148] Previous studies suggested that the preservation of DNA might be also favoured in benthic systems characterised by high organic matter inputs and sedimentation rates, such as continental margins.
[179] Despite the long exposure to degradation under oxic conditions during transport in the water column, and substantially lower concentration of organic matter on the seafloor, there is evidence that planktonic eDNA is preserved in marine sediments and contains exploitable ecological signal.
In addition, if the plankton eDNA is arriving on the seafloor in association with aggregates or shells, it is possible that it withstands the transport through the water column by fixation onto mineral surfaces.
[179] Planktonic foraminifera sedaDNA is an ideal proxy both “horizontally” to assess the spatial resolution of reconstructing past surface ocean hydrographic features and “vertically”, to unambiguously track the burial of its signal throughout the sediment column.
eDNA is a powerful tool to study ecosystem because it does not require direct taxonomic knowledge thus allowing information to be gathered on every organism present in a sample, even at the cryptic level.
[187][188] Importantly, the composition of planktonic foraminifera communities is closely linked to surface hydrography and this signal is preserved by fossil tests deposited on the seafloor.
This can empower local communities (including Indigenous peoples) to be actively involved in monitoring the species in an environment, and help make informed decisions as part of participatory action research model.
