![Longhorn beetle Leptura quadrifasciata](https://upload.wikimedia.org/wikipedia/commons/d/de/Longhorn_beetle_Leptura_quadrifasciata.jpg)
Environmental DNA or eDNA is
DNA that is collected from a variety of environmental samples such as
soil
Soil, also commonly referred to as earth or dirt
Dirt is an unclean matter, especially when in contact with a person's clothes, skin, or possessions. In such cases, they are said to become dirty.
Common types of dirt include:
* Debri ...
,
seawater
Seawater, or salt water, is water from a sea or ocean. On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/L, 35 ppt, 600 mM). This means that every kilogram (roughly one liter by volume) of seawater has appr ...
,
snow
Snow comprises individual ice crystals that grow while suspended in the atmosphere—usually within clouds—and then fall, accumulating on the ground where they undergo further changes.
It consists of frozen crystalline water throughout ...
or
air
The atmosphere of Earth is the layer of gases, known collectively as air, retained by Earth's gravity that surrounds the planet and forms its planetary atmosphere. The atmosphere of Earth protects life on Earth by creating pressure allowing f ...
, rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources.
In recent years, eDNA has been used as a tool to detect endangered wildlife that were otherwise unseen. In 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic.
Example sources of eDNA include, but are not limited to,
feces,
mucus
Mucus ( ) is a slippery aqueous secretion produced by, and covering, mucous membranes. It is typically produced from cells found in mucous glands, although it may also originate from mixed glands, which contain both serous and mucous cells. It ...
,
gametes
A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
,
shed skin,
carcasses and
hair.
Samples can be analyzed by
high-throughput DNA sequencing methods, known as
metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...
,
metabarcoding
Metabarcoding is the barcoding of DNA/ RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does ...
, and single-species detection, for rapid monitoring and
measurement of biodiversity
Conservation biologists have designed a variety of objective means to measure biodiversity empirically. Each measure of biodiversity relates to a particular use of the data. For practical conservationists, measurements should include . For oth ...
. In order to better differentiate between organisms within a sample, DNA
metabarcoding
Metabarcoding is the barcoding of DNA/ RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does ...
is used in which the sample is analyzed and uses previously studied DNA libraries, such as
BLAST
Blast or The Blast may refer to:
*Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film), ...
, to determine what organisms are present.
eDNA metabarcoding
Metabarcoding is the barcoding of DNA/ RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does ...
is a novel method of assessing
biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') l ...
wherein samples are taken from the environment via water, sediment or air from which DNA is extracted, and then
amplified using general or
universal primers in
polymerase chain reaction
The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) ...
and
sequenced
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which suc ...
using
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...
to generate thousands to millions of reads. From this data, species presence can be determined, and overall biodiversity assessed. It is an interdisciplinary method that brings together traditional field-based ecology with in-depth
molecular methods
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
and advanced computational tools.
[ ]
Modified text was copied from this source, which is available under
Creative Commons Attribution 4.0 International License
The analysis of eDNA has great potential, not only for monitoring common species, but to genetically detect and identify other extant species that could influence conservation efforts.
This method allows for biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism. Access to this genetic information makes a critical contribution to the understanding of population size,
species distribution, and
population dynamics for species not well documented. Importantly, eDNA is often more cost-effective compared to traditional sampling methods. The integrity of eDNA samples is dependent upon its preservation within the environment.
Soil,
permafrost, freshwater and seawater are well-studied macro environments from which eDNA samples have been extracted, each of which include many more conditioned
subenvironments.
Because of its versatility, eDNA is applied in many
subenvironments such as freshwater sampling, seawater sampling, terrestrial soil sampling (tundra permafrost), aquatic soil sampling (river, lake, pond, and ocean sediment),
or other environments where normal sampling procedures can become problematic.
On 7 December 2022, ''
The New York Times
''The New York Times'' (''the Times'', ''NYT'', or the Gray Lady) is a daily newspaper based in New York City with a worldwide readership reported in 2020 to comprise a declining 840,000 paid print subscribers, and a growing 6 million paid ...
'' reported that two-million year old eDNA genetic material was found in Greenland, and is currently considered the oldest DNA discovered so far.
Overview
File:Global ecosystem and biodiversity monitoring with environmental DNA metabarcoding.jpg, Global ecosystem and biodiversity monitoring
with environmental DNA metabarcoding
Environmental DNA or eDNA describes the genetic material present in environmental samples such as sediment, water, and air, including whole cells, extracellular DNA and potentially whole organisms.
The analyse of eDNA start with capturing an environmental sample of interest. The DNA in the sample is
extracted and purified. The purified DNA is then
amplified for a specific gene target so it can be
sequenced
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which suc ...
and categorised based on its sequence. From this information, detection and classification of species is possible.
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.
eDNA production is dependent on biomass, age and feeding activity of the organism as well as physiology, life history, and space use.
Despite being a relatively new method of surveying, eDNA has already proven to have enormous potential in
biological monitoring. Conventional methods for surveying richness and abundance are limited by
taxonomic identification
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
, may cause disturbance or destruction of habitat, and may rely on methods in which it is difficult to detect small or elusive species, thus making estimates for entire communities impossible. eDNA can complement these methods by targeting different species, sampling greater diversity, and increasing
taxonomic resolution
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called "sequences"), an indiv ...
.
Additionally, eDNA is capable of detecting
rare species,
but not of determining population quality information such as sex ratios and body conditions, so it is ideal for supplementing traditional studies.
Regardless, it has useful applications in detecting the first occurrences of invasive species, the continued presence of native species thought to be extinct or otherwise threatened, and other elusive species occurring in low densities that would be difficult to detect by traditional means.
Degradation of eDNA in the environment limits the scope of eDNA studies, as often only small segments of genetic material remain, particularly in warm, tropical regions. 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.
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.
While eDNA has numerous applications in conservation, monitoring, and ecosystem assessment, as well as others yet to be described, the highly variable concentrations of eDNA and potential heterogeneity through the water body makes it essential that the procedure is optimized, ideally with a pilot study for each new application to ensure that the sampling design is appropriate to detect the target.
Community DNA
While the definition of eDNA seems straightforward, the lines between different forms of DNA become blurred, particularly in comparison to
community DNA, which is described as bulk organismal samples.
A question arises regarding whole microorganisms captured in eDNA samples: do these organisms alter the classification of the sample to a community DNA sample? Additionally, the classification of genetic material from feces is problematic and often referred to as eDNA.
Differentiation between the two is important as community DNA indicates organismal presence at a particular time and place, while eDNA may have come from a different location, from predator feces, or from past presence, however this differentiation is often impossible.
However, eDNA can be loosely classified as including many sectors of DNA biodiversity research, including fecal analysis and bulk samples when they are applicable to biodiversity research and ecosystem analysis.
selfDNA
The concept of selfDNA stems from discoveries made by scientists from the
University of Naples Federico II
The University of Naples Federico II ( it, Università degli Studi di Napoli Federico II) is a public university in Naples, Italy. Founded in 1224, it is the oldest public non-sectarian university in the world, and is now organized into 26 depar ...
, which were reported during 2015 in the journal ''
New Phytologist
''New Phytologist'' is a peer-reviewed scientific journal published on behalf of the New Phytologist Foundation by Wiley-Blackwell. It was founded in 1902 by botanist Arthur Tansley, who served as editor until 1931.
Topics covered
''New Phytolo ...
'', about the self-inhibitory effect of
extracellular DNA in plants, but also in bacteria, fungi, algae, plants, protozoa and insects. The environmental source of such extracellular DNA is proposed to be
plant litter
Plant litter (also leaf litter, tree litter, soil litter, litterfall or duff) is dead plant material (such as leaves, bark, needles, twigs, and cladodes) that have fallen to the ground. This detritus or dead organic material and its constitue ...
but also other sources in different ecosystems and organisms, with the size of DNA fragments experimentally shown to have an inhibitory effect upon their conspecific organisms typically ranging between 200 and 500 base pairs. The selfDNA phenomenon has been postulated to drive ecological interactions and to be mechanistically mediated by
damage-associated molecular patterns
Damage-associated molecular patterns (DAMPs) are molecules within cells that are a component of the innate immune response released from damaged or dying cells due to trauma or an infection by a pathogen. They are also known as danger-associated ...
(DAMPs) and to have potential for the development of biocidal applications.
eDNA metabarcoding
File:Applications of environmental DNA metabarcoding in aquatic and terrestrial ecosystems.jpg, Applications of environmental DNA metabarcoding in aquatic and terrestrial ecosystems
By 2019 methods in eDNA research had been expanded to be able to assess whole communities from a single sample. This process involves
metabarcoding
Metabarcoding is the barcoding of DNA/ RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does ...
, which can be precisely defined as the use of general or universal
polymerase chain reaction
The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) ...
(PCR) primers on mixed DNA samples from any origin followed by
high-throughput next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...
(NGS) to determine the species composition of the sample. This method has been common in microbiology for years, but is only just finding its footing in assessment of macroorganisms.
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, though it may be limited by false readings due to contamination or other errors.
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.
eDNA metabarcoding has applications to diversity monitoring across all habitats and taxonomic groups, ancient ecosystem reconstruction,
plant-pollinator interactions
A pollination network is a bipartite mutualistic network in which plants and pollinators are the nodes, and the pollination interactions form the links between these nodes. The pollination network is bipartite as interactions only exist between ...
, diet analysis, invasive species detection, pollution responses, and air quality monitoring. eDNA metabarcoding is a unique method still in development and will likely remain in flux for some time as technology advances and procedures become standardized. However, as metabarcoding is optimized and its use becomes more widespread, it is likely to become an essential tool for ecological monitoring and global conservation study.
Extracellular and relic DNA
File:Modeling relic DNA dynamics.jpg, Relic DNA dynamics[ ]
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Creative Commons Attribution 4.0 International License
Extracellular DNA, sometimes called relic DNA, is DNA from dead microbes. Naked extracellular DNA (eDNA), most of it released by cell death, is nearly ubiquitous in the environment. Its concentration in soil may be as high as 2 μg/L, and its concentration in natural aquatic environments may be as high at 88 μg/L.
Various possible functions have been proposed for eDNA: it may be involved in
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
;
it may provide nutrients;
and it may act as a buffer to recruit or titrate ions or antibiotics.
Extracellular DNA acts as a functional extracellular matrix component in the
biofilm
A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular ...
s of several bacterial species. It may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm;
it may contribute to biofilm formation;
and it may contribute to the biofilm's physical strength and resistance to biological stress.
Under the name of environmental DNA, eDNA has seen increased use in the natural sciences as a survey tool for
ecology
Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps wi ...
, monitoring the movements and presence of species in water, air, or on land, and assessing an area's biodiversity.
In the diagram on the right, the amount of relic DNA in a microbial environment is determined by inputs associated with the mortality of viable individuals with intact DNA and by losses associated with the degradation of relic DNA. If the diversity of sequences contained in the relic DNA pool is sufficiently different from that in the intact DNA pool, then relic DNA may bias estimates of microbial biodiversity (as indicated by different colored boxes) when sampling from the total (intact + relic) DNA pool.
Standardised Data on Initiatives (STARDIT) has been proposed as one way of standardising both data about sampling and analysis methods, and taxonomic and ontological relationships.
Collection
Terrestrial sediments
File:Methodological approaches in modern and ancient marine genomics.jpg, (a) Metabarcoding
Metabarcoding is the barcoding of DNA/ RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does ...
is the amplification and analysis of equally sized DNA fragments from a total DNA extract. (b) Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...
is the extraction, amplification, and analysis of all DNA fragments independent of size. (c) Target-capture describes the enrichment and analysis of specific (chosen) DNA fragments independent of size from a total DNA extract.
The importance of eDNA analysis stemmed from the recognition of the limitations presented by
culture
Culture () is an umbrella term which encompasses the social behavior, institutions, and norms found in human societies, as well as the knowledge, beliefs, arts, laws, customs, capabilities, and habits of the individuals in these groups.Tyl ...
-based studies.
Organisms have adapted to thrive in the specific conditions of their natural environments. Although scientists work to mimic these environments, many microbial organisms can not be removed and cultured in a laboratory setting.
The earliest version of this analysis began with ribosomal RNA (
rRNA
Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosoma ...
) in microbes to better understand microbes that live in hostile environments.
The genetic makeup of some microbes is then only accessible through eDNA analysis. Analytical techniques of eDNA were first applied to
terrestrial sediments yielding DNA from both extinct and extant mammals, birds, insects and plants. Samples extracted from these terrestrial sediments are commonly referenced as 'sedimentary ancient DNA' (''seda''DNA or ''dirt''DNA). The eDNA analysis can also be used to study current forest communities including everything from birds and mammals to fungi and worms.
Samples can be obtained from soil, faeces, 'bite DNA' from where leaves have been bitten, plants and leaves where animals have been, and from the blood meals of captured mosquitos which may have eaten blood from any animals in the area. Some methods can also attempt to capture cells with hair traps and sandpaper in areas commonly transversed by target species.
Aquatic sediments
The sedaDNA was subsequently used to study ancient animal diversity and verified using known fossil records in aquatic sediments.
The aquatic sediments are deprived of oxygen and are thus protect the DNA from degrading.
Other than ancient studies, this approach can be used to understand current animal diversity with relatively high sensitivity. While typical water samples can have the DNA degrade relatively quickly, the aquatic sediment samples can have useful DNA two months after the species was present. One problem with aquatic sediments is that it is unknown where the organism deposited the eDNA as it could have moved in the water column.
File:Drilling vessel recovering a sediment core for sedaDNA analysis.jpg, Drilling vessel recovering a sediment core for sedaDNA analysis and hypothetical past marine community composition[ ]
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Creative Commons Attribution 4.0 International License
File:Subglacial aquatic sediment continuous coring.jpg, Subglacial aquatic sediment continuous coring
Aquatic (water column)
Studying eDNA in the water column can indicate the community composition of a body of water. Before eDNA, the main ways to study open water diversity was to use fishing and trapping, which requires resources such as funding and skilled labour, whereas eDNA only needs samples of water.
This method is effective as
pH of the water does not affect the DNA as much as previously thought, and sensitivity can be increased relatively easily.
Sensitivity is how likely the DNA marker will be present in the sampled water, and can be increased simply by taking more samples, having bigger samples, and increasing
PCR.
eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.
Researchers at the
Experimental Lakes Area
IISD Experimental Lakes Area (IISD-ELA, known as ELA before 2014) is an internationally unique research station encompassing 58 formerly pristine freshwater lakes in Kenora District Ontario, Canada. Previously run by Fisheries and Oceans Canada, ...
in
Ontario, Canada
Ontario ( ; ) is one of the thirteen provinces and territories of Canada.Ontario is located in the geographic eastern half of Canada, but it has historically and politically been considered to be part of Central Canada. Located in Central C ...
and
McGill University
McGill University (french: link=no, Université McGill) is an English-language public research university located in Montreal, Quebec, Canada. Founded in 1821 by royal charter granted by King George IV,Frost, Stanley Brice. ''McGill Universit ...
have found that eDNA distribution reflects
lake stratification
Lake stratification is the tendency of lakes to form separate and distinct thermal layers during warm weather. Typically stratified lakes show three distinct layers, the Epilimnion comprising the top warm layer, the thermocline (or Metalimnion) ...
.
As seasons and water temperature change,
water density
Water () is a polar inorganic compound that is at room temperature a tasteless and odorless liquid, which is nearly colorless apart from an inherent hint of blue. It is by far the most studied chemical compound and is described as the "univer ...
also changes such that it forms distinct layers in small
boreal lakes in the summer and winter. These layers
mix during the spring and fall.
Fish habitat Essential Fish Habitat (EFH) was defined by the U.S. Congress in the 1996 amendments to the Magnuson-Stevens Fishery Conservation and Management Act, or Magnuson-Stevens Act, as "those waters and substrate necessary to fish for spawning, breeding, ...
use correlates to stratification (e.g. a cold-water fish like
lake trout
The lake trout (''Salvelinus namaycush'') is a freshwater char living mainly in lakes in northern North America. Other names for it include mackinaw, namaycush, lake char (or charr), touladi, togue, and grey trout. In Lake Superior, it can also ...
will stay in cold water) and so does eDNA distribution, as these researchers found.
Monitoring species
eDNA can be used to monitor species throughout the year and can be very useful in conservation monitoring.
eDNA analysis has been successful at identifying many different taxa from aquatic plants, aquatic mammals,
fishes,
mussels,
fungi and even parasites.
eDNA has been used to study species while minimizing any stress inducing human interaction, allowing researchers to monitor species presence at larger spatial scales more efficiently.
The most prevalent use in current research is using eDNA to study the locations of species at risk, invasive species, and keystone species across all environments.
eDNA is especially useful for studying species with small populations because eDNA is sensitive enough to confirm the presence of a species with relatively little effort to collect data which can often be done with a soil sample or water sample.
eDNA relies on the efficiency of genomic sequencing and analysis as well as the survey methods used which continue to become more efficient and cheaper. Some studies have shown that eDNA sampled from stream and inshore environment decayed to undetectable level at within about 48 hours.
Environmental DNA can be applied as a tool to detect low abundance organisms in both active and passive forms. Active eDNA surveys target individual species or groups of taxa for detection by using highly sensitive species-specific quantitative real-time
PCR or
digital droplet PCR markers. CRISPR-Cas methodology has also been applied to the detection of single species from eDNA; utilising the Cas12a enzyme and allowing greater specificity when detecting sympatric taxa. Passive eDNA surveys employ massively-parallel DNA sequencing to amplify all eDNA molecules in a sample with no ''a priori'' target in mind providing blanket DNA evidence of biotic community composition.
Decline of terrestrial arthropods
File:Differentiation of arthropod communities by plant species.webp, Bipartite plot for the COI gene, showing from which plants each arthropod family is obtained. Plant names: Angeli (''Angelica archangelica
''Angelica archangelica'', commonly known as garden angelica, wild celery, and Norwegian angelica, is a biennial plant from the family Apiaceae, a subspecies of which is cultivated for its sweetly scented edible stems and roots. Like several oth ...
''), Centau ('' Centaurea jacea''), Daucus ('' Daucus carota''), Echium (''Echium vulgare
''Echium vulgare'', known as viper's bugloss and blueweed,Dickinson, T.; Metsger, D.; Bull, J.; & Dickinson, R. (2004) ROM Field Guide to Wildflowers of Ontario. Toronto:Royal Ontario Museum, p. 203. is a species of flowering plant in the bora ...
''), Eupato (''Eupatorium cannabinum
''Eupatorium cannabinum'', commonly known as hemp-agrimony, or holy rope, is a herbaceous plant in the family Asteraceae. It is a robust Perennial plant, perennial native to many areas of Europe. The alkaloids may be present in the plant material ...
''), Solida ('' Solidago canadensis''), Tanace (''Tanacetum vulgare
Tansy (''Tanacetum vulgare'') is a perennial, herbaceous flowering plant in the genus ''Tanacetum'' in the aster family, native to temperate Europe and Asia. It has been introduced to other parts of the world, including North America, and in ...
'').
Terrestrial
arthropod
Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and cuticle made of chiti ...
s are experiencing massive decline in Europe as well as globally, although only a fraction of the species have been assessed and the majority of insects are still
undescribed to science. As one example, grassland ecosystems are home to diverse taxonomic and functional groups of terrestrial
arthropod
Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and cuticle made of chiti ...
s, such as
pollinators,
phytophagous
A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthpar ...
insects, and predators, that use nectar and pollen for food sources, and stem and leaf tissue for food and development. These communities harbor
endangered species, since many
habitat
In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
s have disappeared or are under significant threat. Therefore, extensive efforts are being conducted in order to restore European grassland ecosystems and conserve
biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') l ...
. 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. The vast majority of
flowering plant
Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. The term "angiosperm" is derived from the Greek words ('container, vessel') and ('seed'), and refers to those plants th ...
s are pollinated by insects and other animals both in temperate regions and the tropics. The majority of insect species are herbivores feeding on different parts of plants, and most of these are specialists, relying on one or a few plant species as their main food resource. However, given the gap in knowledge on existing insect species, and the fact that most species are still undescribed, it is clear that for the majority of plant species in the world, there is limited knowledge about the arthropod communities they harbor and interact with.
[ ]
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Creative Commons Attribution 4.0 International License
Terrestrial arthropod communities have traditionally been collected and studied using methods, such as
Malaise traps and
pitfall trap
A pitfall trap is a trapping pit for small animals, such as insects, amphibians and reptiles. Pitfall traps are a sampling technique, mainly used for ecology studies and ecologic pest control. Animals that enter a pitfall trap are unable to esca ...
s, which are very effective but somewhat cumbersome and potentially invasive methods. In some instances, these techniques fall short of performing efficient and standardized surveys, due to, for example,
phenotypic plasticity
Phenotypic plasticity refers to some of the changes in an organism's behavior, morphology and physiology in response to a unique environment. Fundamental to the way in which organisms cope with environmental variation, phenotypic plasticity encompa ...
, closely related species, and difficulties in identifying juvenile stages. Furthermore,
morphological identification depends directly on
taxonomic expertise, which is in decline. All such limitations of traditional biodiversity monitoring have created a demand for alternative approaches. Meanwhile, the advance in
DNA sequencing technologies continuously provides new means of obtaining biological data.
Hence, several new molecular approaches have recently been suggested for obtaining fast and efficient data on arthropod communities and their interactions through non‐invasive genetic techniques. This includes extracting DNA from sources such as bulk samples or insect soups, empty leaf mines, spider webs, pitcher plant fluid, environmental samples like soil, water, and even whole flowers (environmental DNA
DNA,
host plant and predatory diet identification from insect DNA extracts, and predator scat from bats. Recently, also DNA from pollen attached to insects has been used for retrieving information on
plant–pollinator interactions. Many of such recent studies rely on DNA metabarcoding—high‐throughput sequencing of
PCR amplicon
In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication events. It can be formed artificially, using various methods including polymerase chain reactions (PCR) or ligase chai ...
s using generic primers.
Mammals
File:Canadian lynx by Keith Williams.jpg, Canada lynx
File:Brooks Range (19) Lynx trail.jpg, Tracks of a Canada lynx in snow
Snow tracks
Wildlife researchers in snowy areas also use snow samples to gather and extract genetic information about species of interest. 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.
[ ]
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Creative Commons Attribution 4.0 International License
DNA from the air
In 2021, researchers demonstrated that eDNA can be collected from air and used to identify mammals.
Managing fisheries
![EDNA gif without time](https://upload.wikimedia.org/wikipedia/commons/5/5b/EDNA_gif_without_time.gif)
The successful
management
Management (or managing) is the administration of an organization, whether it is a business, a nonprofit organization, or a Government agency, government body. It is the art and science of managing resources of the business.
Management includ ...
of commercial fisheries relies on
standardised surveys to estimate the quantity and distribution of
fish stocks.
Atlantic cod
The Atlantic cod (''Gadus morhua'') is a benthopelagic fish of the family Gadidae, widely consumed by humans. It is also commercially known as cod or codling.[catastrophic stock decline and ensuing economic and social problems. Traditional stock assessments of demersal fish species have relied primarily on ]trawl
Trawling is a method of fishing that involves pulling a fishing net through the water behind one or more boats. The net used for trawling is called a trawl. This principle requires netting bags which are towed through water to catch different speci ...
surveys, which have provided a valuable stream of information to decision makers. However, there are some notable drawbacks of demersal trawl surveys including cost, gear selectivity/catchability, habitat destruction and restricted coverage (e.g. hard-substrate bottom environments, marine protected areas).[ ]
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Environmental DNA (eDNA) has emerged as a potentially powerful alternative for studying ecosystem dynamics. 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 or characterise biodiversity. 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. To further develop the utility of eDNA for fisheries management, understanding the ability of eDNA quantities to reflect fish biomass in the ocean is an important next step.
Positive relationships between eDNA quantities and fish biomass and abundance have been demonstrated in experimental systems. However, known variations between eDNA production and degradation rates is anticipated to complicate these relationships in natural systems. Furthermore, in oceanic systems, large habitat volumes and strong currents are likely to result in physical dispersal of DNA fragments away from target organisms. These confounding factors have been previously considered to restrict the application of quantitative eDNA monitoring in oceanic settings.
Despite these potential constraints, numerous studies in marine environments have found positive relationships between eDNA quantities and complimentary survey efforts including radio-tagging, visual surveys, echo-sounding and trawl surveys. However, studies that quantify target eDNA concentrations of commercial fish species with standardised trawl surveys in marine environments are much scarcer. In this context, direct comparisons of eDNA concentrations with biomass and stock assessment metrics, such as catch per unit effort In fisheries and conservation biology, the catch per unit effort (CPUE) is an indirect measure of the abundance of a target species. Changes in the catch per unit effort are inferred to signify changes to the target species' true abundance. A decr ...
(CPUE), are necessary to understand the applicability of eDNA monitoring to contribute to fisheries management efforts.
Deep sea sediments
File:Extracellular DNA pools from continental margin sediments.webp, OTU (operational taxonomic unit) network of the extracellular DNA pools from the sediments of the different continental margins.[ ]
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Extracellular DNA in surface deep-sea sediments is by far the largest reservoir of DNA of the world oceans. The main sources of extracellular DNA in such ecosystems are represented by in situ DNA release from dead benthic organisms, and/or other processes including cell lysis due to viral infection, cellular exudation and excretion from viable cells, virus decomposition, and allochtonous inputs from the water column. Previous studies provided evidence that an important fraction of extracellular DNA can escape degradation processes, remaining preserved in the sediments. This DNA represents, potentially, a genetic repository that records biological processes occurring over time.
Recent investigations revealed that DNA preserved in marine sediments is characterized by a large number of highly diverse gene sequences. 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.
The diagram on the right shows the OTU (operational taxonomic unit
An Operational Taxonomic Unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, w ...
) network of the extracellular DNA pools from the sediments of the different continental margins. The dot size within the network is proportional to the abundance of sequences for each OTU. Dots circled in red represent extracellular core OTUs, dot circled in yellow are partially shared (among two or more pools) OTUs, dots circled in black are OTUs exclusive of each pool. The core OTUs contributing at least for 20 sequences are shown. The numbers in parentheses represent the number of connections among OTUs and samples: 1 for exclusive OTUs, 2–3 for partially shared OTUs and 4 for core OTUs.
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,. These systems, which represent ca. 15% of the global seafloor, are also hotspots of benthic prokaryotic diversity, and therefore they could represent optimal sites to investigate the prokaryotic diversity preserved within extracellular DNA.
Spatial distribution of prokaryotic diversity has been intensively studied in benthic deep-sea ecosystems through the analysis of "environmental DNA" (i.e., the genetic material obtained directly from environmental samples without any obvious signs of biological source material). However, the extent to which gene sequences contained within extracellular DNA can alter the estimates of the diversity of the present-day prokaryotic assemblages is unknown.
Sedimentary ancient DNA
Analyses of ancient DNA
Ancient DNA (aDNA) is DNA isolated from ancient specimens. Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is more degraded in comparison with contemporary genetic material. Even under the bes ...
preserved in various archives have transformed understanding of the evolution of species and ecosystems. Whilst earlier studies have concentrated on DNA extracted from taxonomically constrained samples (such as bones or frozen tissue), advances in high-throughput sequencing and bioinformatics now allow the analysis of ancient DNA extracted from sedimentary archives, so called sedaDNA. The accumulation and preservation of sedaDNA buried in land and lake sediments have been subject to active research and interpretation. However, studying the deposition of DNA on the ocean floor and its preservation in marine sediments is more complex because the DNA has to travel through a water column
A water column is a conceptual column of water from the surface of a sea, river or lake to the bottom sediment.Munson, B.H., Axler, R., Hagley C., Host G., Merrick G., Richards C. (2004).Glossary. ''Water on the Web''. University of Minnesota-D ...
for several kilometers. Unlike in the terrestrial environment, with pervasive transport of subfossil biomass from land, the largest portion of the marine sedaDNA is derived from planktonic community, which is dominated by marine microbes and marine protists
Marine protists are defined by their habitat as protists that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Life originated as marine single-celled prokaryotes (bacteria an ...
. After the death of the surface plankton, its DNA is subject to a transport through the water column, during which much of the associated organic matter is known to be consumed and respired. This transport could take between 3 to 12 days depending on the size and morphology of test. However, it remains unclear how exactly the planktonic eDNA, defined as the total DNA present in the environment after, survives this transport, whether the degradation or transport are associated with sorting or lateral advection, and finally, whether the eDNA arriving at the seafloor is preserved in marine sediments without further distortion of its composition.[ ]
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Despite the long exposure to degradation under oxic
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