Biodiversity & DNA barcoding
What is DNA barcoding? Why it is important? How are data generated?
The fascination of biodiversity lies in the many levels of richness it manifests. A broad range of habitats provides the basis for rich species diversity. The genetic and morphological variations within species are also often astounding. Biodiversity also means richness in biological resources. This is because every organism exhibits numerous interactions within the ecosystem: it produces, consumes, competes and exerts regulatory, stabilizing, and manipulatory functions. Many of these roles are potentially useful to humans. This makes preserving biodiversity an important goal which – beyond its idealistic motivations – has important material significance.
Which species are present in a particular habitat, which pests are infesting our trees, what kind of meat am I eating and what kinds of herbs are steeping in my tea pot? What can we say about the water quality of a river or lake? Many key questions we need to pose today require precise species identifications. This is as true for nature conservation management as it is quality control in food production, pest control or pharmaceutical or forensic applications, just to name a few examples. In general, biological research, specifically biodiversity research, requires exact species identification.
The exciting challenge of understanding, utilizing and protecting biological diversity in its entirety relies on a wide range of different approaches. DNA barcoding is an important modern instrument for distinguishing species and describing genetic diversity. Combining genetic data with other information and insights opens up a full spectrum of research opportunities and practical applications.
Based on its special geographic position and landscape structure, Austria is a hotspot of biological diversity. Many factors play a role here:
(i) Austria boasts very differentiated landscapes – the high Alpine mountains contrast with remote Alpine valleys, low mountain ranges, and rolling hills that gradually merge into the Pannonian lowlands.
(ii) Austria lies at the transition between the cool, moist Atlantic and dry-warm continental climate, with isolated submediterranean influences in the Southern Alps.
(iii) Austria also has an exciting geological history: our country’s geographic position makes it particularly interesting. The alpine glaciation during the last Ice Ages and the ice-free regions along the eastern margins have led to a very special distribution history of many native organisms. Retreats and recolonizations, along with relict areas, bear witness to these periods of Earth history.
All these factors have contributed to our current high biodiversity, a treasure for which our understanding remains far too incomplete. Documenting this biodiversity in its entirety is a task that is more urgent than ever.
DNA barcoding is a standardized method for the identification of organisms based on specific sections of their genetic material (DNA). DNA barcoding therefore uses sections of specific genes that differentiate species. Thus, these DNA sequences (DNA barcodes) enable to unambiguously assign the DNA to a certain species. In a first step, barcodes of taxonomically classified organisms are inferred and stored in a reference database. These DNA barcodes are then made available for comparisons. Identifying an unknown sample “simply” requires sequencing the DNA barcode section and comparing it with the sequences held in the reference database. This is how DNA barcoding enables quick and reliable species determinations. Nonetheless, the success of the determination depends on how comprehensive the reference database is and on its quality.
The workflow begins by collecting organisms or by selecting the desired material from scientific collections. From tissue samples of such taxonomically determined specimens the DNA is extracted and the gene section used for DNA barcoding (for most organism groups the mitochondrial COI gene) is amplified in the reaction tube via PCR (Polymerase Chain Reaction). The DNA sequences are then made available to a publicly accessible database. The reference specimens themselves are stored in a public scientific collection and are available for future analyses.
Even experts can sometimes reliably identify organisms only in the adult stage. In many cases only one of the two sexes can be identified with certainty. DNA barcoding solves these issues by offering the opportunity to determine difficult-to-identify species as well as to assign eggs, larvae and tissue remains or even traces (e.g., blood) to a specific species. This method innovatively complements classical biological taxonomy by helping to identify species for numerous applications including research, nature conservation and the economic sector.
In the future, the wealth of information on biological diversity can be used for a wide range of applications.
A cornerstone for studying and successfully safeguarding biodiversity is the reliable identification of species and knowledge about their genetic diversity. The establishment of a “DNA barcoding database” provides a solid foundation for this endeavor. Moreover, it also stimulates evolutionary research because comparing the data reveals hidden diversity and speciation processes. Numerous discoveries of previously unknown species are expected. Finally, the affordable and precise analytic possibilities promote our understanding of ecological interrelationships such as food webs and flower–pollinator interactions. Nonetheless, the method has its limits when dealing with species that are very young from an evolutionary biology viewpoint or in species exhibiting exceptional variation. At the same time, this approach is expected to spark and fuel exciting research questions in evolutionary biology and to yield a wealth of new insights.
The method offers significant advantages over traditional monitoring and evaluation procedures, especially for evaluating protected areas and for environmental assessments and will be indispensable in the future as an additional instrument in nature conservation management. Species can also be documented based on developmental stages and tissue remains. This enables capturing a broader spectrum of the species actually present. Organisms shed their DNA into the environment via their feces, skin cells and mucus. This enables testing environmental samples (water samples, soil samples) for their species compositions without requiring sampling the organisms themselves. Such a “metabarcoding” of environmental samples means monitoring tasks can be undertaken at minimal cost. And reporting duties can be solidly supported with precise data.
For agriculture and forestry DNA barcoding offers a variety of effective applications. It is e.g., a precise tool for early detection of harmful organisms, parasites, pathogenic organisms and invasive species, which are not determinable as eggs or larvae by traditional morphological methods, while DNA barcoding allows species determination of these life stages. Further applications include seed control, soil assessment and evaluation of water quality. Even in food control, customs inspection (trading of illegal organisms) and in forensics DNA barcoding is applied successfully.
The international umbrella initiative (iBOL, International Barcode of Life) has devoted itself to establishing a freely accessible reference database of DNA barcodes for all species on a global scale. iBOL determines the standards and has set up an international database (BOLD).
Numerous initiatives have been launched worldwide to contribute to iBOL. Several transnational initiatives focus on specific groups of organisms or on defined issues (e.g. GBOL3: dark taxa). Moreover, national projects have also been established, for example in Germany (GBOL), Switzerland (SwissBOL), Norway (NorBOL) or Croatia (CroBOL).
BOLD already contains data on Austrian organisms. Nonetheless, the majority of the ca. 70,000 species living in Austria are not yet registered. The goal of ABOL is to compile the DNA barcode sequences of all animal, plant and fungus species in Austria, including a consideration of their geographic variation. This information is to be made freely available in an online database. Moreover, ABOL envisions itself as a platform designed to help Austrian biodiversity research to establish networks and make rapid progress.
Can’t we simply use the data for widely distributed organisms already recorded in Germany, Switzerland and other countries? Only to a very limited extent. This is because Austria is a special hotspot of biodiversity with many exclusive (endemic) species and subspecies. Protecting this wealth calls for an in-depth survey.
Country-wide DNA barcoding projects such as ABOL provide up-to-date information for all animal, plant and fungus species, enabling the documentation of biodiversity. For more widely ranging species, the ABOL data compiled for Austria dovetail into a transnational network that also incorporates geographic variation. This helps highlight the intra-specific genetic diversity across wider regions. From a practical perspective, we can now pinpoint the exact origin of a particular organism.
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DNA barcoding workshop at the University of Zambia In early October, ABOL held a DNA barcoding workshop at the University of Zambia (UNZA) in Lusaka together with Prof. Cyprian Katongo. The workshop – as part of the OeAD cooperation development research project “DNA barcoding of Zambia’s biodiversity” (led by the University of Graz) – […]