We perform metabarcoding - fast and accurate analysis of biodiversity
Metabarcoding is an advanced DNA sequencing method that enables the identification of different species of organisms in mixed environmental samples such as soil, water or biological material. With this technology, species monitoring and ecological studies, which are crucial for environmental research, nature conservation or industrial applications, can be carried out effectively and reliably.
Applications
- Healthy soil – Agricultural and forest soil samples can be analyzed for bacteria and fungi, for example, to detect mold and pathogenic bacteria before they damage plants. In addition, the method enables the identification of beneficial microorganisms that act as natural enemies of pests, or monitoring the representation of species with specific functional genes, e.g. for nitrogen fixation in the soil or antibiotic resistance genes. This broad coverage enables accurate monitoring of plant health threats and promotes sustainable pest control. The knowledge gained can help ensure soil health and improve soil yields in the long term.
- Environmental monitoring - DNA metabarcoding provides a record of species diversity in space and time, which is important, for example, in one-time or repeated monitoring of diversity in a certain location. This can be a national park, but also an area intended for development of any kind.
- Environmental Impact Assessment (EIA) – Biodiversity data is needed to assess impacts for example when planning buildings, mining projects, etc.
- Nutritional Ecology - Using metabarcoding, we can analyze the contents of animals' stomachs and intestines to find out what animals feed on. In an agricultural, forestry or water management context, the knowledge of the food webs of species enables the targeted introduction of useful organisms or the management of nutrient cycles and the eutrophication of aquatic ecosystems.
- Aquatic ecology – We provide detailed information on the composition of aquatic communities, which helps assess water quality and habitat condition.
- Microbial ecology – Metabarcoding enables the investigation of complex microbial communities in soil, water or the human body.
- Faeces samples – Animals often cannot be observed directly, but their faeces can almost always be found, samples of which also contain the DNA of their prey. This is key to understanding trophic interactions in nature. Examining the complexity of food webs and their variation over time and space contributes to our understanding of biodiversity and ecosystem functioning.
- Pollen analysis – DNA metabarcoding enables precise identification of the plant species from which the pollen originates. By comparing the sequences of genetic markers, it is possible to determine which plants are present in a given environment and to track changes in their distribution over time. This method can be used, for example, to analyze the composition of honey varieties or to monitor pollination in agriculture.
Why DNA metabarcoding?
Species identification is traditionally carried out by specially trained taxonomists. But this process is time-consuming and to a certain extent it can be subjective, as it is limited by the knowledge of the experts who carry it out, and these can be, for example, locally specific.
The DNA metabarcoding method has a number of advantages compared to this traditional approach. It is objective in the sense that it identifies species based on their DNA. The output is data in digital form that can be easily interpreted, shared, databased and repeatedly analyzed.
- High performance – The method allows hundreds to thousands of samples to be analyzed in parallel, which significantly increases the overall efficiency.
- Complex detection of species - From one sample we can identify a wide range of organisms - microorganisms, plants and animals. Using appropriately designed metabarcoding, all species represented in a sample or perhaps a biotope can be recorded and thus the composition of species communities and flagship species of the respective ecosystem can be analysed. Repeated sampling can provide information on the evolution of individual populations over time.
- Time and cost savings – With automation and fast data processing, you can get results faster and at lower cost than traditional methods.
- High sensitivity – Ability to detect even rare, cryptic or microscopic organisms that could be undetectable by other methods.
What is eDNA?
Environmental DNA (eDNA) is DNA left by organisms in the environment much like fingerprints left at a crime scene. It can come from skin cells, hair, mucus, stool, urine, blood, saliva, or the body remains of deceased individuals. eDNA accumulates in water, sediment, soil, and air, but persists in these environments for varying lengths of time—hours to weeks in water and months to years in sediments.
eDNA analysis is a non-invasive method of biodiversity analysis without the need for direct observation or disturbance of ecosystems.
Case study - Metabarcoding of diatoms
Monitoring of diatoms is of fundamental importance for the assessment of the ecological status of aquatic ecosystems and water quality. Diatoms are one of the main bioindicators because they react sensitively to changes in chemical, physical and biological environmental conditions, such as pollution, eutrophication or pH changes. Regular monitoring of their species composition and abundance provides valuable information about the health of aquatic ecosystems and can be used for early detection of environmental problems.
Metabarcoding of diatoms using rbcL gene sequencing increases the effectiveness of this monitoring by enabling a more accurate and faster analysis of diatom communities, which contributes to a better understanding of the impact of anthropogenic factors on the aquatic environment and to the improvement of water resource protection strategies. Unlike traditional methods such as light microscopy, metabarcoding allows the simultaneous analysis of hundreds of samples and is not burdened by the subjectivity that traditional methods entail.
Case study - Metabarcoding of insect
Some twenty years ago, in search of a simple method for species identification and comparison, DNA barcoding using the mitochondrial gene cytochrome c oxidase (coxI or COI) was proposed as a standardized marker for the classification of animal species.
coxI is a mitochondrial gene expressed in all animal species due to its integral role in energy production. Because the inheritance of mitochondrial genes is in the maternal line, animals typically have only one variant of each mitochondrial gene, and these genes show greater divergence compared to nuclear genes, making coxI an ideal metataxonomy tool.
Metabarcoding using coxI has proven to be a powerful tool for species identification of insects or their prey.
How does metabarcoding work?
The DNA metabarcoding process is designed to meet the individual needs of each customer. Every project therefore requires an initial consultation. A standard procedure typically includes the following steps:
- Sample collection and consultation - We work with our customers to optimize sample collection and storage methods to ensure the highest quality DNA for analysis. We accept samples from various environments, including soil, water, sediments or biological material (e.g. droppings, tissues).
- DNA extraction and in-house laboratory processing - After receiving the samples, our experts perform DNA extraction using proven methods that ensure its high quality. Subsequently, we specifically amplify selected genetic markers (e.g. coxI for animals, ITS for fungi, 16S for bacteria) in order to achieve accurate species identification. A list of available markers is available here.
- DNA Sequencing - Using state-of-the-art DNA sequencing methods, we generate millions of DNA sequences that reflect the biodiversity in your samples. These technologies allow detailed identification of all organisms present.
- Bioinformatic data analysis - Our bioinformaticians analyze the acquired sequencing data using advanced algorithms that filter and group sequences and then assign them to specific taxonomic categories based on comparison with databases. Ideally, the output is a complete list of the species present in the samples.
- Report and Results - Customers receive a detailed report containing species abundancy tables, graphical visualizations and interpretation of ecological data. Our expert team is ready to provide consultation on the results and suggest next steps.
If you are interested in our services in biodiversity analysis, contact us.