Laboratory of Molecular Taxonomy and Ecology
DNA-based methods have become indispensable in contemporary biological research, offering unprecedented levels of precision, efficiency and scope. Techniques such as DNA barcoding, environmental DNA (eDNA) analysis and population genomics are particularly transformative in fields such as taxonomy, ecology and evolutionary biology. They accelerate species identification and discovery, as well as large-scale biodiversity monitoring and conservation. Moreover, DNA methods are expected to progressively replace traditional approaches in biodiversity monitoring, pathogen surveillance and forensics. This means that national institutions and agencies must develop appropriate expertise to comply with European and international standards. Therefore, establishing technological infrastructure and building independent expertise in DNA-based biodiversity research are essential for any research institution seeking to expand its capacity and increase research and training opportunities, in line with international standards and practices. In this context, the National Museum of Natural History at the Bulgarian Academy of Sciences inaugurated its Laboratory of Molecular Taxonomy and Ecology in October 2025.
Aim of the Laboratory
The Laboratory of Molecular Taxonomy and Ecology is entirely dedicated to the application of various DNA techniques to support research, monitoring and conservation of biodiversity. This includes, for example, DNA barcoding and metabarcoding, analysis of environmental DNA (eDNA) samples including metagenomic analyses of microbial and fungal communities, population genetics and genomics, routine genotyping of organisms for genetic monitoring, phylogenetic studies, as well as the assessment of genetic health in species of conservation concern (i.e. characterisation of inbreeding, genetic drift, genetic diversity, gene flow, or genetic bottleneck effects). Future analyses may also include the generation of high-quality reference genomes for Bulgarian species.
In this way, the laboratory meets the research needs of a wide range of scientists and lecturers at the Museum, enabling them to carry out their own research. Following the highest possible standards of methodological rigour and safety, the DNA laboratory is divided into two rooms — pre-PCR and post-PCR.
The pre-PCR room is where most of the laboratory work is conducted, including sample processing, fragmentation, DNA extraction and manipulation, as well as concentration measurements, PCR reagent preparation or library preparation for direct genome sequencing. The post-PCR room is used for PCR amplification and manipulation of amplified DNA such as gel electrophoresis, pooling of amplicons, library preparation for DNA metabarcoding or direct sequencing (e.g. using Oxford Nanopore MinION technology).
Applications
The laboratory supports studies involving a wide range of sample types — animal and plant tissues, soil, water, gastrointestinal contents or faeces — for research ranging from species identification and monitoring to dietary and microbiome analyses, or DNA characterisation of parasites, pathogens and parasitoids. Routine analyses include mixed arthropod samples from field surveys or museum collections.
The laboratory is not designed for molecular analyses of RNA or ancient DNA, although the analysis of historical DNA should be feasible. Likewise, it is currently not equipped for other molecular methods unrelated to DNA, such as proteomics, immunology, hormone assays or other techniques like microbial culturing, karyotyping or histology.
Practical Information
The laboratory aims to be a shared space where everyone feels welcome and free to carry out work and perform protocols independently, according to their own schedule. However, to ensure compliance with and maintenance of the highest standards (which is also essential for ensuring the quality of the data produced), the rules governing the use of the laboratory spaces and equipment must be observed by all users.
The head of the laboratory is Mrs. Iva Karaivanova, who oversees order and adherence to the usage rules. Procedures are in place for initial safety training, waste disposal and hygiene practices (cleaning, use of space, cupboards, refrigerators and freezers, use of shared chemical products, cleaning of lab coats, etc.). Additional procedures apply to movement between the laboratory spaces, particularly the rule that working in the post-PCR room precludes any further use of the pre-PCR room on the same day. Maintaining a controlled environment is crucial for obtaining reproducible results.
The introduction of additional equipment unrelated to DNA analysis significantly increases the risk of contamination, which is particularly problematic for studies involving museum specimens or other sensitive samples. The post-PCR room may store reagents for other laboratory applications, but given its limited size, the integration of additional research functions is restricted.
Aim of the Laboratory
The Laboratory of Molecular Taxonomy and Ecology is entirely dedicated to the application of various DNA techniques to support research, monitoring and conservation of biodiversity. This includes, for example, DNA barcoding and metabarcoding, analysis of environmental DNA (eDNA) samples including metagenomic analyses of microbial and fungal communities, population genetics and genomics, routine genotyping of organisms for genetic monitoring, phylogenetic studies, as well as the assessment of genetic health in species of conservation concern (i.e. characterisation of inbreeding, genetic drift, genetic diversity, gene flow, or genetic bottleneck effects). Future analyses may also include the generation of high-quality reference genomes for Bulgarian species.
In this way, the laboratory meets the research needs of a wide range of scientists and lecturers at the Museum, enabling them to carry out their own research. Following the highest possible standards of methodological rigour and safety, the DNA laboratory is divided into two rooms — pre-PCR and post-PCR.
The pre-PCR room is where most of the laboratory work is conducted, including sample processing, fragmentation, DNA extraction and manipulation, as well as concentration measurements, PCR reagent preparation or library preparation for direct genome sequencing. The post-PCR room is used for PCR amplification and manipulation of amplified DNA such as gel electrophoresis, pooling of amplicons, library preparation for DNA metabarcoding or direct sequencing (e.g. using Oxford Nanopore MinION technology).
Applications
The laboratory supports studies involving a wide range of sample types — animal and plant tissues, soil, water, gastrointestinal contents or faeces — for research ranging from species identification and monitoring to dietary and microbiome analyses, or DNA characterisation of parasites, pathogens and parasitoids. Routine analyses include mixed arthropod samples from field surveys or museum collections.
The laboratory is not designed for molecular analyses of RNA or ancient DNA, although the analysis of historical DNA should be feasible. Likewise, it is currently not equipped for other molecular methods unrelated to DNA, such as proteomics, immunology, hormone assays or other techniques like microbial culturing, karyotyping or histology.
Practical Information
The laboratory aims to be a shared space where everyone feels welcome and free to carry out work and perform protocols independently, according to their own schedule. However, to ensure compliance with and maintenance of the highest standards (which is also essential for ensuring the quality of the data produced), the rules governing the use of the laboratory spaces and equipment must be observed by all users.
The head of the laboratory is Mrs. Iva Karaivanova, who oversees order and adherence to the usage rules. Procedures are in place for initial safety training, waste disposal and hygiene practices (cleaning, use of space, cupboards, refrigerators and freezers, use of shared chemical products, cleaning of lab coats, etc.). Additional procedures apply to movement between the laboratory spaces, particularly the rule that working in the post-PCR room precludes any further use of the pre-PCR room on the same day. Maintaining a controlled environment is crucial for obtaining reproducible results.
The introduction of additional equipment unrelated to DNA analysis significantly increases the risk of contamination, which is particularly problematic for studies involving museum specimens or other sensitive samples. The post-PCR room may store reagents for other laboratory applications, but given its limited size, the integration of additional research functions is restricted.