Welcome to CLP1 ‘Environmental genomics and transcriptomics – terrestrial habitats’!
In Brief
CLP1 is foreseen for:
- Undergraduates: B.Sc. students; EQF 6
- Graduates: M.Sc. students; EQF 7
CPL1 Summary
The advancement of DNA-based approaches for genome data generation and interpretation encompasses, among others, the study of the genomes at an environmental scale using environmental DNA (eDNA). eDNA is the genetic material of nuclear and mitochondrial origin released from an organism in the environment. It is obtained directly from environmental samples (terrestrial or aquatic) without the necessity of biomaterial availability and used as an efficient, easy-to-manipulate, and standardized, non-invasive sampling approach. Thus, eDNA sampling is applied for species distribution monitoring and operates through sensitive and cost-effective protocols. Although the current technical challenges and drawbacks that scientists face are related mainly to the pitfalls in eDNA obtaining, sequencing, and data interpretation, the potential of eDNA applications is undoubtful. The perspectives on eDNA applications cover the field methods and laboratory protocols improvement for its detection and technical advancements in eDNA application as a biodiversity inventory and monitoring tool.
Landscape transcriptomics explores RNA transcripts (mRNA and different small RNAs) in a given environmental sample at the time of its collection. This emerging branch of transcriptomics reveals the links between genetic and phenotypic variations and landscape-scale processes to determine how genome expression patters reflect the environmental landscape through organismal functioning and genetic differentiation among populations. Landscape transcriptomics performs gene flow, genetic drift, and local adaptation studies across large spatial scales. It explores high-throughput, standardized, and readily applied to a diversity of organisms, techniques (DNA microarrays and RNAseq technology). Landscape transcriptomics assesses the impact of natural environmental stimuli and their fluctuations (e.g., stress conditions) on gene expression and transcriptomic responses at population level. Furthermore, it provides useful data for organism – environment relations in conservation practices management. Landscape transcriptomics possesses great potential to study organisms with no genomic resources, identify novel transcripts, and elucidate the role of transcriptional modulation.
Environmental biotechnology is the application of biotechnology principles and techniques to study and manage the natural environment. It involves microorganisms and other biological agents’ usage for the performance of environmentally beneficial tasks such as cleaning up contaminated sites, enhancing soil health, and reducing greenhouse gas emissions. Examples of environmental biotechnology applications include the use of bacteria to break down pollutants in water and soil, the use of algae to absorb excess nutrients from wastewater, and the use of fungi to decompose organic matter in landfills. Environmental biotechnology has the potential to contribute to finding sustainable solutions to environmental problems, and it is an area of active research and development. Environmental database provides access to international scientific literature relating to all aspects of environmental quality, monitoring, resource management, and conservation. Bioinformatics is essential for understanding ecological processes, managing data, and developing tools to address global challenges.
Soil is responsible for providing Earth’s ecosystems with vital services for their existence. Human activities and climate change effects negatively affect soil health. There is an urgent need for strategies empowering the minimization of these impacts and protecting the soils. A rational approach is the employment of bioindicators to characterize variations in soil health. Microorganisms are versatile biomarkers of soil health since soil microbiome responds rapidly to environmental changes. The application of genomics/metagenomics tools contributes to revealing the full potential of these biomarkers. Genomics/Metagenomic studies of soil microbial communities highlight the structural and functional microorganisms’ diversity, species identification, characterization of new genes, and discovery of enzymatic activities and active compounds. Guided metagenomics (metabarcoding), shotgun metagenomics, One-Health approach towards soil health, eco-genomics, and global inventory of soil microbiome are impactful techniques that allow for exploration of the biodiversity, community structure, and potential functions of the soil microbial communities.
Educational Goals
This CLP1 offers new knowledge and skills about:
- eDNA as a tool for monitoring species, populations and communities at molecular level
- eDNA sampling ant its technical challenges and drawbackse
- DNA application areas and future potential
- Transcriptomics and Landscape transcriptomics essentials
- Performance of transcriptomic studies of non-model microorganisms in natural environments
- Challenges and perspectives of landscape transcriptomics
- Bioinformatics methods and software tools for understanding biological data
- Data science – environmental databases that provide access to a wealth of information related to environmental science
- Environmental science – field that study the environment and solve environmental problems
- Challenges and perspective of environmental bioinformatics
- Use of microorganisms as soil health biomarkers
- Theoretical and practical insights in genomics/metagenomic studies of soil microbial communities
- Modern applications of genomics towards soil health: One-Health approach, ecogenomics, and global inventory of soil microbiome
Learning Outcomes
Upon completion of this CLP the learners will be able to:
- Define eDNA as a tool for monitoring species, populations and communities at molecular level
- Explain the application areas of eDNA of microbial origin and macro-organisms in different habitats and time frames
- Recognize and apply eDNA sampling protocols for monitoring species distribution
- Explain the technical challenges and drawbacks of eDNA sampling and data interpretation
- Understand the eDNA applications potential
- Describe the principles of transcriptomics / landscape transcriptomics
- Apply Landscape transcriptomics approaches in ecology, evolution, and conservation
- Define the main categories of Landscape transcriptomics studies of wild systems in natural environments
- Explain the approaches for collection, analysis, and explanation of transcriptomics data from natural environments
- Understand the gene expression as a time-based and tissue specific process
- Describe the principles and key aspects of environmental bioinformatics and its methods and software tools
- Use different environmental databases that cover all aspects of human impact on the environment.
- Define the major categories of environmental science
- Explain the application of environmental bioinformatics
- Define the challenges, limits and perspective of environmental bioinformatics
- Present the metagenomics as a bioindicator tool for soil health evaluation
- Use soil metagenomics for association of specific members to the microbial communities with transformations that certain soils are experiencing
- Understand the guided metagenomics (metabarcoding) principles and its advantages and disadvantages
- Uprise the shotgun metagenomics technique to understand taxonomic composition and functional potential of soil microorganism communities
- Use metagenomics approach in approximations of “OneHealth” and EcoGenomics
Composition
This CLP comprises two Units of Learning Outcomes (ULO1 & ULO 5)
- ULO 1:
- Module 1 Genomics: environmental DNA and sampling
- Module 2 Transcriptomics: addressing ecological niches
- ULO 5
- Module 6 Environmental database and bioinformatics
- Module 8 Genomics approach to develop soil biomarkers
Learning Content
Access here the CLP1 learning content!
👉 Genomics: environmental DNA and sampling
👉 Transcriptomics: addressing ecological niches
👉 Environmental database and bioinformatics
👉 Genomics approach to develop soil biomarkers
Knowledge Assessment
Check your knowledge!
ECTS Credit Points & Certificate
Get your certificate!