Welcome to CLP9 “Integrated environmental omics – biotechnology applications”
In Brief
CLP9 is foreseen for:
- Academic professionals (Teachers, Mentors, Supervisors); EQF 8
CLP9 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.
Contemporary environmental protection has emphasized how molecular and “omics” technologies can be used to determine the nature, behavior, and functions of microbial communities present in ecosystems to limit and eliminate pollution. Environmental “omics” aim to understand better the metabolic processes of a wide range of organisms and/or complex microbial communities to improve phenotype-genotype relationships, thereby providing new insights into the key molecules and processes responsible for the adaptation of organisms in response to environmental changes. Advances in new omics approaches (metagenomics, metatranscriptomics, metaproteomics, metabolomics, and fluxomics) and the applied multi-omics approach have led to invaluable information on microbial communities and essential biotechnological applications – from pollutant bioremediation to the design of innovative biosensors, screening for new catalysts or biological production of materials and products. The progress in “omics” technologies will allow us to explore and characterize new environments and processes to develop and optimize new biotechnological applications.
Environmental proteomics is a proteomics application area studying the effects of growth environments on organism development in natural, non-controlled conditions. This proteomics branch contributes to the proteins expressed in the cell, identification and quantitative determination, the discovery of the mechanisms of essential cellular processes, and the elucidation of phenomena like syntrophy, gene exchange, and cell-to-cell communication at the molecular level. Environmental proteomics investigates microbial-dominated organisms’ assemblages and designs differential protein production and expression patterns that reflect physiological responses to environmental changes (in norma and under stress). It performs laboratory surveys with model environmental microorganisms and studies natural microbial communities, analysing their collective proteome (metaproteomics). Environmental proteomics has diverse research and application areas (e.g., metabolic engineering, microbial ecology, environmental stress tolerance, etc.) due to the methodological and technical innovations (e.g., 2D PAGE, LC, ICAT, MS, phage display, bioinformatics. etc.) that allow protein identification and structural characterization.
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.
Educational Goals
This CLP9 offers new knowledge and skills about:
- eDNA as a tool for monitoring species, populations and communities at molecular level
- eDNA sampling and its technical challenges and drawbacks
- eDNA application areas and future potential
- Мultiomics holistical approach in ecological research by using omics technologies
- Omics techniques and approaches for biotechnological applications: biodegradation, bioremediation, sustainable agriculture, reduction/mitigation environmental damage
- Prospects and challenges in bio-technological application of ”оmics“ techniques
- Proteomics and Environmental proteomics essentials
- Main categories of environmental proteomics and the relevant to them methodological and technical innovations
- Challenges, frontiers, and perspective of environmental proteomics applications
- 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
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 omics approaches in ecological research
- Present the role of a holistic multiomics approach for bioremediation and environmental protection.
- Reveal the potential of multiomics techniques and approaches for biotechnological applications in an environmental context
- Explain a multimix solution for developing biotechnology to reduce oil pollution and mitigate environmental damage
- Define the main perspectives and challenges in the application of Omics techniques for biotechnological applications in an environmental context
- Describe the principles of proteomics / environmental proteomics
- Apply proteiomics studies for assessment of protein diversity of ecosystems and communities
- Define the main categories of environmental proteomics studies
- Explain the application of environmental proteomics for metabolic engineering, microbial ecology surveys and environmental stress tolerance assessment
- Specify the challenges, frontiers, and perspective of environmental proteomics
- 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
Composition
This CLP9 comprises two Units of Learning Outcomes (ULO 4 & ULO 6)
- ULO 4:
- Module 1 Genomics: environmental DNA and sampling
- Module 11 Omics techniques for biotechnological applications
- ULO 6
- Module 3 Advanced environmental proteomics
- Module 6 Environmental database and bioinformatics
Learning Content
Access here the CLP9 learning content!
>> Genomics: environmental DNA and sampling
>> Omics techniques for biotechnological applications
>> Advanced environmental proteomics
>> Environmental database and bioinformatics
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