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2023-1-BG01-KA220-HED-000155777 – DigiOmica

Welcome to CLP5 “Integrated environmental omics in soil biomarkers establishment”

In Brief

 

CLP5 is foreseen for:

      • Postgraduates: Ph.D. students; EQF 7
      • Postdoctoral researchers & Research associates; EQF 8

CLP5 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.

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.

Ecotoxicology is the study of the effects of environmental pollutants on living organisms. The use of omics technologies in this field provides a molecular level understanding of biological responses in organisms, enabling more comprehensive and sensitive analyses. Within the scope of omics technologies, genomics investigates the genetic structure of organisms and how changes in this structure respond to environmental stressors; transcriptomics investigates gene expression profiles; proteomics investigates the structure and function of proteins; metabolomics investigates metabolite profiles and changes in metabolic pathways; and epigenomics investigates the effects of environmental factors on epigenetic modifications. The ecotoxicological aspects of aquatic and terrestrial ecosystems and their possible relationship with omics concepts are examined. In addition, air pollution is examined within the framework of omics concepts. The relationship of the human organism, which has an important place in food webs, with pollutants is explained with omics concepts.

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

Authors

  • Aleksandar Dolashki, IOCCP-BAS
  • Aysel Çağlan Günal, Gazi University
  • Gamze Yücel Işıldar, Gazi University
  • Iliyana Rasheva, SU “St. Kliment Ohridski”
  • Lyudmila Velkova, IOCCP-BAS
  • Maria Vassileva,University of Granada
  • Nikolay Vassilev, University of Granada
  • Pavlina Dolashka, IOCCP-BAS
  • Trayana Nedeva, SU “St. Kliment Ohridski”

Educational Goals

This CLP5 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
  • 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
  • Provision of background information on the fields of ecotoxicology and the basic principles and types of omics technologies
  • Understanding how to interpret omics data in ecotoxicology research
  • Highlighting the application of the omics data in environmental risk assessments
  • 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
  • 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
  • Have general information about the science of ecotoxicology integrated with omics technologies
  • Integrate the data from omics technologies to assess the molecular responses of organisms to environmental toxicants
  • Explain how ecotoxicology uses omics technology to assess biomarkers of exposure, impacts, and susceptibility in organisms.
  • Learn the usage areas of omics technologies in aquatic and terrestrial ecosystems
  • Learns the usage areas of omics technologies in the field of human health
  • 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 CLP5 comprises two Units of Learning Outcomes (ULO1 & ULO 8)

  • ULO 1:
    • Module 1 Genomics: environmental DNA and sampling
    • Module 8 Genomics approach to develop soil biomarkers
  • ULO 8
    • Module 5 Integrated omics in ecotoxicology
    • Module 6 Environmental database and bioinformatics

Learning Content

Access here the CLP5 learning content!

>> Genomics: environmental DNA and sampling

>> Genomics approach to develop soil biomarkers

>> Integrated omics in ecotoxicology

>> Environmental database and bioinformatics

Knowledge Assessment

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ECTS Credit Points & Certificate

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