Introduction to Environmental DNA (eDNA) Applications of Metagenomics (PDF)

Introduction to Environmental DNA: Applications of Metagenomics Welcome to Lecture 6. Today, we'll explore the exciting field of environmental DNA (eDNA), focusing on its applications in metagenomics. eDNA refers to genetic material extracted from environmental samples, providing insights into the o...

Introduction to Environmental DNA: Applications of Metagenomics Welcome to Lecture 6. Today, we'll explore the exciting field of environmental DNA (eDNA), focusing on its applications in metagenomics. eDNA refers to genetic material extracted from environmental samples, providing insights into the organisms present in a particular ecosystem. ha by Dr. Hadil Alahdal Lecture Outline eDNA Extraction Metabarcoding Data Analysis Applications Environmental DNA is eDNA metabarcoding uses Data analysis involves eDNA has diverse applications extracted from various sources, genetic barcodes to identify analyzing the sequence data to in various fields, including including water, soil, and species present in an identify and quantify species conservation, biosecurity, and sediment, and then analyzed. environmental sample. present in the environment. ecological monitoring. What is Genomics? Genomics is the study of an organism's complete set of genetic instructions. This includes genome sequencing, annotation of gene function, and understanding genome architecture. Loading… Genomics also involves studying patterns of gene expression (transcriptomics), protein expression (proteomics), and metabolite flux (metabolomics). The collective term "omics" is used to address the transcriptome, proteome, and genome.  Environmental Perspective Genome Research The Human Genome Project has led to a surge in genomic research across different species, including model organisms. Risk Assessment Understanding the genome of various organisms is essential for accurate environmental risk assessment. Ecotoxicogenomics This new field combines environmental toxicology and genomics, offering a powerful approach to assess the impact of pollutants. Understanding Environmental DNA Environmental DNA (eDNA) is genetic material that originates from organisms and is found in environmental samples like soil, water, or air. It offers a non- Loading… invasive approach to studying biodiversity, complementing traditional methods. The presence of eDNA in an environment indicates the presence of a specific organism. Researchers can extract, amplify, and sequence the DNA to identify the species present and quantify their abundance. This innovative approach has revolutionized ecological research, particularly in detecting elusive species and monitoring populations. Visual Representation of eDNA eDNA is a powerful tool for studying biodiversity. It can be used to detect the presence of species in a particular environment. The image represents a visual representation of eDNA. Sources of eDNA Feces Skin Animal excrement contains Shedding of skin cells, scales, DNA shed from the animal's and hair provides genetic digestive tract. material. Gametes Carcasses Reproductive cells, such as Decomposing remains of dead eggs and sperm, contain DNA organisms release DNA into the for offspring. environment.  eDNA Metabarcoding Methodology Environmental Sampling 1 Collect environmental samples like water, sediment, or air. DNA Extraction 2 Isolate DNA from the collected sample. Amplification 3 Amplify specific DNA regions using PCR. Sequencing 4 Sequence the amplified DNA using next-generation sequencing. Data Analysis 5 Analyze sequence data to identify species and assess biodiversity. eDNA metabarcoding is a powerful tool for biodiversity assessment. This method combines field-based ecology with molecular techniques and computational tools. Benefits of eDNA Non-Invasive Sampling Cost-Effectiveness eDNA analysis allows for biomonitoring eDNA is often more cost-effective without requiring the collection of the compared to traditional sampling living organism, eliminating the need methods. This makes it a valuable tool for invasive sampling. for monitoring biodiversity. Taxonomic Resolution Detection of Rare Species eDNA can target different species, eDNA can detect rare species, invasive sampling greater diversity, and species, the presence of native species increasing taxonomic resolution. This is thought to be extinct or otherwise crucial for a comprehensive threatened, and other elusive species understanding of biodiversity. that would be difficult to detect by traditional means.  Drawbacks of eDNA Degradation Variability eDNA degrades in the environment. This limits the scope of eDNA Degradation time varies with environmental conditions. DNA can also studies. Only short segments of genetic material remain, especially in travel through media such as water. This impacts inference of fine-scale warm, tropical regions. spatiotemporal trends of species and communities. 1. What is the primary advantage of using environmental DNA (eDNA) in biodiversity monitoring? A) It allows the collection of live organisms for study. B) It enables non-invasive sampling, reducing the need to disturb ecosystems. C) It is more expensive than traditional sampling methods. D) It can only detect common species in an environment. Loading… Answer: B) It enables non-invasive sampling, reducing the need to disturb ecosystems. The Metabarcoding Approach Metabarcoding is a powerful tool for biodiversity analysis. It uses DNA sequencing to identify multiple species simultaneously from a single sample. ha The metabarcoding approach  Why the metagenomic approach Biodiversity Functional Diversity Metagenomics is a powerful tool for Metagenomics can reveal the functional studying biodiversity. It allows researchers potential of a community. It can identify to identify all the organisms present in a the genes present in the community and sample, regardless of whether they can be the metabolic pathways that are active. cultured in the lab. Genome Assembly Metagenomics enables the assembly of complete genomes, even for organisms that cannot be cultivated or are extinct. It provides insights into the evolution and adaptation of organisms. Consortia and International Networks Global Collaboration Biological Diversity International networks foster These programs focus on documenting collaboration among researchers. and understanding biological diversity. Phylogenetic Relationships Functional Traits Defining evolutionary relationships Investigating connections between among species. genetic patterns and organismal traits.  Examples of Metagenomics Programs Fungi Arthropods Vertebrates Human Fungi metagenomics analyzes the Arthropod metagenomics explores Vertebrate metagenomics Human metagenomics focuses on the DNA of fungal communities, the genetic makeup of arthropod investigates the genetic diversity of collective genetic material of revealing the diversity of fungi in an communities, focusing on insects, vertebrates, including mammals, microorganisms that inhabit the environment. Researchers can arachnids, and crustaceans. This birds, reptiles, amphibians, and fish. human body, such as bacteria, fungi, identify new fungal species and approach identifies arthropod By studying their genomes, and viruses. Understanding the investigate their roles in ecosystems. diversity, their interactions with other researchers can understand their human microbiome is crucial for organisms, and their contributions to evolutionary relationships, studying human health, disease, and ecosystem function. adaptation to different environments, the interactions between the host and and disease resistance. its microbial inhabitants. What is the main difference between metabarcoding and metagenomics in eDNA analysis? A) Metabarcoding identifies multiple species using genetic markers, while metagenomics sequences the entire DNA in a sample. B) Metabarcoding is more expensive than metagenomics. C) Metagenomics uses PCR to amplify specific DNA regions, while metabarcoding sequences the whole genome. D) Metabarcoding is only used for studying plants, while metagenomics is for animals. Answer: A) Metabarcoding identifies multiple species using genetic markers, while metagenomics sequences the entire DNA in a sample. Fungi Programs Fungal Genomics Functional Features Diverse Groups of Fungi Carbon Cycle The 1,000 Fungal Genomes These initiatives study the links Fungi play a crucial role in (1KFG) and Mycorrhizal between functional features and These programs focus on controlling the carbon cycle in Genomics Initiative are genetic patterns. various fungal groups, terrestrial and aquatic important programs for including saprophytes, ecosystems. understanding fungi. symbionts, and pathogens. Fungi genomic targets They target fungal genomes of three domains: Vegetable health, Biorefinery and Fungal diversity. The sequencing and analysis of the genome of about 50 ectomycorrhizal symbionts, 100 pathogenic agents and 100 brown and white rots. Comparing the inventories of genes of these fungi highlighted the key role that decompose the polysaccharides of the plant cell wall (CAZyme). Arthropods Program Details 1 i5k Program 2 Genomic Targets The i5k program aims to sequence Genomes selected for sequencing 5,000 arthropod genomes in 5 years, are potentially useful in energy emphasizing species of agricultural, production. food, or medical significance. 3 Applications 4 Research Focus The i5k program contributes to the The project investigates chemical- fight against pests and pathogens, sensory reception mechanisms, advances forensic applications, trophic relations between plants, improves aquaculture, and aids insects, and vectors, and the role of biodiversity conservation. insects in carbon and methane capture. Vertebrates Project Overview The Genome 10k project proposes a collection of genomic banks of tissues and DNA of 10,000 species of vertebrates. The aim is to gather one specimen of each known genus. The program aims to document the genetic modifications that have shaped the diversity of past and current forms, including reorganization, duplications, and gains and loss of genes. This knowledge will be an essential reference resource for proposals of new paradigms in biology and for the understanding of functions that are essential to life.  Human Societies Insights Genetic Variation Human Lineage Reconstruction Next-generation sequencing (NGS) provides data that enables Within the framework of the us to document the genetic program, the collected data can variations whose frequency is less be used to reconstruct the history than 1% when different human of the human lineage. populations are compared. Disease Research This data can also be used to fight rare or common diseases that arise from our industrial societies, such as some cancers.  Human Societies Insights Many international projects address issues related to human health. For example, the National Institute of Environmental Health Sciences (NIEHS) focuses on human-environment interactions. The National Human Genome Research Institute (NHGRI) studies human biology and seeks to document the impact of the environment on human health. NHGRI researches the biological mechanisms that control the response to environmental stress. Exploring Microbiomes and Genomics: A Global Perspective Genomics and microbiome research have revolutionized our understanding of life. These fields explore the intricate relationships between organisms and their environments. From human health to global ecosystems, genomic studies provide crucial insights. The Human Microbiome Project 1 Ethical Implications 2 International Collaboration The Human Genome Project coordinates research with a The International Human focus on ethical, legal, and Microbiome Consortium societal impacts. (IHMC) aims to improve disease prevention through microbiome study. 3 Intestinal Microbiome Groups MetaHIT project revealed three distinct intestinal microbiome groups, independent of demographics or health status.  Expanding Genomic Research Programs Beyond Human Research International Collaboration Descriptive to Analytical Next-generation sequencing technologies Numerous programs involve global Research is transitioning from descriptive are revolutionizing research methods scientific communities. This cooperation to analytical approaches. This shift allows across species. These advancements facilitates knowledge sharing and for more comprehensive understanding of enable deeper insights into diverse accelerates discoveries. complex biological systems. organisms.  Earth Microbiome Project 1 Sample Analysis Over 200,000 samples analyzed using metagenomics, metatranscriptomics, and metabarcode sequencing techniques. Atlas Construction 2 Building a global atlas of genes and proteins from diverse ecosystems. 3 Metabolic Modeling Developing environment-specific metabolic models of microbial communities and assembling 500,000 microbial genomes. 4 Data Visualization Creating an online portal for interactive visualization of the collected information. What is the primary goal of the Earth Microbiome Project? A) To analyze human microbiomes for medical research. B) To sequence the genomes of 10,000 vertebrate species. C) To create a global atlas of genes and proteins from diverse ecosystems. D) To identify plant species using genetic barcodes. Answer: C) To create a global atlas of genes and proteins from diverse ecosystems. Terragenome: Exploring Soil Microbiomes Project Scope Initial Focus The Terragenome project aims to Research began with studying soil fully sequence metagenomes of from an agricultural experimental various soils worldwide. station. Loading… Metagenomic Approach Multidisciplinary Collaboration Utilizes metagenomics to study hundreds of thousands of soil Involves experts in microbiology, microorganism species. ecology, molecular biology, bioinformatics, and soil physico- chemistry. Marine Genomics: Oceanomics Project Ecosystem Exploration Oceanomics studies oceanic plankton, Earth's largest planetary ecosystem. It investigates all planktonic communities, including viruses. Advanced Technologies Combines NGS sequencing with fast-rate imaging for taxonomic information extraction. Data Integration Compares biological data with environmental metadata to understand marine diversity. Biomonitoring Applications Transfers new technologies to aquatic biomonitoring case studies.  Oceanomics: Beyond Science Research Focus Application Phenotyping Analysis of environmental samples and chosen strains Bioactive Compounds Screening for pharmaceutical and nutritional potential Legal Framework Developing balanced models for marine bioprospection Marine Biotechnologies: Seaweed Project Genomic Study Explores the diverse genomics of marine macroalgae for industrial applications. Genetic Tools Develops new genetic tools to identify populations with industrially interesting properties. Genetic Mapping Creates genetic maps to understand adaptation mechanisms and phenotype- environment interactions.  Genomic Observatories: A Global Network Facility Purpose 1 Genomic Observatories produce long-term, contextualized biodiversity observations at the 2 Ecosystem Coverage genomic level. Represent marine and continental ecosystems worldwide, from polar to Research Goals 3 tropical regions. Quantify biotic interactions and build biodiversity models to 4 Technological predict ecosystem services. Approach Apply cutting-edge genomics to monitor genetic variations in human and natural ecosystems. Integrating Genomic and Environmental Data Data Integration Predictive Modeling Expansion Opportunities Genetic data is systematically related to Models map biodiversity quality and New genomic observation sites can be biophysical and socio-economic metadata. distribution of ecosystem services. They established in developing countries. These This integration enables comprehensive consider various scenarios of future sites will study biodiversity vulnerability predictive modeling of ecosystems. change and human activity. in diverse ecosystems. Natural History Museums: Key Roles in Conservation Preserving Integrity DNA Preservation Natural history museums are crucial for Beyond physical specimens, museums now safeguarding the long-term integrity of house genetic material, enabling researchers biological collections, ensuring the samples to study evolutionary relationships and remain representative and reliable for future biodiversity. research. Global Collaboration Barcoding Life Museums like the French MNHN, the These museums contribute to the Barcode National Museum of Natural History in the of Life initiative, a global project aiming to US, and the Natural History Museum in barcode all living organisms, advancing London serve as hubs for international biodiversity research. collaboration, fostering research on a global scale. Challenges in Biodiversity Data Management 1 Specimen-Data Link 2 Unidentified Organisms Connecting genomic data to Samples from diverse specific museum specimens environments contain numerous poses a significant challenge, unknown organisms, requiring hindering comprehensive extensive taxonomic work for analysis. identification. 3 Specialist Shortage The vast amount of data generated by modern molecular biology techniques requires specialized expertise, which is often limited. Ecoinformatics: A New Paradigm for Biodiversity Data 1 Methodological Advancements 2 Cultural Shift Ecoinformatics involves the development of This approach represents a significant new methodologies and software tools change in how researchers work, specifically designed for analyzing and emphasizing collaboration, data sharing, and managing biodiversity data. standardized data formats. 3 Open Data Sharing 4 Data Infrastructure Ecoinformatics promotes the sharing of data A key component is the establishment of sets online, making them accessible to a secure and accessible data platforms, such as broader scientific community. Ecological Data and DataOne, which facilitate data curation, standardization, and long-term preservation. The Future Integrated Data Systems 1 Seamless integration of collections data, genomics, and environmental information. Citizen Science Engagement 2 Encouraging public participation in research and data collection. Virtual and Augmented Reality 3 Immersive experiences for understanding biodiversity and conservation. Predictive Modeling and Conservation 4 Using data to forecast environmental changes and guide conservation strategies. Ethical Considerations 5 Addressing ethical challenges in data ownership, access, and responsible research.  Omics Technologies: A New Era for (Eco)Toxicology Risk Assessment Population Responses "Omics" technologies offer significant potential to reduce These technologies enable a deeper understanding of how uncertainties in risk assessments. By analyzing molecular level populations respond to environmental change, including toxic information, researchers can evaluate a chemical's potential exposures. The insights gained from "omics" data can be used to toxicity more accurately and rapidly. identify sensitive and insensitive species and phenotypes. What is one of the challenges in managing biodiversity data in genomic observatories? A) The inability to sequence microbial DNA. B) Difficulty in linking genomic data to specific specimens. C) Lack of interest in documenting environmental DNA. D) Limited use of open data sharing platforms. Answer: B) Difficulty in linking genomic data to specific specimens. References https://sci- hub.se/https://www.sciencedirect.com/science/article/abs/pii/ B9781785481468500010 https://youtu.be/gfDIkwoAbPk?si=AG6db0rrsVWNWdsp https://youtu.be/10y_FkPjkwo?si=2qulZKMrGMF2Sy14 https://youtu.be/B9RruLkAUm8?si=hKcsxg0UlhviCND0 Which metagenomics application do you find most relevant for ecological monitoring?