Introduction To Environmental DNA 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 preencoded.png Lecture Outline eDNA Extraction Metabarcoding Data Analysis Applications Environmental DNA is eDNA metabarcoding uses Data analysis involves eDNA has diverse extracted from various genetic barcodes to identify analyzing the sequence data applications in various fields, sources, including water, species present in an to identify and quantify including conservation, soil, and sediment, and then environmental sample. species present in the biosecurity, and ecological analyzed. environment. monitoring. preencoded.png 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. 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. preencoded.png  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. preencoded.png Understanding Environmental 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-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. preencoded.png 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. preencoded.png Sources of eDNA Feces Skin Animal excrement contains Shedding of skin cells, DNA shed from the animal's scales, and hair provides digestive tract. genetic material. Gametes Carcasses Reproductive cells, such as Decomposing remains of eggs and sperm, contain dead organisms release DNA for offspring. DNA into the environment. preencoded.png  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. preencoded.png Benefits of eDNA Non-Invasive Sampling Cost-Effectiveness eDNA analysis allows for eDNA is often more cost-effective biomonitoring without requiring the compared to traditional sampling collection of the living organism, methods. This makes it a valuable eliminating the need for invasive tool for monitoring biodiversity. sampling. Taxonomic Resolution Detection of Rare Species eDNA can target different species, eDNA can detect rare species, sampling greater diversity, and invasive species, the presence of increasing taxonomic resolution. This native species thought to be extinct is crucial for a comprehensive or otherwise threatened, and other understanding of biodiversity. elusive species that would be difficult to detect by traditional means. preencoded.png  Drawbacks of eDNA Degradation Variability eDNA degrades in the environment. This limits the scope of eDNA Degradation time varies with environmental conditions. DNA can studies. Only short segments of genetic material remain, also travel through media such as water. This impacts inference especially in warm, tropical regions. of fine-scale spatiotemporal trends of species and communities. preencoded.png 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. Answer: B) It enables non-invasive sampling, reducing the need to disturb ecosystems. preencoded.png 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 preencoded.png The metabarcoding approach The metabarcode approach enables the analysis of the diversity of organism communities of current and past times. It uses genetic markers of the barcode type, which are specific to a particular taxon (depending on scale, a taxon is specific to the species, the genus or the family) such as the 16S rDNA for bacteria, the 18S rDNA, Cyt-b or COI for animals, rbcL and matK for plants or ITS for fungi. This approach can also be used to determine the biodiversity of genes that code for ecologically interesting functions, like those involved in the nitrogen cycle in soil bacteria.  Why the metagenomic approach Biodiversity Functional Diversity Metagenomics is a powerful tool for Metagenomics can reveal the studying biodiversity. It allows functional potential of a community. It researchers to identify all the can identify the genes present in the organisms present in a sample, community and the metabolic regardless of whether they can be 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. preencoded.png Consortia and International Networks Global Collaboration Biological Diversity International networks foster These programs focus on collaboration among researchers. documenting and understanding biological diversity. Phylogenetic Relationships Functional Traits Defining evolutionary relationships Investigating connections between among species. genetic patterns and organismal traits. preencoded.png  Examples of Metagenomics Programs Fungi Arthropods Vertebrates Human Fungi metagenomics analyzes the Arthropod metagenomics Vertebrate metagenomics Human metagenomics focuses DNA of fungal communities, explores the genetic makeup of investigates the genetic diversity on the collective genetic material revealing the diversity of fungi in arthropod communities, focusing of vertebrates, including of microorganisms that inhabit an environment. Researchers can on insects, arachnids, and mammals, birds, reptiles, the human body, such as bacteria, identify new fungal species and crustaceans. This approach amphibians, and fish. By studying fungi, and viruses. Understanding investigate their roles in identifies arthropod diversity, their their genomes, researchers can the human microbiome is crucial ecosystems. interactions with other organisms, understand their evolutionary for studying human health, and their contributions to relationships, adaptation to disease, and the interactions ecosystem function. different environments, and between the host and its microbial disease resistance. inhabitants. preencoded.png 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. preencoded.png Fungi Programs Fungal Genomics Functional Features Diverse Groups of Fungi Carbon Cycle Fungi The 1,000 Fungal Genomes These initiatives study the Fungi play a crucial role in (1KFG) and Mycorrhizal links between functional These programs focus on controlling the carbon cycle Genomics Initiative are features and genetic various fungal groups, in terrestrial and aquatic important programs for patterns. including saprophytes, ecosystems. understanding fungi. symbionts, and pathogens. preencoded.png 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 Genomes selected for sequence 5,000 arthropod sequencing are potentially genomes in 5 years, useful in energy production. emphasizing species of agricultural, food, or medical significance. 3 Applications 4 Research Focus The i5k program contributes to The project investigates the fight against pests and chemical-sensory reception pathogens, advances forensic mechanisms, trophic relations applications, improves between plants, insects, and aquaculture, and aids vectors, and the role of insects biodiversity conservation. in carbon and methane capture. preencoded.png 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. preencoded.png  Human Societies Insights Genetic Variation Human Lineage Reconstruction Next-generation sequencing (NGS) provides data that Within the framework of the enables us to document the program, the collected data genetic variations whose can be used to reconstruct the frequency is less than 1% history of the human lineage. when different human 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. preencoded.png  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. preencoded.png 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. preencoded.png The Human Microbiome Project 1 Ethical Implications 2 International Collaboration The Human Genome Project coordinates The International Human research with a focus on Microbiome Consortium ethical, legal, and societal (IHMC) aims to improve impacts. disease prevention through microbiome study. 3 Intestinal Microbiome Groups MetaHIT project revealed three distinct intestinal microbiome groups, independent of demographics or health status. preencoded.png  Expanding Genomic Research Programs Beyond Human Research International Collaboration Descriptive to Analytical Next-generation sequencing Numerous programs involve global Research is transitioning from technologies are revolutionizing scientific communities. This descriptive to analytical approaches. research methods across species. cooperation facilitates knowledge This shift allows for more These advancements enable deeper sharing and accelerates discoveries. comprehensive understanding of insights into diverse organisms. complex biological systems. preencoded.png  Earth Microbiome Project 1 Sample Analysis Over 200,000 samples analyzed using metagenomics, metatranscriptomics, and metabarcode sequencing techniques. 2 Atlas Construction 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. preencoded.png 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. preencoded.png 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. Metagenomic Approach Multidisciplinary Collaboration Collaboration Utilizes metagenomics to study hundreds of thousands of soil Involves experts in microbiology, microorganism species. ecology, molecular biology, bioinformatics, and soil physico- chemistry. preencoded.png 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. preencoded.png  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 preencoded.png 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. preencoded.png  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 Technological Approach predict ecosystem services. 4 Apply cutting-edge genomics to monitor genetic variations in human and natural ecosystems. preencoded.png Integrating Genomic and Environmental Data Data Integration Predictive Modeling Expansion Opportunities Genetic data is systematically related Models map biodiversity quality and New genomic observation sites can to biophysical and socio-economic distribution of ecosystem services. be established in developing metadata. This integration enables They consider various scenarios of countries. These sites will study comprehensive predictive modeling of future change and human activity. biodiversity vulnerability in diverse ecosystems. ecosystems. preencoded.png Natural History Museums: Key Roles in Roles in Conservation Preserving Integrity DNA Preservation Natural history museums are crucial Beyond physical specimens, museums for safeguarding the long-term integrity now house genetic material, enabling of biological collections, ensuring the researchers to study evolutionary samples remain representative and relationships and biodiversity. reliable for future research. Global Collaboration Barcoding Life Museums like the French MNHN, the These museums contribute to the National Museum of Natural History in Barcode of Life initiative, a global the US, and the Natural History project aiming to barcode all living Museum in London serve as hubs for organisms, advancing biodiversity international collaboration, fostering research. research on a global scale. preencoded.png Challenges in Biodiversity Data Management 1 Specimen-Data Link 2 Unidentified Organisms Connecting genomic data to Samples from diverse specific museum specimens environments contain poses a significant challenge, numerous unknown hindering comprehensive organisms, requiring analysis. extensive taxonomic work for identification. 3 Specialist Shortage The vast amount of data generated by modern molecular biology techniques requires specialized expertise, which is often limited. preencoded.png Ecoinformatics: A New Paradigm for Biodiversity Data 1 Methodological Advancements 2 Cultural Shift Ecoinformatics involves the This approach represents a significant development of new methodologies change in how researchers work, and software tools specifically emphasizing collaboration, data designed for analyzing and managing sharing, and standardized data formats. biodiversity data. 3 Open Data Sharing 4 Data Infrastructure Ecoinformatics promotes the sharing of A key component is the establishment data sets online, making them of secure and accessible data accessible to a broader scientific platforms, such as Ecological Data and community. DataOne, which facilitate data curation, standardization, and long-term preservation. preencoded.png 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. preencoded.png  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 populations respond to environmental change, including level information, researchers can evaluate a chemical's toxic exposures. The insights gained from "omics" data can potential toxicity more accurately and rapidly. be used to identify sensitive and insensitive species and phenotypes. preencoded.png 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. preencoded.png 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 preencoded.png Which metagenomics application do you find most relevant for ecological monitoring? preencoded.png