Environmental DNA and Metabarcoding

Environmental DNA (eDNA)

• eDNA is genetic material found in environmental samples (water, soil, air)
• It provides insights into the organisms present within a given ecosystem
• eDNA analysis can detect the presence of a species even when the organism itself is not present
• Common sources of eDNA include feces, skin, gametes and carcasses

Metabarcoding

• Metabarcoding uses genetic barcodes to identify species present in an environmental sample
• It combines field-based ecology with molecular techniques and computational tools
• Allows for the identification and quantification of species in a sample
• Is more cost effective than traditional monitoring methods

Genomics

• Genomics is the study of an organism's complete set of genetic instructions
• Includes genome sequencing, annotation of gene function, and understanding genome architecture
• Also involves studying patterns of gene expression (transcriptomics), protein expression (proteomics), and metabolite flux (metabolomics).

Environmental Genomics

• Environmental genomics is a field that combines environmental toxicology and genomics
• This has led to a surge in genomic research across different species
• It is used in risk assessment for environmental factors

Benefits of eDNA Analysis

• Non invasive sampling, does not require collection of the living organism
• Can be used to detect rare species, invasive species, and species considered to be extinct
• Cost effective solution

Fungi Programs

• The 1,000 Fungal Genomes (1KFG) and Mycorrhizal Genomics Initiative are important programs for understanding fungi
• They study functional features and genetic patterns for different groups of fungi: saprophytes, symbionts, and pathogens
• Fungi play a crucial role in controlling the carbon cycle in terrestrial and aquatic ecosystems

Arthropods Program Details

• The i5k program aims to sequence 5,000 arthropod genomes in 5 years, focusing on species of agricultural, food, or medical significance
• The program contributes to the fight against pests and pathogens, advances forensic applications, improves aquaculture, and aids biodiversity conservation

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

Earth Microbiome Project

• Over 200,000 samples have been analyzed using metagenomics, metatranscriptomics, and metabarcode sequencing techniques
• The goal of the project is to create a global atlas of genes and proteins from diverse ecosystems

Terragenome: Exploring Soil Microbiomes

• The Terragenome project aims to fully sequence metagenomes of various soils worldwide
• Uses metagenomics to study hundreds of thousands of soil microorganism species
• Involves experts in various fields including microbiology, ecology, molecular biology, bioinformatics, and soil physico-chemistry

Marine Genomics: Oceanomics Project

• Oceanomics studies oceanic plankton, Earth's largest planetary ecosystem
• Combines NGS sequencing with fast-rate imaging for taxonomic information extraction
• Compares biological data with environmental metadata to understand marine diversity

Marine Biotechnologies: Seaweed Project

• Explores the diverse genomics of marine macroalgae for industrial applications
• Develops new genetic tools to identify populations with industrially interesting properties
• Creates genetic maps to understand adaptation mechanisms and phenotype-environment interactions

Genomic Observatories: A Global Network

• Genomic Observatories produce long-term, contextualized biodiversity observations at the genomic level
• Represent marine and continental ecosystems worldwide
• Apply cutting-edge genomics to monitor genetic variations in human and natural ecosystems
• Aims to quantify biotic interactions and predict ecosystem services