SU Case Metagenomics 18/10 Flashcards
Abstract
Lichens are symbiotic organisms primarily composed of a fungal partner (lichen-forming fungi) and a photobiont (algal or cyanobacterial), with a diverse array of bacterial associates. Recent advances in metagenomics have revealed more complexity in these associations than previously thought, showing additional fungal species and varied bacterial communities within lichens. To explore these relationships, metagenomic sequencing across hundreds of lichen species was performed. Analyses included genome assembly, binning, and occurrence studies to identify core symbionts, bacterial functions, and their ecological roles. Using tools like CONCOCT and MetaBAT2, genomes were reconstructed, revealing high diversity and strain-level variations. The study highlights how sequencing depth impacts genome recovery, with some metagenomes yielding no high-quality fungal or photobiont genomes. The work underscores the importance of microbial diversity in lichen symbiosis and how bacteria may play essential, yet understudied, roles in lichen ecology and metabolism.
Lichen Symbiosis
Lichens are formed by a symbiotic relationship between a fungus (lichen-forming fungi, often an ascomycete) and a photobiont, which can be an alga or a cyanobacterium. However, recent studies reveal that this relationship includes a diverse microbiome, including bacterial and additional fungal symbionts. These microbial partners likely contribute to nutrient exchange, defense, and overall stability of the lichen.
Metagenomic Analysis
Metagenomics involves sequencing the DNA from entire microbial communities without isolating individual organisms
Binning and Genome Assembly
Binning refers to the process of grouping DNA fragments into bins representing individual genomes. These bins were analyzed to understand which organisms consistently co-exist within lichens. Genome assembly follows the binning process, piecing together the short sequencing reads into longer, continuous sequences.
binning is commonly used to group sequences from metagenomic datasets based on similarity, often to reconstruct genomes from mixed microbial communities. It helps in organizing large datasets into meaningful groups for further analysis
Sequencing Depth
Sequencing depth refers to the number of times a base in the genome is sequenced -> accuracy of genome sequencing, higher better
The study shows that deeper sequencing leads to the recovery of more complete genomes. However, in cases of shallow sequencing, even core symbionts like the fungal and algal partners might not be recovered with high quality. This highlights the importance of sequencing depth for accurate metagenomic analysis and complete genome recovery.
Co-Occurrence Networks
look at relationships between the microbial community for example symbiotic relationships
are graphical representations used to visualize relationships between entities, often based on the frequency with which they appear together in a dataset
The study analyzes co-occurrence networks to identify patterns in how different organisms (such as bacteria and fungi) are found together within lichen communities. This network approach helps to uncover ecological relationships between different symbiotic partners and determine whether certain bacterial species consistently co-occur with specific fungal hosts, suggesting possible functional associations or symbiotic relationships.
Bacterial Functions that help the Lichen
- Nutrient Cycling: The process by which bacteria decompose organic matter and recycle essential nutrients in ecosystems.
- Antibiotic Production: The synthesis of antimicrobial compounds by bacteria to inhibit or kill competing microorganisms.
- Metabolic Support: Bacteria assist in metabolic processes essential for other organisms’ survival and growth.
These bacteria likely play roles in enhancing the lichen’s ability to adapt to environmental stressors.
