Chapter 12 Microbial Ecology

They are in constant physical and molecular interactions includes syntropy. - They never work alone.

• byproducts of some microbes needed by other microbes.

False : It is essential for survival. Especially since they NEVER WORK ALONE

• Microbes of any kind found in a “defined” habitat.

Metagenomics.

4.

Use and recycle all compounds present in one environment–> new and accessible resources for other organisms.

• Amplicon Analysis • Biological Genome Functions.

-Targets one specific gene in the microbiomes of SSU of rRNAs and amplifies that gene in all the organisms they’re studying

Looks at what genomes are there by using metagenomics.

• Illumina - produces short DNA reads • PacBio/Nanopore -Long DNA reads

• uses a targeted approach which searches for one gene. • amplicon sequencing of partial 16S/18S rRNA genes –> detection of microbial taxonomic diversity (requires amplification) • Targeted Microbial Sequencing –> detection of antimicrobial resistance genes or viral targets diversity in certain environments (required read mapping on a reference). • Low genome resolution • Higher output

-Amplicon Sequencing of complete 16S/18S rRNA–detection of microbial taxonomic diversity –> higher resolution. - Acquisition of Complete Bacterial Genomes - detection of microbial taxonomic + genomic diversity. - High gene/genome resolution - Lower output.

Long DNA read- we only only produce a little bit of them with a high resolution Short DNA reads - we can produce a lot of them with a low resolution

• Amplification: amplifies select DNA (16S or the 18S rRNA) using polymerase chain reaction (PCR) and universal primers. • Sequencing : Once the selected DNA is extracted, those products are then sequenced into its specific groups with Illumina Procedure (special machine) where it then organizes the genes into categories BUT KNOW that we will only obtain a little bit of the gene that will be sequenced. Output : many billions of sequencing short reads of 50-300bp in length. • Taxanomic Assignment : the 16S or 18S rRNA reads need to be classified! • Allows relative abundance within communities in specific environments – or switches in one community over time or due to environmental change.

Primers may amplify off-target sequences and not all sequences similarly amplified.

Assumes sequenced amplicons accurately represent the rRNA diversity and abundance of the target region in the sample—FACT: rRNA copied vary in sequence/ number

DNA sequence obtained from a mixture of genomes–obtained using short (illumination) or long-read sequencing technologies (Pacific BioSciences or Nanopore).

Finding what genes/biological functions/cellular pathways are there. -We are going to take the entire DNA and sequence everything and not just one little part of it. We always start with the total genome before we start getting fancy with it.

• Allows determination of changes in AB resistance. • Identification of Problematic Taxa. Allows for predictions based on certain aspects like seasonality or location.

Metagenome -Assembled Genomes : more detailed view of community functions. For example, what do the bacteria do?

• We would assemble MAGS to help us go into detail. We will map the genes and see which overlap (what he means by overlap) and from that we will find pathways and then we will see what pathways they take. Long reads is better than short reads.

Long reads are easier because think of them like bigger pieces of the puzzle. They’re easier to put together than a lot of short reads. this makes it easier for us to find overlap.

because these overlaps create contigs