BIOL 220 Lecture Notes - Lecture 16: Species Richness, 16S Ribosomal Rna, Asymptote
Lecture 16
BIO 220
Eukaryotes/ Microbial Ecology/ Biogeochemistry
Microbial Ecology
oPopulation
Is a group of individuals of one species living in a common location
oEcosystem
Consists of populations of species plus their habitat or environment
oCommunity
The sum of all the populations of different species constitute
oMicrobial communities critically impact other organisms in all habitats, from oceans and
forests to the interstices of rock
Sampling requires that we first define a target community to study
Community Information Storage
oThe metagenome is the sum total of all DNA sequenced from an environmental sample
othe small subunit SSU rRNA sequence is the standard for identifying environmental taxa
othe term metagenome refers to the DNA sequence obtained directly from a mixture of
genomes
Harvesting the community DNA
oEvery multicellular organism possesses a microbiome
oTo sequence a metagenome requires a series of steps, each of which presents important
choices
oThe cells of the target community must be separated from their surroundings without
loss of DNA
Sampling requirements
oSeparating the microbes from their physical environment
oFiltering the organisms of interest
oBreaking open the cells
oPurifying the DNA
find more resources at oneclass.com
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Document Summary
Is a group of individuals of one species living in a common location: ecosystem. Consists of populations of species plus their habitat or environment: community. The sum of all the populations of different species constitute: microbial communities critically impact other organisms in all habitats, from oceans and forests to the interstices of rock. Sampling requires that we first define a target community to study. Sampling requirements: separating the microbes from their physical environment, filtering the organisms of interest, breaking open the cells, purifying the dna. Steps in high throughput sequencing: once the dna samples are obtained how do we sequence them, in most cases, the sample dna must be amplified by pcr, this is followed by high throughput sequencing. The choice of method depends on several factors. Functional interest: once the dna sequences are obtained how to we assemble them into the genome, note that the genome of a single organism requires assembly of overlapping fragments into contigs.
