BIOM-360 Lecture Notes - Lecture 9: Nucleic Acid Thermodynamics, Gc-Content, Nitrification
2 May 2018
School
Department
Course
Professor
Microbial Taxonomy and the Evolution of Diversity
Nitrogen Fixation
Atmospheric N fixed by nitrogenases.
Nitrification: A chemolithotrophic process.
1. Ammonium oxidized to nitrite
2. Nitrite oxidized to nitrate
iClicker Question
Nitrification is the process that converts ammonium to nitrate. What is the fate of this compound?
Phosphorus cycle does not have a gas component (P can be less available). Differs from N and C cycles
this way.
Within-species Variation
Bacteria/Archaea: Strains, type strains.
Strains → descendants of a single pure culture
Type strains → used to describe a species
Molecular Aspect
Microbial taxonomy is mainly molecular.
Nucleic acids are the most reliable and widely used approach.
Important: nucleic acid base composition.
G/C content varies a lot within groups, but not within genera.
Easy access, higher DNA melting temp = higher G/C content.
Nucleic acid hybridization assesses how different genomes are. DNA is denatured (heated up so the two
strands separate) and different strains allowed to pair. Then slowly bring temp down so that DNA binds
again.
*What parts of the DNA would you predict to match between a cyanobacterium and human DNA?
Would not expect photosynthesis genes to match.
Mitochondrial would be somewhat matching.
rRNA
would try to match, as we all need it.
Nucleic acid sequencing: whole genome versus specific regions.
Sequencing whole genomes: more more information provided but is expensive and technically
challenging.
Target specific regions that are informative as an alternative.
rRNA is the most widely used molecule to infer microbial phylogenies.
Large subunit and small subunit. Present in all organisms.
Proteins synthesis and little variation.
Do not suffer horizontal gene transfer.
rRNA has short conserved signatures that are shared by specific phylogenetic groups.
Document Summary
Nitrification: a chemolithotrophic process: ammonium oxidized to nitrite, nitrite oxidized to nitrate iclicker question. Nitrification is the process that converts ammonium to nitrate. Phosphorus cycle does not have a gas component (p can be less available). Differs from n and c cycles this way. Strains descendants of a single pure culture. Type strains used to describe a species. Nucleic acids are the most reliable and widely used approach. G/c content varies a lot within groups, but not within genera. Easy access, higher dna melting temp = higher g/c content. Nucleic acid hybridization assesses how different genomes are. Dna is denatured (heated up so the two strands separate) and different strains allowed to pair. Then slowly bring temp down so that dna binds again. Mitochondrial would be somewhat matching. rrna would try to match, as we all need it. Nucleic acid sequencing : whole genome versus specific regions. Sequencing whole genomes: more more information provided but is expensive and technically challenging.
