16S rRNA
This computational step clusters sequences at 97% identity.
What is OTU clustering?
The famous saying “Everything is everywhere…” was coined by this person.
Who is Baas Becking?
This HGT mechanism involves uptake of free DNA from the environment.
What is transformation?
Frequent antibiotic pulses in the gut represent this type of disturbance.
What is a pulse disturbance?
The LTEE studies evolution in this model organism.
What is Escherichia coli?
These variable regions of the 16S gene are commonly amplified for microbial community profiling—though exactly which one researchers use is a matter of spirited debate.
What are the V3-V4 regions?
This term describes microbes that inhabit extreme environments like hydrothermal vents or hot springs.
What are extremophiles?
This type of mobile genetic element can hop around the genome, sometimes bringing neighbors with it.
What is a transposon?
Fire, floods, or storms can open new niches, triggering this post-disturbance recovery process.
What is succession?
One population famously evolved the ability to metabolize this unexpected carbon source under aerobic conditions.
What is citrate?
This phenomenon explains why 16S copy number variation can inflate perceived abundance in amplicon datasets.
What is rRNA operon copy number bias?
Microbial similarity decreases as sites are further apart, according to this relationship.
What is the distance-decay relationship?
HGT often complicates microbial phylogenies because these genes do not follow the typical parent-to-offspring pattern known as this.
What is vertical inheritance?
Microbes on medical devices resist antibiotics thanks to these protective, sticky compounds.
What are extracellular polymeric substances?
Reproducible increases in fitness over time illustrate this concept.
What are adaptive trajectories?
These “semi-mythical” organisms famously eluded cultivation but were identified thanks to their 16S signatures.
What is the candidate phyla radiation?
This process can be seen in metagenomic surveys when environmental parameters like pH or salinity exert strong effects on microbial communities.
What is habitat filtering?
This type of plasmid carries genes for conjugation machinery, enabling it to spread rapidly.
What is an F plasmid?
Highly disturbed ecosystems often favor fast-growing, opportunistic microbes known by this name.
What are r-strategists?
The LTEE’s frozen “fossil record” works because populations are preserved using this method.
What is glycerol freezing or -80C storage?
This property of the 16S rRNA gene makes it great for phylogeny but terrible for resolving species- or strain-level variation.
What is the rate of evolution of the 16S gene?
Endemism in microbes is difficult to demonstrate due to this confounding factor in global sequence databases.
What is sampling bias? (or) what is uneven sampling?
Gene exchange across distantly related lineages is one reason microbial phylogenies sometimes produce this contradictory pattern in trees.
What is phylogenetic incongruence?
When disturbances knock microbial populations below critical thresholds, demographic randomness can dominate recovery dynamics due to this process.
What is ecological drift?
Clonal interference is common in the LTEE because beneficial mutations compete in this type of population.