Transcript Growth rates of SAR11 in the Delaware estuary - C-MORE

Growth rates of heterotrophic
bacteria determined by 16S
rRNA:rDNA ratios
Tom S. Lankiewicz
The microbial loop
Why do growth rates matter?
½ of population controls
Bottom-up controls
• Addition of new cells to
population
(growth)
• Resource limitation (organic
carbon)
• Growth rate determined by
extent of resource limitation
Top-down controls
• Removal of cells from
population
(grazing and viral lysis)
Ribosomes as a measure of growth
Some very basic assumptions:
More ribosomes = more protein synthesis
More protein synthesis = more growth
Past applications of this concept
rRNA:rDNA ratios
# of 16 S rRNA copies
# of 16S rDNA copies
rRNA: could be quantified with high throughput
sequencing or with Q-PCR
rDNA: can be inferred from abundances
rRNA:rDNA ratios:
recent studies
Current limitations in using
rRNA:rDNA as a measure of growth
With current knowledge data is relative: X is
growing fast compared to other populations of X
We don’t know what the growth rate of X is in
relation to Y
Some unique relationship between rRNA:rDNA ratio
and growth rate for each bacterial strain
Phase 1: In lab
Hypothesis
Higher rRNA:rDNA ratios are indicative of faster
growth within one organism,
But there is a unique relationship between
rRNA:rDNA and growth rate for each strain.
Growth of heterotrophic bacteria in culture
What is the relationship between rRNA:rDNA
ratios and growth rate?
Leucine incorporation and growth rate? (easy bulk
measurement of growth)  double check
Samples Taken:
•rRNA (QPCR)
•Cell abundance
(DAPI)
•Leucine Inc (bulk
incorporation assay)
•Organic acid uptake
(bulk incorporation)
•(Respiration)
Dilution rate (D) = Growth Rate (μ)
Test several different μ to
determine a relationship
Complementary to work with
heterotrophic bacterial respiration
Will be run in parallel with rRNA:rDNA ratio
experiment
Respiration, uptake, and growth rates will
provide a robust picture of carbon utilization
during diff. rates of growth
Possible strains
Organism
Clade
Habitat where
isolated
Sequenced?
Max growth
rate (d-1)
Pelagibacter
ubique
SAR11
Oligotrophic
Yes
0.4
Ruegeria
pomeroyi
Roseobacter
Copiotrophic
Yes
0.4
Polaribacter
Flavobacteria
Copiotrophic
Yes
.8
HTCC2207
SAR92
Oligotrophic
Yes
2.0
Phase 2: Delaware Bay sampling
Growth rates of natural populations
Which organisms in the Delaware Bay estuary are
growing rapidly and which are growing slowly?
Is abundance negatively related to growth rate?
Delaware Bay estuary bacterial
biogeography
Kirchman et al. (2005)
Questions