Following on from my previous post, here are notes from day 2 of ISME. This is the last of my ISME notes, I only attended the first half of the meeting.
crispr repeats — history of host-viral interaction
200 of 1300 spacers match known virii
blast spacers against viral genomes
more similarity to viral genomes from geographically local places
strains from same location have spacers matching same virii (geographic correlation)
more matches to SIRV virus in north american populations
vice versa for SSV/kamchakta
shifting gears to new topic:
39 strains from one hot springs.
predator prey oscillations?
most of the time there should be a single dominant strain.
MLST of 39 strains
appears to be one dominant clone
small number of coexisting strains branching deeper in MLST tree
look at CRISPRs in 12 genomes sequenced from these isolates
3 CRISPR/Cas loci. hypervariable.
tried to amplify with primers to sequence but only works 60% of time
lots of rearrangements in the crispr region, preventing amplification
C locus deletions in some strains
possible recombination in CRISPRs
need an alternative model:
do CRISPRs maintain host population diversity?
notion is that CRISPRs match different parts of the virus so an escape mutation in the virus will only affect part of the host population
Question by David Ward: can the dominant population be subdivided into several different subpopulations?
A: yes, the dominant strains actually group into three groups based on genome-wide similarity
Qeustion by Matt Kane: how does this relate to the rate of genetic communication? are the virii driving local speciation and diversification?
Vibrio paracholerae/cholerae genome conversion
paracholerae sister taxa to cholerae. not usually human pathogenic.
isolates from bangladesh and wood’s hole.
phylogeny of strains using 6 marker genes shows a mix of topology
look at integron for markers. variable part of the genome, 3%.
attI shuffling locus for homologous recombination-mediated rearrangement of integron genes
integron cassette phylogeny clusters by geography, not by species (as defined by housekeeping genes).
integrons are highly variable in gene content, the integron gene pool families are not part of the main vibrio gene pool.
that is: integron genes are always in integron regions, never in the rest of the genome.
annotated gene functions in integrons appear to be “ecologically relevant”?
Why does cross-feeding occur in Microbial communities?
Why are microbial communities so diverse, and how is the diversity maintained?
How are communities assembled?
Substrate cross-feeding: does it maintain diversity?
Studying denitrification .. Nitrate to N2
Some bugs do total denitrification, other bugs only have part of the pathway and assemble into communities that create a complete pathway.
Why don’t bugs with the complete pathway do better?
Mathematical model of fitness of each approach to denitrification.
assumptions: cell has a limited number of enzymes
convex constraint function creates cross-feeding, concave constraint function creates complete pathway organisms
nitrogen mutants of Pseudomonas stutzeri, measure the shape of the constraint function by assembling communities of mutants where each community member carries out part of the pathway
Had to delete the complete transformation system in order to get experiment to work.
pathogen: any organism that reduces the fitness of a host
bacteriophage: strongly select for phage resistance
- may indirectly select for less pathogenic bacteria
investigated selection by parasitic phages and thermal environments on evolution of bacterial pathogenicity
microcosm experiment with serratia marescens
bacteria cultured with lytic phage PPV in low and high temp
changes in pathogenicity measured in vivo using wood tiger moth larvae
temp and phage treatment had little effect on bacterial growth traits
previous phage exposure allowed larger population sizes in subsequent exposure
S. marescens becomes more pathogenic when cultured at 37c without phage, but not with phage.
is it due to reduced maximum population size caused by phage??
motility maladaptive in presence of phage, but good for pathogenicity?
cell-to-cell electron transfer in geobacter
interspecies hydrogen transfer — one organism exports H2 other exports H+ to reduce CO2 to CH4
Geobacter, non fermenters, iron citrate respiration
create cocultures of sulfurreducesn and metallireducens
syntrophic when growing on ethanol fumarate media.
metallireducens oxidizes ethanol, sulfurreduces consumes H2+acetate, reduces fumarate.
grew slowly at first.
serial transfer to select for fast growers on the media.
large aggregates emerged!
1mm in size. large spherical structures by transfer #30.
channels in aggregates, possibly to promote exchange with the environment around them
One organism exists in 15% abundance, other is 85%.
spatial arrangement determined by FISH, nice mix of organisms.
solexa resequencing from transfer 15. found single mutation in pilR regulator that causes frameshift and premature stop codon.
possible up-regulation of OmcS.
conductive pili — proposed mechanism of syntrophy.
interconnected web of pili in the aggregate, electrons go thru pili from metallireducens to sulfurreducens
test conductance using 2 plate gold with aggregates in gap between plates. yep, conducts electricity.
Q: able to separate the species from aggregates?
Q: can the organism abundances be explained metabolically?
A: the metallireducens (electron donor) organism is in lower abundance, not sure yet about metabolism.