university of essex
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University of Essex. BIODEEP-WP3. Analysis of species diversity, community structures and phylogeny of microorganisms and meiofauna in the Mediterranean deep-sea hypersaline anoxic basins (DHAB). Andrea Sass , Terry McGenity. Community structure fingerprinting via t-RFLP of 16S rDNA. - PowerPoint PPT PresentationTRANSCRIPT
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University of EssexUniversity of Essex
BIODEEP-WP3
Analysis of species diversity, community structures and phylogeny of microorganisms and meiofauna in the Mediterranean deep-sea hypersaline anoxic basins (DHAB)
Andrea Sass , Terry McGenity
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Amplification with fluorescent eubacterial primers successful Water, brine and interface samples were all investigated
Not successful: amplification with Archaeal primers DNA extraction from most sediment samples amplification from Discovery brine and interface
Summary of achievements up to date:
Community structure fingerprinting via t-RFLP of 16S rDNA
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Summary of previously presented results:
brines of each basin unique patterns l’Atalante and Bannock brines more similar patterns stable over time same patterns from Urania brines 1 and 2 number of fragments relatively small
Brine samples:
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new achievements:
amplification from l‘Atalante and Bannock basin sediments successful
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Bannock sediment sample and brine
Sediment top
Brine
Fragment length
RF
U
Amplification with eubacterial primers, digestion with AluI
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Brine samples taken at same location and depth?
Brine
Sediment
L’Atalante sediment and brine
Sediment top covered with black ooze
Cruise 2002
Cruise 2002
Cruise 2001
amplification with -casein
Sediment top
Sediment top
Sediment top
Sediment bottom
amplification with -
caseine
extraction with phenol-chloroform
RF
U
Fragment length
Amplification with eubacterial primers, digestion with AluI
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patterns from sediment samples very similar to brine samples no unique fragments found in sediment samples
Community in the sediments widely the same as in brines?
sediments consist mainly of brine both sediments and brine are anoxic
Extraction methods yield DNA only from the brine fraction of the sediment?
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Interfaces
Patterns from interfaces unique for each basin and different from brines and oxic seawater
Certain fragments occur only at certain salinities within the interface
Unique community or accumulation of microorganisms from the water column?
Bannock interface samples taken in intervals at different salinities
Summary of previous presented results:
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Salinity 25%= brine
Salinity 21.5%
Salinities 13.8-15.9%
Salinity 12.7%
Salinities 8.7-10.8%
Salinities 3.8-7.6%
Oxic water, 3000 m depth
Fragment length
Bannock interface
Amplification with eubacterial primers, digestion with AluI
RF
U
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Sediment traps
2 weeks
6 months
12 months
Amplification with eubacterial primers, digestion with AluI
Fragment length
RF
U
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new achievements:
investigation of Urania basin interface with greater spatial resolution
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Salinity 5.7 ‰
Salinity 15.4 ‰
Salinity 6.3 ‰
Salinity 9.0 ‰
Salinity 13.1 ‰
Salinity 21.1 ‰
Salinity 15.6 ‰
Salinity 18.4 ‰
Brine
Urania interface
Amplification with eubacterial primers, digestion with AluI
Fragment length
RF
U
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fingerprints change gradually from interface to brine no succession of microbial communities within interface
interface not as stable as Bannock interface?
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Bannock and Urania upper interfaces:
community fingerprints are different from oxic deep-sea water
change in communcity structure starts at seawater salt concentration above the sampled interface?
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Amplification with eubacterial primers, digestion with AluI
Fragment length
Urania interface compared with oxic water samples
samples taken 2001
RF
U
Urania interface
oxic water 3500m depth
oxic water 3000m depth
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Different pattern in water and interface samples due to different amount of water filtered ?
Amplification with eubacterial primers, digestion with AluI
Patterns from the same DNA extract with different amounts of DNA addes to PCR reaction
Fragment length
RF
U
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Summary of newly achieved results:
Microbial community in Bannock and l‘Atalante sediments similar to those in corresponding brines
Succession of different comminties at different salinities within the interface more pronounced in Bannock interface than in Urania interface
Upper interfaces different from sea water