Microbial Communities at Seamounts

1
Microbial Communities at Seamounts
Iron finger chimneys at Loihi
2
Microbial Community Characterization

• What microorganisms are present and how many?
• the potential for biogeochemical processes to
  occur
• just because organisms are present doesn't
  necessarily mean they are active
• What are they doing and how fast?
• activities biogeochemical reactions
• rates
• What are the physical and chemical properties of
  the system?

3
Relative Voltage (Peo(W))
Relative Voltage (Peo(W))
FUELS OXIDANTS
-10
-10
Photoreductants
- 8
- 8

The Geological Environment Supplies Many
Oxidants And Reductants That Life has Learned
to Utilize !! Volcanic Hydro- thermal Etc.
H2 H2S So Fe(II) NH4 Mn(II)
- 6
- 6
CO2 SO4 AsO43- FeOOH SeO3 NO2- NO3- MnO2 NO3
-/N2 O2
- 4
- 4
- 2
- 2
0
0
2
2
4
4
6
6
8
8
10
10
12
12
14
14
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What microorganisms are present and how many?
Whole cell assays

• Cultivation and identification
• lt1 of the microbes observed have been cultured
• Cell counts
• Total epifluorescent counts
• Particle counts
• Specific group assays (molecular probes)

5
What microorganisms are present and how many?
Cell extract assays

• Biomarkers biomass indicators
• Lipids, pigments, etc.
• Microbial community snapshots (PCR based)
• 16S ribosomal gene clone libraries sequencing
• Denaturing gradient gel electrophoresis (DGGE)
• Terminal restriction length fragment polymorphism
  (TRFLP)
• Automated ribosomal intergenic spacer analysis
  (ARISA)
• Polymerase chain reaction-single-strand
  conformation polymorphism (PCR-SSCP)
• Quantitative polymerase chain reaction (QPCR) for
  specific phylotypes

6
What are they doing and how fast?

• (Geo)chemical methods
• Detection of processes
• Rate measurements of chemical reactions
• Molecular methods
• Detection of functional genes
• Measurements of gene expression
• Diagnostic proteins
• Gene transcripts (mRNA)

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Cutting edge approaches

• Omics
• Genomics/metagenomics (genes)
• Proteomics (proteins)
• Transcriptomics (mRNA)
• Spatially-resolved mineralogical phylogenetic
  approaches using synchotron technologies

8
Todays session

• Katrina Edwards (WHOI) CARD-FISH approaches for
  characterizing endolithic rock-hosted microbial
  populations
• David Emerson (ATCC) Cultivation of novel
  marine Fe-oxidizing bacteria from the Loihi
  Seamount
• Craig Moyer (WWU) Spatial and temporal
  variability in microbial mat communities from
  pre- and post-eruption Loihi Volcano

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General Approaches for Studying Basalt Weathering
Figure courtesy of Alexis Templeton