Download Measurement of Microbial Numbers and Activity

Microbial Communities at Seamounts
Iron finger chimneys at Loihi
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?
I
I
I
I
I
I
O2
I
I
+ 14
I
I
NO3-/N2
I
I
+ 12
0
+2
I
I
MnO2
+ 10
-2
+4
I
I
Mn(II)
-4
+6
I
I
NH4+
SeO3
NO2NO3-
-6
+8
I
I
Fe(II)
CO2
SO4=
AsO43FeOOH
Organic
Carbon
-8
+ 10
I
Organic H2
Carbon
H2S
So
I
Volcanic
Hydrothermal
Etc.
Photoreductants
I
The
Geological - 6
Environment
-4
Supplies
-2
Many
Oxidants
0
And
Reductants + 2
That
+4
Life has
Learned to + 6
Utilize !!
+8
I
-8
Relative Voltage (Pεo(W))
OXIDANTS
-10
+ 12
I
I
Relative Voltage (Pεo(W))
FUELS
-10
+ 14
What microorganisms are present and
how many? – Whole cell assays
• Cultivation and identification
– <1% of the microbes observed have been cultured
• Cell counts
– Total epifluorescent counts
– Particle counts
– Specific group assays (molecular probes)
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
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)
Cutting edge approaches
• “–Omics”
– Genomics/metagenomics (genes)
– Proteomics (proteins)
– Transcriptomics (mRNA)
• Spatially-resolved mineralogical &
phylogenetic approaches using synchotron
technologies
Today’s session
• Katrina Edwards (WHOI) – CARD-FISH
approaches for characterizing endolithic rockhosted 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
General Approaches for Studying
Basalt Weathering
Geochemical Characterization
Diffraction, Electron Microscopy, Microprobe
Biofilm Experiments
LOIHI
Molecular Characterization
Pure culture & consortia, surface chemistry
T-RFLP, sequencing, RubisCO
Enrichment cultures & Isolations
Aerobic and anaerobic
Figure courtesy of Alexis Templeton