Microbial Life on Earth : Engines of the BiosphereThermodynamics, microbial diversity, and...
Transcript of Microbial Life on Earth : Engines of the BiosphereThermodynamics, microbial diversity, and...
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Microbial Life on Earth : Engines of the BiosphereMicrobial Life on Earth : Engines of the Biosphere
Earth history & microbial evolutionEarth history & microbial evolution
Thermodynamics, microbial diversity, and biogeochemical cyclesThermodynamics, microbial diversity, and biogeochemical cycles
New ways to study microbes :New ways to study microbes :Microbial genomics in the environmentMicrobial genomics in the environment
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Early Earth conditions (not so different than our planetary neighbors !)
Lots of bolide impacts, volcanic activity
Much warmer average global temperature than today (80 C ?)
Mildly reducing conditions in the atmosphere (C02, N2, H2, NH4, CH4)
Oceans likely formed > 3.8 bya (condensation from atm as Earth cooled)
No free oxygen
Whats needed for life in generalEnergy (light, oxidants, reductants)Water (liquid)Basic elements : C, H, N, O, P, S + trace metals
Microbes thrive at the extreme ranges of temperature, salinity, pH, pressure, water activity …..
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Science, Vol 289, Issue 5485, 1703-1705 , 8 September 2000
D. J. Des Marais
STROMATOLITES
Stromatolites are formed through the activity ofprimitive unicellular organisms: cyanobacteria(which used to be called blue-green algae) andother algae. These grow through sediment and sand, binding the sedimentary particles together,resulting in successive layers which, over a long period of time, harden to form rock. For at least three-quarters of the earth's history stromatoliteswere the main reef building organisms, constructing large masses of calcium carbonate.
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Anoxygenic photoautotrophs utilize cyclicphotophosphorylation
Cyclic photophosphorylation
Cyclic photosynthesis (anoxygenic)
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OXYGENIC PHOTOSYNTHESIS OXYGENIC PHOTOSYNTHESIS -- SPLITTING WATER WITH LIGHT !SPLITTING WATER WITH LIGHT !
1. ATP synthesis2. Reducing power (NADPH)3. Use energy for C02 fixation
Animals Animals BacteriaBacteria
Chemical Chemical energy or heatenergy or heat
RespirationRespiration
Life on Earth TodayLife on Earth Today
COCO22 + H+ H22OOcarbon watercarbon waterdioxidedioxide
CC66HH1212OO66 + O+ O2 2 organic oxygenorganic oxygencarboncarbon
Plants Plants PhytoplanktonPhytoplankton
PhotosynthesisPhotosynthesisSolar energySolar energy
N,P,S,Fe….N,P,S,Fe….
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Microbial Life on Earth : Engines of the BiosphereMicrobial Life on Earth : Engines of the Biosphere
Earth history & microbial evolutionEarth history & microbial evolution
Thermodynamics, microbial diversity, and biogeochemical cyclesThermodynamics, microbial diversity, and biogeochemical cycles
New ways to study microbes :New ways to study microbes :Microbial genomics in the environmentMicrobial genomics in the environment
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Barns et al.,1996
{PlantsAnimalsFungi
• EXIST @ EXTREMES OF TEMPERATURE, pH, SALINTY, PRESSURE
• MAKE ENERGY and FOOD FROM LIGHT -> PRIMARY PRODUCTION
• MAKE ENERGY and FOOD FROM ROCKS ! -> “CHEMOSYNTHESIS”
• INVENTED BIOLUMINESCENCE, MAGNETIC NAVIGATION, etc…
TREMENDOUS FUNCTIONAL DIVERSITY in MICROBESTREMENDOUS FUNCTIONAL DIVERSITY in MICROBES
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TEMPERATURE : TEMPERATURE : --20 to 121 degrees 20 to 121 degrees CelciusCelcius !!
pH: < pH 1.0 to pH 12pH: < pH 1.0 to pH 12
PRESSURE: 1 PRESSURE: 1 atmatm to > 1000 to > 1000 atmatm
SALINITY: 0 % to saturated brines (5 M SALINITY: 0 % to saturated brines (5 M NaClNaCl))
MICROBES INHABIT “EXTREME” ENVIRONMENTSMICROBES INHABIT “EXTREME” ENVIRONMENTS
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Animals Animals BacteriaBacteria
Chemical Chemical energy or heatenergy or heat
RespirationRespiration
Life on Earth TodayLife on Earth Today
COCO22 + H+ H22OOcarbon watercarbon waterdioxidedioxide
CC66HH1212OO66 + O+ O2 2 organic oxygenorganic oxygencarboncarbon
Plants Plants PhytoplanktonPhytoplankton
PhotosynthesisPhotosynthesisSolar energySolar energy
N,P,S,Fe….N,P,S,Fe….
LIFE IS ELECTRIC ! METABOLIC PROCESS ARE LARGELYLIFE IS ELECTRIC ! METABOLIC PROCESS ARE LARGELYENERGY SWAPPING REACTIONS, THAT USE ELECTRONS AS CURRENCYENERGY SWAPPING REACTIONS, THAT USE ELECTRONS AS CURRENCY
(“REDOX” CHEMISTRY)(“REDOX” CHEMISTRY)
CC66HH1212OO6 6 + 6O+ 6O2 2 ++ 12H12H++ 6CO6CO22 + 6H+ 6H22O O + heat+ heat
CC66HH1212OO66
6CO6CO22 6H6H22O O
6O6O2 2 ++ 12H+ 12H+
ee--
Electron donorElectron donor Electron acceptorElectron acceptor
+ heat+ heat
ETCETC
((ETC=electron transport chain)ETC=electron transport chain)
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Electrons are passed from NADH via the electron transport chainto oxygen. Simultaneously, protons are “pumped” outside cell.
Inside cell
Outside cell
H+
H+
H+
H+
H+
H+
electron transport chainembrane
The enzyme ATPase can use the energy from the proton gradient to make ATP.
Inside cell
Outside cellNADH/NAD+ -0.32
-0.5
-0.3
-0.1
+0.1
+0.3
+0.5
+0.7
E o ’ ( v o lt s )
0.5O2/H2O +0.82
MICROBIALMICROBIALMETABOLIC METABOLIC DIVERSITYDIVERSITY
Relative VoltageRelative VoltageFUELS (EAT) OXIDANTS (BREATHE)
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4
+ 6
+ 8
+ 10
+ 12
+ 14
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4+ 6
+ 8
+ 10+ 12
+ 14
OrganicCarbon
CO2SO4
=
AsO43-
FeOOH
SeO3NO2
-
NO3-
MnO2
NO3-/N2
O2
H2
H2SSo
Fe(II)
NH4+
Mn(II)
A
B
Photoreductants
Microbes can
eat & breathe just
about anything !
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MICROBIALMICROBIALMETABOLIC METABOLIC DIVERSITYDIVERSITY
Relative VoltageRelative VoltageFUELS (EAT) OXIDANTS (BREATHE)
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4
+ 6
+ 8
+ 10
+ 12
+ 14
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4+ 6
+ 8
+ 10+ 12
+ 14
OrganicCarbon
CO2SO4
=
AsO43-
FeOOH
SeO3NO2
-
NO3-
MnO2
NO3-/N2
O2
H2
H2SSo
Fe(II)
NH4+
Mn(II)
A
B
Photoreductants
Microbes can
eat & breathe just
about anything !
METABOLIC DIVERSITYMicrobes can eat “rocks”(inorganic e- donors) and fix CO2
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MICROBIALMICROBIALMETABOLIC METABOLIC DIVERSITYDIVERSITY
Relative VoltageRelative VoltageFUELS (EAT) OXIDANTS (BREATHE)
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4
+ 6
+ 8
+ 10
+ 12
+ 14
-10
- 8
- 6
- 4
- 2
0
+ 2
+ 4+ 6
+ 8
+ 10+ 12
+ 14
OrganicCarbon
CO2SO4
=
AsO43-
FeOOH
SeO3NO2
-
NO3-
MnO2
NO3-/N2
O2
H2
H2SSo
Fe(II)
NH4+
Mn(II)
A
B
Photoreductants
Microbes can
eat & breathe just
about anything !
E- acceptor ∆Go’ (using glucose as e- donor)
Oxygen -3190 kJ/mol
NO3- -3030
Mn (IV) -3090
Fe(III) -1410
Sulfate -380
CO2 -350
METABOLIC DIVERSITYMETABOLIC DIVERSITY - MICROBES CAN USE LOTS
OF DIFFERENT TERMINAL ELECTRON ACCEPTORS
((∆Go’ is Gibbs free energy of reaction = energy available to do work)
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2-
-
2
4
3
-
22 2
3
THE NITROGEN
CYCLE
With Microbes
3
3
THE NITROGEN
CYCLE
Without Microbes
2-
-
2
4
3
-
22 2
3
X X
XX
X
XWithout Microbes
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2-
-
2
4
3
-
22 2
3
THE NITROGEN
CYCLE
NHNH44++
NONO22--
NONO33--
NitrosospiraNitrosospira
NitrospiraNitrospira
Nitrosospira
3
3
LIGHT from ENERGYBIOLUMINESCENT MICROBES
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FLASHLIGHT FISH USELIGHT from
BACTERIAL SYMBIONTS
MAGNETOTACTIC BACTERIA
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Microbial Life on Earth : Engines of the BiosphereMicrobial Life on Earth : Engines of the Biosphere
Earth history & microbial evolutionEarth history & microbial evolution
Thermodynamics, microbial diversity, and biogeochemical cyclesThermodynamics, microbial diversity, and biogeochemical cycles
New ways to study microbes :New ways to study microbes :Microbial genomics in the environmentMicrobial genomics in the environment
How much do we really know?Seawater plate count
100s microbes/mlDirect counts1,000,000/mlVERSUS
WHAT ARE WE MISSING ???
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CULTIVATIONCULTIVATIONINDEPENDENT INDEPENDENT SURVEYSSURVEYS
A la Pace, 1986A la Pace, 1986
Known Bacterial Phylogenetic Divisions
Courtesy N. Pace 2006
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GENOMIC ANALYSES ?UNCHARACTERIZED NATIVE TAXA
Community DNA encodes the network instructions that drive Community DNA encodes the network instructions that drive organism function, organism function, organismalorganismal interactions & ecosystem functioninteractions & ecosystem function
GENOMES to BIOMES
Community DNA
Community compositionand interactions
Community metabolism
Ecosystem functions
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XX
X
X
X
X
X (oxygen min)
X
X
MontereyBay BAC libraries
X
XX
X
X (oxygen min)
MB BAC libraries
1
SAR86 130 kbp BAC
1
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“SAR86” 130kb GENOME FRAGMENT
Bacteriorhodopsin is light driven proton pump
Inside cell
Outside cell
Inside cell
Outside cell
cellmembrane
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Fast photcycle kinetics
ON
OFF
5 min
OFF
ON
Retinal Proteorhodopsin
+-+
+
-+ -
-
pH 0.02
LIGHT-DRIVEN PROTON PUMPING IN E. COLI(via ŅSAR86Ó PROTEORHODOPSIN)
Expression of proteorhodopsin in E. coli
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Venter et al., Environmental Genome Shotgun Sequencing of the Sargasso Sea
Science 394:66-74 (2004)
Venter et al., Environmental Genome ShotgunSequencing of the Sargasso Sea,
Science 394:66-74 (2004)
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Depth-specific differences in proteorhodopsin variants
Béjà Nature 411:786-789 (2001)
PROTEORHODOPSIN NATURAL VARIATION = FUNCTIONAL VARIATIONPROTEORHODOPSIN NATURAL VARIATION = FUNCTIONAL VARIATION
“Blue” rhodopsin“Green” rhodopsin
DIFFERENT ‘FLAVORS” of RHODOPSINBeja et al, 2003
Leu105 -> Gln105
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(Thanks, NSF !)
GenomeLibraries
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KEGG PZ Enriched
KEGG DW Enriched
PZPZ DWDW
PZPZ DWDW
F. Azam (1998)Science 280: 694
PHOTIC ZONE -CHEMOTACTIC ?
DEEP WATER -PREFERNTIALLY
ATTACHED ?
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1) Prochlorococcus phylotypes evident2) Viral recovery maxima - 70 m3) Viral recovery decrease below PZ