microbial life on earth : engines of the biospherethermodynamics, microbial diversity, and...
TRANSCRIPT
1
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
2
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 …..
3
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.
4
Anoxygenic photoautotrophs utilize cyclicphotophosphorylation
Cyclic photophosphorylation
Cyclic photosynthesis (anoxygenic)
5
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….
6
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
7
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
8
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
9
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)
10
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 !
11
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
12
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)
13
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
14
2-
-
2
4
3
-
22 2
3
THE NITROGEN
CYCLE
NHNH44++
NONO22--
NONO33--
NitrosospiraNitrosospira
NitrospiraNitrospira
Nitrosospira
3
3
LIGHT from ENERGYBIOLUMINESCENT MICROBES
15
FLASHLIGHT FISH USELIGHT from
BACTERIAL SYMBIONTS
MAGNETOTACTIC BACTERIA
16
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 ???
17
CULTIVATIONCULTIVATIONINDEPENDENT INDEPENDENT SURVEYSSURVEYS
A la Pace, 1986A la Pace, 1986
Known Bacterial Phylogenetic Divisions
Courtesy N. Pace 2006
18
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
19
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
20
“SAR86” 130kb GENOME FRAGMENT
Bacteriorhodopsin is light driven proton pump
Inside cell
Outside cell
Inside cell
Outside cell
cellmembrane
21
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
22
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)
23
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
24
(Thanks, NSF !)
GenomeLibraries
25
KEGG PZ Enriched
KEGG DW Enriched
PZPZ DWDW
PZPZ DWDW
F. Azam (1998)Science 280: 694
PHOTIC ZONE -CHEMOTACTIC ?
DEEP WATER -PREFERNTIALLY
ATTACHED ?
26
1) Prochlorococcus phylotypes evident2) Viral recovery maxima - 70 m3) Viral recovery decrease below PZ