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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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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-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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-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

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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

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LIGHT from ENERGYBIOLUMINESCENT MICROBES

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FLASHLIGHT FISH USELIGHT from

BACTERIAL SYMBIONTS

MAGNETOTACTIC BACTERIA

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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

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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

microbial life on earth : engines of the biospherethermodynamics, microbial diversity, and...

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