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

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