2/4/11

1

Microbes:driversofglobal

biogeochemistry1/28/2011

VirginiaRich‐EEB

With material from Drs. Sco2 Saleska (U of Az), Gene Tyson (U of Queensland, Australia) and Kostas KonstanBnidis (Georgia Tech)  

prop

ortal.m

it.ed

u

Prochlorococcus marinus 

forces.si.edu

Soilfungus

Soilbacteria

www.bioqu

est.org

Diatom

Den

nisKu

nkel

Coccolithophore

ww

w.n

hm.a

c.uk

ww

w.m

orni

ng-e

arth

.org

/Gra

phic

-E/

Bios

pher

e/Bi

os-M

icro

be-I

mag

e/M

-PC

ophr

yosc

olex

RumenproFstOphryoscolex  

forces.si.edu

TermiteproFst

Outline I.  BigPictureII.  Howdomicrobesmakealiving(andthusinteract

withbiogeochemicalcycles)?III.  Microbes&theCcycle–thehighlights

A.  PrimaryProducFonB.  DecomposiFon

SoilrespiraFon,oceanrespiraFon

IV.  MenFonofothercycles,&Summary

2/4/11

2

I.Bigpicture:microbesdrivebiogeochemicalcycles

If all multi-cellular life disappeared tomorrow the major biogoechemical cycles would likely proceed with very little change... 

•  ~ Half planetary primary production (C fixation): forests &

other big green stuff

marine microorganisms (cyanobacteria & phytoplankton)

•  Biomass: ~109 microbial cells/gram surface soil and ~106 cells/ml seawater. (You have more microbial cells in your body than human cells). 50-90% of marine biomass is microbial (Census of Marine Life).

Without microbial recycling, nutrients would be locked up & become unavailable.

•  Organic matter degradation:

cour

ses.

wor

ldca

mpu

s.ps

u.ed

u

•  Metabolic diversity:Microbes perform all major metabolic pathways, and periodically reveal entirely new ones (e.g. proteophodopsin, anaerobic methane oxidation). ht

tp:/

/new

scen

ter.l

bl.g

ov/

II.Howdomicrobesmakealiving?•  “Microbes”canmeanseveralthings!!!Forthisoverviewdefinedas

single‐celledorganisms:bacteriaandarchaea(togetheroZencalledthe“prokaryotes”,also“microbes”)plussingle‐celledeukaryotes(aka“protozoans”,andthemajorityof“proFsts”)

Howaremicrobesinvolvedinallthesebiogeochemicalcycles?Whatdomicrobes–indeedallcells–needtomakealiving?

•  CARBONforbulkofbiomass•  NUTRIENTS(N,P,S)andmicronutrientsforproteins,nucleicacids,

etc.•  WATERasasolvent(andareactantinbiomassproducFon)•  ENERGYtoallowthemtoworkagainstentropy•  ELECTRONStotransferenergyviaredoxreacFons,andperform

chemicaltransformaFons–soasourceandasinkforelectrons‐

2/4/11

3

Let’stakeanexamplewe’remorefamiliarwith:us.Inourspecialcase,ourfoods(complexorganiccompounds)provideuswithCarbon,withBondenergy,ANDwithelectrons.Howareorganiccompoundsusedforallthesethings?Recallthemitrochondria?(Whichare,asyou’llrecallfromhighschoolbio,descendentsoffree‐livingbacteriathattookupresidenceinsideeukaryoFccellslongago).

Wikipedia

Mitochondrialelectrontransportchain

aka Krebs cycle

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

SourceforC,energy+electrons=carboncompounds

2/4/11

4

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

SourceforC,energy+electrons=carboncompounds

biosynthesis

biosynthesis

biosynthesis

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

biosynthesis

biosynthesis

biosynthesis

ATP

2/4/11

5

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

biosynthesis

biosynthesis

biosynthesis

ATP

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

biosynthesis

biosynthesis

biosynthesis

ATP

2/4/11

6

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

biosynthesis

biosynthesis

biosynthesis

ATP

Wikipedia

Mitochondrialelectrontransportchain

Carboncompounds(=“food”)

ww

w.p

ower

2fitn

ess.

com

/im

ages

/kre

bs_c

ycle

-lrg

.gif

Sinkforelectrons=O2(producingwater)

biosynthesis

biosynthesis

biosynthesis

ATP

2/4/11

7

Words we use to describe where organisms get their carbon, energy, and electrons 

1.Carbon•  AutotrophGreek autos=self,trophe=nutriFon.Sowhat

istheirCsource?Howdotheygetit?Whataresomeexamples?

•  Heterotrophheteros=other,trophe=nutriFon.SowhatistheirCsource?Howdotheygetit?Examples?

prop

orta

l.mit.

edu

eart

hobs

erva

tory

.nas

a.go

v

wikiped

ia

Asso

ciat

ed P

ress

prot

istu

ser.u

ni-

fran

kfur

t.de.

~sch

aude

r.ter

mite

s.pr

oto7

_bg

ww

w.m

orni

ng-e

arth

.org

/Gr

aphi

c-E/

Bios

pher

e/Bi

os-

Mic

robe

-Im

age/

M-

PCop

hryo

scol

ex.jp

g

2.Energy•  Phototrophphoto=lightEnergycomesfromphotons

•  Chemotrophchemo=chemicalEnergycomesfromconverFngenergystoredinchemicalbonds(viatheirelectrons)

Inbothcases,capturedenergyisstoredasATP,carbs,lipidsorproteins.

3.ElectronSource•  Organotrophorganic=C‐containing.Usecarboncompoundsas

electrondonors.Thisincludesus!

•  Lithotrophlithos=rockUseinorganiccompoundsaselectrondonors

4.ElectronSink•  AerobicrespiraFonusesO2asterminalelectronacceptor.Whenit’s

available,itgetsusedbecauseofhighlyfavorableenergeFcs.

•  AnaerobicrespiraFonoccursinabsenceofO2,usingalternateterminalelectronacceptor.E.g.denitrificaBon usesnitrate(NO3

‐),sulfate reducBonusessulfate(SO4

2‐),methanogenesisusescarbon(CO2oracetate)

2/4/11

8

Examples

not so important to memorize terms as to understand that a diversity of lifestyles exist, & thus a diversity of interactions with biogeochem. cycles

•  Howwouldlandplantsbeclassified?–  FixCO2 –  Usesunforenergy– Whatistheirelectronsource?Isitorganicorinorganic

http

://w

ww

.mis

sour

ipla

nts.

com

/Fe

rns/

Equi

setu

m_h

ymen

ale_

stem

s

ThereforeweareChemoorganoheterotrophs,asareallmulFcellularcarnivores,herbivores,andmanymanymicrobes.

Photolithoautotrophs

http

://w

ww

.pop

artu

k.co

m/g

/l/l

gsb0

015+

da-v

inci

s-vi

truv

ian-

man

-hom

er-s

imps

on-t

he-s

imps

ons-

art-

prin

t.jpg

•  Howwouldwebeclassifiedunderthistrophicnomenclature?–  GetCfromothers–  GetelectronsfromCcompounds–  Getenergyfrombondenergy

Many biogeochemical transformations are unique to Bacteria and Archaea, and not found in Eukaryotes, e.g.

Nitrogen fixation N2 ⇒ NH3

Nitrification NH3 ⇒NO2- ⇒NO3

-

Anaerobic respiration Use of electron acceptors

other than O2 Examples Methanogenesis CO2 (or CH3COOH) ⇒ CH4

Denitrification NO3- ⇒ N2

Sulfate reduction SO42- ⇒ H2S

What jumps out just of this brief sampling? The N cycle is dominated by

microbial transformations.

2/4/11

9

Scok(andothers)says:

“Carbon is the currency of life”:

photosynthesis

H2O + CO2 CH2O + O2

respiration Carbon in

atmospheric CO2 Reduced Carbon in organic matter (biomass & energy supply)

III. Microbes & the Carbon Cycle

A.PrimaryProducFonakaautotrophy

•  OceanNPP~landNPP.Muchsparserbiomass,sowhy?

•  Theoceanscoveralotofterritory(~71%oftheearth’ssurface)

•  NotalotofmulF‐cellularprimaryproducersintheoceans–seagrasses&mostseaweedslimitedtocoasts,etc.–soit’sallaboutthemicrobes

earthobservatory.nasa.gov

Field et al. 1998 Science

≈

OceanNPP LandNPP

2/4/11

10

Whoisdoingthismarinephototrophy?

prop

ortal.m

it.ed

u

CYANOBACTERIA(e.g. Prochlorococcus marinus)  Diatom

Den

nisKu

nkel

Coccolithophore

ww

w.n

hm.a

c.uk

ea

rtho

bser

vato

ry.n

asa.

gov

30-60% of ocean primary production

EUKARYOTICPHYTOPLANKTON

http

://w

ww

.pho

tolib

.noa

a.go

v/bi

gs/fi

sh18

80.JP

G

40-70% of ocean primary

production

Butthat’sjustphotoautotrophy…whataboutchemoautrophy?

•  Intheoceans,chemoautrophyoccursin:

–  highorganic‐makercoastalzonewaters,

–  oxygenminimumzones(lowO2‐horizontalstretchesoftheoceans,theexpansionofwhichislinkedtoclimatechangeinseveralways.“Deadzones”areanextremeanthropogenictypeofoxygenminimumzone),

–  hydrothermalventsystems,

–  marinesediments,

–  marinebasalts,

–  thewatercolumnoftheopenocean,

–  ….

Basically everywhere in the sea, to varying degrees 

NS

F pr

ess

rele

ase

for D

eLon

g et

al 2

006

Sci

ence

2/4/11

11

Example:Chemolithoautotrophslivingonandbelowtheseaflooronbasalt.

“Laserconfocalphotomicrographofamicrobialbiofilmakachedtothesurfaceofbasaltchipsfromadepthof1500meters.GreenisreflectedlightfromthebasaltsurfaceandredisfromNilered–stainedbacterialcells.”

Stevens & McKinley, 1995 Science.

Subseafloor microbes = 10–30% of the total living biomass of Earth - Whitman et al. 1998 PNAS.

Santelli et al., 2008 Nature

Howdynamicmightthesepoolsbe?ANYdataonSIZEofchemoautotrophicCfixaFon?

“Total[autotrophic]biomassproducFonbyarchaeaindeepwatersis...1%ofannualmarineprimaryproduc>on...ofamagnitudesignificanttotheglobalcarboncycleandgreaterthan...thatburiedinmarinesediments.”(It’sonscaleof1/10thannualhumanCaddiFontoatmosphere.

Veryfew.Oneelegantexampleinadeep‐sea,low‐carbon,open‐oceanhabitat:

Used carbon isotopes in microbial biomass to track autotrophy (“you are what you eat”). Ingalls et al., 2006 PNAS

Walker et al., 2010 PNAS

Whatkindofchemoautotrophy? NH3

nitrification, by ammonia-

oxidizing archaea (ammonia is

electron DONOR)

2/4/11

12

Summaryofmicrobialautotrophy

•  Marine~terrerstrialNPP•  MarineNPP~microbial

•  MarineNPP=cyanos+eukaryoFcphytoplankton

•  Butwait,there’salotofnon‐phoFchabitatontheplanet

•  Chemoautrophsareabundantanddiverse

•  UnclearhowmuchCtheymaybefixing

eart

hobs

erva

tory

.nas

a.go

v

Ste

vens

& M

cKin

ley,

199

5.

NS

F fo

r DeL

ong

et a

l 200

6 Microbes&theCCycle:B.Heterotrophy•  Hetero.sgettheirCfromothers:

–  predaFon&herbivoryoflivingFssues–  scavengingofdeadbiomass

•  Resultsinbreakdownof organicmaker

Microbes are master decomposers

https://courses.worldcampus.psu.edu/welcome/turf230/images/microbial

http//berkeley.edu/news/media/releases/2007/01/images/leaf_bags

Will

iam

S. C

urrie

TERRESTRIAL

http

://w

ww

.who

i.edu

/cm

s/im

ages

/lsto

key/

2005

/1/v

40n2

-hon

jo2e

n_49

50.jp

g

Stocker et al Cover of Science Feb 2010

MARINE

2/4/11

13

MicrobialdecomposiFon

•  Providesenergyformicrobialgrowth (heteroTROPHY)

•  Releasesnutrients

Vitalforsustaininglife

e.g.Recyclednutrientsinocean’ssurfacewatersfuel78%ofmarineprimaryproducFon(Duceetal2008).

MicrobialdecomposiFonimpactsclimate

•  Influencesecosystemcarbonstorageandthereforeclimate....

•  RespiraBon =  the measurable output of all life’s breakdown of organic ma2er (thus both autotrophic and heterotrophic respiraBon.) 

•  CO2isreturnedtotheatmospherebyrespiraFonofmulFcellularorganismsandchemoorganotrophicmicrobes,plusanthropogenicacFviFes 

Soilbacteria

www.bioqu

est.org

forces.si.edu

Soilfungus

2/4/11

14

TerrestrialandmarinerespiraBon

IPCC2007,Ch.7;1990sdata

Soil respiration is the largest natural source of CO2 released to the atmosphere.

Marine respiration isn’t far behind.

Both much larger annually than human addition of CO2 to atmosphere.

Values in black are natural, values in red are anthropogenic.

The Global C Cycle

TerrestrialandmarinerespiraBon

IPCC2007,Ch.7;1990sdata

Soil respiration is the largest natural source of CO2 released to the atmosphere.

Marine respiration isn’t far behind.

Both much larger annually than human addition of CO2 to atmosphere.

Values in black are natural, values in red are anthropogenic.

The Global C Cycle

2/4/11

15

TerrestrialrespiraFon:

•  Insoils,theannualimbalancebetweenplantphotosynthesisand(plant+microbial)respiraFondefinesNEP=NetEcosystemProduc>on=CO2takenupbyanecosystem.

•  SoilrespiraFon=~½autotrophic(plantroots)and½heterotrophic(microbial+fungaldecomposiFon)(e.g.Trumbore2006GCB)

•  In oceans, the imbalance between production (+ terr. C input) and respiration defines the amount of C exported into the deep sea, where it has the potential to be buried and sequestered from the atmosphere.

•  e.g. in oceans, <0.1% of NPP reaches the sediment and gets buried (Falkowski & Oliver, 2007, Nature Rev. Micro.)

•  marinerespiraFon=~20%autotrophic(phytoplanton)and80%heterotrophic(microbes+metazoans)(e.g.delGiorgio&Duarte2002Nature)

•  ofheterotrophicrespiraFon,metazoansaccountfor<1%upto50%dependingontheregion,producFvity,depth,etc.(delGiorgio&Duarte2002Nature).

MarinerespiraFon:

Side Q: are fungi important decomposers in the oceans? 

2/4/11

16

Variantsonthebasics(a):MicrobialdecomposiFonisamajorprocessnotonlyin

soils&water,butinguts•  Ruminants.Hard‐to‐degradecellulosicplant

materialsrequiremicrobialenzymes–gutislikeamicrobialbioreactor…

•  Termites.Ifyoulivedoffgnawingwood,you’dneedhelptoo–termitegutsarefilledwitharichcommunityofsymbioFcmicrobes

•  Etc…BasicallyallmulF‐cellularheterotrophs–includingus…(yourveryown–likelyuniquetoyou!–commensalgutbacteria)

ww

w.m

orni

ng-e

arth

.org

/Gra

phic

-E/

Bios

pher

e/Bi

os-M

icro

be-I

mag

e/M

-PC

ophr

yosc

olex

RumenproFstOphryoscolex  

forces.si.edu

TermiteproFst

Variantsonthebasics(b):Non‐canonicalheterotrophy

SFllusingorganiccarbonastheircarbonsource–sosFlltrueheterotrophs–butge|ngaddiFonalenergyfromthesunorfrominorganicchemicalbonds.Inset example: proteorhodopsin.

assigned reading

http

://w

ww

.mba

ri.or

g/tw

enty

/imag

es/p

rote

o.jp

g

2/4/11

17

Summaryofmicrobialheterotrophy

•  microbesaremasterdegraders•  releasesnutrients•  organicmakerbreakdownquanFfiedbyrespiraFon•  controlsecosystemCstorage(imbalancebetweenPP&

respiraFon)–alsoseeScok’slecture9/28•  soilresp.=½autotrophic+½heterotrophic•  marineresp.=1/5autotrophic+4/5heterotrophic•  decomposiFonisthemajoravenueofcarbonlossfrom

ecosystems,&isdominatedbymicrobes•  metazoanheterotrophyenabledbysymbioFcmicrobial

decomposiFoninguts•  biogeochemicallyimportanttwistsonheterotrophywhereenergyissupplementedfromothersources.

Tipoftheiceberg:Microbial“hands”inmanybiogeochemicalcookiejars

•  OnlyhadFmetointroducethebasicmicrobialC‐cyclingphototrophyandheterotrophy

•  alsodrivethemethanecycleasproducersandconsumers

•  AlsodrivetheNcycle–ScokdidthoroughoverviewofNcyclingon9/30.AsmenFoned,it’sallmicrobial.

•  AndFecycling•  AndScycling•  etc…

2/4/11

18

Summary

I.  MicrobeshaveanamazingvarietyofmetabolismsthatplacethematthefocaltransformaFonsofbiogeochemicalcycles

II.  Microbial(whenincl.single‐celledeukaryotes)autotrophsperform~50%oftheprimaryproducFonontheplanet

III.  MicrobialheterotrophdecomposersplayamajorroleinterrestrialandmarineorganicmakerdegradaFon

I.  RespiraFonismajorsourceofCO2toatmosphere

II.  DegradaFonliberatesaccessibleformsofnutrients