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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
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Prochlorococcus marinus
forces.si.edu
Soilfungus
Soilbacteria
www.bioqu
est.org
Diatom
Den
nisKu
nkel
Coccolithophore
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RumenproFstOphryoscolex
forces.si.edu
TermiteproFst
Outline I. BigPictureII. Howdomicrobesmakealiving(andthusinteract
withbiogeochemicalcycles)?III. Microbes&theCcycle–thehighlights
A. PrimaryProducFonB. DecomposiFon
SoilrespiraFon,oceanrespiraFon
IV. MenFonofothercycles,&Summary
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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
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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‐
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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”)
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SourceforC,energy+electrons=carboncompounds
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Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
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SourceforC,energy+electrons=carboncompounds
biosynthesis
biosynthesis
biosynthesis
Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
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biosynthesis
biosynthesis
biosynthesis
ATP
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Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
ww
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biosynthesis
biosynthesis
biosynthesis
ATP
Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
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biosynthesis
biosynthesis
biosynthesis
ATP
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Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
ww
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biosynthesis
biosynthesis
biosynthesis
ATP
Wikipedia
Mitochondrialelectrontransportchain
Carboncompounds(=“food”)
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Sinkforelectrons=O2(producingwater)
biosynthesis
biosynthesis
biosynthesis
ATP
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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?
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l.mit.
edu
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wikiped
ia
Asso
ciat
ed P
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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)
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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
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Equi
setu
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ale_
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ThereforeweareChemoorganoheterotrophs,asareallmulFcellularcarnivores,herbivores,andmanymanymicrobes.
Photolithoautotrophs
http
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• 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.
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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
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Whoisdoingthismarinephototrophy?
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CYANOBACTERIA(e.g. Prochlorococcus marinus) Diatom
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Coccolithophore
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30-60% of ocean primary production
EUKARYOTICPHYTOPLANKTON
http
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tolib
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v/bi
gs/fi
sh18
80.JP
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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
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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)
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Summaryofmicrobialautotrophy
• Marine~terrerstrialNPP• MarineNPP~microbial
• MarineNPP=cyanos+eukaryoFcphytoplankton
• Butwait,there’salotofnon‐phoFchabitatontheplanet
• Chemoautrophsareabundantanddiverse
• UnclearhowmuchCtheymaybefixing
eart
hobs
erva
tory
.nas
a.go
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Ste
vens
& M
cKin
ley,
199
5.
NS
F fo
r DeL
ong
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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
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Stocker et al Cover of Science Feb 2010
MARINE
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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
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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
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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?
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Variantsonthebasics(a):MicrobialdecomposiFonisamajorprocessnotonlyin
soils&water,butinguts• Ruminants.Hard‐to‐degradecellulosicplant
materialsrequiremicrobialenzymes–gutislikeamicrobialbioreactor…
• Termites.Ifyoulivedoffgnawingwood,you’dneedhelptoo–termitegutsarefilledwitharichcommunityofsymbioFcmicrobes
• Etc…BasicallyallmulF‐cellularheterotrophs–includingus…(yourveryown–likelyuniquetoyou!–commensalgutbacteria)
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forces.si.edu
TermiteproFst
Variantsonthebasics(b):Non‐canonicalheterotrophy
SFllusingorganiccarbonastheircarbonsource–sosFlltrueheterotrophs–butge|ngaddiFonalenergyfromthesunorfrominorganicchemicalbonds.Inset example: proteorhodopsin.
assigned reading
http
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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…
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Summary
I. MicrobeshaveanamazingvarietyofmetabolismsthatplacethematthefocaltransformaFonsofbiogeochemicalcycles
II. Microbial(whenincl.single‐celledeukaryotes)autotrophsperform~50%oftheprimaryproducFonontheplanet
III. MicrobialheterotrophdecomposersplayamajorroleinterrestrialandmarineorganicmakerdegradaFon
I. RespiraFonismajorsourceofCO2toatmosphere
II. DegradaFonliberatesaccessibleformsofnutrients
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