Microbial Ecology of the Dark Ocean above, at, and below the Seaffoor

62 Pages·2011·9.26 MB·English

MICROBIOLOGYANDMOLECULARBIOLOGYREVIEWS,June2011,p.361–422 Vol.75,No.2
1092-2172/11/$12.00 doi:10.1128/MMBR.00039-10
Copyright©2011,AmericanSocietyforMicrobiology.AllRightsReserved.
Microbial Ecology of the Dark Ocean above, at, and
below the Seafloor†
Beth N. Orcutt,1,2 Jason B. Sylvan,2 Nina J. Knab,2 and Katrina J. Edwards2,3*
CenterforGeomicrobiology,AarhusUniversity,8000Aarhus,Denmark1;MarineEnvironmentalBiologySection,Departmentof
BiologicalSciences,UniversityofSouthernCalifornia,LosAngeles,California900892;andDepartmentofEarthSciences,
UniversityofSouthernCalifornia,LosAngeles,California900893
INTRODUCTION.......................................................................................................................................................362 D
DARKOCEANHABITATS—ANOVERVIEW......................................................................................................362 o
w
METABOLICREACTIONSINTHEDARKOCEAN..........................................................................................367
n
ElectronSources.....................................................................................................................................................369 lo
Organicmatter....................................................................................................................................................369 a
d
Hydrogen..............................................................................................................................................................369
e
Methane................................................................................................................................................................369 d

Reducedsulfurcompounds...............................................................................................................................370 f
r
Reducedironcompounds...................................................................................................................................370 o
m
Ammonium...........................................................................................................................................................370

Otherelectrondonors........................................................................................................................................371 h
t
ElectronSinks.........................................................................................................................................................371 tp
Oxygen..................................................................................................................................................................371 :/
/
Nitrateandnitrite..............................................................................................................................................371 m
Manganeseandironoxides...............................................................................................................................372 m
Oxidizedsulfurcompounds(sulfate,sulfite,elementalsulfur,andthiosulfate)......................................372 b
r
Carbondioxide....................................................................................................................................................372 .a
OtherMicrobialProcessesintheDarkOcean..................................................................................................372 s
m
DOMINANTREACTIONSANDMICROORGANISMSINDARKOCEANHABITATS...............................372
.
TheAphoticPelagicOcean....................................................................................................................................374 o
r
Generalphysicalandchemicalparameters....................................................................................................374 g
/
Metabolicreactions............................................................................................................................................374 o
Microbialdistributionanddiversity................................................................................................................375 n

MarineSediments...................................................................................................................................................377 A
p
Generalphysicalandchemicalcharacteristics..............................................................................................378 r
Metabolicreactions............................................................................................................................................378 il
4
Microbialdistributionanddiversity................................................................................................................382 ,

OceanicCrust..........................................................................................................................................................384 2
0
Generalphysicalandchemicalcharacteristics..............................................................................................384 1
Metabolicreactions............................................................................................................................................385 9

Microbialdistributionanddiversity................................................................................................................386 b
y
HydrothermalVents—VentFluidsandHydrothermalChimneys...................................................................387
g
Generalphysicalandchemicalcharacteristics..............................................................................................388 u
Metabolicreactions............................................................................................................................................388 e
s
Microbialdistribution........................................................................................................................................390 t
HydrothermalPlumes............................................................................................................................................391
Generalphysicalandchemicalcharacteristics..............................................................................................391
Metabolicreactions............................................................................................................................................392
Microbialdistributionanddiversity................................................................................................................393
MICROBIALECOLOGYOFTHEDARKOCEAN..............................................................................................395
BroadPatternsinProkaryoticMicrobialBiogeography...................................................................................395
TaxonomyofDarkOceanProkaryoticMicrobialCommunities......................................................................396
CultivatedProkaryotesfromtheDarkOcean....................................................................................................403
*Correspondingauthor.Mailingaddress:DepartmentofBiological
Sciences,UniversityofSouthernCalifornia,3616TrousdaleBlvd.,
Los Angeles, CA 90089. Phone: [phone]. Fax: (213) 740-
8123.E-mail:[email protected].
†Supplemental materialfor thisarticlemaybefoundathttp://mmbr
.asm.org/.
361
362 ORCUTT ET AL. MICROBIOL.MOL.BIOL.REV.
MicrobialEukaryotesandVirusesintheDarkOcean.....................................................................................408
MAGNITUDEOFPROKARYOTICBIOMASSINTHEDARKOCEAN.........................................................408
CONCLUSIONSANDFUTUREDIRECTIONS....................................................................................................409
ACKNOWLEDGMENTS...........................................................................................................................................410
REFERENCES............................................................................................................................................................410
INTRODUCTION and,thus,society.Microbesaretheprincipalcustodiansofthe
environment,balancingandmaintainingEarth’sglobalbiogeo-
The majority of the Earth’s habitable environments are chemical cycles. Although researchers have recognized for
physicallylocatedinenvironmentsthatdonotreceivesunlight. many years the importance of studying the dark ocean, our
Indeed, the largest potential habitats on Earth are located in understandingofthisrealmhaslaggedbehindthatofitssunlit
the ocean, which covers approximately 70% of the Earth’s counterparts in the terrestrial and marine realms due to the
surface (Fig. 1). The ocean’s average depth is 4,000 m and difficultyinaccessingit,asstudiesinthedarkoceanareboth
reachesasdeepas11,000mintheMarianasTrench.Depend- technicallychallengingandexpensive.Despitetheseobstacles,
D
ing on the quantity of particulate matter in the water, signifi- new generations of researchers and experimental tools have
o
cant levels of sunlight—the driver of photosynthesis—pene- emerged, in the last decade in particular, owing to dedicated w
trateonlyafewtenstohundredsofmeters(300mmaximum) researchprogramstoexplorethedarkoceanbiosphere.Inthis n
lo
intothewater.Thus,fromaquantitativeperspective,mostof review, we summarize the current understanding of microbi- a
theocean—roughly1.27(cid:1)1018m3—existsinthedark,witha ologyinthedarkocean,outliningsalientfeaturesofthevari- d
minorvolume(3.0(cid:1)1016m3)actuallypenetratedbysunlight oushabitattypesthatexistinthisvastrealm,discussingknown ed
(Table 1). Considering that other habitats exist beneath the (andspeculative)typesofmicrobialmetabolismandtheircon- fr
o
oceanwatercolumn,suchasmarinesediments,oceaniccrust, sequencesinglobalbiogeochemicalcycling,reviewingpatterns m
and hydrothermal vents (Table 1), these dark ocean environ- of microbial diversity in the dark ocean, and highlighting im-
h
ments(Fig.2to5)togethercomprisethelargestcollectionof portant new areas of research presently emerging for future tt
habitatsbyvolumethatlife—inparticular,microbiallife—can study.Beforedelvingintothedetailsofthemicrobialprocesses p:
/
occupyonEarth. andcommunitiesthatarecharacteristicofthevarioushabitats, /m
Ourknowledgeofmicrobialprocessesinthedarkoceanhas we present an overview of the classification scheme for dark m
increased enormously in recent decades, owing in part to the oceanhabitatsandareviewofthefundamentalunderpinnings b
r
exciting discoveries of hydrothermal vents, cold seeps, and thatgovernmicrobialprocessesinthedarkocean. .a
whale falls at the bottom of the ocean in the late 1970s and s
m
1980s (91, 249, 439, 504). Studies that try to decipher the
DARKOCEANHABITATS—ANOVERVIEW .o
activityofmicroorganismsinthedarkocean,wherewecannot
r
g
easilyobservethem,continuallyyieldparadigm-shiftingdiscov- Thedarkoceancanbeconsideredanyhabitatexistingbelow /

eries,fundamentallychangingourunderstandingoftheroleof thephoticzoneoftheocean.Figure2presentsaschematicof o
n
thedarkoceanintheglobalEarthsystemanditsbiogeochemi- these different habitats, and photographs in Fig. 3 to 5 high-
A
calcycles.Asoneexample,thediscoveryoftheexistenceand light some of these. Other than permanent darkness and iso- p
predominance of psychrophilic and mesophilic Crenarchaeota lation from photosynthetic pathways as a local means of gen- ril
belowthephoticzoneintheworld’socean(111,177,270)has erating new carbon at the trophic base, another common 4
,
radicallychangedourunderstandingofthedistributionofar- unifying feature of the dark ocean is relatively high pressures 2
chaeaonEarthandraisedquestionsaboutthefunctionofthe (pressureincreasesby(cid:2)1atmwithevery10mofwaterdepth). 01
Crenarchaeota in this global habitat. Further research led to Habitatsinthedarkoceanspanawiderangeoftemperatures, 9

theisolationofrepresentativesofthisarchaealcladewiththe from relatively cold (some below 0°C) deep-water masses to b
y
capability of oxidizing ammonium to nitrate (288), the au- high-temperature hydrothermal vents (up to 400°C in some g
totrophicmicrobialprocessofnitrificationthatwasheretofore places).Byvolume,lowtemperaturesandhighpressuresdom- u
e
knowntooccuronlywithinthebacterialdomain.Thesestudies inatehabitabledarkoceanenvironments.Althoughsuchcon- s
t
providedsomeindicationofapotentialbiogeochemicalfunc- ditions are often referred to as “extreme,” considering their
tion for related Crenarchaeota in the dark ocean, with signifi- ubiquityintheenvironment,theseconditionsareactuallyquite
cantramificationsforglobalbudgetsandcyclesofnitrogenand averageonaglobalscale.
carbon. Another revolutionary discovery emerged from re- The body of water below the photic zone in the world’s
search of deeply buried sediments of the dark ocean, where oceans represents the largest water mass on Earth and the
active microorganisms are now known to persist in sediments largestaqueoushabitatformicrobiallife(Table1).Thiswater
hundreds of meters below the ocean floor that are millions massblanketsthebenthichabitatsofthedarkocean,servingas
of years old (433). These discoveries prompted a recent afilterbetweentheoceanbottomandthesunlitsurfaceworld.
waveofstudiestounderstandtheextent,function,andimpor- Theaphoticwatercolumncanbehighlydiversechemicallyand
tanceofadeepsedimentarybiosphereinthedarkocean(45, physically,rangingfrompolartotemperatetoequatorialcon-
47,240,323,355,487,488). ditions and from deep open oceans to shallower seas and
These two examples demonstrate that in addition to their containingverticaldivisionsofwatermassesbasedontemper-
importantcontributiontohumanhealthanddisease,microor- ature and salinity. In addition to the water mass above the
ganismsalsodominatedarkoceanecosystemsandarerelevant seafloor,largevolumesofwaterresideandcirculatewithinthe
to global processes that influence the Earth’s environment basementrocksoftheoceancrust—avolumeofwaterreferred
VOL.75,2011 MICROBIAL ECOLOGY OF THE DARK OCEAN 363
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FIG. 1. Globalmapsofoceanwaterdepth(A)andsedimentthickness(B).Thewaterdepthscaleisfromlessthan500m(red)to6,000(cid:3)m
(purple). The sediment thickness scale is from 0 m (purple) to (cid:4)2,000 m (red). Maps were created using GeoMapApp (www.geomapapp.org
[474a]).
to as the subseafloor ocean (this moniker does not apply to (Fig. 5F and G) and a cooler, more diffuse emission across
fluidscontainedinporespaceswithinmarinesediments,how- large areas of the seafloor (137). The subseafloor ocean har-
ever,asadvectiveprocessestypicallydonotcharacterizethem boredinoceaniccrustisestimatedtocirculatetheentirevol-
[see below]). In this subsurface ocean, deep seawater enters umeoftheoceanthroughthecrustontheorderofevery105
intoexposedoutcropsoftheocean’scrustduetothermaland to106years(137,604),allowingforchemicalexchangeduring
pressuregradients(239,600,605),replacingtheliquidvolume fluid-rockinteractionsthatgreatlyimpactmanyglobalelemen-
lost as the discharge of hydrothermal fluids. This discharge tal budgets. Where hydrothermal fluid is discharged into the
process occurs as both spatially confined, rapidly advective overlying water column (Fig. 5F and G), mixing of reduced
fluid flow (i.e., as hydrothermal vents along midocean ridges) hydrothermal fluid with cool, oxygenated seawater occurs,
364 ORCUTT ET AL. MICROBIOL.MOL.BIOL.REV.
TABLE 1. Estimatedvolumesofvarioushabitatsinthedarkocean, leading to the formation of positively and neutrally buoyant
withthevolumeoftheoceanphoticzoneincludedforreference “plumes” of distinct, hydrothermally derived water masses in
Habitat Vol(m3) Reference thewatercolumn.Althoughmanychemicalcompoundspre-
cipitate out of the plumes early on, due to the change in
Watercolumn 3.0(cid:1)1016 608
((cid:5)200mbelowsealevel) temperatureoroxidation,chemicalsignalsofhydrothermal
Watercolumn 1.3(cid:1)1018 608 input persist in plumes over large spatial areas, many of
(200(cid:3)mbelowsealevel) which are kilometers away from the source venting (185).
Hydrothermalplumesa 7.2(cid:1)1013(/yr) 43
At the seafloor below hydrothermal plumes are areas of
Subsurfaceocean (cid:2)1016 131
intense hydrothermal activity, related either to the formation
Sediment,all 4.5(cid:1)1017 283 ofnewoceancrustatmidoceanridgesandmidplatehotspots
Shelfsediment 7.5(cid:1)1016 283 (Fig.1and2)ortocompressionalsubductionprocessesoccur-
Slopesediment 2(cid:1)1017 283
Risesediment 1.5(cid:1)1017 283 ringwheretwotectonicplatescollidewitheachother.Hydro-
Abyssalsediment 2.5(cid:1)1016 283 thermal activity is also generated in back-arc basins, which
0-to10-cmlayer 3.6(cid:1)1013 608 derive from a combination of seafloor spreading and subduc- D
tion processes, therefore producing a unique geological envi- o
Oceancrustb 2.3(cid:1)1018 w
ronment(125).Thegeneralgeologicalpropertiesofmidocean n
aThevolumeofhydrothermalplumesisgivenasthevolumeofplumefluid ridges, such as topography and age, depend on whether the lo
producedperyear(adaptedfromreference43). a
bThevolumeofoceaniccrustwasassumedbymultiplyingtheaveragethick- ridgeislocatedonaslow-spreadingcenterthattendstohave d
nessoftheoceaniccrust(7km(cid:6)89(cid:7))bytheassumedareaofseafloorunderlain steeper,blockierridgeaxessculptedbytectonicforcesorona e
bycrust(65%ofEarth’ssurface,or3.3(cid:1)1014m2). fast-spreading axis that is characterized by smoother ridge d
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flanks and well-defined axial valleys at the ridge center (for a o
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moredetaileddiscussion,seereference492).Offaxisfromthe

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FIG. 2. Schematics depicting a stylized cross section of dark ocean habitats (top; adapted from reference 259 by permission of Macmillan
PublishersLtd.,copyright2007)andrepresentationsofsedimentbiogeochemicalzonation(bottom).Notethattheupperpanelisnotdrawnto
scale.Inthelowerpanel,dominantelectronacceptorsinthevarioussedimenthabitatsareindicatedbyverticaldepthintosediment(notethe
logarithmicsedimentdepthscale).Therelativequantityoforganicmatterdepositedineachsedimenttypeandthescaleofmetabolicratesin
sedimentareindicatedbythegrayscalebar,withdarkshadesindicatinghigherrates.
VOL.75,2011 MICROBIAL ECOLOGY OF THE DARK OCEAN 365
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FIG. 3. Photographs of representative sediment habitats in the dark ocean. (A) Surficial sediment from a methane seep in the Black Sea.
(B)Matsofsulfur-oxidizingBeggiatoaonthesedimentsurfaceoftheNorthwesternBlackSeashelf.(C)PacificOceanabyssalplainsediment
surface.(D)CompilationofdeepsedimentlayerscoredatHole1231(PeruMargin)duringOceanDrillingProgramExpedition201.(PanelA
courtesyofT.Treude,IfMGeomar,Kiel,Germany;panelBcourtesyofK.Hissmann,JAGO-Team/IfMGeomar,Kiel,Germany;panelCwas
reprintedwithpermissionoftheMontereyBayAquariumResearchInstitute[courtesyofKenSmith].)
midocean ridges, the ridge flanks subside and become buried protrudefromthesedimentcover,formingoutcropsofoceanic
bysediment“raining”downthroughthewatercolumn,derived rockbasementthatareexposedtoseawater.Inaddition,mid-
fromeithersurfaceoceanparticulatematterformationorcon- platevolcanichotspotscanalsoleadtonewcrustformationin
tinental inputs. Topographic highs on former ridge axes can theformofseamounts(suchastheHawaiianIslandchainand
366 ORCUTT ET AL. MICROBIOL.MOL.BIOL.REV.
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FIG. 4. Photographsofrepresentativemarinesedimentseepandwhalefallhabitats.(A)Crosssectionofamethane-oxidizingmicrobialmat r
g
fromacarbonatechimneyformedattheseafloorintheanoxicBlackSea.(B)WhalefallecosystemattheseafloorinthePacificOcean.(C)Barite
/
chimneyatamudvolcanointheGulfofMexico.(D)Close-upimageoforangeandwhiteBeggiatoabacteriaoverlyingsulfidicsedimentataGulf o
ofMexicocoldseep.(PanelAcourtesyofT.Treude,IfMGeomar,Kiel,Germany;panelBcourtesyofCraigSmith,UniversityofHawaii;panels n

CandDcourtesyofI.R.MacDonald,FloridaStateUniversity.) A
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Iceland), which also subside and are partially covered in sed- surebuild-up,leadingtotheformationofsubmarinecanyons 2
0
iment as the seamounts move off the hot spot. Eventually, intheslopefaceandtofansofsedimentdepositatthebaseof 1
oceanic plates are recycled at convergent margins, where one the slope in the abyssal plain (577). The abyssal plain is a 9

platesubductsbeneathanother.Thisprocessleadstothefor- relatively flat expanse of seafloor sediment overlying oceanic by
mationofoceanictrenchesbetweenthesubductingplateand crust, with an average water depth of 4 km. The sedimen- g
the convergent margin, which can reach depths of almost 11 tation rate over the abyssal plain is generally much lower ue
km below sea level, as at the Marianas Trench, and to the than the rate closer to shore, and thus the sediments, on s
t
formationofback-arcvolcanicsystemsontheoverridingplate.
average, are shallow, on the order of tens to hundreds of
Formoredetailsabouttheclassificationofoceaniccrusthab-
meters thick.
itats,athoroughreviewwasrecentlypublished(491).
Thick sedimentary sections, occurring in such places as the
The highest deposition rate of sediment to the dark ocean
continental shelves and slopes and at convergent margins
occurs at the continental margin, where terrestrial sediment
above subduction zones, host unique features in the form of
inputs aggregate with water column particulate formation in
mud volcanoes, gas seeps, and gas hydrates (Fig. 4). Mud
the biologically productive continental margin waters. The
volcanoesandcoldgasseepsarecharacterizedbytheemission
thickest sedimentary units typically occur on the continental
shelf, overlying the contact between continental and oceanic offluidizedmudand/orgas-chargedfluids,resultingfromthe
crust.Sedimentsintheseshelfareascanreachdepthsof(cid:4)10 build-upofporepressureand/orgascontentwithinsediments.
km (Fig. 1 and 2). Adjoining the shelf environments is the Pressurebuild-upcanbeattributedtothemovementofburied,
continental slope, which receives less sediment input, has a neutrally buoyant salt, to sediment slumps, or to gas produc-
steeper gradient than the shelf, and constitutes a transition tionfromthermalandbiologicalprocesses.Inareaswithhigh
between the shelf environment and the deeper abyssal plain. gas content, some of the gas can become trapped in gas hy-
Slopefailuresareknowntooccurinareaswithunstablepres- drates,gas-richice-likestructuresformedfromthereactionof
VOL.75,2011 MICROBIAL ECOLOGY OF THE DARK OCEAN 367
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FIG. 5. Photographsofrepresentativeoceaniccrustandhydrothermalventhabitatsinthedarkocean.(A)Nine-meter-tallextincthydrother- r.
a
malsulfidechimneyoffaxisoftheEastPacificRise.(B)ActiveandinactivehydrothermalchimneysatTu’IMalilaventfield,ValuFaRidge.
s
(C)RiftiapachyptilatubewormsatEastPacificRise.(D)PieceofalteredbasalticoceaniccrustfromtheLoihiSeamountbeingpickedupbythe m
ROVJasonsubmersiblemanipulator.(E)YoungbasaltflowsoverlayingolderbasaltflowsattheEastPacificRise.(F)Whitesmokerhydrothermal .
o
chimneyatMarinerventfield,ValuFaRidge.(G)BlacksmokerhydrothermalchimneybeingsampledbythesubmersiblearmofDSVAlvinat r
theJuandeFucaRidge.(H)Sixty-meter-tallcarbonatechimneyattheLostCityhydrothermalventfield.(PanelsA,D,andGcourtesyofWoods g
/
HoleOceanographicInstitution;panelsB,C,andFtakenwiththeNDSFROVJasonII,operatedbytheWoodsHoleOceanographicInstitution, o
courtesy of C. Fisher [PSU] and the National Science Foundation Ridge 2000 program; panel E courtesy of Adam Soule, Woods Hole n

OceanographicInstitution;panelHcourtesyofDebKelly.) A
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2
gas with water under certain conditions of pressure and tem- METABOLICREACTIONSINTHEDARKOCEAN 0
perature(296,298). 1
To understand the microbiology and ecology of microbial 9
Sedimentsthatoccurbelowthemostactivesurficialdepths
habitats in the dark ocean, it is important to consider how b
are often referred to as deep sediment (Fig. 3D) (121, 543, y
microorganisms utilize substrates and gain energy in these g
608). In these sediments, rates of microbial activity and also
environments.AtthesurfaceoftheEarth,diverseautotrophic u
celldensitiesaremuchlowerthanintheuppersedimentlayers e
organismsproduceenergy-richorganicmatterbyfixingcarbon s
duetoreducedabundancesofcarbonandenergysources.The t
dioxide through photosynthesis, and this organic matter then
upper boundary of the deep biosphere is often operationally
servesasfoodforotherorganismsthatconvertitbacktoCO
defined as somewhere between 10 cm and 10 m of sediment 2
viarespiration.Thesereactionsareoftencloselycoupledspa-
depth(121,608).Acquisitionofsedimentsbelowafewmeters
tiallyandfunctionally,andourecosystem-levelunderstanding
of sediment depth requires the use of technologically sophis- of the biological carbon cycle is based in large part on the
ticated (and expensive) oceanic drilling vessels to drill bore- balance between these processes. A fundamental distinguish-
holes into the seafloor, akin to drilling a well on land. Ocean ing factor in the dark ocean is that metabolic strategies are
drilling has been used for decades in the oil industry and in based on chemical redox reactions rather than the photosyn-
geoscience research (geology and paleoclimatology), but our thetic processes occurring in the sunlit world. Furthermore,
ability to explore the existence of life below a few meters in respirationpathwaysandthereactionsusedforenergygener-
sediments occurred only relatively recently (102, 119, 433). ation in the dark ocean are more variably coupled—spatially,
Finally, although macrofauna (fish, sponges, corals, inverte- temporally, and functionally. In addition to sinking organic
brates,etc.)existinthedarkoceanwatercolumnandanchored mattercreatedviaphotosynthesis,additionalpathwaysofpri-
insedimentsandrocksattheseafloor,thedeepsubsurfaceis maryproductivityexistinthedarkoceanthatareoftenunac-
onlyknowntobeinhabitedbymicroorganisms. countedforinbiogeochemicalbudgets.Understandingecolog-
368 ORCUTT ET AL. MICROBIOL.MOL.BIOL.REV.
TABLE 2. Commonredoxreactionsandassociatedstandardfreeenergiesofreactionthatoccurinthedarkoceanand
canbeexploitedformetabolicenergy
Pathway Reaction (cid:9)G°(kJ/mol)a
Oxicrespiration CHO(cid:3)O 3CO (cid:3)H O (cid:8)770
Denitrification CH2O(cid:3)4/52NO (cid:8)32 1/5C2O (cid:3)2/5N (cid:3)4/5HCO(cid:8)(cid:3)3/5H O (cid:8)463
MnO reduction CH2O(cid:3)3CO (cid:3)3 H O(cid:3)2M2nO 322Mn2(cid:3)(cid:3)4H3CO(cid:8) 2 (cid:8)557
Fe(III2)oxidereduction CH2O(cid:3)7CO2(cid:3)4F2e(OH) 342Fe3(cid:3)(cid:3)8HCO(cid:8)(cid:3)33H O (cid:8)697
Sulfatereduction CH2O(cid:3)1/2SO2 2(cid:8)3HCO3(cid:8)(cid:3)1/2H S 3 2 (cid:8)98
Sulfatereduction(frommethane) CH2(cid:3)SO 2(cid:8)34 HCO(cid:8)(cid:3)3HS(cid:8)(cid:3)H2O (cid:8)33
4 4 3 2
Methanogenesis(fromacetate) CHCOOH3CH (cid:3)CO (cid:8)24
Methanogenesis(fromH/CO) H (cid:3)3 1/4HCO(cid:8)(cid:3)41/4H(cid:3)231/4CH (cid:3)3/4H O (cid:8)57
2 2 2 3 4 2
Fermentation(fromethanol) CHCH OH(cid:3)H O3CH COOH(cid:3)2H (cid:8)181
Fermentation(fromlactate) CH3CH2COO(cid:8)(cid:3)23H O33CH COOH(cid:3)2HCO(cid:8)(cid:3)3H (cid:8)1,075
Acetogenesis H (cid:3)3 1/22CO(cid:8)(cid:3)1/4H2(cid:3)31/4C3H COO(cid:8)(cid:3)H O3 2 (cid:8)90
2 3 3 2
Hydrogenoxidation H (cid:3)1/2O 3H O (cid:8)263
2 2 2
MSuelfithdaenoexoidxaidtiaotnion HCHH2SS4(cid:3)(cid:3)(cid:3)228OO/52N233OC(cid:8)SOO3242(cid:3)(cid:8)SO(cid:3)2H22(cid:8)2HO(cid:3)(cid:3)4/5N (cid:3)4/5H O(cid:3)2/5H(cid:3) (cid:8)(cid:8)(cid:8)778515049 Dow
Fe(II)oxidation Fe22(cid:3)(cid:3)1/4O 3(cid:3)H(cid:3)34Fe3(cid:3)(cid:3)1/22H O 2 (cid:8)48 n
Fe2(cid:3)(cid:3)1/5NO2 (cid:8)(cid:3)6/5H(cid:3)3Fe3(cid:3)(cid:3)23/5H O(cid:3)1/10N (cid:8)44 lo
Fe2(cid:3)(cid:3)MnO 3(cid:3)2H(cid:3)3Fe3(cid:3)(cid:3)MnO(cid:3)H2 O 2 ND a
Mn(II)oxidation MMnn22(cid:3)(cid:3)(cid:3)(cid:3)O2/52N32OM(cid:8)n(cid:3)O24/5H O3MnO (cid:3)1/52N (cid:3)8/5H(cid:3) (cid:8)(cid:8)14799 ded
Nitrification NH(cid:3)(cid:3)2O 33NO(cid:8)(cid:3)22H(cid:3)(cid:3)H O2 2 (cid:8)302 f
Anammox NH4(cid:3)(cid:3)NO2(cid:8)3N3 (cid:3)2H O 2 (cid:8)345 ro
4 2 2 2 m
aValuesfor(cid:9)G°calculationsweretakenfromreference15.ND,notdetermined. h
t
t
p
:
/
/
m
ical diversity and microbial metabolic reactions in the dark is oxidized while another substrate is reduced), but often cat- m
ocean is a centerpiece of dark ocean research. Furthermore, abolicandanabolicreactionsareseparated. b
r
understandingtheprinciplesaffectingmicrobiologyinthemost The metabolic activities of microorganisms in the dark .
a
extremeorenergy-limitedenvironmentsonEarth—forexam- ocean depend on the availability and speciation of electron s
m
ple,hydrothermalventsorthedeepmarinesubsurface,respec- donors(oxidizablecompounds)andacceptors(reducablecom-
.
o
tively—provides valuable parameters for constraining the pounds) (174). Distinct zonations of microbial activity based r
g
search for life elsewhere in our solar system and for under- onavailableelectrondonorsandacceptorsarewelldescribed /

standingtheevolutionoflifeonEarth. andcharacteristicformarinesediments,whichhavebeenstud- o
n
Microbiologists studying life in the dark ocean and the po- ied intensively compared to some other dark ocean habitats.
A
tential for life on other planets are developing key unifying Figure 2 provides a representation of this metabolic zonation p
r
reference frames concerning “habitability” of different envi- inmarinesediments,illustratingthetypicalcascadeofusageof il
ronments(491).Energeticconstraintsthatexaminethepoten- preferredelectronacceptorsandtheimpactofdeliveryratesof 4
,
tialofchemicalreactionstoprovideenergyforlifeinthedark electron donors (i.e., organic matter) on the gradient of met- 2
0
provide one such useful construct (27, 223). Approaches that abolic rates. Although this sequence of usage of electron do- 1
defineenergeticconstraintshavebeenappliedinanumberof nors and acceptors is well studied for some environments, 9

darkoceanhabitats(forexample,seereferences26,359,and recentresearchindicatesthatlow-level,crypticbiogeochemical b
y
360) and allow geological and geochemical information to be cyclingmaystilloccurinzoneswhereitisnotexpected(228). g
usedforthepurposeofpredictingwhichmetabolicandphys- The availability of metabolic substrates and substrate con- u
e
iological processes might characterize dark microbial ecosys- centration gradients is determined by diffusive and advective s
t
tems. Such information guides strategies for cultivation and transportprocesses(forfurtherreview,seereference59).Dif-
ecological studies as well as for understanding the biogeo- fusion,therandommovementofmolecules,leadstoaspread
chemical consequences of dark microbial ecosystems for the of substances from areas of higher concentrations to areas of
globalenvironment. lower concentrations, depending on concentration gradients
All life on Earth requires access to sources of energy and andthespeedofdiffusionofthemolecules,whichistypically
carbon.Intheabsenceoflight,metabolicenergyisharnessed on the order of 10(cid:8)9 m2 s(cid:8)1. In deep ocean water, chemical
from the coupling of reducing and oxidizing (“redox”) reac- exchange occurs via the movement of water in currents and
tions(forexamples,seeTable2).Energyisobtainedwhenthe along isopycnal gradients, upwelling and downwelling near
coupledredoxreactionsarethermodynamicallyfavorableand coastlines and the equator, and mixing with hydrothermal,
yieldenoughenergyforATPgeneration.Microorganismsex- groundwater, and riverine fluid inputs. Chemical exchange in
ploittheavailablechemicalenergybydevelopingstrategiesto marine sediments is dictated mostly by molecular diffusion,
overcome the activation energy of reaction and kinetic con- withadvectiveprocesseslimitedtothebioturbationandbioir-
straintsorbycouplingenergeticallyunfavorablereactionswith rigationactivitiesofanimalslivinginsurfacesediment;tothe
otherenergy-yieldingpathways.Carbonacquisitionandenergy migration of fluids, fluidized mud, and gasses from deep gas
generationarelinkedinsomecases(i.e.,whenorganicmatter sources or salt deposits; and to the movement of fluids along
VOL.75,2011 MICROBIAL ECOLOGY OF THE DARK OCEAN 369
faultsandfracturesinthesediment.Inoceaniccrust,advective mentsindicatethatmicroorganismscapableofcouplinghydro-
processesincludefluidflowthroughpermeable,fractured,and gen oxidation to the reduction of electron acceptors such as
porous hard rock, driven by pressure and temperature gradi- metaloxides,sulfate,andcarbondioxideareabletosuppress
ents. Hydrothermal vents provide conspicuous evidence of thehydrogenconcentrationtolevelsthatmakethelessfavor-
crustal fluid flow; however, a large fraction of fluid flow in able pathways uncompetitive (222, 339). Hydrogen is also an
oceaniccrustoccursatlowertemperatures((cid:2)20°C)andover important intermediate in syntrophic relationships between
broadspatialscales(239). different groups of microorganisms, a process referred to as
interspecieshydrogentransfer(reviewedinreference569).For
example,fermentingmicroorganismsareoftenfoundcoupled
ElectronSources
with methanogens, since methanogenic activity keeps the hy-
The dominant electron sources in the dark ocean include drogen concentration low enough to make the fermentation
organic matter, hydrogen, methane, reduced sulfur compounds, pathway energetically favorable. Furthermore, hydrogen can
reducedironandmanganese,andammonium.Theseelectron alsobeproducedduringironoxidationinsediments,whereby
donors have different abundances and energy potentials and it is rapidly consumed by hydrogenophilic microorganisms
D
thereforedifferinsignificanceassubstratesformicrobialme- (340). Interspecies hydrogen transfer has been speculated to
o
tabolism.Below,wediscusseachofthevariouselectrondonors occur in other processes, such as in sulfate-dependent anaer- w
in order, starting from that with the most negative relative obic methane oxidation (221), but such associations remain n
lo
reductionpotential. controversial(403,427,571). a
Organicmatter.Thehighredoxpotentialoforganicmatter Inenvironmentswithhighhydrogenconcentrations,suchas d
e
comparedwithmostotherelectrondonors(Table2),coupled in some hydrothermal fluids (particularly in mantle rock- d

with its broad availability, renders it the dominant electron hosted hydrothermal systems), hydrogen oxidation can be a f
r
o
donorinmostmarineenvironments,especiallyinthosewhere major metabolic pathway. In these systems, hydrogen is pro- m
itisavailableinabundance,suchasatproductivecontinental ducedduringserpentinizationreactionsoccurringwithinultra-
h
margins(Fig.2).Organicmatteriscomposedofdifferentcom- mafic rocks and can reach millimolar concentrations. It has t
t
p
pounds—simple and complex sugars, proteins, lipids, humics, beenspeculatedforover50yearsthattheradiolysisofwaterto
:
/
ligands, organic acids, etc.—each characterized by different form hydrogen, fueled by the radioactive decay of naturally /m
reactivities (i.e., susceptibilities to chemical/biological degra- radioactiveelements(i.e.,uraniumandpotassium),maysupply m
dation). Thus, utilization of organic compounds as an energy this electron donor to organic matter-starved sediment mi- b
r
source depends on both the quantity and quality/reactivity of crobes(52,381),althoughdefinitiveproofofthismechanismis .
a
the substrates (58, 212, 308, 330, 418). For example, fresh lacking. The diverse sources and the fast, often immediate s
m
organicmatterisutilizedfasterthanagedorganicmaterialin turnoverofhydrogenbymicroorganismsincloseproximityto
.
o
sediments, evidencing the generally more refractory (i.e., re- thesourcemakeitdifficulttoquantifytheoverallsignificance r
g
sistant to degradation) nature of aged organic matter. Low- ofhydrogenasanelectrondonorformarinemicroorganisms, /

molecular-weight compounds are preferentially consumed thoughpursuitofthishypothesisremainsactive.Technological o
n
(22), although the patterns of organic consumption can be advancesinhydrogenquantificationareneededtoremedythis
A
affected by external forces such as temperature change (597). gapinknowledge. p
r
Organicmaterialinthedarkoceancanbeproducedinsituby Methane.Byfar,thelargestreservoirofmethaneonEarth il
extantmicroorganismsordeliveredfromadistantsource,such occurs buried in marine sediments (607), as dissolved or free 4
,
astheoverlyingphoticzoneorterrestrialsources.Ingeneral, gas or in the form of gas hydrate (297). Methane in marine 2
0
terrestrially derived organic matter is more difficult to utilize sedimentsoriginatesfrombothabioticandbioticsources.Abi- 1
than water column- and in situ-derived organic matter due to otic methane can be generated in the marine environment 9

differences in material composition (i.e., primarily plant resi- either by the thermal degradation of buried organic matter b
y
duesversusphytoplankton[32]).Depositionalconditions,such (329) or by the reaction of H2 and CO2 during reaction be- g
as bioturbation activity by benthic macrofauna in sediments, tweenmafic(i.e.,magnesium-andiron-rich)rocksintheoce- u
e
alsoaffecttheturnoveroforganicmatterbymicroorganismsin aniccrustthroughaprocessknownasserpentinization(279). s
t
sediments(418). Globally, the largest fraction (80%) (299) of methane in the
Inordertobecomeaccessibleformicrobialremineralization marinerealmisformedbiologicallyfromreductionofCO or
2
(i.e., conversion of organic matter to inorganic carbon diox- otherlow-molecular-weightorganiccompounds—suchascar-
ide),theparticulateanddissolvedorganicmatterinsediments bonmonoxide(CO),acetate(CH COOH),formate(COOH),
3
aredegradedbyhydrolysisandfermentationmediatedbyboth methanol (CH OH), methanethiol (CH SH), and methyl-
3 3
microbial eukaryotes and prokaryotes to form smaller mole- amine (CH NH )—by methanogenic archaea, as discussed in
3 3
cules such as short-chain fatty acids, alcohols, and amines. moredetailbelow.
Thesedegradationproductsarethenusedbydiversegroupsof Asanelectrondonor,microbiallymediatedmethaneoxida-
microorganisms and remineralized with various electron ac- tionoccurswithdifferentelectronacceptors,withsulfatebeing
ceptorstoformcarbondioxide. quantitativelythedominantelectronacceptorformethaneox-
Hydrogen. Molecular hydrogen is one of the most energet- idationbecausemethaneproductionoccursbelowthesulfate-
ically favorable electron sources for microorganisms. There- rich zone in sediments, and thus sulfate is the first available
fore, the concentration of hydrogen in the environment is electron acceptor for methane oxidation. Sulfate-dependent
generally very low due to tight competition for this energetic methaneoxidationoccursinwell-definedzonesinanoxicma-
resource. Studies of hydrogen consumption in marine sedi- rinesediments,whereupwardlydiffusingoradvectingmethane
370 ORCUTT ET AL. MICROBIOL.MOL.BIOL.REV.
meetssulfatebeingdeliveredtodepthfromthewatercolumn actions to H S with several electron acceptors, including
2
(118, 247). These zones are often referred to as the sulfate- Fe(III)oxidesandnitrate(16,156).Insedimentsandatsulfur-
methanetransitionzone(SMTZ).Onaglobalscale,morethan rich hydrothermal vents, free H S reacts, both biotically and
2
90%ofthepotentialmethanefluxfromsedimentsisrecycled abiotically, with reduced iron to form pyrite (490), which can
via microbial methane oxidation before reaching the water- serveasanothersourceofenergyformicroorganismsinboth
sediment interface (218). Thus, taking into account the mag- oxicandanoxicenvironments(130).
nitude of methane generated in marine sediments (218, 460), Reducedironcompounds.Reducediron[i.e.,Fe(II)-bearing
microbial methane oxidation is one of the most important speciessuchasaqueousFe2(cid:3)andmineral-boundformssuchas
controlsongreenhousegasemissionandclimateonEarth.At pyrite (FeS )] can also be used as an electron donor in dark
2
coldseeps,theupwardfluxofmethaneissohighthatitisnot oceanhabitats.Intheopenocean,Fe(II)derivesfromaltera-
entirely oxidized in the SMTZ but reaches the sediment sur- tionreactionsoccurringbetweencrustalmaterialsandfluidsin
face and water column. At these sites, methane may be oxi- hydrothermal settings, whereas in sediments, Fe(II) derives
dizedbyotherelectronacceptorsbesidessulfate,suchasoxy- mainlyfromdepositionandfromanaerobicreductionofiron
gen. Aerobic methane oxidation is a chemosynthetic energy oxides.Inmarinesediments,thesolubleferrousironmigrates,
D
sourcewithinsomesymbiont-containinganimalsthatresideat via diffusive and advective processes, into zones with suitable
o
gas seeps and hydrothermal vents (80, 81, 126). Additionally, oxidizing species—oxygen, nitrate, and manganese oxides— w
aerobic methane oxidation also occurs at hydrothermal vents whichcanbecoupledtometabolicreactions(Table2).Fe(II) n
lo
whereaerobicseawatermixeswithmethane-richhydrothermal also diffuses to where it reacts with reduced sulfur species to a
fluids (106, 416, 417, 570, 587). Nitrite-dependent methane form iron sulfides, such as pyrite, which can also be used as d
e
oxidation has been observed in freshwater sediments and en- electron donors, although some empirical evidence suggests d

richmentcultures(149,151,452)andcouldtheoreticallyoccur thatthisprocessmaynotbeimportantformicroorganismsin f
r
o
in cold seep sediments, although the discovery of these pro- marine sediments (486). A microbiological role for Fe oxida- m
cesses is so recent that their existence in marine habitats has tioninmarinesedimentshasbeenstudiedinonlyafewcases
h
notyetbeenwelldocumented.Inmarinesediments,methane (486), as it was previously assumed that life could not exploit t
t
p
is usually depleted by sulfate reduction before it reaches ni- Feoxidationreactionswithrapidabiotickineticsunderaerobic
:
/
trite-containing sediments, thus limiting significant rates of conditionsatcircumneutralpH. /m
nitrate-dependent methane oxidation to environments with Recentevidenceshowsthatmicroorganismsareresponsible m
relativelyhighnitrateandlowsulfateconcentrations.Basedon forFeoxidationinsomehydrothermallyderivedmineralsub- b
r
thermodynamic energy yields, methane oxidation could theo- strates under cold, microaerobic conditions (144, 145), when .
a
retically also be coupled to metal (i.e., iron and manganese) abiotickineticsaremoresluggish,indicatingthatmicrobialFe s
m
reduction, and some preliminary evidence suggests that this oxidation may be more prevalent than previously assumed.
.
o
processdoesoccur(39),butitsglobalsignificancehasnotbeen Hydrothermalironinputstotheglobaldeepoceanrivalwhat r
g
demonstrated. is delivered to the oceans from riverine sources (605). Simi- /

Reduced sulfur compounds. Many reduced sulfur com- larly, Fe that is released from rock and minerals in the deep o
n
pounds (e.g., sulfides)—such as elemental sulfur (S0), hydro- ocean during oxidative alteration has been shown to support
A
gen sulfide (H S), methanethiol (CH SH), dimethylsulfide activities of Fe-oxidizing bacteria (26, 132–134). Fe(II) is the p
2 3 r
[(CH3)2S], pyrrhotite (Fe1-xS), pyrite (FeS2), chalcopyrite mostabundantreducedelementinEarth’scrustandmakesup il
(CuS),andsphaelerite(ZnS)—havebeendemonstratedtobe 7 wt%, on average, of the elemental abundance of the ocean 4
,
used as electron donors by microorganisms. Hydrothermal crust underlying the oceans (26); consequently, reactions be- 2
0
ventfieldshostedwithinbasalticcrustareoftenrichinsulfide tween oxygen and Fe are commonly catalyzed by microbes, 1
deposits due to the precipitation of particulates from H S although this process is poorly studied. Even less well under- 9
2
and/ormetal-richfluidsthatmixwithcoldoxygenatedseawa- stoodaremicrobiallymediatedreactionsintheoceanbetween b
y
ter. Sediments can have significant levels of H2S, and some- Fe(II) and nitrate, as there are conflicting reports of their g
timesironsulfidesandS0,duetothegenerationofsulfidefrom occurrence(238,516),orwithmanganeseoxides,asthereare u
e
sulfatereduction. fewdataavailable. s
t
In sedimentary environments and at hydrothermal systems, Ammonium.Ammoniumisthemostreducedformofnitro-
H S and S0 produced by microbial sulfate reduction or geo- gen and an important electron donor in the dark ocean. In
2
thermalprocessesareoxidizedbyanumberofelectronaccep- mostoftheocean,ammoniumderivesfromthebreakdownof
tors, including oxygen, nitrate, and metal oxides [i.e., Fe(III) nitrogen-containingorganicmatterbyeitherbiologicaldegra-
andMn(IV)oxides],throughbothabioticandmicrobiallyme- dation or hydrothermal alteration. At smaller quantities, am-
diatedprocesses(16,57,127,262,269).AnaerobicH Soxida- moniumisalsogeneratedviaamicrobialprocessreferredtoas
2
tionwithironoxides,manganeseoxides,andnitratealsocon- dissimilatorynitratereduction(62).Somerecentstudiesindi-
sumes some sulfide in marine sediments (168). In sediments catethatmicrobialnitrogenfixation,wherebydinitrogengasis
with high H S fluxes, allowing H S to reach the sediment convertedintoammonium,isanothersourceofammoniumin
2 2
surface, both free-living and symbiotic bacteria gain energy thedarkocean,asinthecaseofnitrogenfixationlinkedtothe
fromsulfideoxidationwithnitrate(see“MarineSediments”). anaerobicoxidationofmethaneorsulfatereductioninmarine
Other sulfide oxidizers reside as chemosynthetic symbionts in sediments(44,107).Othergenomicsurveysindicatethepres-
mussels, clams, snails, and polychaete worms (Fig. 5C) (126, ence of nitrogen-fixing microorganisms inhabiting the surface
406)anduseoxygenasanelectronacceptor.S0canbeoxidized ofseafloor-exposedbasalticcrustalrocks(354).Thesefindings
microbiallythroughbothdisproportionationandoxidationre- indicate that nitrogen fixation may contribute more ammo-