Geobiology. 2017;15:817–835. wileyonlinelibrary.com/journal/gbi | 817© 2017 John Wiley & Sons Ltd
Received:03October2016 | Accepted:21September2017
DOI: 10.1111/gbi.12266
O R I G I N A L A R T I C L E
Microbial diversity and iron oxidation at Okuoku- hachikurou
Onsen, a Japanese hot spring analog of Precambrian iron
formations
L. M. Ward1 | A. Idei2 | S. Terajima3 | T. Kakegawa3 | W. W. Fischer1 |
S. E. McGlynn2,4,5
1Division of Geological and Planetary
Sciences,CaliforniaInstituteofTechnology,Pasadena,CA,USA2DepartmentofBiology,TokyoMetropolitanUniversity,Tokyo,Japan3DepartmentofGeosciences,TohokuUniversity,SendaiCity,Japan4Earth-LifeScienceInstitute,TokyoInstituteofTechnology,Tokyo,Japan5BlueMarbleSpaceInstituteofScience,Seattle,WA,USA
Correspondence
L.M.Ward,CaltechGPSDivision,Pasadena,CA,USA.Email:[email protected]
S.E.McGlynn,Earth-LifeScienceInstitute,TokyoInstituteofTechnology,Tokyo,Japan.Email:[email protected]
Funding informationNASANESSF,Grant/AwardNumber:(#NNX16AP39H;NSF,Grant/AwardNumber:#OISE1639454;NSFGROW,Grant/AwardNumber:#DGE1144469;MEXTKAKENHI,Grant/AwardNumber:15K14608;NASAExobiology,Grant/AwardNumber:#NNX16AJ57G;DavidandLucilePackardFoundation;StanfordUniversityBlausteinFellowship
AbstractBanded iron formations (BIFs) are rock deposits common in the Archean andPaleoproterozoic (andregionallyNeoproterozoic)sedimentarysuccessions.Multiplehypothesesfortheirdepositionexist,principallyinvokingtheprecipitationofironviathemetabolicactivitiesofoxygenic,photoferrotrophic,and/oraerobiciron-oxidizingbacteria.SomeisolatedenvironmentssupportchemistryandmineralogyanalogoustoprocessesinvolvedinBIFdeposition,andtheirstudycanaidinuntanglingthefactorsthat lead to ironprecipitation.OnesuchprocessanalogsystemoccursatOkuoku-hachikurou (OHK)Onsen inAkitaPrefecture,Japan.OHK isan iron-andCO
2-rich,
circumneutralhotspringthatproducesarangeofprecipitatedmineraltexturescon-tainingfinelaminaeofaragoniteandironoxidesthatresembleBIFfabrics.Here,wehaveperformed16SrRNAgeneampliconsequencingofmicrobialcommunitiesacrosstherangeofmicroenvironments inOHKtodescribethemicrobialdiversitypresentand to gain insight into the cycling of iron, oxygen, and carbon in this ecosystem.TheseanalysessuggestthatproductivityatOHKisbasedonaerobic iron-oxidizingGallionellaceae.IncontrasttootherBIFanalogsites,Cyanobacteria,anoxygenicpho-totrophs, and iron-reducing micro-organisms are present at only low abundances.Theseobservationssupportahypothesiswherelowgrowthyieldsandthehighstoi-chiometry of iron oxidized per carbon fixed by aerobic iron-oxidizing chemoauto-trophs like Gallionellaceae result in accumulation of iron oxide phases withoutstoichiometricbuildupoforganicmatter.Thissystemsupportslittledissimilatoryironreduction,furthersettingOHKapartfromotherprocessanalogsiteswhereironoxi-dationisprimarilydrivenbyphototrophicorganisms.ThispositionsOHKasastudyareawherethecontrolsonprimaryproductivityiniron-richenvironmentscanbefur-therelucidated.Whencomparedwithgeologicaldata,themetabolismsandmineral-ogyatOHKaremost similar to specificBIFoccurrencesdepositedafter theGreatOxygenationEvent,andgenerallydiscordantwiththosethataccumulatedbeforeit.
818 | WARD et Al.
1 | BACKGROUND
Banded iron formation (BIF) is a characteristic lithotype in manyPrecambrian basins. These finely laminated, iron-rich (>15% Fe byweight) sedimentary deposits are not only economically criticalsourcesofironore(particularlyafterpost-depositionalweatheringandhydrothermalprocessesoxidize, leach,andupgrade theore,Morris,1980;Beukes,1984),butmayprovidearecordofbiologicalactivityontheearlyEarth(e.g.,Harder,1919;Kappler,Pasquero,Konhauser,&Newman,2005;Konhauseretal.,2002).
Despitetheirprevalenceintheearlyrockrecord,theprocessesbywhichBIFsaredepositedarenotwellunderstood.Itisgenerallyhy-pothesizedthatBIFsformedasaresultoftransportandconcentrationof ferrous iron (as Fe
2+
(aq))inseawaterunderanoxicandsulfur-poorcon-ditions,followedbyoxidationandprecipitationof ironasferric ironphases(Drever,1974;Holland,1973,1984).However,itisimportanttonotethattheprimarymineralogythatmadeuptheprecursorsed-imentstoBIFremainsuncertaininmanycases,andthesignificanceofironoxidationduringBIFdepositionremainsanareaofactivede-bate (Bekker etal., 2014;Kappler&Newman,2004;Kappler etal.,2005; Konhauser etal., 2002; Posth, Konhauser, & Kappler, 2013;Rasmussen,Krapež,Muhling,&Suvorova,2015;Rasmussen,Meier,Krapež,&Muhling,2013;Rasmussen,Muhling,Suvorova,&Krapež,2016;Tosca,Guggenheim,&Pufahl,2016).DifferenthypothesesforBIFdeposition invokearangeof ironoxidationprocesses, includingabioticironoxidationbyUVlight(e.g.,Cairns-Smith,1978;Francois,1986),indirectlybiologicallybyO
2sourcedfromoxygenicphotosyn-
thesisbyCyanobacteria(e.g.,Cloud,1973),ordirectlybiologicallybyaerobiciron-oxidizingbacteria(e.g.,Chan,Emerson,&Luther,2016)or by anaerobic iron-oxidizing phototrophic bacteria (e.g., Kappleretal., 2005;Widdel etal., 1993). BIFs do not form inmarine sedi-mentarybasinstodayduetotheO
2 and sulfate content of seawater
(Canfield, 1998), which prevents the mobilization and concentra-tionofsufficientamountsofdissolvedironinseawaterandshallowpore fluids (Holland, 1973). However, a range of potential analogenvironmentscanbeobservedtodaythatmayrevealkeyprocessesassociatedwith the deposition of BIFs. These include permanentlystratifiedlakes,suchasLakeMatanoinIndonesia(Croweetal.,2008),and iron-rich hot springs, such as Chocolate Pots in YellowstoneNational Park (Pierson, Parenteau, & Griffin, 1999). These systemscontainanoxic, iron-richwaters thatproduce ironoxidesandotherFe-bearingphasesthrougharangeofprocesses.InLakeMatano,ironoxideproductionisthoughttobedrivenlargelybyphotoferrotrophy(Croweetal.,2008),whileatChocolatePots,hotspring ironoxida-tion isdrivenprimarilybyabioticreactionof ironwithO
2produced
byCyanobacteria (Pierson&Parenteau, 2000;Piersonetal., 1999;Trouwborst,Johnston,Koch,Luther,&Pierson,2007).Terrestrialhotsprings can provide unique environments inwhich high concentra-tionsofdissolved ironcanexist at circumneutral conditionsdue torockweathering by anoxic sourcewaters; they also provide accesstonovelmicrobialdiversitywhichisrareorabsentfromtypicalsur-faceenvironments.Whilethesehotspringfluidsarenotperfectcom-positional mimics of Precambrian seawater, the geomicrobiological
processestheysupportandtheresultingfaciesandfabricscanpro-videprocessanalogsforunderstandingdepositionalmechanicsofatleastsomeBIFs.Thisisparticularlyusefulforevaluatingtherelativerolesthatdifferentmicrobiologicalprocesses(e.g.,photoferrotrophy,aerobicironoxidation,andoxygenicphotosynthesis)mayhaveplayedinthedepositionofdifferentBIFfacies.Acrucialbutunderstudiedas-pectofBIFdepositioninmodernanalogenvironmentsistherelativedelivery fluxesof ironoxidesandorganiccarbon tosediments,andtheaverageoxidation stateof the resultant iron formations; trendsin theproportionof ferrous to ferric iron inancientBIFshave longbeenobserved in the rock record (e.g.,Klein,2005)—andthesecanreflecttheredoxstateoftheenvironmentatthetimeofdeposition,aswellastheparticularphysiologiesandmetabolismsresponsibleforironoxidation (Fischer&Knoll,2009) (AppendixS1).Although littleexplored,themetabolicyieldandefficiencyofthemicrobialmetab-olisms driving iron oxidationwill be a factor in themineralogy andredoxchemistryofdiageneticallystabilizedironformationlithologies.Currently, knowledge of the microbial metabolisms and processesthat leadtodifferentmineralassemblages (andferric:ferrous ratios)inmodernenvironmentsremainsmeager.Characterizationofthemi-crobialcommunitiesinthecontextoftheorganiccarboncontentandredoxstateofironinthesolidsaccumulatinginBIFanalogsdepositeddifferentially by photoferrotrophs, Cyanobacteria, and aerobic ironoxidizerswillhelptoconnectobservationsofancientBIFstothegeo-biologicalprocessesresponsibleforironoxidedeposition.
Inthisstudy,weinvestigatedanovelBIFanalogenvironmentatOkuoku-hachikurou Onsen (OHK) in Akita Prefecture, Japan. OHKis an iron- andcarbonate-rich, circumneutralhot springwithanoxicsource waters, which produces extensive iron oxide and aragonitetravertine with mineralogical and textural features resembling BIF(Takashima, Okumura, Nishida, Koike, & Kano, 2011). To study themicrobialdiversityofOHKandevaluatethepotentialrolesofdiffer-entmicrobialmetabolismsinproducingmineraldepositsatOHK,wecollectedmineral precipitates and filtered springwater from pointsalong the outflow of the stream for analysis usingmicroscopy andcharacterizationofthemicrobialcommunityvia16SrRNAgeneam-pliconsequencing.Thesedatarevealthatproductivityandironoxida-tionatOHKisprimarilydrivenbyaerobic,iron-oxidizingtaxarelatedto the genusSideroxydans, and consequently, the environment pro-ducessedimentsthatareorganic-leanandcontainahighproportionof ferric ironphases—anearlydiageneticprecondition to thehighlyoxidizedBIFfaciesdepositedincertainenvironmentsaftertheGreatOxygenationEvent.
2 | MATERIALS AND METHODS
2.1 | Geological context and sedimentology of OHK
OHK is located in Akita Prefecture, Japan, at 40.407925N,140.754744E(Figure1),inanactiveregionoftheTohokuvolcanicarc, generated by the subduction of the Pacific Plate; the localbedrock geology consists of Miocene–Holocene green tuff andfelsicvolcanicrocks (Shimazu,Yamada,Narita,&Igarashi,1965).
| 819WARD et Al.
OHKconsistsofasinglesubsurfacewatersourcethatoriginatesfromaminingexplorationboreholedrilledinthe1960s.Thisbore-holeemergesintoa2-m-diametersourcepool,withasubmergedshelfaroundtheedgeoftheboreholeat1.2mdepth.Atthetimeof our study inNovember 2015,water emerged from the bore-holeat44.3°C,highinFe(II),verylowinoxygen(Table1),anddis-playedcontinuousandvigorousebullitionofCO
2 (Figure2).The
source pool contains abundant suspended fine flocs of hydrousironoxides.TheearlycrystallineironoxidephasesatOHKconsistof ferrihydrite (Takashimaetal.,2011), thoughthismayage intomore ordered iron oxideminerals such as hematite, goethite, orlepidocrociteintravertines.Fromthesourcepooltotherotenburo(Figure2), the stream flows over a mineralized substrate com-prisedofwell-lithified, finely laminatedaragonite and ironoxidetravertinewith a smooth texture andmottled coloration rangingfrom white aragonite to orange and red iron oxides (Figure2).Surfacesofpools,channels,andcanalsarecoatedinfine,orange-colored ironoxideflocs.Mature ironoxidephaseswithintraver-tine appear dark red. Travertine accumulates around pool edgesas lobate walls ~10cm in width.Where spring water overflowstheedgesofpools travertine terracesdevelopwith a character-istic~5cmstepsizeanduptoaboutahalfmeterintotalheight.Theseterracessuperficiallyresemblethosefoundinbothcircum-neutralandacidic iron-richsystemselsewhere (e.g.,YellowstoneNationalPark,Fouke,2011;andtheTintilloRiver,Spain,España,SantofimiaPastor,&LópezPamo,2007);theoccurrenceofsimilarlarge-scalemorphologiesacrossverygeochemicallydifferenten-vironmentssuggeststhathydrology—asmuchasgeochemistryor
microbial processes—plays a role in the travertinemorphologies(Fouke,2011).
Anoldoutflowchannel emerges from the sourcepool, butwaslargelyinactiveatthetimeofoursampling;flowintothischannelhasbeen blocked and redirected through canals to the rotenburo.Thischannel is ~5cmdeep, partiallymixeswith the source pool due toswashing caused byCO
2 ebullition, but is otherwise stagnant.Thin
platesofaragonite(<1mm)coatthewatersurfaceofthechannel,andinsomeareas,thinmicrobialbiofilmshavedevelopedonthebottomofthechannel.
Wateremergingfromthesourcepoolpredominantlyflowsthroughshallow(5–10cm)canalsintoa~1-m-diameterpoolusedforbathing(rotenburo).Rocksurfacesinthecanalsandrotenburoarecoatedin
F IGURE 1 LocationofOkuoku-hachikurouOnsen(OHK)inAkitaPrefecture,Japan.InsethighlightsthelocalgeologyoftheLakeTowadaregion,modifiedfromGeologicalSurveyofJapan(2012).ThebedrockgeologyatOHKconsistspredominantlyoffelsicvolcanics[Colourfigurecanbeviewedatwileyonlinelibrary.com]
TABLE 1 GeochemicalcharacteristicsofOHKsourcewater
T 44.3°C
pH 6.8
DO <15μm
Fe2+114 μm
NH3/NH
4
+22 μm
Cl− 38 mm
SO4
2−6.5 mm
NO3
− <1.6μm
NO2
− <2.2μm
HPO4
− <1μm
TOC <0.005Cwt%
820 | WARD et Al.
ironoxide flocs.Water flowsout from the rotenburo throughaddi-tionalshallowcanalsandultimatelydevelopsintoasheetedflowonthehillslope,wherecontinualdegassingofCO
2 leads to formation of
bubbles.Manybubblesbecomeencrustedwitharagoniteandminer-alized(Figure2).
While no substantial accumulation of microbial biomass is visi-blewithinthesourcepool,rotenburo,orcanals,thin(<1mm)patchygreenbiofilmsoccuralongtherimofthesourcepoolandoldstream(Figure2d). These were sampled for the Shallow Source and OldStreamMineralsamples.
Downstream, OHK preserves unique mineralized bubbles. AsCO
2degassesfromthespringwater,thepHrises,dissolvedinorganic
carbon concentrations drop, and the carbonate saturation state in-creases prompting aragonite precipitation. This occurs sufficientlyquickly inOHK that bubbles develop coatings of aragonite and aremineralized in situ. These bubbles encrust and provide a possiblepreservation mechanism for a wide range of organic materials, in-cludingleaves,arthropods,andbiofilmsinthissectionofthespring.Preservationoforganicstructuresbyironmineralshasbeenobservedpreviouslyinacidiciron-richenvironmentsatRioTinto,Spain,wherefossil structures endure formillions of years (Fernández-Remolar &Knoll,2008).TherapidmineralizationofironoxidesandaragoniteatOHKmaythereforealsoserveasamechanismforpreservingkeybio-logicalfeaturesofthisenvironmentovergeologictimescales.
F IGURE 2 ContextphotographsofOHK.(a)PhotographofOHKfacingnorthtowardsourcepool.Sourcepool(1),oldstream(2),canal(3),androtenburo(4)visible.Peopleforscale(~1.8m).(b)ImageofOHKfacingsouthwesttowardrotenburoandbubblepool.Waterflowingfromtherotenburo(4)developsintoasheetedflowwhichspreadsacrossthehillside,fillingthebubblepool(5)wheredegassingCO
2
bubbles become encrusted in aragonite.
Personforscale(~1.8m).(c)Underwaterphotographofsource.WaterandCO
2
bubblesemergefromtheboreholeatright.Scalebaris10cm.(d)Lobatewalloftravertineattherimofthesourcepool,withgreen-pigmentedbiofilms(sampledasShallowSourceMineralsample)visible.Scalebaris10cm.(e)Close-upoftravertineonthewestedgeofthesourcepool.Scalebaris50cm.(f)Close-upphotographofthebubblepool,showingaragonite-mineralizedCO
2bubbles.Scale
bar5cm.(g,h)Close-upsofferrihydriteand aragonite laminations in travertine.
Redlayersareprimarilycomposedofferrihydrite,whilewhitelayersarepredominantlyaragonite.Scalebarsshownare5mm[Colourfigurecanbeviewedatwileyonlinelibrary.com]
(a) (b)
(c) (d)
(e) (f)
(g) (h)
| 821WARD et Al.
2.2 | Sample collection
Samples for sequencing and geochemical analysis were collectedfromfivesitesatOHK(Figure2):DeepSource(1.2mdeepinthesourcepoolattheborehole),ShallowSource(surfacewaterandathinbiofilmalongtheedgeofthesourcepool),OldStream(waterand thin biofilm along the semi-stagnant blocked outflow), Canal(alongtheflowfromthesourcepooltotherotenburo),andBubblePool (downstream in a 15cm deep pool coated in mineralizedbubbles).
Fromeachsite,botha“Mineral”anda“Water”samplewerecol-lectedfor16Sampliconsequencing,targetingsurface-associatedandpelagicmicrobial communities, respectively. “Mineral” samples con-sistedofscrapingsofthinbiofilms,mineralprecipitates,orwholemin-eralizedbubblesfromsurfacesoftravertinesorcobblesinthebottomofwaterchannels.Mineral sampleswerecollectedusingsterile for-cepsandspatulas(~0.25cm3ofmaterial).“Water”samplesconsistedof cells and sediment filtered from water using sterile syringes and
0.2-μmSansyo (SansyoCo.,Tokyo,JP) filters (~50–200ml ofwaterfiltered,untilfilterbegantoclog).CellswerelysedandDNA-preservedinthefieldusingZymoTerralyzerBashingBeadMatrixandXpeditionLysisBuffer(ZymoResearch,Irvine,CA).Cellsweredisruptedimme-diatelybyattachingtubestothebladeofacordlessreciprocatingsaw(Black&Decker,Towson,MD)andoperatingfor1minute.Samplesforgeochemical analysis consistedofwatercollectedvia sterile syringeandfilteredimmediatelythrougha0.2-μmSansyofilter.
2.3 | Geochemical analysis
Dissolved oxygen (DO), pH, and temperature measurements wereperformedinsituusinganExtechDO7008-in-1PortableDissolvedOxygen Meter (FLIR Commercial Systems, Inc., Nashua, NH). Ironconcentrations were measured using the ferrozine assay (Stookey,1970)followingacidificationwith40mmsulfamicacidtoinhibitironoxidation byO
2 or oxidized nitrogen species (Klueglein & Kappler,
2013).Ammonia/ammoniumconcentrationsweremeasuredusingaTetraTestNH
3/NH
4
+Kit(TetraPond,Blacksburg,VA)followingman-ufacturer’s instructions butwith colorimetry of samples andNH
4Cl
standardsquantifiedwithaThermoScientificNanoDrop2000cspec-trophotometer(ThermoFisherScientific,Waltham,MA)at700nmtoimprovesensitivityandaccuracy.Anionconcentrationsweremeas-ured via ion chromatography on a Shimadzu Ion Chromatograph(ShimadzuCorp.,Kyoto,JP)equippedwithaShodexSI-904Eanioncolumn(ShowaDenko,Tokyo,JP).
Total organic carbon (TOC) contents were assessed for filteredwaterandmineralprecipitatesfromthesourcepool,aswellasmineralprecipitates near the canal. For dissolved organic carbon measure-ments, 3L of springwaterwas filtered using 0.45-μmSansyo glassfiberfilters.Formineralprecipitates,approximately300gofsampleswas collected. Carbonate carbonwas removed via dissolutionwithHCl,andresidueswerefoldedintotincapsulesandanalyzedforcar-bon content via elemental analyzer (Thermo Scientific Flash 2000)withadetectionlimitof0.005%Cbyweight.
SamplesofsedimentfromthesourcepoolwerecharacterizedviaSEM-EDS (SU5500;Hitachi, Tokyo, JP) and μm X-ray diffraction byTEM(JEM-3010;JEOL,Tokyo,JP).
2.4 | 16S rRNA gene amplicon sequencing and analysis
Followingreturntothelaboratory,microbialDNAwasextractedandpurifiedwithaZymoSoil/FecalDNAextractionkit.TheV4-V5regionofthe16SrRNAgenewasamplifiedfromeachextractusingarchaealandbacterialprimers515F(GTGCCAGCMGCCGCGGTAA)and926R(CCGYCAATTYMTTTRAGTTT) (Caporaso etal., 2012). DNA wasquantifiedwithaQubit3.0fluorimeter(LifeTechnologies,Carlsbad,CA)accordingtomanufacturer’s instructionsfollowingDNAextrac-tionandPCRsteps.AllsamplesyieldedPCRampliconswhenviewedonagel after initialpre-barcodingPCR (30cycles).DuplicatePCRswerepooledandreconditionedforfivecycleswithbarcodedprimers.SamplesforsequencingweresubmittedtoLaragen(CulverCity,CA)foranalysisonanIllumniaMiSeqplatform.Sequencedatawerepro-cessed using qiimeversion1.8.0(Caporasoetal.,2010).Rawsequencepairswere joinedandquality-trimmedusing thedefaultparametersin qiime. Sequences were clustered into de novo operational taxo-nomicunits (OTUs)with99%similarityusinguclustopenreferenceclusteringprotocol(Edgar,2010).Then,themostabundantsequencewaschosenasrepresentativeforeachdenovoOTU(Wang,Garrity,Tiedje,&Cole,2007).Taxonomicidentificationforeachrepresenta-tivesequencewasassignedusingtheSilva-115database(Quastetal.,2012)clusteredatseparatelyat99%andat97%similarity.Singletonsandcontaminants(OTUsappearinginthenegativecontroldatasets)were removed; 16S sequences were aligned using mafft (Katoh,Misawa,Kuma,&Miyata, 2002), and a phylogenywas constructedusing fasttree(Price,Dehal,&Arkin,2010).Alphadiversitywasesti-matedusingtheShannonindex(Shannon,1948)andinverseSimpsonmetric(1/D)(Hill,1973;Simpson,1949).Allstatisticswerecalculatedusing scripts inQIIME and are reported at the99%and97%OTUsimilarity levels.Multidimensional scaling (MDS) analyses and plotstoevaluatethesimilaritybetweendifferentsamplesandOHKenvi-ronmentswereproducedinrusingthevegan and ggplot2packages(Oksanenetal.,2016;RCoreTeam2014;Wickham,2009).
3 | RESULTS AND DISCUSSION
3.1 | Geochemistry
GeochemistrymeasurementsofOHKsourcewateraresummarizedinTable1,whilegeochemicalgradientsalongthestreamoutflowaresummarizedinFigure3.Wateremergingfromthesourcewas44.3°C,very lowindissolvedoxygen(<15μm),hadapH6.8,andcontainedsubstantial concentrations of dissolved iron (114 μmFe2+),and22μm
NH3/NH
4
+.Afteremergingfromtheborehole,thespringwaterrapidlyexchangesgaseswiththeairduetoturbulentmixingassociatedwithwaterflowandCO
2ebullition,andDOroseto30μmattheShallow
Source.Dissolvedorganiccarbon in thesourcepoolwasbelowthe
822 | WARD et Al.
limitofdetection (0.005%Cbyweight).Organiccarboncontentofmineralprecipitatesatthesourcepoolwas0.01%byweight,risingto0.02%nearthecanal.SEM-EDSanalysisofsourcepoolprecipitatesdetectedFeandOasthemajorelements,andselectedareaX-raydif-fractionbyTEMrevealedamorphousFehydroxidesasthesolidphasewithnodetectionofhematiteorothercrystallinephases (Figure4).Aswater flows downstream from the source pool, it cools slightly,degassesCO
2,andcontinuestoabsorbatmosphericO
2.Bythetime
waterreachestheBubblePoolthespringwateris40°C,pH7.5,con-tains 7.7 μmNH
3/NH
4
+,109μm O2,andnodetectabledissolvediron.
Concentrationsofmajoranionswere largelystablealongthespringoutflow, with 1,350mg/L Cl−, 620mg/L SO
4
2−, and no detectableNO
2
−,NO3
−,orHPO4
−(limitofdetection0.1mg/L).
LikemanymodernBIFanaloghotspringsites,undertheenviron-mentalconditionsatOHK,abioticironoxidationisexpectedtopro-ceedspontaneously.FollowingrateequationsforabioticironoxidationfromSingerandStumm(1970),therateofabioticironoxidationpro-ceedsproportionatelytoconcentrationsofdissolvedFe2+,O
2,andthe
activityofOH−,oftheform—d[Fe2+]/dt = k[Fe2+
]PO2[OH−]2,wherek is
arateconstantequaltoabout8×1013L2 mole
−2 atm
−1 min
−1at25°C,andincreasingapproximately10-foldforevery15°Coftemperatureincrease (Stumm&Lee,1961).AttheDeepSource,where[O
2] was
belowthedetectionlimitof0.5mg/L(~15μm),abioticironoxidationratesare thereforeexpected tobe less than~4.35μm/min.Thisex-pectedratewouldbeexpectedto increasebetween~8.7μm/min at
theShallowSourcesiteand~12.7μm/minattheCanalsite,the last
F IGURE 3 Summaryofthegeochemistryandiron-oxidizingcommunitycompositionofOHKordinatedalongtheflowpathsinthesystem.(a)SchematicofOHKflowpaths,keyedtothesamplenames.MineralandWatersampleswerecollectedfromOldStream,DeepSource,ShallowSource,Canal,andBubblePoollocalities.(b)Relativeabundanceofphototrophicandiron-oxidizingtaxainthewater(top,solidbars)andmineral(bottom,crosshatchedbars)samplesalongtheflowpath.DatahereincludetaxalistedinTable3anddiscussedinthetextwithconfidentlyassignedmetabolisms,butnotincludingtaxasuchasAnaerolineaewhosemetabolismscannotbepredictedwithavailabletaxonomicresolution.Aerobicironoxidizersareshowninred,anoxygenicphototrophsinpurple,andoxygenicCyanobacteriaingreen.Aerobicironoxidizersarecommonthroughoutthewatersamples,andintheDeepSourcemineralsample,butdecreaseinrelativeabundancesomewhatdownstream.AnoxygenicphototrophsareconcentratedintheOldStreamandShallowSourceMineralsamples,whileoxygenicCyanobacteriaincreaseinabundancedownstream,particularlyinwatersamples.(c)ConcentrationsofdissolvedO
2andFe2+.Sourcewatersaredepletedin
O2buthighindissolvediron,whiledownstreamFe2+concentrationsdropandO
2increases.Themajorityofironoxidationappearstooccur
undermicrooxicconditionswhereaerobicironoxidizersaremostprevalent,whileanoxygenicphototrophsarelargelyrestrictedtopatchybiofilms,andCyanobacteriaareonlysignificantaftertheironhasalreadybeenremovedfromsolution.Changesintemperature(44.3–40.7°C)andconcentrationsofchloride(~37–39mm)andsulfate(~6.3–6.65mm)alongthehotspringoutflowwereminorandnotexpectedtocontributesignificantlytochangesinmicrobialcommunityormineralprecipitates,andsoarenotdisplayedhere[Colourfigurecanbeviewedatwileyonlinelibrary.com]
(a)
(b)
(c)
| 823WARD et Al.
samplinglocationatwhichdissolvedironwasdetectable.Thesevaluesaresignificant,andasaresult,abioticironoxidationlikelycontributessubstantially to theproductionof ironoxidesatOHK.Nonetheless,theabundanceofiron-oxidizingbacteriaandmorphologyofironoxideprecipitates demonstrate that there is aviable and active niche for
biologicalironoxideproduction.Thisisfurthersupportedbyestimatesof flowrates throughOHKcorrelatedagainstchanges in ironoxideabundance from theedgeof theShallowSourcePool to theCanal,whereflowratesof~0.33m/sthroughcanalswithcrosssectionsof~10cmby5cmsuggestflowratesof~1.67L/s.Overdistancesof2mfromtheShallowSourcetotheCanal, [Fe2+
] declines from ~114 μm
to ~83 μm, ora changeof31μm inapproximately6seconds; this isequivalenttoabout100-foldfasterthanexpectedforpurelyabioticrates. Even assuming substantial backflow andmixing, this leaves asubstantialroleforaerobiciron-oxidizingbacteriainexplainingthede-clineinironconcentrationsalongthehotspringoutflow.TheseresultsarealsoconsistentwithestimatesfromKasamaandMurakami(2001)that suggest aerobic iron-oxidizingbacteria can increase ironoxida-tionratesbyupto4ordersofmagnitudeabovethoseexpectedfrompurelyabioticreactions.
3.2 | Recovered microbial diversity
In total, we recovered 141,125 sequences from the 10 samples atOHK (Table2). Reads per sample ranged from 2,176 for theCanalMineralsample to27,454reads for theOldStreamMineralsample(median15,247,mean14,112, and standarddeviation8,654).WiththeexceptionoftheOldStreamMineralsample,watersamplescon-sistentlyrecoveredmoresequencereadsthanmineralsamples(meanof5,926versus18,983).AssessmentofsamplingdepthwasestimatedusingGood’sCoverage(Good,1953).Onaverage,90%ofthemicro-bialcommunitywasrecoveredfromOHKsamplesatthe99%OTUlevel(rangingfrom75%coverageintheCanalMineralsampleto96%in theOld StreamMineral sample) and94%at the97%OTU level(83%fortheCanalMineralsampleto98%fortheOldStreamsample).
Mostofthetaxonomicandabundancevariationwasrelatedtolo-cationalong theoutflowand therefore the localenvironmental andredoxconditionsandconsequentmetabolicopportunities (Figures3and5).Thecommunitycompositionofthewatersamplesallappearedrelativelysimilartoeachother,with lowdissimilaritybetweenwatersamplesandmineralsamplesfromthesourcepool.Downstream,min-eralsamplesappeardissimilarbothfromwatersamplesandfromeachother(Figure5).
Relativeabundancesofmicrobialtaxaasrevealedby16Ssurveyscanbeuseful forpredictingmetabolismsdrivinggeochemicalcyclesand producing themineral deposits observed at OHK (Table3 andFigure3).Inparticular,thecontributionsofvariousironoxidizersandphototrophstoprimaryproductivityalongthespringpath (Figure3)can be estimated due to these metabolisms being fairly well con-servedwithinbacterialtaxa(e.g.,Chanetal.,2016;Emerson,Fleming,&McBeth,2010).AnalysisofthemostabundanttaxaatOHKrevealedsignificant roles fororganismsassociatedwithdiverse ironmetabo-lisms, including aerobic and phototrophic iron oxidation, aswell astraceironreducers.Whiletherelativecontributionofabioticironoxi-dationatOHKisnotconstrained,sequencedatasuggestthataerobiciron-oxidizingbacteriaarethedominantbiologicaldriversofironoxi-dationinthehotspring.Alsopresentwerediversephototrophsasso-ciatedwithbothoxygenicandanoxygenicphototrophicclades;these
F IGURE 4 Electronmicroscopyimagingofprecipitatesfromsourcepoolwall.Back-scatteredelectronimagescollectedbySEMofthinsectionsamplesofsolidscollectedfromthetravertinewallofthesourcepool(Figure2d).Thissampleshowsalternatinglaminationsofaragonite-richzonesandironoxide-richzones.(a)Overviewimageillustratesalternationofcarbonate-andironoxide-richlayers.(b)Enlargedimageofironoxide-richzoneof(a),showingaggregationofironoxidenanoparticlesintoadendritictexture.(c)ImageofdendriticironoxideaggregatesfollowingremovalofcarbonatephasesviatreatmentwithHCl,revealingsheath-liketubularandamorphousparticulateironoxidemorphotypes
(a)
(b)
(c)
824 | WARD et Al.
organismswereobservedatonly traceabundance inmostsamples,butanoxygenicphototrophswereenriched inbiofilmsfromtheOldStream,therimoftheSourcePool,whileCyanobacteriawereabun-dantintheBubblePool.AsmallbutdiverseassortmentofmicrobesassociatedwithnitrogencyclingwaspresentatOHK,despitelowcon-centrationsofnitrogencompoundsinthespringwater(AppendixS1).
3.3 | Aerobic iron- oxidizing bacteria
AmongthemostabundanttaxaatOHKaremembersofthebetapro-teobacterialfamilyGallionellaceae,mostlikelymembersorcloserela-tivesoftheaerobiciron-oxidizinggeneraGallionella or Sideroxydans.
Gallionella and Sideroxydans are neutrophilic iron oxidizers that usemolecularoxygentooxidizedissolvedFe(II)toFe(III)oxideswhilecon-servingenergyforgrowthandautotrophiccarbonfixation(Emerson&Moyer,1997;Emersonetal.,2013;Kucera&Wolfe,1957);theyarecommonlyfoundinterrestrialiron-richsystems(Emersonetal.,2010).Aerobic iron-oxidizing bacteria have characteristically low growthyields (Neubauer, Emerson,&Megonigal, 2002) due to themodestpotentialsofFe(II)/Fe(III)redoxcouplesandresultingrequirementforreverseelectrontransfertoachievethesufficientlylowpotentialelec-tronsneededforcarbonfixation(Bird,Bonnefoy,&Newman,2011).
Gallionellaceaeareabundantinboththemineralandwaterfrac-tionsoftheDeepSource(37%and18%,respectively),butotherwiseappeartobedominantlyassociatedwiththewaterfractionofothersamples(28%averageinwatersamples,8.5%averageinmineralsam-ples) (Table3).Thismay indicateapreferenceof theGallionellaceaeat OHK for a planktonic over surface-attached modes of growth,althoughthis is impossible tostatewithcertainty in theabsenceofcellquantificationbetweenthesesampletypesanddeterminationofdifferencesinabsoluteratherthanrelativeabundance.Basedonthesequencedata,membersoftheGallionellaceaeappeartobethefirstironoxidizersandprimaryproducers toacton theupwelling springwaterasitmixeswithatmosphericO
2,drivingthebulkofearlybio-
logical ironoxidationatOHKandproducingmuchofthe ironoxidesedimentthatistransportedalongthespringoutflow.Gallionellaceaewere fairly diverse, including169OTUs at the97% identity cutoff;however, the twomost abundantOTUswereboth~97% similar toSideroxydans lithotrophicusES-1andrepresentedmorethan92%ofthetotalGallionellaceaesequencesatOHK.TheabundanceofthesetwoOTUsdrivestheoveralltrendinironoxidizerabundance(Figure3).
Also present, albeit at lower abundance (up to ~1.5% relativeabundance) (Table3),aremembersof thezetaproteobacterial familyMariprofundaceae,anothergroupofneutrophilicironoxidizers.Iron-oxidizing Zetaproteobacteria are more commonly found in marinesettings,particularlyindeepoceanbasinsassociatedwithhydrother-malironsources(Emersonetal.,2010).Despiteasimilarphysiology,MariprofundaceaearenotcloselyrelatedtoGallionellaceaeorotheraerobic iron oxidizers, instead forming a distinct class within theProteobacteria(Emersonetal.,2007).Zetaproteobacteriahaveprevi-ouslybeenidentifiedinrelativelysalineterrestrialiron-andCO
2-rich
systems(e.g.,Emerson,Thomas,Alvarez,&Banfield,2016),sometimesco-occurringwithGallionella(Crosseyetal.,2016);thediscoveryoftheT
ABLE 2 DiversitymetricsofOHKsequencing.Diversitymetricscalculatedforboth99%and97%sequenceidentitycutoffsforassigningOTUs
Dee
p So
urce
M
ine
ra
l
Dee
p So
urce
W
ate
r
Shal
low
Sou
rce
Min
era
l
Shal
low
So
urce
Wat
erO
ld S
trea
m
Min
era
l
Old
Str
eam
W
ate
r
Ca
na
l
Min
era
lC
an
al
Wa
te
r
Bubb
le P
ool
Min
era
l
Bubb
le P
ool
Wa
te
r
Re
ad
s6,456
20,067
6,512
25,306
27,454
19,052
2,176
17,893
3,608
12,601
ObservedOTUs(99%)
906
1,928
1,045
2,450
1,775
1,842
74
02,455
85
71,595
Goodcoverage(99%)
0.9035
0.9388
0.8948
0.941
0.9615
0.9423
0.7
46
80.9076
0.8
28
70.911
Shannonindex(99%)
5.9544
6.0339
7.6849
6.4
78
56
.83
02
6.3
40
38
.11
36
.84
82
7.2
74
75.896
InverseSimpson(99%)
9.4959
12.9196
62
.63
37
11
.50
82
37
.01
68
11.4379
10
5.3
15
31
2.7
88
13
2.6
02
58
.64
75
ObservedOTUs(97%)
43
1895
57
21,059
74
7869
490
1,281
55
5910
Goodscoverage(97%)
0.9588
0.9737
0.9459
0.9768
0.9834
0.9738
0.8359
0.9529
0.8911
0.951
Shannonindex(97%)
4.7
60
34.6789
6.4739
5.0
55
45
.57
85
5.0959
7.0
60
35
.47
67
6.1
73
64
.57
11
InverseSimpson(97%)
6.5
62
38.4309
33
.13
31
7.5
28
82
2.6
65
87
.70
54
55
.62
31
8.1
76
31
8.5
50
45
.56
7
| 825WARD et Al.
co-occurrenceof theseorganisms atOHKprovides further supporttotheoverlappingecologicalnichesoftheseclassically“marine”and“terrestrial” iron-oxidizingbacteria.Thismayberelatedtothe inter-mediatesalinityofOHKwater(~38mmCl−,~6.5mmSO
4
2−),providinganenvironmentconducivetoorganismsadaptedtobothfreshwaterandsaltwater,resultinginthemixedpopulationofGallionellaceaeandMariprofundaceae.
MembersoftheGallionellaceaearetypicallyassociatedwithcoldiron-oxidizingenvironments,andnothotsprings(Hallbeck&Pedersen,2013);whilemembersoftheMariprofundaceaehavebeenobservedtohaveanuppergrowthtemperatureof30°C(Emersonetal.,2010).OHK,withsourcewatertemperatures~44°Cmaythereforesupportuniquethermotolerantstrainsofthesebacteria.
Members of the family Comamonadaceae were also fairlyabundant (~1%–12%) in OHK samples (Table3). This family ofBetaproteobacteria includes members such as Acidovorax ebreus, a
nitrate-reducing anaerobic iron oxidizer (Byrne-Bailey etal., 2010),aswell as iron reducers such asRhodoferax ferrireducens (Finneran,Johnsen,&Lovley,2003)andtheiron-oxidizingbacteriumLeptothrix
(vanVeen,Mulder,&Deinema,1978).However,thetaxonomicaffin-ityoftheComamonadaceaeatOHKisinsufficientlyresolvedtocon-fidently assess the contribution of this group to iron cycling in thisenvironment.
Electronmicroscopyofmineralprecipitatesfromthesourcepoolandcanalrevealedalternatinglaminationsofaragonite-richandironoxide-richmaterial;imagingofironoxidebandsfollowingdissolutionofcarbonateswithHClrevealedthatironoxidesweremadeupofamixture of amorphous and sheath-like tubular structures (Figure4).While iron oxide sheaths are typically associatedwith the betapro-teobacterial iron-oxidizing genus Leptothrix (Emerson etal., 2010),they can alsobeproducedbydiverse ironoxidizers including somestrainsofZetaproteobacteria(Flemingetal.,2013).Althoughweten-tatively regard thesemineralized filaments as biological in origin, it
isunclearwhatorganismsareresponsiblefortheproductionof ironoxide sheaths observed at OHK, particularly as structures appearhighly mineralized, potentially reflecting encrustation of biogeniciron oxides by subsequent abiotic precipitation. Sub-micrometer,amorphous particulate iron oxides are characteristic of iron oxida-tion by Sideroxydans(Emerson&Moyer,1997),andsotheprevalenceof this iron oxide morphology is consistent with this genus of theGallionellaceaebeingmajorcontributorstoironoxidationatOHK.Theabundance of amorphous iron oxide particles also supports the as-signmentofGallionellaceaeOTUsatOHKtoSideroxydansratherthanstalk-formingGallionella(Emersonetal.,2010).However,asdiscussedabove,asignificantportionofironoxidationatOHKlikelyproceedsabioticallyandmaycontributesimilarmorphologiesofamorphousironoxideparticles,sothepresenceoftheseformsisconsistentwith,butnotnecessarilydiagnosticof,theactionofSideroxydans and may in-steadreflectthecombinedactionoftheseorganismswithabioticironoxidation.
3.4 | Cyanobacteria
Cyanobacteria were abundant in the Bubble Pool Water sam-ple,where theymadeup~37%of all sequence reads, butwere ofmuch lower abundance in samples collectedupstream (Table3 andFigure3).AlthoughCyanobacteria are sometimesunderrepresentediniTagdatasetsasaresultofpoorDNAyieldoramplificationbiases(e.g.,Parada,Needham,&Fuhrman,2015;Trembath-Reichertetal.,2016), thepaucityofCyanobacteria inupstreamOHKsampleswasconfirmed by epifluorescencemicroscopy, inwhich cells displayingcyanobacterial autofluorescence were observed abundantly in sam-ples from thedownstreamBubblePool but not in the SourcePool(Fig.S2).
It has been demonstrated that in iron-rich systems whereCyanobacteriaareabundantandproductive,only~1%ofO
2 released
F IGURE 5 MultidimensionalscalinganalysisofOHKsamples.Eachpointrepresentstherecoveredmicrobialcommunityfromagivensample,withsitesidentifiedbycolorandsampletypebyshape.Pointsclosetoeachotherinthistwo-dimensionalspaceshareasimilarcommunitycomposition.Relativeabundance data were transformed by
the4throottodown-weighttheeffectofabundanttaxainthesamples.Watersamplesclustertogether,andwithSourcepoolmineralsamples,whiletheBubblePoolWaterandtheotherMineralsamplesstandoutalongdifferentcurvesinthisspace.Stressvalueis0.0465[Colourfigurecan be viewed at wileyonlinelibrary.com]
Water
Mineral
Bubble Pool
Canal
Deep Source
Old Stream
Shallow Source
826 | WARD et Al.TABLE 3 RelativeabundanceoftaxatotheFamilylevel.Overall,10mostabundanttaxalisted,aswellasothertaxaofinterestmentionedinthetextandSI,orderedbyrelativeabundance
averagedacrossallsamples.Taxacolorcodedbyputativemetabolism:redforaerobicironoxidizers,purpleforanoxygenicphototrophs,greenforoxygenicphototrophs,bluefornitrifiers,and
yellowfortaxawithmembersperformingadiverserangeofmetabolismsthatcannotberesolvedwithtaxonomicresolutionofavailabledata[Colourtablecanbeviewedatwileyonlinelibrary.com]
Taxo
nD
eep
Sour
ce
Min
era
l (%
)
Dee
p So
urce
W
ate
r (
%)
Shal
low
So
urce
M
ine
ra
l (%
)
Shal
low
So
urce
W
ate
r (
%)
Old
Str
eam
M
ine
ra
l (%
)
Old
Str
eam
W
ate
r (
%)
Ca
na
l
Min
era
l (%
)
Ca
na
l W
ate
r
(%)
Bubb
le P
ool
Min
era
l (%
)
Bubb
le P
ool
Wa
te
r (
%)
Ave
rage
(%)
Bacteria;__
Proteobacteria;__
Betaproteobacteria;__
Nitrosomonadales;__
Gallio
ne
llace
ae
36.94
18
.23
1.09
34
.05
3.2
73
3.5
70
.46
31
.77
0.4
42
3.5
81
8.3
4
Bacteria;__
Proteobacteria;__
Zetaproteobacteria;__
Mariprofundales;__
Mariprofundaceae
0.6
51
.32
0.0
50
.52
1.5
10
.52
1.0
10
.58
0.1
70
.17
0.6
5
Bacteria;__
Cyanobacteria;__
Cyanobacteria;__
SubsectionIII;__FamilyI
0.1
50
.24
2.5
04
.46
0.2
11
.41
0.4
62
.30
0.3
33
7.4
54.95
Bacteria;__
Cyanobacteria;__
Cyanobacteria;__
SubsectionV;__FamilyI
0.0
80
.11
0.09
5.1
60
.01
0.3
10
.00
1.29
0.0
60
.20
0.7
3
Bacteria;__
Proteobacteria;__
Alphaproteobacteria;__
Rhodospirillales;Other
0.09
0.0
56
.68
0.0
42
.57
0.1
70.09
0.1
30.19
0.0
31
.00
Bacteria;__
Proteobacteria;__
Betaproteobacteria;__
Rhodocyclales;__
Rhodocyclaceae
0.94
0.5
50
.15
0.4
22
.61
3.3
10
.00
0.99
0.5
30
.38
0.99
Bacteria;__
Proteobacteria;__
Alphaproteobacteria;__
Rhodobacterales;__
Rhodobacteraceae
0.1
10
.34
1.8
00
.47
2.8
50
.26
0.7
40
.87
0.2
50
.14
0.7
8
(Continues)
| 827WARD et Al.
Taxo
nD
eep
Sour
ce
Min
era
l (%
)
Dee
p So
urce
W
ate
r (
%)
Shal
low
So
urce
M
ine
ra
l (%
)
Shal
low
So
urce
W
ate
r (
%)
Old
Str
eam
M
ine
ra
l (%
)
Old
Str
eam
W
ate
r (
%)
Ca
na
l
Min
era
l (%
)
Ca
na
l W
ate
r
(%)
Bubb
le P
ool
Min
era
l (%
)
Bubb
le P
ool
Wa
te
r (
%)
Ave
rage
(%)
Bacteria;__
Proteobacteria;__
Alphaproteobacteria;__
Rhodospirillales;__
Rhodospirillaceae
0.0
30
.01
3.1
30
.04
0.0
70
.06
0.09
0.3
00.19
0.29
0.4
2
Bacteria;__Chloroflexi;__
Chloroflexia;__
Chloroflexales;__
Chloroflexaceae
0.0
00
.00
0.0
50
.02
0.0
00
.00
1.19
0.2
70
.83
0.1
20
.25
Bacteria;__Chlorobi;__
Chlorobia;__
Chlorobiales;__OPB56
0.09
0.2
10
.06
0.0
30
.17
0.3
00
.14
0.1
70
.03
0.0
20
.12
Bacteria;__
Proteobacteria;__
Gammaproteobacteria;__
Chromatiales;__
Chromatiaceae
0.4
20
.00
0.0
00
.04
0.0
00
.18
0.0
00
.01
0.0
30
.21
0.09
Bacteria;__
Proteobacteria;__
Gammaproteobacteria;__
Xanthomonadales;__
Xanthomonadaceae
0.2
20
.61
3.0
60
.41
10
.01
0.3
09.33
1.7
024.89
1.39
5.19
Bacteria;__Chloroflexi;__
Anaerolineae;__
Anaerolineales;__
Anaerolineaceae
7.1
31
0.7
51
0.1
03
.52
2.3
20.91
1.4
73
.67
2.2
20
.60
4.2
7
Bacteria;__
Proteobacteria;__
Betaproteobacteria;__
Burkholderiales;__
Comamonadaceae
1.5
01
.88
2.0
32
.35
12
.12
1.5
11
.42
4.1
52
.52
4.3
83.39
Bacteria;__Nitrospirae;__
Nitrospira;__
Nitrospirales;__
Nitrospiraceae
0.39
1.19
0.2
55
.07
4.6
51
2.8
10
.18
3.8
20
.03
2.1
03
.05
Archaea;__
Thaumarchaeota;__
Marine_Group_I;__o;__f
0.99
0.2
30
.00
0.09
0.0
10.98
0.0
00
.44
0.0
00
.04
0.2
8
TABLE 3 (Continued)
(Continues)
828 | WARD et Al.
Taxo
nD
eep
Sour
ce
Min
era
l (%
)
Dee
p So
urce
W
ate
r (
%)
Shal
low
So
urce
M
ine
ra
l (%
)
Shal
low
So
urce
W
ate
r (
%)
Old
Str
eam
M
ine
ra
l (%
)
Old
Str
eam
W
ate
r (
%)
Ca
na
l
Min
era
l (%
)
Ca
na
l W
ate
r
(%)
Bubb
le P
ool
Min
era
l (%
)
Bubb
le P
ool
Wa
te
r (
%)
Ave
rage
(%)
Bacteria;__Chlorobi;__
Ignavibacteria;__
Ignavibacteriales;Other
6.7
23
4.2
53
.67
5.3
812.95
2.2
30
.37
11
.85
4.49
1.6
68
.36
Bacteria;__
Proteobacteria;__
Deltaproteobacteria;__
Bdellovibrionales;__
Bacteriovoracaceae
2.29
0.97
0.2
14
.31
0.2
11
1.3
80
.14
4.2
10
.08
3.7
52
.76
Bacteria;__Candidate_divi-
sion_OP11;__c;__o;__f
0.1
51
.73
0.1
40
.46
2.09
0.4
26
.34
0.2
51
1.0
30
.06
2.2
7
Bacteria;__
Bacteroidetes;__
Sphingobacteriia;__
Sphingobacteriales;__env.
OPS_17
4.2
03
.28
0.2
57.09
0.1
40
.68
1.2
43
.85
1.1
40
.64
2.2
5
Bacteria;__
Proteobacteria;__
Gammaproteobacteria;__
Enterobacteriales;__
En
tero
bacte
riace
ae
3.4
41
.01
3.49
1.1
60.69
1.4
74
.18
0.39
2.19
0.5
31
.86
Bacteria;__
Proteobacteria;__
Deltaproteobacteria;__
Desulfuromonadales;__
Ge
ob
acte
race
ae
0.0
20.79
0.0
00
.03
0.1
40
.03
0.0
50
.06
0.0
00
.14
0.1
3
Bacteria;__
Cyanobacteria;__
ML635J-21;__o;__f
0.0
30
.06
0.0
20
.06
0.0
00
.34
0.0
00
.02
0.0
00
.23
0.0
8
Bacteria;__
Cyanobacteria;__SHA-
109;__o;__f
0.0
00
.00
0.1
00
.00
0.90
0.0
00
.00
0.0
00
.00
0.0
00
.10
TABLE 3 (Continued)
| 829WARD et Al.
oxidizesferrousiron,withtheremainderescapingtotheatmosphere(Rantamäki etal., 2016). Thus, given the inefficiency of cyanobac-terial oxygen fluxes for oxidizing dissolved iron, and the scarcity ofCyanobacteriaupstreamatOHKwhereironoxidationistakingplace,Cyanobacteriadonotappeartobemajorcontributorstoironoxida-tionatOHK.
CyanobacteriapresentarepredominantlymembersofSubsectionIII,FamilyI.ThisgroupincludesLeptolyngbya,agenusoffilamentousnon-heterocystousCyanobacteriathathasappearedinclonelibrariesfromOHK(Takashimaetal.,2011)andiscommoninotherhotspringsofsimilartemperatures(e.g.,Bosaketal.,2012;Roeselersetal.,2007).
Members of deeply branching non-phototrophic CyanobacteriacladesareaminorbutnotablecomponentofOHKsamples(upto0.9%abundance).While theCyanobacteriaphylumhas traditionallybeenconsideredtoexclusivelycontainoxygenicphototrophs,severaldeep-branching non-phototrophic clades have recently been describedwithintheCyanobacteriaphylum, includingMelainabacteria,asistergroup tooxygenicCyanobacteria (i.e.,Oxyphotobacteria), aswell asdeeper-branchingclades(DiRienzietal.,2013;Johnsonetal.,2013b;Leyetal.,2005;Soo,Woodcroft,Parks,Tyson,&Hugenholtz,2015;Soo etal., 2014).These deep-branching Cyanobacteria—particularlythecladesSHA-109andML635J-21,whichbranchbasaltoallotherCyanobacteria—are thought to be ancestrally non-phototrophic andcanhelptobetterconstraintheevolutionaryhistoryofCyanobacteriaandthereforeoxygenicphotosynthesis(e.g.,Fischer,Hemp,&Johnson,2016;Shih,Hemp,Ward,Matzke,&Fischer,2017;Soo,Hemp,Parks,Fischer,&Hugenholtz,2017).Thesecladesarefoundathigherabun-danceatOHKthanmostotherenvironments,andOHKcouldprovidea valuable resource for investigatingmembers of this understudiedgroupviametagenomicsequencing,incubations,orisolation.
3.5 | Anoxygenic phototrophs and relatives
Membersofseveraltaxamadeupoforcontaininganoxygenicphoto-trophswerepresentatlowabundanceinOHKsamples(Table3).Theseinclude the Rhodospirillales, Rhodobacteraceae, Rhodocyclaceae,Chloroflexaceae, Chlorobiales, and Chromatiaceae. Some of thesetaxa (e.g.,Chloroflexaceae,Chlorobiales)aremadeupalmostexclu-sivelyofphototrophs,whileothers(e.g.,Rhodobacteraceae)containmemberswithawidediversityofmetabolisms,onlysomeofwhichare phototrophic (Fischer etal., 2016; Overmann & Garcia-Pichel,2013).Shotgunmetagenomicorculture-basedanalysiswillbeneces-sarytoconfirmwhetherthemembersofthesetaxapresentatOHKarephototrophic.Althoughthesetaxaindividuallyrepresentnomorethanafewpercentofthesequencereadsatanygivensite(overallav-erage~0.88%ofreadspertaxon),thispopulationisquitediverseandinsumrepresentsasizablefractionofthetotalmicrobialcommunity(3%–20%)(Figure3).Putativeanoxygenicphototrophsaremostabun-dant intheShallowSourceandOldStreamMineralsamples(13.8%and20.4%oftotalabundance,respectively),droppingto~3%intheDeepSourcesample.EveninthedownstreamBubblePoolsamples,anoxygenicphototrophsmakeup~5%ofthetotalabundanceofse-quences. Sequences associated with anoxygenic phototrophs were
more abundant inmineral samples than inwater samples (~9% vs.~5%),thoughasdiscussedaboveinthecaseofGallionellaceae, it isunclearwhetherabsoluteabundancescaleswithrelativeabundanceandthereforewhethertheseorganismsgrowpreferentiallyattachedtosolidsurfacesratherthanplanktonically.
All samples contained relatively abundant sequence reads be-longingtotheChlorobiphylum(Table3).TheChlorobiareclassicallyknown as the Green Sulfur Bacteria due to the anaerobic sulfur-oxidizing anoxygenic phototrophic lifestyle of its earliest describedmembers (Bryant & Liu, 2013; Davenport, Ussery, & Tümmler,2010). This includes iron-oxidizing anoxygenic phototrophs such asChlorobium ferrooxidans (Heising, Richter, Ludwig, & Schink, 1999),which employ ametabolism thought to be relevant toArcheanBIFdeposition(e.g.,Kappleretal.,2005).Duetoincreasedenvironmentalsequencingandnewisolationefforts,however,theChlorobiphylumis nowknown to also contain aerobic photoheterotrophs (Liu,Klattetal., 2012; Stamps, Corsetti, Spear, & Stevenson, 2014) and non-phototrophs(Podosokorskaya,Kadnikovetal.,2013).ThemajorityofChlorobisequencesfoundinOHKappeartofallwithintheChlorobiorderIgnavibacteria,abasalcladeofChlorobiwhoseknownmembersincludeversatileheterotrophicmetabolismsbutnoknownphototro-phypathways(Iinoetal.,2010;Liu,Frigaardetal.,2012).ItthereforeappearsthatphotoferrotrophybyChlorobi isnotdriving ironoxida-tionatOHK,althoughmetagenomicsequencingandassemblyofOHKChlorobi genomeswill be necessary to confirm that phototrophy isnotpresent in theseorganisms. Ignavibacteria appear tobe a com-moncomponentofhotspringmicrobialcommunities:theseorganismswerefirstisolatedfromaJapanesehotspring(Iinoetal.,2010)andarefoundathighabundanceinChocolatePotshotspringsinYellowstoneNationalPark(Fortneyetal.,2016).
The Ignavibacteria found atOHKhadonly low similarity to de-scribedstrains,withmorethan50%of Ignavibacteriareads (primar-ily from the Deep Source and CanalWater samples) from anOTU~91%similartoMelioribacter roseusP3M,amoderatelythermophilicfacultative anaerobe (Kadnikov etal., 2013). Approximately 20% ofIgnavibacteriareads(primarilyfromtheDeepSourceWaterandOldStreamMineralsamples)were93%similartoIgnavibacteria albumJCM16511.
Members of the bacterial phylum Chloroflexi were remarkablyabundant inOHKsamples (Table3).TheChloroflexiwereclassicallydescribedasthegreennon-sulfurbacteriaduetotheanoxygenicpho-totrophicmetabolismoftheirearliestdescribedmembers(Overmann,2008),butitisnowrecognizedthatthephylumismuchmoregeneti-callyandmetabolicallydiverse(Yamada&Sekiguchi,2009).Metaboliccharacters in the Chloroflexi largely follow class-level taxonomicpatternsbutwithanumberofnotableexceptions,suchas thenon-phototrophicpredatoryHerpetosiphonwithinthepredominantlypho-totrophic Chloroflexia class (Kiss etal., 2011;Ward,Hemp, Pace,&Fischer,2015b).ThemostabundantChloroflexiatOHKbelongtotheclassAnaerolineae,whichwereabundantinallsamples(upto~11%).TheAnaerolineaehavegenerallybeen isolatedasobligatelyanaero-bicheterotrophs(e.g.,Sekiguchietal.,2003;Yamadaetal.,2006),butgenomesequencinghasrevealedthecapacityforaerobicrespiration
830 | WARD et Al.
indiversemembersofthisclade(e.g.,Hemp,Ward,Pace,&Fischer,2015a, 2015b; Pace, Hemp, Ward, & Fischer, 2015; Ward, Hemp,Pace, & Fischer, 2015a). Furthermore, a genome for an organismcloselyrelatedtotheAnaerolineaewithgenesforphotosynthesishasbeenassembledfromaYellowstoneNationalParkmetagenome(Klattetal.,2011;Tank,Thiel,Ward,&Bryant,2017;Thieletal.,2016).Itisthereforeunclearwhatmetabolismsmaybepresent inAnaerolineaeatOHK,andisolationormetagenomicsequencingoftheseorganismswillbenecessarytodeterminewhatroletheymaybeplayinginthisenvironment.TheAnaerolineaeatOHKwereverydiverse, including480OTUsatthe97%cutoff.ThisincludedadistinctpopulationattheDeepSource (bothWaterandMineralSamples), theShallowSourceMineralsample,andmoredownstreamsamples.Thethreemostabun-dantAnaerolineaeOTUsweremostcloselyrelatedtoThermomarilinea lacunifontana (84%–88% similarity); T. lacunifontana is an anaerobic
heterotroph isolated from a shallow hydrothermal system in Japan(Nunouraetal.,2013).ThemostabundantAnaerolineaeOTUintheShallowSourceWatersample(makingup~7%ofallAnaerolineaeatOHK)was89% identical toOrnatilinea apprima.Themost abundantOTUintheOldStreamMineralsamplewas91%identicaltoLongilinea arvoryzae. Both O. apprima and L. arvoryzae are described as obli-gatelyanaerobicfermenterscapableofdegradingsugarsandproteins(Podosokorskaya, Bonch-Osmolovskaya etal., 2013; Yamada etal.,2007).
3.6 | Low biomass yield of the OHK microbial community
OHKisauniqueecosystemsupportingnovelmicrobialcommunitiesaswellasservingasanintriguingprocessanalogforPrecambrianbandedironformationdeposits.Futureactivitymeasurementsofcommunitymembers,forexample,bymetagenomicsandstableisotopeprobingwillbenecessarytofurtherdefinemicrobialactivitiesinthissystem.Basedonmicroscopyand16Samplicondata,themicrobialcommuni-tiesatOHKappeartobesupportedprimarilybyaerobicironoxida-tionoccurring in andnear the sourcepool.At theOldStream site,mineral-attached anoxygenic phototrophs becomemore significant,whileCyanobacteriabecomeabundantonlyinthemostdownstreamsamples (Figure3).Thispredominanceof lithoautotrophsoverpho-totrophsisrareattheearth’ssurfacetodayandprovidesacontrasttoothermodernBIFanalogsites.Forinstance,inLakeMatano,ironoxidationisthoughttobedrivenlargelybyphotoferrotrophs(Croweetal., 2008). AtChocolate Pots hot spring in YellowstoneNationalPark—perhaps themost geochemically similar system toOHK thathasbeenextensivelystudied—ironoxidationisthoughttobeprimar-ily driven abiotically by O
2 produced in situbycyanobacterialmats
(Trouwborst etal., 2007). Furthermore, relative to Chocolate Pots,OHKsupportsverylittleinthewayofwell-developedmicrobialmats,withonlythin,patchybiofilms.
TheabsenceofsubstantialmicrobialbiomassaccumulationnearthesourcepoolatOHKcanbeconsideredtheresultoftwoseparatephenomena:(i)thepaucityofphotosyntheticCyanobacteriaand(ii)thepoorgrowthyieldsoftheiron-oxidizingbacteriathatdooccur.Neither
oftheseissuesisfullyresolved,buthypothesesfortheircausescanbemadebasedonthegeochemistryandmineralogyofOHKandrelatedsystems,aswellasaspectsofthephysiologiesdrivingironoxidation.
It has been proposed that high iron concentrations are toxic toCyanobacteria and that thismayhaveplayed a role indelaying theoxygenation of the Archean atmosphere (Swanner etal., 2015).In principle, ferrous iron toxicity may help explain the absence ofCyanobacteria in OHK until the most downstream samples, wheremostironhasalreadybeenoxidizedandprecipitated.TheabsenceofCyanobacteriaatOHKischallengingtoexplain,however,asotheriron-richsystems(e.g.,ChocolatePotsHotSpring,Trouwborstetal.,2007)supportproductivecyanobacterialpopulations,andinothersystems,oxygenicphotosynthesisandaerobicironoxidationhavebeenshownto co-occur (Hegler, Lösekann-Behrens, Hanselmann, Behrens, &Kappler,2012;Morietal.,2015).AtFuschnaSpringintheSwissAlps,Gallionella-dominatedcommunitiesoccurintheiron-rich,low-oxygen,high-flowconditionswithintheflowchannel,butCyanobacteria-andiron reducer-richmicrobialmats accumulate along the edgeswhereflowislesspronounced(Hegleretal.,2012).Thissuggeststhatflowregimemayalsoplayarole indeterminingthemicrobialcommunityofiron-richsystems;OHKexperienceshighflowrates,andturbulentmixinginthesourcepool,andthismayplayaroleinlimitingthede-velopmentofphototrophicmicrobialmats.Turbulencemayinhibitthedevelopment of phototrophic microbial mats, while simultaneouslybeingadvantageoustoaerobiciron-oxidizingbacteriabyhelpingthemshed accumulated iron oxides, limiting encrustation by their meta-bolic byproducts.However, futureworkwill be necessary to betterdeterminetheroleoffluidflowregimeandotherfactorsininhibitingCyanobacteriaatOHK.
Areasonablehypothesisforthepoordevelopmentofbiofilmsbyaerobic iron-oxidizing bacteria atOHK could be related to the lowgrowthyieldofaerobic iron-oxidizingmicrobesrelativetophototro-phs. Based on electron balance and assuming an average oxidationstateofzerofororganiccarbon,themaximumpossibleefficiencyofautotrophicironoxidationis1moleofCO
2fixedforevery4molesof
Fe(II)oxidized.However,measuredyieldsofaerobicironoxidizersaretypicallymuch lower,ontheorderof1moleofCO
2 fixedforevery
40molesofFe(II)oxidized (Neubaueretal.,2002).Yieldsforphoto-ferrotrophsappeartobemuchmoreefficient,approximatingtheidealstoichiometryof4Fe:1C (Ehrenreich&Widdel,1994).Whileelec-tron transfer inneutrophilic ironoxidizershasnotbeenextensivelycharacterized,thisdifferenceinyieldappearstofundamentallycomedowntotheredoxpotentialofironoxidationreactions,which(whilequitevariabledependingonenvironmentalpHandmineralogyofironoxides)aretooelectrochemicallypositivetodirectlyreduceNAD(P)+
andthereforebeusefulforcarbonfixation(Birdetal.,2011).Inordertogrow, theseorganismsmustconsumeprotonmotiveforce (PMF)torunelectrons“uphill”tolowerredoxpotentialsinordertogeneratetheNAD(P)HneededtoreduceCO
2(Birdetal.,2011).Inaerobiciron
oxidizers,thisrequireslargefluxesofironoxidationtomaintainsuffi-cientPMFtofixcarbon,whilephototrophicironoxidizerscanrelyoncyclicelectronflowthroughtheirreactioncenterstobuildPMFsuffi-cientlytoallowstoichiometricironoxidationandcarbonfixation.The
| 831WARD et Al.
relativelypoorgrowthyieldofaerobiciron-oxidizingbacteriaatOHKresults in organic carbon-lean mineral precipitates (<0.02% organiccarbonbyweight),incontrasttophototroph-dominatediron-richsys-tems likeChocolatePotshot springwhereorganic carboncontentscanbeinexcessof1%organiccarbonbyweight(Parenteau&Cady,2010).Ultimately,itislikelythattheoverproductionofferricironrel-ativetocarbonfixationduringaerobicironoxidationsetsthebudgetsforsubsequentcarbonandironcyclinginthisenvironment.
Significantly, 16S sequence reads associated with environ-mentally common iron-reducing microbes (e.g., Shewanellaceae,Geobacteraceae) occur at only very low abundances at OHK,with a maximum abundance of the Deltaproteobacteria familyGeobacteraceaeof0.79%intheDeepSourceWatersample(Table3).Thisisincontrasttootheriron-rich,neutralpHsystemsincludinghotandcoldspringsandgroundwaterseeps(e.g.,Blöthe&Roden,2009;Fortneyetal.,2016;Hegleretal.,2012;Rodenetal.,2012).Thismaypartiallyreflecttherelativefluxesofironoxidationversusorganiccar-bonfixationatOHK;thatis,thereisinsufficientorganiccarbonbeingfixed in this environment to fuel substantial iron oxide respiration.Meanwhile,turbulentmixingensuresthatoxygen-poormicroenviron-mentsdonotdevelop.Asmolecularoxygenisavailableinsubstantialexcessoforganiccarbon,heterotrophyatOHKneverdepletesO
2 suf-
ficientlytomakeironoxidesafavorableelectronacceptor.Incontrast,insystemswithmoresubstantiallydevelopedmicrobialmatsor lessefficientmixing,oxygencanbecomedepleteddeeperinmatfabricsorindiffusion-limitedboundarylayers,drivinglocalanoxiaandtheshifttowardironrespiration.ThelackofsubstantialironreductionatOHKisconsistentwiththepredominanceofferricironmineralsintheOHKdeposits(Takashimaetal.,2011)(Figure3).
4 | CONCLUSIONS
The relative paucity of organic carbon, the dominantly ferric ironcontentofsedimentary laminations,andtheprimaryroleofaerobicironoxidationtogethermakeOHKmostsimilartoProterozoic-typeBIFs,depositedaftertheGOE.BIFcompositionvariesthroughtime,with BIFs of different ages likely forming via different processes.Thisvariabilityislikelydrivenbychangesinprimaryproductivityandremineralizationpathwayscausedbytheevolutionofoxygenicpho-tosynthesisinCyanobacteriaandthesubsequentoxygenationoftheatmosphere at theGOE ca. 2.3Ga.While substantial debate existsabouttheantiquityofCyanobacteria,multiplelinesofevidencesug-gest that oxygenic photosynthesis evolved only shortly before theGOE (Fischer etal., 2016; Johnson etal., 2013a; Shih etal., 2017;Ward,Kirschvink,&Fischer,2016),andtherefore,molecularoxygenderivedfromphotosynthesiswasunlikelytoplayaroleinArcheanBIFformation.ThehypothesisthatthedepositionoftheseBIFsoccurredviaphototrophicironoxidationisconsistentwiththepredominantlyferrous composition of Archean and early Paleoproterozoic ironformations (Fischer&Knoll,2009) (AppendixS1), and isdiscordantwithmechanismsrelyingonaerobicironoxidation;photoferrotrophyresults in stoichiometric amounts of iron oxide and organic carbon
delivered to sediments,whichpromotes an environment conduciveto substantial amounts of iron reduction during burial and diagenesis
(Johnson,Beard,Klein,Beukes,&Roden,2008;Konhauser,Newman,& Kappler, 2005; Li, Konhauser, Kappler, & Hao, 2013). After theGOE,molecularoxygenwassufficientlyabundantintheatmosphereEarthsurfaceenvironmentsthatitcouldbeusedtodriveaerobicironoxidation.Additionally,ithasbeenobservedthattheorganiccarboncontentofBIFtendstobeinverselycorrelatedtotheproportionofresidualferriciron,withthemostironoxide-dominatedBIFscontain-ingontheorderof0.01%orlessorganiccarbonbyweight(Fischeretal., 2014; Klein, 2005). Proterozoic BIFs, such as the syn-glacialiron formations that co-occurwith Snowball Earth episodes late inNeoproterozoic (Cryogenian) time (Hoffman, Kaufman, Halverson,&Schrag,1998;Kirschvink,1992),aredominantlycomprisedoffer-ricironphases.Thisisconsistentwithexpectationsfortheirdeposi-tionviaaerobic ironoxidation (i.e.,excessdepositionof ironoxidesrelative to organic carbon, limiting subsequent iron reduction), andmost closely resembles the mineralogy of the materials currentlybeingdepositedatOHK.BycontrastingOHKwithotherBIFprocessanalogsiteswhereironoxidationpredominantlyoccursbydifferentprocesses (e.g.,phototrophy), itmaybepossible toopenawindowintotheecology,mineralogy,productivity,andotheraspectsofBIFdeposition across theGOE,withOHK representing an endmemberinwhich the ironoxide componentofBIF sedimentwasdepositedprimarilybyaerobicironoxidation.
ACKNOWLEDGMENTS
LMW acknowledges support from NASA NESSF (#NNX16AP39H),NSF (#OISE1639454),andNSFGROW(#DGE1144469).SEMac-knowledges support from MEXT KAKENHI grant-in-aid for chal-lenging exploratory research (grant award number 15K14608).WWF acknowledges the support of NASA Exobiology award#NNX16AJ57G, the David and Lucile Packard Foundation, and aStanford University Blaustein Fellowship. The authors would liketo thank Katsumi Matsuura and the Environmental MicrobiologylaboratoryatTokyoMetropolitanUniversity for laboratorysupport,VictoriaOrphanandStephanieConnonattheCaliforniaInstituteofTechnology for sequencing support, and Nancy Merino and NorioKitadaiattheTokyoInstituteofTechnologyforassistancewith ionchromatographymeasurements.TheauthorswouldalsoliketothankElizabethTrembath-Reichert,JamesHemp,andRolandHatzenpichlerforhelpfuldiscussion,aswellasClaraChanandfouranonymousre-viewersforhelpfulcommentsonthemanuscript.
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How to cite this article:WardLM,IdeiA,TerajimaS,KakegawaT,FischerWW,McGlynnSE.MicrobialdiversityandironoxidationatOkuoku-hachikurouOnsen,aJapanesehotspringanalogofPrecambrianironformations.Geobiology.
2017;15:817–835. https://doi.org/10.1111/gbi.12266