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Seediscussions,stats,andauthorprofilesforthispublicationat::ExploringmicrofluidicstocreatemicrobialhabitatstructuresArticle  in  TheISMEJournal·November2017DOI:10.1038/ismej.2017.184CITATIONS3READS1586authors,including:Someoftheauthorsofthispublicationarealsoworkingontheserelatedprojects:SoilChipprojectViewprojectKristinAleklettLundUniversity10PUBLICATIONS   137CITATIONS   SEEPROFILEVictorCaldasVrijeUniversiteitAmsterdam9PUBLICATIONS   60CITATIONS   SEEPROFILEEdithCHammerLundUniversity24PUBLICATIONS   553CITATIONS   SEEPROFILEAllcontentfollowingthispagewasuploadedbyKristinAlekletton16November2017.Theuserhasrequestedenhancementofthedownloadedfile.OPENPERSPECTIVEBuildyourownsoil:exploringmicrofluidicstocreatemicrobialhabitatstructuresKristinAleklett1,ETobyKiers2,PelleOhlsson3,ThomasSShimizu4,VictorEACaldas2,4andEdithCHammer11DepartmentofMicrobialEcology,LundUniversity,Lund,Sweden;2DepartmentofEcologicalScience,VrijeUniversiteitAmsterdam,Amsterdam,TheNetherlands;3DepartmentofBiomedicalEngineering,LundUniversity,Lund,Swedenand4AMOLFInstitute,Amsterdam,TheNetherlandsSoilislikelythemostcomplexecosystemonearth.Despitetheglobalimportanceandextraordinarydiversityofsoils,theyhavebeennotoriouslychallengingtostudy.Weshowhowpioneeringmicrofluidictechniquesprovidenewwaysofstudyingsoilmicrobialecologybyallowingsimulationandmanipulationofchemicalconditionsandphysicalstructuresatthemicroscaleinsoilmodelhabitats.TheISMEJournaladvanceonlinepublication,14November2017;doi:10.1038/ismej.2017.184Soil—achallenginghabitattostudySoilpresentsmicrobeswithphysicalandchemicalenvironmentsthatvarystronglyacrossthree-dimensional(3D)spaceandtime.Evensinglesoilaggregatescanconsistofcontrastingmineralmateri-alsinamatrixofair,waterandorganicmatter,exhibitingalternatinghotspotsand‘desertareas’ofnutrientsandtoxins.Thiscomplexenvironmentchallengessoilorganismsthatrequirefoodandshelterwithinthelabyrinthofporesinthesoil.Fragmentingbarriersarelikelyresponsibleforseeminglyparadoxicalobservations,suchastheaccumulationoforganicmaterialinthedirectvicinityofdecomposers,andmakesoilsoneofthemostspecies-denseecosystemsintheworld(Eisenhaueretal.,2017;Rilligetal.,2017).Earlierapproachestoaddresstherecognizedspatialandchemicalcomplexityofsoilecosystems,suchasglassbeadorartificialsoilmodelsystems,andinsituanalysisofsoilwithmicroelectrodesortomography,haveprovidedimportantinsightsintosoilfunction.However,theyhavenotbeenabletosimulate,ormanipulate,thespatio-temporalhetero-geneityofsoilsatthemicroscale,thescalethatmicroorganismsexperience.Innovativemicro-technologiesarenowemerging(TextBox1),allow-ingresearcherstomimicandmanipulatespatiallyandchemicallycomplexgrowthenvironmentsatthescaleofsoilparticles(Figure1).Theseapproachesareopeningnewpossibilitiesforaddressingunansweredquestionsinsoilmicrobialecology(Table1)byallowingresearcherstoconstructmicroscopichabitats,andstudyinteractionsamongindividuals,distinctpopulations,multi-speciesandorganism–environmentinteractionsattherelevantscale,includingatthelevelofsinglecellsandhyphaltips.Inthisperspectivespaper,weshowhowmicro-fluidicscanbeappliedinsoilmicrobialecology,wepresentinspirationalexamplesofmicrofluidicapproachesinotherfieldssuchasbiomedicalcellresearch,andcriticallyreflectonpotentialdraw-backsandchallengestostudyingsoilecologywiththistechnology.NovelexperimentalpossibilitiesusingmicrofluidicsMicrofluidicplatformshavethepotentialtoaddressfourmajorchallengesinstudyingsoilsystems,namely(1)theirenormousspatio-temporalhetero-geneity,(2)thelackofcurrentmethodstomimicsoilrealisticallyattheappropriatescale,(3)thedifficul-tiesinstudyinginteractionsamongsoilmicrobesand(4)thelackofopticalaccessinrealsoilsystems.Wediscusstheseissuesinturn,highlightingimpor-tantadvancesdrivingthetransferofthistechnologytosoilsystems,butalsoidentifypotentialchallenges.SimulatingstructuralandchemicalhabitatheterogeneityAmajordisadvantageofclassicalsolidnutrientmediummodelsystemsistheabsenceofhabitatheterogeneity.Whenphysicalbarriersareabsent,organismsandcompoundshavenoconstraintstoCorrespondence:ECHammer,DepartmentofMicrobialEcology,Biology,LundUniversity,Lund,22362Sweden,E-mail:[e-mail]11April2017;revised25August2017;accepted15September2017TheISMEJournal(2017),1–8(Figures1a–d),siliconandglassetchingor3Dprinting.Thesemicro-structuredchipsystemsprovideanewplatformforstudyingmicrobialinteractionswiththeirphysicalenvironment,forexample,thealgorithmsusedbyfungitoexplorespaceinsearchofnutrients(Heldetal.,2010).Conglomerationsofsoilparticlesofdifferentsizescanbemimickedbyimprintingarraysofcylindersorwallswithvaryingdiametersandshapes(Figures1gandh),si