Psychrophiles: From Biodiversity to Biotechnology PDF
Preview Psychrophiles: From Biodiversity to Biotechnology
Rosa Margesin Editor Psychrophiles: From Biodiversity to Biotechnology Second Edition Psychrophiles: From Biodiversity to Biotechnology Rosa Margesin Editor Psychrophiles: From Biodiversity to Biotechnology Second Edition Editor RosaMargesin InstituteofMicrobiology UniversityofInnsbruck Innsbruck,Austria ISBN978-3-319-57056-3 ISBN978-3-319-57057-0 (eBook) DOI10.1007/978-3-319-57057-0 LibraryofCongressControlNumber:2017943539 The1stedition©Springer-VerlagBerlinHeidelberg2008waseditedbyRosaMargesin,FranzSchinner, Jean-ClaudeMarxandCharlesGerday. ©SpringerInternationalPublishingAG2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthis book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained hereinor for anyerrors oromissionsthat may havebeenmade. Thepublisher remainsneutralwith regardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface to the Second Edition The Earth is a cold planet. The majority of the Earth’s biosphere is exposed to temperaturesbelow5(cid:1)Cthroughouttheyear.Coldecosystemsareverydiverseand rangefromhighmountainstodeepoceans.Eventhemostextremecoldandfrozen environments harbour enormously diverse and metabolically active microbial populations. The key feature of microorganisms living in these habitats is the successful surmounting of the negative effects of low temperatures. Cold adapta- tionincludesacomplexrangeofstructuralandfunctionaladaptationsatthelevelof allcellularconstituents.Cold-adaptedmicroorganismsplayakeyecologicalrolein their natural habitats, and their mechanisms and strategies to cope with the cold renderthemparticularlyusefulforbiotechnologicalapplications. Why a second edition of the book “Psychrophiles: from Biodiversity to Bio- technology”?Thefirsteditionofthisbookwaspublishedin2008.Sincethen,there was a continuously increasing interest in the microbiology of the Earth’s cryobiosphere. This can be attributed to several factors, such as the awareness of theconsequencesoftheglobalclimatechangeontheresponseofmicroorganisms in cold ecosystems, the development of the emerging fields of omics approaches enabling the study of the versatility and functional roles of life in the cold bio- sphere,theinterestintheexistenceofextraterrestriallifeandtheneedforenviron- mentallyfriendlyandsustainableperspectivesinbiotechnology. Thesecondeditionofthebookpresents,attheleadingedgeofknowledge,the newest insights into the psychrophilic lifestyle. Both fundamental and applied aspectsareconsidered.Allchapterswerewrittenbyleadingscientistsandauthor- ities in the respective field. Some of the chapters are updated contributions to the firsteditionofthebook,whileseveralnewlyintroducedchaptersoutlinetopicsof interestemerginginthelastdecade.ThebookisorganizedintofourthematicParts: Part I, “Boundary Conditions for Microbial Life in the Cold”, addresses the conditions that influence the low-temperature limit of microbial life. Climatic factorsandbiologicalconstraintsinthecoldarediscussedinChaps.1and2. Part II, “Microbial Diversity and Activity in Cold Ecosystems”, presents the current knowledge of microbial communities in the atmosphere and in glacial environments, deep oceans and permafrost. The diversity and activity of bacteria, v vi PrefacetotheSecondEdition archaea and eukaryotes as well as of viruses in these habitats are described in Chaps.3–9. PartIII,“MolecularandPhysiologicalAdaptationstoColdHabitats”,isfocused on the characteristics and roles of the key features of microbial cold adaptation, such as cold-active enzymes, cryoprotectants, exopolysaccharides and cell mem- branecomponents,andreportsthelatestdevelopmentsingenomics,metagenomics, proteomics, transcriptomics and metatranscriptomics of psychrophiles. These topicsareoutlinedinChaps.10–18. Part IV, “Biotechnological Perspectives”, considers the significance of psychrophiles in various biotechnological applications. The role of psychrophiles asasourceofnovelcold-activeenzymes,antimicrobialsandotherbiopolymers,as expressionsystemsforrecombinantproteinproduction,inbiomedicalapplications andinthebioremediationofcontaminatedsoilandwaterisoutlinedinChaps.19–29. I wish toexpressmy gratitude toall authors for their excellent contributions. I alsothanktheSpringerteam,especiallyHannaHensler-Fritton,IsabelUllmannand Dr. Andrea Schlitzberger, for their valuable and continuous support during the preparationofthisbook. Innsbruck,Austria RosaMargesin March2017 Preface to the First Edition Most scientists in the middle of the twentieth century would probably not have believedthatlifewaspossibleatextremevaluesofenvironmentalfactors,suchas pH values close to 0 (e.g. sulphurous environments) or to 14 (e.g. soda lakes), salinitiesof6MNaCl(e.g.DeadSea),hydrostaticpressuresapproaching0.1MPa (deepsea)andtemperaturesexceeding100(cid:1)C(thermalventsorhotsprings)oras low as (cid:3)20 (cid:1)C (e.g. polar regions). Of the current studies on extremophiles, approximately 30,000 articles by the year 2007, almost two-thirds have been performed on organisms adapted to outstanding temperatures, but much more attention has been paid to thermophiles than to psychrophiles. However, over the past 10 years, scientific publications on cold-adapted microorganisms have increasedbyafactoroften. If one considers the extent of cold habitats, psychrophiles, i.e. cold-loving organisms, should largely lead in this comparison with thermophiles because a great proportion of the Earth’s biosphere never reaches temperatures above 5 (cid:1)C. Nearlythree-quartersoftheEarthiscoveredbyoceanswhosedeepwatermasses, irrespectiveoflatitude,are constantly between 2and4(cid:1)C.Thelarge continentof Antarctica also provides a permanently cold terrestrial environment as well as an aquaticnicheinthesurroundingicethatmeltsduringthesummer.Otherexamples ofcold habitats inpolarandalpine regions are permafrostsoils, high alpine soils, colddeserts,coldcaves,marinesediments,snow,glacierandseaice.Coldecosys- tems host a wide diversity of psychrophiles, including bacteria, archaea, yeasts, filamentous fungi and algae. These microorganisms have evolved a number of strategies to thrive successfully in cold habitats where they play key roles in nutrient cycling, such as nitrogen fixation, nitrification and denitrification, photo- synthesis, sulphur oxidation and reduction, methanogenesis and transformation of organiccompounds. Thisbookisfocusedonpsychrophilesanddescribes,attheedgeofknowledge, representative groups of cold-adapted microorganisms as well as the habitats in whichtheyliveandtheirstrategiestocopewiththecold.Itissubdividedintofour mainsections: vii viii PrefacetotheFirstEdition 1. Boundaryconditionsformicrobiallifeatlowtemperatures 2. Biodiversity 3. Molecularadaptations 4. Biotechnologicalaspects thuscoveringalmostallthefieldsofknowledgein“cold”microbiologicalresearch. ItiscertainlynotbychancethatthisbookispublishedduringtheInternational Polar Year 2007–2008, which is the fourth polar year following those in 1882– 1883,1932–1933and1957–1958andinvolvingover200projects,withthousands of scientists from over 60 nations examining a wide range of physical, biological and social research topics. Therefore, this book perfectly matches the current demands and trends and provides an additional source of information to all those scientistswhoareinterestedin“cold”microbiology. Lastbutcertainlynotleast,theeditorsofthisbookwanttothankalltheauthors, whoaretheleadingscientistsintherespectivefield,forhavingacceptedtowritea chapter of this book, even though all these persons are also very busy and highly solicited scientists. We also thank Springer—Life Sciences, especially Dr. Dieter Czeschlik and Dr. Jutta Lindenborn, for their continuous support and trust in our capacitytosuccessfullyachievetheeditingofthisbook. Innsbruck,Austria RosaMargesin Innsbruck,Austria FranzSchinner Liege,Belgium Jean-ClaudeMarx Liege,Belgium CharlesGerday July2007 Contents PartI BoundaryConditionsforMicrobialLifeintheCold 1 TheClimateofSnowandIceasBoundaryCondition forMicrobialLife. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 MichaelKuhnandAndrewG.Fountain 2 DeterminingtheLimitsofMicrobialLifeatSubzero Temperatures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 CorienBakermans PartII MicrobialDiversityandActivityinColdEcosystems 3 Aeromicrobiology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 LewisCuthbertsonandDavidA.Pearce 4 MicrobialLifeinSupraglacialEnvironments. . . . . . . . . . . . . . . . . 57 ArwynEdwardsandKarenA.Cameron 5 MicrobiologyofSubglacialEnvironments. . . . . . . . . . . . . . . . . . . 83 AmandaM.Achberger,AlexanderB.Michaud,TristaJ.Vick-Majors, BrentC.Christner,MarkL.Skidmore,JohnC.Priscu, andMartynTranter 6 VirusesinGlacialEnvironments. . . . . . . .. . . . . . . . . . . . . . . . .. . 111 SaraM.E.Rassner 7 MicrobialLifeintheDeepSea:Psychropiezophiles. . . . . . . . . . . . 133 YuichiNogi 8 MicrobialLifeinPermafrost. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 IaninaAltshuler,JacquelineGoordial,andLyleG.Whyte 9 CyanobacteriainPolarandAlpineEcosystems. . . . . . . . . . . . . . . 181 AnneD.JungblutandWarwickF.Vincent ix x Contents PartIII MolecularandPhysiologicalAdaptationstoColdHabitats 10 EnzymeCatalysisinPsychrophiles. . . . . . . . . . . . . . . . . . . . . . . . . 209 TonyCollinsandCharlesGerday 11 CryoprotectantsandIce-BindingProteins. . . . . . . . . . . . . . . . . . . 237 HidehisaKawahara 12 TheRoleofExopolysaccharidesinMicrobialAdaptation toColdHabitats. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259 JodyW.DemingandJodiN.Young 13 MolecularStructureofLipopolysaccharidesofCold-Adapted Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285 MariaMichelaCorsaro,AngelaCasillo,ErmenegildaParrilli, andMariaLuisaTutino 14 PolarMicroalgae:FunctionalGenomics,Physiology, andtheEnvironment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305 AmandaHopes,DavidN.Thomas,andThomasMock 15 GenomicsofPsychrophilicBacteriaandArchaea. . . . . . . . . . . . . . 345 JohnP.Bowman 16 MetagenomicAnalysisofLow-TemperatureEnvironments. . . . . . 389 HabibuAliyu,PieterDeMaayer,SaraSj€oling,andDonaldA.Cowan 17 ProteomicInsightsofPsychrophiles. . . . . . . . . . . . . . . . . . . . . . . . 423 JunKawamoto,TatsuoKurihara,andNobuyoshiEsaki 18 FromTranscriptomestoMetatranscriptomes:ColdAdaptation andActiveMetabolismsofPsychrophilesfromColdEnvironments... 437 IsabelleRaymond-BouchardandLyleG.Whyte PartIV BiotechnologicalPerspectives 19 BiotechnologicalAspectsofCold-ActiveEnzymes. . . . . . . . . . . . . 461 Ma´rioBarroca,GustavoSantos,CharlesGerday,andTonyCollins 20 BiotechnologicalImprovementsofCold-AdaptedEnzymes: CommercializationviaanIntegratedApproach. . . . . . . . . . . . . . . 477 KhawarSohailSiddiqui,AhsanMushirShemsi,GeaGuerriero, TahriaNajnin,Taha,andHalukErtan 21 HeterologousProteinExpressioninPseudoalteromonashaloplanktis TAC125. .. . . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . . .. . . .. 513 ErmenegildaParrilliandMariaLuisaTutino 22 PsychrophilesasaSourceofNovelAntimicrobials. . . . . . . . . . . . . 527 ErikBorchert,StephenA.Jackson,FergalO’Gara, andAlanD.W.Dobson
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