Psychrophiles: From Biodiversity to Biotechnology

685 Pages·2017·12.491 MB·English

by  Rosa Margesin (eds.)

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
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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