The microbial diversity and function of Arctic supraglacial biomes.

375 Pages·2016·10.09 MB·English

The microbial diversity and function of
Arctic supraglacial biomes.
Stefanie Lutz
Submitted in accordance with the requirements for the
degree of Doctor of Philosophy
The University of Leeds
School of Earth & Environment
December 2015
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Declaration
The candidate confirms that the work submitted is her own, except where work
which has formed part of jointly authored publications has been included. The
contribution of the candidate and the other authors tothis work has been explicitly
indicated below. The candidate confirms that appropriate credit has been given
withinthethesiswherereferencehasbeenmadetotheworkofothers.
TheworkinChapter4ofthethesishasappearedinpublicationasfollows:
Lutz,S.,Anesio,A.M.,Villar,S.E.J.&Benning,L.G.(2014)Variationsofalgal
communities cause darkening of a Greenland glacier. FEMS Microbiology
Ecology,89(2),402-414.
Field work was carried out by SL, LGB and AMA. All analyses, data
interpretation, writing and production of figures and tables were completed by SL.
SEJVcarriedouttheRamanspectroscopicanalyses.ManuscriptwaswrittenbySL
anddiscussionswithallco-authorshelpedimproveit.
TheworkinChapter5ofthethesishasappearedinpublicationasfollows:
Lutz, S., Anesio, A. M., Edwards, A. & Benning, L. G. (2015) Microbial diversity
onIcelandicglaciersandicecaps.FrontiersinMicrobiology,6,307.
Field work was carried out by SL and LGB. All analyses, data interpretation,
writingandproductionoffiguresandtableswerecompletedbySL.AllDNAwork
was carried out by SL at Aberystwyth University. Manuscript was written by SL
anddiscussionswithallco-authorshelpedimproveit.
TheworkinChapter6ofthethesishasappearedinpublicationasfollows:
Lutz, S., Anesio, A. M., Field, K. & Benning, L. G. (2015) Integrated ‘omics’,
targeted metabolite and single-cell analyses of Arctic snow algae functionality and
adaptability.FrontiersinMicrobiology,6,1323.
Field work was carried out by SL and LGB. All analyses, data interpretation,
writing and production of figures and tables were completed by SL. Metabolomics
workwas carriedout bySLatthe Universityof SheffieldundersupervisionofKF.
Manuscript was written by SL and discussions with all co-authors helped to
improveit.
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The work in Chapter 7 of the thesis reproduces a manuscript in review with
NatureCommunications(since09.09.2015):
Lutz, S., Anesio, A. M., Raiswell, R., Edwards, A., Newton, R. J., Gill, F. &
Benning, L. G. (in review) Algae Melt Arctic Glaciers: The Biogeography and
FunctionofSnowMicrobiomes.
Field work was carried out by SL, AMA and LGB. All analyses, data
interpretation, writing and production of figures and tables were completed by SL.
All DNA work was carried out by SL at Aberystwyth University. CNP work was
carried out by SL under supervision of RJN. Fatty acid analyses were carried out
by SL under supervision of FG. Albedo model was developed by RR with data
provided bySL. Manuscript was written bySL and discussions with all co-authors
helpedtoimproveit.
The workin Chapter 8 of the thesis reproduces a manuscript in the final stages of
preparationforsubmissiontotheISMEJournal:
Lutz, S., Anesio, A. M., Edwards, A, Newton, R. J. & Benning, L. G. (in prep)
LinkingmicrobialdiversityandfunctionalityofArcticglacialsurfacehabitats.
Field work was carried out by SL, AMA and LGB. All analyses, data
interpretation, writing and production of figures and tables were completed by SL.
All DNA work was carried out by SL at Aberystwyth University. CNP work was
carried out by SL under supervision of RJN. Manuscript was written by SL and
discussionswithallco-authorshelpedtoimproveit.
This copy has been supplied on the understanding that it is copyright material and
that no quotation from the thesis may be published without proper
acknowledgement.
©2015TheUniversityofLeedsandStefanieLutz
Theright of Stefanie Lutztobe identifiedas Author ofthis workhas beenasserted
byherinaccordancewiththeCopyright,DesignsandPatentsAct1988.
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Acknowledgements
IwouldliketothankLianeG.Benningforalwaysbeingimmenselysupportiveand
encouraging, for giving me endless opportunities to gain new experiences and
enlargemyknowledgeandforherendlessoptimism.
Special thanks to Alexandre M. Anesio for great support, his always encouraging
wordsandformanyhilariousmomentsinthefieldthatIwillneverforget.
I would like to thank the whole Cohen geochemistry group for a great time and a
lotoffun.MassivethanksgoesalsotoourITguyswhoareabsoluteheroes.
I am grateful to SEE and a Vice Chancellor Fellowhsip Contribution to LGB for
funding my PhD and the following societies for additional grants awarded during
my PhD: National Geographic, the European Association for Geochemistry, the
Society for General Microbiology, the Royal Geographical Society, and the
EuropeanAstrobiologyNetworkAssociation.
I am very grateful for my family, who has always supported me, no matter what I
decidedtodo.WithoutthemIwouldnotbewhoIamtoday.
I am also very grateful to Aleš, Andrea and all my friends for distracting me from
work with climbing, caving, squash (thanks Ekbal!), coffee and tea breaks (thanks
James!), after-work G&T (thanks again James!), and Catan (thanks Andy, Pieter,
Adam!).
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Abstract
The main aim of this research project was to improve our understanding of the
diversity, function and ecology of glacial microbiomes. Snow and ice algae are
critical players in supraglacial habitats and form extensive blooms in spring and
summer. Here I present results on the diversity and the function of snow and ice
algaeon21glaciersin4Arcticsettings:Greenland,Iceland,SvalbardandSweden.
For the first time, Ihave evaluated the full microbial communitycomposition(i.e.,
algae, bacteria, archaea) in the main supraglacial habitats, namely green snow, red
snow, biofilms, dirty ice, and cryoconite holes. I have cross-correlated these data
with metabolic analyses (i.e., metabolomics, pigments, fatty acids) and critical
physico-chemicalparameters.
Ifoundthatsnowandicealgaewerethefirstcommunitiestoappearaftertheonset
of melting and they showed positive net photosynthetic rates indicating
accumulation of organic matter. Furthermore, for the first time I have described
these communities in Iceland. My data reveal that red pigmented snow algae are
cosmopolitan, and independent of location specific geochemical and mineralogical
factors. Only six taxa made up >99% of the algal communities: two uncultured
Chlamydomonadaceae, Chloromonas polyptera, Chloromonas nivalis,
Chloromonas alpina and Raphidonema sempervirens. In contrast, the composition
of green snow varied between the studied locations with higher relative abundance
of Raphidonema sempervirens and Microglena sp. in Svalbard, and Chloromonas
polyptera in Sweden. Furthermore, I show that green and red snow are not
successive stages but two independent phenomena with different adaptation
strategies.
In all sites, bacteria were mostly represented by the phyla Bacteriodetes,
Proteobacteria and Cyanobacteria. The bacterial community composition varied
between the different habitats on the phylum level, whereas on the class level they
alsoshowedstrongbiogeography.Archaeashowedoveralllowspeciesdiversity.
Thesynthesisofpigmentsandfattyacidsinsnowandicealgaeweremainlydriven
by nitrogen and less so by phosphorus limitation. This is especially important for
pigments which cause a darkening of glacial surfaces. I show that snow and ice
algae dramatically decrease surface albedo which will eventully result in higher
meltingratesofglaciers.
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List of contents
Declaration................................................................................................................3
Acknowledgements...................................................................................................5
Abstract.....................................................................................................................7
Listofcontents..........................................................................................................8
Listoffigures..........................................................................................................11
Listoftables............................................................................................................17
Listofabbreviations...............................................................................................25
Chapter1:Introduction...........................................................................................26
1.1Background...................................................................................................26
1.2Researchhypotheses.....................................................................................28
1.3Thesisoutline................................................................................................29
Chapter2:Literaturereview...................................................................................32
2.1Introduction...................................................................................................32
2.2Stressfactorsofsnowandiceenvironments................................................32
2.3Snowfields....................................................................................................34
2.4Supraglacialice.............................................................................................45
2.5Englacialandsubglacialice..........................................................................48
2.6Bacteria.........................................................................................................48
2.7Archaea.........................................................................................................49
2.8Genomicsofglacialenvironments................................................................49
2.9Applications/Significance.............................................................................50
Chapter3:Methodology.........................................................................................62
3.1Fieldsites......................................................................................................62
3.2Fieldmeasurements......................................................................................62
3.3Fieldsamplingstrategy.................................................................................63
3.4Fieldsamplepreservationandhandling........................................................64
3.5Aqueousorganic(DOC)andinorganicanalyses..........................................65
3.6Totalcarbon,totalnitrogen,totalsulphur,totalphosphateandcarbonand
nitrogenisotopes.................................................................................................65
3.7Mineralogy....................................................................................................66
3.8Imaging.........................................................................................................66
3.9Fouriertransforminfraredspectroscopy.......................................................67
3.10Ramanspectroscopy...................................................................................68
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3.11Pigmentanalysis.........................................................................................68
3.12Fattyacidsanalysis.....................................................................................69
3.13DNAanalyses.............................................................................................70
3.14Metabolomics..............................................................................................72
3.15Statisticalanalyses......................................................................................73
Chapter4:VariationsofalgalcommunitiescausedarkeningofaGreenlandglacier.
................................................................................................................................76
Abstract...............................................................................................................77
4.1Introduction...................................................................................................77
4.2Methods.........................................................................................................79
4.3Results...........................................................................................................85
4.4Discussion.....................................................................................................95
Chapter5:MicrobialdiversityonIcelandicglaciersandicecaps........................104
Abstract.............................................................................................................105
5.1Introduction.................................................................................................105
5.2Materialsandmethods................................................................................107
5.3Results.........................................................................................................115
5.4Discussion...................................................................................................131
Chapter6:Integrated‘omics’,targetedmetaboliteandsingle-cellanalysesof
Arcticsnowalgaefunctionalityandadaptability..................................................143
Abstract.............................................................................................................144
6.1Introduction.................................................................................................144
6.2MaterialandMethods.................................................................................147
6.3Results.........................................................................................................154
6.4Discussion...................................................................................................168
Chapter7:AlgaeMeltArcticGlaciers:TheBiogeographyandFunctionofSnow
Microbiomes.........................................................................................................184
Abstract.............................................................................................................185
7.1Introduction.................................................................................................185
7.2ResultsandDiscussion...............................................................................187
7.3Conclusions.................................................................................................198
7.4 Methods......................................................................................................198
Chapter8:LinkingmicrobialdiversityandfunctionalityofArcticglacialsurface
habitats..................................................................................................................210
Abstract.............................................................................................................211
8.1Introduction.................................................................................................211
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8.2MaterialsandMethods................................................................................213
8.3Results.........................................................................................................216
8.4Discussion...................................................................................................227
Chapter9:Synthesisdiscussion............................................................................239
9.1Snowandicealgaeareimportantprimarycolonisersandnetproducers...239
9.2Redsnowalgaearecosmopolitanandindependentoflocationspecific
factors................................................................................................................240
9.3Greenandredsnowaretwoindependentandnotsuccessivephenomena.240
9.4Icealgaecommunitycompositionseeminglyinfluencedbyexternalsnow
andsoilinput.....................................................................................................242
9.5Possiblediscrepanciesbetweensequencingandmicroscopydata.............242
9.6Bacteriashowbiogeographyanddifferencesbetweenhabitats..................243
9.7Archaeashowlowspeciesdiversity...........................................................244
9.8RelationshipsforsolidC/N/Pratiosbutnotaqueousgeochemistrywith
communitycompositionandmetabolites.........................................................244
9.9 Metabolitemeasurementsshowlargeheterogeneityatthebeginningandno
differencestowardstheendofthemeltseason.................................................246
9.10Snowandicealgaedecreasesurfacealbedo.............................................247
Chapter10:Conclusions.......................................................................................252
Chapter11:Outlook..............................................................................................255
AppendixA:Supplementaryinformationforchapter4.......................................258
AppendixB:Supplementaryinformationforchapter5........................................275
AppendixC:Supplementaryinformationforchapter6........................................287
AppendixD:Supplementaryinformationforchapter7.......................................298
AppendixE:Supplementaryinformationforchapter8........................................321