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Structural Biology. 7,828-834. DEININGER, C. A., MUELLER. G. M. and WOLBER, P. K. (1988). Immunolgical characterisation of ice nucleation proteins from Pseudomonas syringae. Pseudomonas f uorescens and Erwina herbicola. Journal of Bacteriology. 170.1 669-675. DELONG, E. F. and YAYANOS, A. A. (1985). Adaptation of the membrane lipids of a deep-sea bacterium to changes in hydrostatic pressure. Science. 228,1101-1102. De MENDOZA, D. and CRONAN, J. E., Jr. (1983). Thermal regulation of membrane lipid fluidity by bacteria. Trends in Biochemical Science. 8,49-52. DEMIRJIAN, D. C., MORIS-VARAS, F. and CASSIDY, C. S. (2001). Enzymes from extremophiles. Current Opinion in Chemical Biology. 5.144-151. DENKER, E. B. M., MARK, B., BUSSE, H. J., TURKIEWICZ, M. and LUBITZ, W. (2001). Psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the Antarctic krill Euphausia superba Dana, excreting a cold-adapted metalloprotease. Systematic and Applied Microbiology. 24.44-53. DeVRIES, A. L. (1971). Glycoproteins as biological antifreeze agents in Antarctic fishes. Science. 172,1152-1155. DeVRIES, A. L. and LIN, Y. (1977). Structure of a peptide antifreeze and mechanism of adsorption to ice. Biochimica et Biophysica Acta. 495,388-392. DeVRIES, A. L. and CHENG, C. -H. C. (1992). The role of antifreeze glycopeptides and peptides in the survival of cold water fishes. In: Water and Life. (Eds. G. N. Somero, C. B. Osmond and C. L. Bolis). Springer-Verlag, New York, Berlin. Pp. 31-315. DOBSON, S. J., COLWELL, R. R., McMEEKIN, T. A. and FRANZMANN, P. D. (1993). Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov., two new species from a hypersaline lake. International Journal of Systematic Bacteriology. 43,77-83. DONACHIE, S. P.. HOU, S., GREGORY. T. S.. MALAHOFF. A. and ALAM. M. Bacterial diversity and identification of a new species in hydrothermal fluids at the Loihi submarine volcano, Hawaii. Unpublished. 202
DRICKAMER, K. (1999). C-type lectin-like domains. Current Opinion in Structural Biology. 9,585-590. DUILIO, A. TUTINO, M. L., MATAFORA. V., SANNIA, G. and MARINO. G. (2001 ) Molecular characterisation of a recombinant replication protein (Rep) from the Antarctic bacterium Psychrobacter sp. TA 144. FEMS Microbiology- Letters. 198. 1,49-55. DUINEVELD, B. M., KOWALCHUK, G. A., KEIJZER, A., VAN ELSAS, J. D. and VAN VEEN, J. A. (2001). Analysis of bacterial communities in the Rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Applied and Environmental Microbiology. 67,1,172-178. DUMAN, J. G. (1977). Variations in macromolecular antifreeze levels in larvae of the darkling beetle, Meracantha contracta. The Journal of Experimental 7_oologi-. 201,1,85-92. DUMAN, J. G., NEVEN. L. G., BEALS, J. M., OLSON, K. R. and CASTELLINO, F. J. (1985). Freeze-tolerance adaptations, including haemolymph protein and lipoprotein nucleators, in the larvae of the cranefly, Tipula trivittata. Journal of Insect Physiology. 31,1-8. DUMAN, J. G., XU, L., NEVEN, L. G., TURSMAN, D. and WU, D. W. (1991). Haemolymph proteins involved in insect subzero temperature tolerance: Ice nucleators and antifreeze proteins. In: Insects at Low Temperatures. (Eds.) R. E. Lee and D. L. Denlinger. Chapman & Hall, New York/London. Pp. 94-127. DUMAN, J. G. and OLSEN, T. M. (1993). Thermal hysteresis protein activity in bacteria, fungi, and phylogenetically diverse plants. Cryobiology. 30.322-328. DUMAN, J. G. and SERIANNI, A. S. (2002). The role of endogenous antifreeze protein enhancers in the haemolymph thermal hysteresis activity of the beetle Dendroides canadensis. Journal of Insect Physiology. 48,1,103-111. DUNBAR, J., TICKNOR, L. O. and KUSKE, C. R. (2000). Assessment of microbial diversity in four South-western United States soils by 16S rRNA gene terminal restriction fragment analysis. Applied and Environmental Microbiologi'. 66.7, 2943-2950. 203
Page 1 and 2:
COLD ADAPTATION STRATEGIES AND DIVE
Page 3 and 4:
, 71 "If you march your Winter Jour
Page 5 and 6:
1.6.3. Molecular typing techniques
Page 7 and 8:
3.2.1.2.3. DOC and chlorophyll a ..
Page 9 and 10:
5.3.2.5. The Sphingomonas group, is
Page 11 and 12:
LIST OF FIGURES Figure I. I. Diagra
Page 13 and 14:
Figure 3.17a Mean bacterial abundan
Page 15 and 16:
LIST OF TABLES Table 1.1. Types of
Page 17 and 18:
List of Abbreviations AFP AFGP AFLP
Page 19 and 20:
ACKNOWLEDGEMENTS This study was fun
Page 21 and 22:
Chapter 1: INTRODUCTION 1.1 - Tempe
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1999 ; Hand & Burton, 1981) or iden
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Cold adaptation is dependant on the
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not at 25°C is a function of the a
Page 29 and 30:
The most prolific literature on col
Page 31 and 32:
process known as thermal hysteresis
Page 33 and 34:
dominant, role in the ice-growth in
Page 35 and 36:
explanation for this diversity is t
Page 37 and 38:
1.5.3.5 - Membrane bound solute tra
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een well established (Russell & Nic
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& Bowman, 2001; Labrenz & Hirsch, 2
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The reaction mix contains both deox
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gene mixtures and hence can be used
Page 47 and 48:
displaying a high number of common
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AACGTCGAAA AACCTCGAAA (Organism A)
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particular set of environmental par
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Lake Maximum Depth (m) Approximate
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Larsemann Hills __ rp3rtrnent of th
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Sampling trips took two days during
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Sigma, Sigma-Aldrich Company Ltd.,
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oxidized and the sample then conver
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sample. An appropriate volume was l
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min to ensure complete extension of
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Figure 2.3 - Lane delineation image
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Figure 2.6b - Molecular weights are
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RNA 41F (5'-GCT CAG ATT GAA CGC TGG
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I min. The spin column was removed
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compiled using Seqman and any erron
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ecorded and related to the level of
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information regarding the cold adap
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50ppt to 186ppt. Thirteen were sali
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M N N 't M M \p \p 00 kf) M kf) bA
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as would normally be expected, as b
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1444 6ý L CC vý O Q O O NO u 'c z
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5 - 250 3 245 240 G (, -3 235 a 0-
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3.2.2.2.5 - Dissolved organic carbo
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d 14 12 10 14 12 7 10 8 6 4 2 0 00/
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SRP ('g L- 05 10 15 20 2 3 Depth4 5
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3.2.2.3 - Biological characteristic
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a 0 Bacterial Abundance (x 106 ml-1
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3.3 - Discussion 3.3.1 - Summer sam
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to high surface water temperatures
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chemocline (Rankin et al., 1999). M
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a 250 200 150 100 50 70 60 50 40 ý
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The temperature (Fig 3.2a) through
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et al., 1999). No melt out was obse
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increase in ammonium is probably du
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10 7 9 6 8 E ö 7 5 Co u c m c 40 w
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main pigments were chlorophylls a a
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Inorganic nitrogen (NO2, NO3 and NH
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744 -- 7 644 6 19 ü SE 400-- 4 2s
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salinity decreased from July to Sep
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a Bacterial abundance (x 106 1.1) 0
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8 ö a N Ö oý L _> Q O O 4 0 rn O
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undoubtedly true of Club Lake. The
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suggested that input of bacteria an
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Pendant Lake is an unstratified, sa
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non-AFP active peptides from inhibi
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. ter rý :. 'ý Figure 4.2 -Fryka
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-ý- ---- ,. r. __-_-. ___. r. ýý
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4.2 - Results 4.2.1 - Sampling and
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SPLAT score. It has been shown that
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3'E t ý _d M! .PJ r rn 15 3.5 4 3
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4.3 - Discussion Of the 866 bacteri
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arisen in very few species due to c
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Chapter 5: BACTERIAL MOLECULAR TYPI
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Fig 5.1 - Photographs of ARDRA gel
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Coefficient: Dice Algorithm: lPGMAA
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The closest published relative for
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identification was made based on 15
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Isolate number Closest phylogenetic
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e included due to its small sequenc
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5.3.2 - Identification of the AFP a
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explains the fluctuation in related
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contamination was lower as the PCR
Page 171 and 172: seen to a certain extent in the ARD
Page 173 and 174: American Type Culture Collection (A
Page 175 and 176: Phylogenetic cluster alignment of t
Page 177 and 178: et al., 1994) and the Antarctic SIM
Page 179 and 180: Chapter 6: BACTERIAL COMMUNITY ANAL
Page 181 and 182: 6.2.1 - Detection of AFP active iso
Page 183 and 184: using the same PCR protocol as orig
Page 185 and 186: Figure 6.1 - Denaturing gradient ge
Page 187 and 188: 6.2.2 - Temporal and spatial variat
Page 189 and 190: Figure 6.4c - Gel I image showing b
Page 191 and 192: Coefficient: Dice Algorithm: UPGMA
Page 193 and 194: etween Om and 2m was obviously the
Page 195 and 196: All PCR-based rRNA molecular techni
Page 197 and 198: 6.3.2.3 - Cellular lysis and DNA pu
Page 199 and 200: hybrids should be equal. However, S
Page 201 and 202: contain contaminants. If the profil
Page 203 and 204: (Section 6.3.2.4.3 ) could not be r
Page 205 and 206: most dominant species in the commun
Page 207 and 208: study was characterised as M protea
Page 209 and 210: 11 species) showed AFP activity. Th
Page 211 and 212: that AFP activity could have evolve
Page 213 and 214: 7.2 - Future Work The 19 AFP active
Page 215 and 216: REFERENCES ABYZOV, S. S. (1993). Mi
Page 217 and 218: BELL, E. M. and LAYBOURN-PARRY, J.
Page 219 and 220: Symposium on Environmental Biogeoch
Page 221: Research. 5,477-493. CLESCERI, L. S
Page 225 and 226: antifreeze proteins from Atlantic s
Page 227 and 228: FRANZMANN, P. D. and DOBSON, S. J.
Page 229 and 230: GRIFFITH, M., ALA, P., YANG. D. S.
Page 231 and 232: IVANOVA, E. P., KIPRIANOVA, E. A.,
Page 233 and 234: Antarctic Ecosystems. G. A. Llano (
Page 235 and 236: Howard-Williams and I. Hawes). Balk
Page 237 and 238: W. (1998). Rep-PCR-mediated genomic
Page 239 and 240: putida strains from Antarctica. Mic
Page 241 and 242: NICHOLS, D., BOWMAN, J., SANDERSON,
Page 243 and 244: PEARCE, D. A. and BUTLER, H. G. (20
Page 245 and 246: (1999). Palaeohydrological modellin
Page 247 and 248: tracers of biogeochemical processes
Page 249 and 250: R. G. Landes Company, Austin, Texas
Page 251 and 252: partial 16S rDNA sequencing. Applie
Page 253 and 254: YABUUCHI, E., WANG, L., ARAKAWA, M.
Page 255 and 256: APPENDICES Al. Media Tryptic Soya A
Page 257 and 258: "D C 'O I. .. r .. r 6 rr E , 4mo .
Page 259 and 260: . + + + I I I I I I + I + + I I I I
Page 261 and 262: Ö ON N M 1 O - N 'zt "o l'" 00 C N
Page 263 and 264: 1 T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Page 265 and 266: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Page 267 and 268: 1 1 1 1 I 1 + I I 1 I 1 1 I 1 1 1 I
Page 269 and 270: 1 1 1 1 1 1 1 I I 1 I 1 I 1 1 I T I
Page 271 and 272: Cl M 'tt tn '. p t- 00 O\ N M O - (
Page 273 and 274:
d' O - (N M 'nt V) \O N. 00 O> N M
Page 275 and 276:
1 1 T 1 1 1 T 1 1 1 1 1 1 1 1 1 1 1
Page 277 and 278:
+ + i i i i i i " i " . + + + + " +
Page 279 and 280:
e O --ý N M t Vn 1,0 [-- 00 O> N M
Page 281 and 282:
FT ce + I I r. to \, O t- 00 O\ N M
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kn 110 r- 00 Oý N M O - N M Itt vn
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, It N M "t N M Iýt N M M M M Oý
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gj a - - - - - - - - - - - - - - -
show all

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