Phylogenetic analyses of bacteria in sea ice at Cape Hallett, Antarctica

New Zealand Journal of Marine and Freshwater Research

Volumn 46, Issue 1, 2012, Pages 3-12

  Maas, E W ^a   Simpson, A M ^b   Martin, A ^b,c   Thompson, S ^b   Koh, E Y ^b   Davy, S K ^b   Ryan, K G ^b   O'Toole, R F ^b  

^a NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

^b VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

16S rRNA; Antarctica; bacterial community composition; sea ice

Indexed keywords

BACTERIUM; COMMUNITY COMPOSITION; CYANOBACTERIUM; GENE; HETEROTROPHY; MICROBIAL COMMUNITY; MITOCHONDRIAL DNA; PHOTOAUTOTROPHY; PHYLOGENETICS; POLYMERASE CHAIN REACTION; RNA; SEA ICE;

ANTARCTICA; CAPE HALLETT; EAST ANTARCTICA; SOUTHERN OCEAN;

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES (CLASS); CYANOBACTERIA; CYTOPHAGA; FLAVOBACTERIA; POSIBACTERIA; PROTEOBACTERIA;

EID: 84859123279     PISSN: 00288330     EISSN: 11758805     Source Type: Journal    
DOI: 10.1080/00288330.2011.579981     Document Type: Article

References (45)

1. Andreoli C, Moro I, LaRocca N, Dalle Valle L, Masiero L, Rascio N, Dalla Vecchia F 2000. Ecological, physiological and biomolecular surveys on microalgae from Ross Sea (Antarctica). Italian Journal of Zoology 67: 147-156.
2. Arrigo KR, Thomas DN 2004. Largescaleimportance of sea ice biology in the Southern Ocean. Antarctic Science 16: 471-486. (Pubitemid 40008769)
3. Atamna-Ismaeel N, Sabehi G, Sharon I, Witzel KP, Labrenz M, Jurgens K, Barkay T, Stomp M, Huisman J, Beja O 2008. Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME Journal 2: 656-62. (Pubitemid 351793251)
4. Atkinson A, Siegel V, Pakhomov E, Rothery P. 2004. Long term decline in krill stock and increase in salps within the Southern Ocean. Nature432: 100-103. (Pubitemid 39490834)
5. Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods 55: 541-555. (Pubitemid 37357207)
6. Bano N, Ruffin S, Ransom B, Hollibaugh JT 2004 Phylogenetic composition of Arctic Ocean Archaeal assemblages and comparison with Antarctic assemblages. Applied and Environmental Microbiology 70: 781-789. (Pubitemid 38568199)
7. Bowman JP, McCuaig RD 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Applied and Environmental Microbiology 69: 2463-2483. (Pubitemid 36560319)
8. Bowman JP, McCammon SA, Brown MV, Nichols DS, McEeekin TA 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Applied and Environmental Microbiology 63: 3068-3078. (Pubitemid 27337795)
9. Bowman JP, Rea SM, McCammon SA, McMeekin TA. 2000. Diversity and community structure within anoxic sediment from marine salinity meromictic lakes and a coastal meromictic marineb asin, Vestfold Hills, Eastern Antarctica. Environmental Microbiology 2: 227-237. (Pubitemid 33136717)
10. Brinkmeyer R, Glö ckner FO, Helmke E, Amann R. 2004. Predominance of b-proteobacteria in summer melt pools on Arctic pack ice. Limnology and Oceanography 49: 1013-1021. (Pubitemid 39048047)
11. Brinkmeyer R, Knittle K, Jurgens J, Weyland H, Amann R, Helmke E 2003. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Applied and Environmental Microbiology 69: 6610-661.
12. Brown MV, Bowman JP 2001. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiology Ecology 35: 267-275. (Pubitemid 32320003)
13. Castiglioni B, Rizzi E, Frosini A, Sivonen K, Rajaniemi P, Rantala A, Mugnai MA, Ventura S, WilmotteA, BoutteC, Grubisic S, Balthasart P, Consolandi C, Bordoni R, Mezzelani A, Battaglia C, De Bellis G 2004. Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of Cyanobacteria. Applied and Environmental Microbiology 70: 7161-7172. (Pubitemid 39643779)
14. DeLong EF 1992. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America 89: 5685-5689.
15. DeLong EF, Ying Wu K, Prezelin BB, Jovine RVM 1994. High abundanceof Archaea in Antarctic marinepicoplankton. Nature371: 695-697. (Pubitemid 24327326)
16. Garrison DL 1991. Antarctic sea ice biota. American Zoologist 31: 17-33.
17. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature345: 60-63.
18. Gordon DA, Priscu J, Giovannoni S 2000. Origin and phylogeny of microbes living in permanent Antarctic lakeice . Microbial Ecology 39: 197-202. (Pubitemid 30454195)
19. Gosink JJ, Staley JT 1995. Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water. Applied and Environmental Microbiology 61: 3486-3489. (Pubitemid 26463233)
20. Gradinger R, Ikavalko J 1998. Organism incorporation into newly forming Arctic sea ice in the Greenland Sea. Journal of Plankton Research 20: 871-886. (Pubitemid 28309858)
21. Gross L 2005. As the Antarctic ice pack recedes, a fragile ecosystem hangs in the balance. PLoS Biology 3: 557-561.
22. Hugenholtz P 2002. Exploring prokaryotic diversity in the genomic era. Genome Biology 3: 1-8.
23. Iizuka H, TanabeI, Meguro H 1966. Microorganisms in plankton-iceof theAntarctic Ocean. Journal of General and Applied Microbiology 12: 101-102.
24. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In Munro H ed. Mammalian protein metabolism. New York, Academic Press. Pp. 21-132.
25. Junge K, Eicken H, Deming JW 2004. Bacterial activity at 2 to 208C in Arctic wintertime sea ice. Applied and Environmental Microbiology 70: 550-577.
26. Junge K, Imhoff F, Staley T, Deming JW, 2002. Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature. Microbial Ecology 43: 315-328. (Pubitemid 36953118)
27. Kirchman DL, Yu L, Cottrell MT. 2003. Diversity and abundanceof uncultured Cytophaga-like bacteria in the Delaware Estuary. Applied and Environmental Microbiology 69: 6587-6596. (Pubitemid 37420194)
28. Koh EY, Atamna-Ismaeel N, Martin A, Cowie RO, Beja O, Davy SK, Maas EW, Ryan KG 2010. Proteorhodopsin-bearing bacteria in Antarctic sea ice. Applied and Environmental Microbiology 76: 5918-5925.
29. Lane DJ 1991. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M eds. Nucleic acid techniques in bacterial systematics. Chichester, John Wiley & Sons Ltd. Pp. 115-175.
30. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, Lai T, Steppi S, Jobb G et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Research 32: 1363-1371. (Pubitemid 38854737)
31. Mock T, Thomas DN 2005. Recent advances in seaicemicrobiology. Environmental Microbiology 7: 605-619.
32. Murray AE, Grzymski JJ 2007. Diversity and genomics of Antarctic marine micro-organisms. Philosophical Transactions of theRoyal Society B: Biological Sciences 362: 2259-2271.
33. Nü bel U, Garcia-Oichel F, Muyzer G 1997. PCR primers to amplify 16S rRNA genes from Cyanobacteria. Applied and Environmental Microbiology 63: 3327-3332.
34. Oz A, Sabehi G, Koblizek M, Massana R, Beja O 2005. Roseobacter-like bacteria in red and mediterranean sea aerobic anoxygenic photosynthetic populations. Applied and Environmental Microbiology 71: 344-353. (Pubitemid 40116288)
35. Pradella S, Allgaier M, Hoch C, Pauker O, Stackebrandt E, Wagner-Dobler I 2004. Genomeorganization and localization of thepufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Applied and Environmental Microbiology 70: 3360-3369. (Pubitemid 38745879)
36. Reysenbach AL, Pace NR 1995. Archaea a laboratory manual thermophiles. In: Robb FT, Place AR eds. New York, Cold Spring Harbour Press. Pp. 101-107.
37. Sambrook J, Russell D.W. 2001. Molecular cloning: a laboratory manual. 3rd ed. New York, Cold Spring Harbor Press Ltd.
38. Shiba T, Shioi Y, Takamiya KI, Sutton DC, Wilkinson CR 1991. Distribution and physiology of aerobic bacteria containing bacteriochlorophyll a on theEast and West Coasts of Australia. Applied and Environmental Microbiology 57: 295-300.
39. Staley JT, Gosink JJ 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annual Review of Microbiology 53: 189-206.
40. Staley JT, Reysenbach AL 2002. Biodiversity of microbiological life. New York: Wiley-Liss.
41. Sullivan CW, Palmisano AC 1984. Sea ice microbial communities: distribution, abundance, and diversity of Ice bacteria in McMurdo Sound, Antarctica, in 1980. Applied and Environmental Microbiology 47: 788-795.
42. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL 1999. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Applied and Environmental Microbiology 65: 4375-4384.
43. Vincent WF, Bowman JP, Rankin LM, McMeekin TA 2000. Phylogenetic diversity of picocyanobacteria in Arctic and Antarctic ecosystems. In Bell CR, Brylinsky M, Johnson-Green P eds. Microbial biosystems: new frontiers. Proceedings of the8th International Symposium on Microbial Ecology. Atlantic Canada Society for Microbial Ecology, Halifax, Canada. Pp. 317-322.
44. Wagner-Dö bler I, Biebl H 2006. Environmental biology of the marine Roseobacter lineage. Annual Review of Microbiology 60: 255-280.
45. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glockner FO, Rossello-Mora R 2008. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Systematic and Applied Microbiology 31: 241-250.