Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the high Arctic

Applied and Environmental Microbiology

Volumn 78, Issue 2, 2012, Pages 549-559

  Varin, Thibault ^a   Lovejoy, Connie ^a   Jungblut, Anne D ^b,c   Vincent, Warwick F ^b   Corbeil, Jacques ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b CENTRE D ÉTUDES NORDIQUES   (Canada)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOBACTERIA; ANTARCTIC ICE SHELVES; ANTARCTICA; COLD SHOCK; COPPER HOMEOSTASIS; CYANOBACTERIAL MATS; ENVIRONMENTAL STRESS; EXOPOLYSACCHARIDES; FREEZE-UP; FUNCTIONAL RESPONSE; GENES CODING; GENOMIC RESPONSE; HIGH ARCTIC; HIGH-THROUGHPUT; MEMBRANE MODIFICATION; METAGENOMES; METAGENOMIC ANALYSIS; MICROBIAL COMMUNITIES; OPEN OCEAN; OSMOTIC STRESS; POLAR HABITATS; PROTEIN-CODING GENES; PROTEOBACTERIA; PYROSEQUENCING; STATISTICAL COMPARISONS;

CODES (SYMBOLS); MICROORGANISMS;

GENES;

ADAPTATION; ALPINE ENVIRONMENT; COPPER; CYANOBACTERIUM; ECOSYSTEM RESPONSE; ENVIRONMENTAL STRESS; FUNCTIONAL CHANGE; GENETIC ANALYSIS; GENOMICS; HOMEOSTASIS; HYPOTHESIS TESTING; ICE SHELF; MICROBIAL COMMUNITY; MICROBIAL MAT; POLAR REGION; PROPAGULE; PROTEIN;

ANTARCTICA; ARCTIC; ARTICLE; BACTERIUM; BIOTA; CLASSIFICATION; DNA SEQUENCE; GENETICS; METAGENOME; MICROBIOLOGY; SEDIMENT;

ANTARCTIC REGIONS; ARCTIC REGIONS; BACTERIA; BIOTA; GEOLOGIC SEDIMENTS; METAGENOME; SEQUENCE ANALYSIS, DNA;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; PROTEOBACTERIA;

EID: 84855733160     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06354-11     Document Type: Article

References (61)

1. Allewalt JP, Bateson MM, Revsbech NP, Slack K, Ward DM. 2006. Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the Octopus Spring microbial mat community of Yellowstone National Park. Appl. Environ. Microbiol. 72:544-550.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Ayala-del-Rio HL, et al. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl. Environ. Microbiol. 76:2304-2312.
4. Bottos EM, Vincent WF, Greer CW, Whyte LG. 2008. Prokaryotic diversity of arctic ice shelf microbial mats. Environ. Microbiol. 10: 950-966.
5. Braissant O, et al. 2007. Exopolymeric substances of sulfate-reducing bacteria: interactions with calcium at alkaline pH and implication for formation of carbonate minerals. Geobiology 5:401-411.
6. Cavicchioli R. 2006. Cold-adapted Archaea. Nat. Rev. Microbiol. 4:331-343.
7. Crump EM, Perry MB, Clouthier SC, Kay WW. 2001. Antigenic characterization of the fish pathogen Flavobacterium psychrophilum. Appl. Environ. Microbiol. 67:750-759.
8. Franzmann PD, Springer N, Ludwig W, Conway de Macario E, Rohde M. 1992. A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov. Syst. Appl. Microbiol. 4:573-581.
9. Gomez-Alvarez V, Teal TK, Schmidt TM. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3:1314-1317.
10. Gorbushina AA. 2007. Life on the rocks. Environ. Microbiol. 9:1613-1631.
11. Gosink JJ, Woese CR, Staley JT. 1998. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus ' as Polaribacter glomeratus comb. nov. Int. J. Syst. Bacteriol. 48:223-235.
12. Harding T, Jungblut AD, Lovejoy C, Vincent WF. 2011. Microbes in High Arctic snow and implications for the cold biosphere. Appl. Environ. Microbiol. 77:3234-3243.
13. Hawes I, Safi K, Sorrell B, Webster-Brown J, Arscott D. 2011. Summerwinter transitions in Antarctic ponds. I. The physical environment. Antarct. Sci. 23:235-242.
14. Hawes I, Safi K, Webster-Brown J, Sorrell B, Arscott D. 2011. Summerwinter transitions in Antarctic ponds. II. Biological responses. Antarct. Sci. 23:243-254.
15. Hazel J, Williams EE. 1990. The role of alterations in membrane lipid composition in enabling physiological adaptation of organisms to their physical environment. Prog. Lipid Res. 29:167-227.
16. Hoffman L. 1999. Marine cyanobacteria in tropical regions: diversity and ecology. Eur. J. Phycol. 34:371-379.
17. Ito H, et al. 2009. Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus. Proc. Natl. Acad. Sci. U. S. A. 106:14168-14173.
18. Jungblut AD, Lovejoy C, Vincent WF. 2010. Global distribution of cyanobacterial ecotypes in the cold biosphere. ISME J. 4:191-202.
19. Junge K, Imhoff F, Staley T, Deming JW. 2002. Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature. Microb. Ecol. 43:315-328.
20. Kandror O, DeLeon A, Goldberg AL. 2002. Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures. Proc. Natl. Acad. Sci. U. S. A. 99:9727-9732.
21. Kenne L, Lindberg B. 1983. Bacterial polysaccharides, p 287-363. In Aspinall GO (ed), The polysaccharides. Academic Press, New York, NY.
22. Kennedy AF, Sutherland IW. 1987. Analysis of bacterial exopolysaccharides. Biotechnol. Appl. Biochem. 9:12-19.
23. Klein W, Weber MHW, Marahiel MA. 1999. Cold shock response of Bacillus subtilis: isoleucine-dependent switch in the fatty acid branching pattern for membrane adaptation to low temperatures. J. Bacteriol. 181: 5341-5349.
24. Klock J-H, Wieland A, Seifert R, Michaelis W. 2007. Extracellular polymeric substances (EPS) from cyanobacterial mats: characterisation and isolation method optimisation. Mar. Biol. 152:1077-1085.
25. Krembs C, Eicken H, Junge K, Deming JW. 2002. High concentrations of exopolymeric substances in Arctic winter sea ice: implications for the polar ocean carbon cycle and cryoprotection of diatoms. Deep Sea Res. Part I Oceanogr. Res. Pap. 49:2163-2181.
26. Margulies M, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376-380.
27. Maslova IP, Mouradyan EA, Lapina SS, Klyachko-Gurvich GL, Los DA. 2004. Lipid fatty acid composition and thermophilicity of Cyanobacteria. Russ. J. Plant Physiol. 51:353-360.
28. Meyer F, et al. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386.
29. Mueller DR, Vincent WF, Bonilla S, Laurion I. 2005. Extremotrophs, extremophiles and broadband pigmentation strategies in a High Arctic ice shelf ecosystem. FEMS Microbiol. Ecol. 53:73-87.
30. Mueller DR, Vincent WF, Jeffries MO. 2006. Environmental gradients, fragmented habitats, and microbiota of a northern ice shelf cryoecosystem, Ellesmere Island, Canada. Arct. Antarct. Alp. Res. 38:593-607.
31. Muir DCG, et al. 2009. Spatial trends and historical deposition of mercury in eastern and northern Canada inferred from lake sediment cores. Environ. Sci. Technol. 43:4802-4809.
32. Murray AE, Grzymski JJ. 2007. Diversity and genomics of Antarctic marine micro-organisms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362: 2259-2271.
33. Mykytczuk NCS, Trevors JT, Twine SM, Ferroni GD, Leduc LG. 2010. Membrane fluidity and fatty acid comparisons in psychrotrophic and mesophilic strains of Acidithiobacillus ferrooxidans under cold growth temperatures. Arch. Microbiol. 192:1005-1018.
34. Nichols CM, Bowman JP, Guezennec J. 2005. Effects of incubation temperature on growth and production of exopolysaccharides by an Antarctic sea ice bacterium grown in batch culture. Appl. Environ. Microbiol. 71:3519-3523.
35. Nichols CM, et al. 2005. Chemical characterization of exopolysaccharides from Antarctic marine bacteria. Microb. Ecol. 49:578-589.
36. Nicolaus B, Kambourova M, Oner ET. 2010. Exopolysaccharides from extremophiles: from fundamentals to biotechnology. Environ. Technol. 31:1145-1158.
37. Overbeek R, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33:5691-5702.
38. Parks D, Beiko R. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715-721.
39. Phadtare S. 2004. Recent developments in bacterial cold-shock response. Curr. Issues Mol. Biol. 6:125-136.
40. Poli A, Anzelmo G, Nicolaus B. 2010. Bacterial exopolysaccharides from extreme marine habitats: production, characterization and biological activities. Mar. Drugs 8:1779-1802.
41. Ponder M. 2005. Ph.D. thesis. Characterization of physiological and transcriptome changes in the ancient Siberian permafrost bacterium Psychrobacter arcticum 273-4 with low temperature and increased osmotica. Michigan State University, East Lansing, MI.
42. Powell LM, Bowman JP, Franzmann PD, Burton HR. 2005. Ecology of a novel Synechococcus clade occurring in dense populations in saline Antarctic lakes. Mar. Ecol. Prog. Ser. 291:65-80.
43. Rabus R, et al. 2004. The genome of Desulfotalea psychrophila, a sulfatereducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6:887-902.
44. Riley M, et al. 2008. Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9:210.
45. Rodrigues DF, Tiedje JM. 2008. Coping with our cold planet. Appl. Environ. Microbiol. 74:1677-1686.
46. Rosen R, Ron EZ. 2002. Proteome analysis in the study of the bacterial heat-shock response. Mass Spectrom. Rev. 21:244-265.
47. Scherer S, Neuhaus K. 2006. Life at low temperatures, p 210-262. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (ed), The prokaryotes, 3rd ed. Springer, New York, NY.
48. Schmidt S, Moskall W, de Mora SJ, Howard-Williams C, Vincent WF. 1991. Limnological properties of Antarctic ponds during winter freezing. Antarct. Sci. 3:379-388.
49. Schneider DW, Frost TM. 1996. Habitat duration and community structure in temporary ponds. J. North Am. Benthol. Soc. 15:64-86.
50. Simon C, Wiezer A, Strittmatter AW, Daniel R. 2009. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol. 75:7519-7526.
51. Tang EPY, Tremblay R, Vincent WF. 1997. Cyanobacterial dominance of polar freshwater ecosystems: are high-latitude mat-formers adapted to low temperatures? J. Phycol. 33:171-181.
52. Tillett D, Neilan BA. 2000. Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. J. Phycol. 36:251-258.
53. Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J. 2010. Metagenomic profiling of Arctic microbial mat communities as nutrient scavenging and recycling systems. Limnol. Oceanogr. 55:1901-1911.
54. Vincent WF, Castenholz RW, Downes MT, Howard-Williams C. 1993. Antarctic cyanobacteria: light, nutrients, and photosynthesis in the microbial mat environment. J. Phycol. 29:745-755.
55. Vincent WF. 2000. Cyanobacterial dominance in the polar regions, p 321-340. In Whitton BA, Potts M (ed), The ecology of cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
56. Vincent WF. 2007. Cold tolerance in cyanobacteria and life in the cryosphere, p 287-301. In Seckbach J (ed), Algae and cyanobacteria in extreme environments. Springer, Heidelberg, Germany.
57. Visscher PT, Reid RP, Bebout BM. 2000. Microscale observations of sulfate reduction: correlation of microbial activity with lithified micritic laminae in modern marine stromatolites. Geology 28:919-922.
58. B-dependent general stress regulon confers multiple stress resistance in Bacillus subtilis. J. Bacteriol. 181:3942-3948.
59. Ward DM, et al. 2006. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:1997-2008.
60. Yergeau E, Hogues H, Whyte LG, Greer CW. 2010. The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J. 4:1206-1214.
61. Zhao D, Chen X, He H, Shi M, Zhang Y. 2007. Gene cloning and sequence analysis of the cold-adapted chaperones DnaK and DnaJ from deep-sea psychrotrophic bacterium Pseudoalteromonas sp. SM9913. Acta Oceanol. Sin. 26:91-100.