Dissimilatory sulfur cycling in oxygen minimum zones: An emerging metagenomics perspective

Biochemical Society Transactions

Volumn 39, Issue 6, 2011, Pages 1859-1863

  Stewart, Frank J ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Autotrophic denitrification; Eastern Tropical South Pacific (ETSP); Oxygen minimum zone; Sulfate reduction; Sulfur oxidation; SUP05

Indexed keywords

NITRATE; NITRATE REDUCTASE; NITRATE REDUCTASE NARGH; NITRIC OXIDE REDUCTASE; NITRIC OXIDE REDUCTASE NORCB; NITRITE; NITRITE REDUCTASE; NITRITE REDUCTASE NIRK; OXYGEN; SULFUR; UNCLASSIFIED DRUG;

BACTEROIDETES; CHEMICAL ENVIRONMENT; CHLOROBI; CONFERENCE PAPER; DELTAPROTEOBACTERIA; DENITRIFICATION; DESULFATIBACILLUM; DESULFOBACTERIUM; EPSILONPROTEOBACTERIA; GAMMAPROTEOBACTERIA; MARINE ENVIRONMENT; METAGENOMICS; NONHUMAN; OXYGEN MINIMUM ZONE; PRIORITY JOURNAL; RUTHIA MAGNIFICA; SULFUR CYCLE; SULFUR OXIDIZER; VESICOMYOSOCIUS OKUTANII;

METAGENOMICS; OXIDATION-REDUCTION; OXYGEN; SULFATES; SULFUR; WATER MICROBIOLOGY;

EID: 81855220883     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20110708     Document Type: Conference Paper

References (39)

1. Bopp, L., Le Quere, C., Heimann, M., Manning, A.C. and Monfray, P. (2002) Climate-induced oceanic oxygen fluxes: implications for the contemporary carbon budget. Global Biogeochem. Cycles 16, 1-13
2. Pauly, D. (2010) Gasping fish and panting squids: oxygen, temperature, and the growth of water-breathing animals. In Excellence in Ecology, Book 22 (Kinne, O., ed.), International Ecology Institute, Oldendorf (Luhe)
3. Diaz, R.J. and Rosenberg, R. (2008) Spreading dead zones and consequences for marine ecosystems. Science 321, 926-929
4. Stevens, H. and Ulloa, O. (2008) Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific. Environ. Microbiol. 10, 1244-1259 (Pubitemid 351499241)
5. Ulloa, O. and Pantoja, S. (2009) The oxygen minimum zone of the eastern South Pacific. Deep-Sea Res. Part II 56, 987-991
6. Zehr, J.P. and Kudela, R.M. (2011) Nitrogen cycle of the open ocean: from genes to ecosystems. Annu. Rev. Mar. Sci. 3, 197-225
7. Thamdrup, B., Dalsgaard, T., Jensen, M.M., Ulloa, O., Farias, L. and Escribano, R. (2006) Anaerobic ammonium oxidation in the oxygen-deficient waters off northern Chile. Limnol. Oceanogr. 51, 2145-2156 (Pubitemid 44520911)
8. Lam, P., Lavik, G., Jensen, M.M., van de Vossenberg, J., Schmid, M., Woebken, D., Dimitri, G., Amann, R., Jetten, M.S.M. and Kuypers, M.M.M. (2009) Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. U.S.A. 106, 4752-4757
9. Lam, P. and Kuypers, M.M.M. (2011) Microbial nitrogen cycling processes in oxygen minimum zones. Annu. Rev. Mar. Sci. 3, 317-345
10. Lavik, G., Stuhrmann, T., Bruchert, V., Van der Plas, A., Mohrholz, V., Lam, P., Mussmann, M., Fuchs, B.M., Amann, R., Lass, U. and Kuypers, M.M.M. (2009) Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457, 581-586
11. Zaikova, E., Walsh, D.A., Stilwell, C.P., Mohn, W.W., Tortell, P.D. and Hallam, S.J. (2010) Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ. Microbiol. 12, 172-191
12. Korom, S.F. (1992) Natural denitrification in the saturated zone. Water Resour. Res. 28, 1657-1668
13. Canfield, D.E., Stewart, F.J., Thamdrup, B., De Brabandere, L., Dalsgaard, T., Delong, E.F., Revsbech, N.P. and Ulloa, O. (2010) A cryptic sulfur cycle in oxygen minimum zone waters off the Chilean coast. Science 330, 1375-1378
14. Walsh, D.A., Zaikova, E., Howes, C.G., Song, Y.C., Wright, J.J., Tringe, S.G., Tortell, P.D. and Hallam, S.J. (2009) Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326, 578-582
15. Stewart, F.J., Ulloa, O. and DeLong, E.F. (2011) Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ. Microbiol., doi:10.1111/j.1462-2920.2010.02400.x
16. Brettar, I., Labrenz, M., Flavier, S., Botel, J., Kuosa, H., Christen, R. and Hofle, M.G. (2006) Identification of a Thiomicrospira denitrificans-like epsilonproteobacterium as a catalyst for autotrophic denitrification in the central Baltic Sea. Appl. Environ. Microbiol. 72, 1364-1372 (Pubitemid 43271248)
17. Chistoserdov, A.Y., Madrid, V.M., Taylor, G.T. and Scranton, M.I. (2001) Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco Basin. Appl. Environ. Microbiol. 67, 1663-1674 (Pubitemid 33644937)
18. Glaubitz, S., Labrenz, M., Jost, G. and Jurgens, K. (2010) Diversity of active chemolithoautotrophic prokaryotes in the sulfidic zone of a Black Sea pelagic redoxcline as determined by rRNA-based stable isotope probing. FEMS Microbiol. Ecol. 74, 32-41
19. Sunamura, M., Higashi, Y., Miyako, C., Ishibashi, J. and Maruyama, A. (2004) Two bacteria phylotypes are predominant in the Suiyo Seamount hydrothermal plume. Appl. Environ. Microbiol. 70, 1190-1198 (Pubitemid 38568248)
20. Fuchs, B.M., Woebken, D., Zubkov, M.V., Burkill, P. and Amann, R. (2005) Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquat. Microb. Ecol. 39, 145-157 (Pubitemid 40885735)
21. Woebken, D., Teeling, H., Wecker, P., Dumitriu, A., Kostadinov, I., DeLong, E.F., Amann, R. and Glockner, F.O. (2007) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J. 1, 419-435 (Pubitemid 47373248)
22. Newton, I.L.G., Woyke, T., Auchtung, T.A., Dilly, G.F., Dutton, R.J., Fisher, M.C., Fontanez, K.M., Lau, E., Stewart, F.J., Richardson, P.M. et al. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998-1000 (Pubitemid 46281189)
23. Kuwahara, H., Yoshida, T., Takaki, Y., Shimamura, S., Nishi, S., Harada, M., Matsuyama, K., Takishita, K., Kawato, M., Uematsu, K. et al. (2007) Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Curr. Biol. 17, 881-886 (Pubitemid 46702672)
24. Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W. and DeLong, E.F. (2008) Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. U.S.A. 105, 3805-3810 (Pubitemid 351723480)
25. Stewart, F.J., Sharma, A.K., Bryant, J.A., Eppley, J.M. and Delong, E.F. (2011) Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol. 12, R26
26. Chisholm, S.W., Martiny, A.C. and Coleman, M.L. (2006) Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc. Natl. Acad. Sci. U.S.A. 103, 12552-12557 (Pubitemid 44267296)
27. Cypionka, H. (2000) Oxygen respiration by Desulfovibrio species. Annu. Rev. Microbiol. 54, 827-848
28. Dugdale, R.C., Goering, J.J., Barber, R.T., Smith, R.L. and Packard, T.T. (1977) Denitrification and hydrogen sulfide in the Peru upwelling region during 1976. Deep-Sea Res. 24, 601-608
29. Bruchert, V., Jorgensen, B.B., Neumann, K., Riechmann, D., Schlosser, M. and Schulz, H. (2003) Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central Namibian coastal upwelling zone. Geochim. Cosmochim. Acta 67, 4505-4518 (Pubitemid 37470951)
30. Zopfi, J., Bttcher, M.E. and Jorgensen, B.B. (2008) Biogeochemistry of sulfur and iron in Thioploca-colonized surface sediments in the upwelling area off central Chile. Geochim. Cosmochim. Acta 72, 827-843
31. Teske, A. (2010) Cryptic links in the ocean. Science 330, 1326-1327
32. Meyer, B. and Kuever, J. (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl. Environ. Microbiol. 73, 7664-7679
33. Peek, A.S., Feldman, R.A., Lutz, R.A. and Vrijenhoek, R.C. (1998) Cospeciation of chemoautotrophic bacteria and deep sea clams. Proc. Natl. Acad. Sci. U.S.A. 95, 9962-9966 (Pubitemid 28415277)
34. Stewart, F.J., Young, C.R. and Cavanaugh, C.M. (2008) Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Mol. Biol. Evol. 25, 673-687 (Pubitemid 351398323)
35. Stewart, F.J., Young, C.R. and Cavanaugh, C.M. (2009) Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol. Biol. Evol. 26, 1391-1404
36. Imhoff, J.F., Sahling, H., Suling, J. and Kath, T. (2003) 16S rDNA-based phylogeny of sulphur-oxidising bacterial endosymbionts in marine bivalves from cold-seep habitats. Mar. Ecol. Prog. Ser. 249, 39-51 (Pubitemid 36400138)
37. Stramma, L., Johnson, G.C., Sprintall, J. and Mohrholz, V. (2008) Expanding oxygen minimum zones in the tropical oceans. Science 320, 655-658 (Pubitemid 351928345)
38. Shaffer, G., Olsen, S.M. and Pedersen, J.O.P. (2009) Long-term ocean oxygen depletion in response to carbon dioxide emissions from fossil fuels. Nat. Geosci. 2, 105-109
39. Keeling, R.F., Kortzinger, A. and Gruber, N. (2010) Ocean deoxygenation in a warming world. Annu. Rev. Mar. Sci. 2, 199-229