Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Detoxification of sulphidic African shelf waters by blooming chemolithotrophs


Coastal waters support 90 per cent of global fisheries and are therefore an important food reserve for our planet1. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide—toxic to multi-cellular life—with disastrous consequences for coastal ecosytems2,3,4,5. Here we show that an area of 7,000 km2 of African shelf, covered by sulphidic water, was detoxified by blooming bacteria that oxidized the biologically harmful sulphide to environmentally harmless colloidal sulphur and sulphate. Combined chemical analyses, stoichiometric modelling, isotopic incubations, comparative 16S ribosomal RNA, functional gene sequence analyses and fluorescence in situ hybridization indicate that the detoxification proceeded by chemolithotrophic oxidation of sulphide with nitrate and was mainly catalysed by two discrete populations of γ- and ε-proteobacteria. Chemolithotrophic bacteria, accounting for 20 per cent of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters and, thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Spatial and temporal distribution of sulphidic shelf waters off Namibia during 2004–2005.
Figure 2: Chemical zonation and distribution of indicators for bacterial sulphide oxidation.
Figure 3: Affiliation and morphology of sulphide-oxidizing bacteria from the Namibian shelf waters.

Accession codes

Primary accessions


Data deposits

Sequences for the 16S rRNA, aprA and rdsrA genes obtained in this study have been submitted to GenBank under the accession numbers FM246507FM246787, FM246819FM246832 and FM246788FM246818, respectively.


  1. Pauly, D. et al. Towards sustainability in world fisheries. Nature 418, 689–695 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Diaz, R. J. & Rosenberg, R. Marine benthic hypoxia: a review of its ecological effects and the behavioral responses of benthic macrofauna. Oceanogr. Mar. Biol. Annu. Rev. 33, 245–303 (1995)

    Google Scholar 

  3. Naqvi, S. W. A. et al. Increased marine production of N2O due to intensifying anoxia on the Indian continental shelf. Nature 408, 346–349 (2000)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Rabalais, N. N., Turner, R. E. & Scavia, D. Beyond science into policy: Gulf of Mexico hypoxia and the Mississippi River. Bioscience 52, 129–142 (2002)

    Article  Google Scholar 

  5. Malakoff, D. Death by suffocation in the Gulf of Mexico. Science 281, 190–192 (1998)

    Article  ADS  CAS  Google Scholar 

  6. Carr, M.-E. Estimation of potential productivity in eastern boundary currents using remote sensing. Deep-Sea Res. II 49, 58–80 (2002)

    Google Scholar 

  7. Copenhagen, W. J. The periodic mortality of fish in the Walvis Bay region. Investl Rep. Div. Sea Fish S. Afr. 14, 1–35 (1953)

    Google Scholar 

  8. Hart, T. J. & Currie, R. I. The Benguela current. Discovery Rep. 31, 123–297 (1960)

    Google Scholar 

  9. Emeis, K. C. et al. Shallow gas in shelf sediments of the Namibian coastal upwelling ecosystem. Continent. Shelf Res. 24, 627–642 (2004)

    Article  ADS  Google Scholar 

  10. Weeks, S. J., Currie, B. & Bakun, A. Satellite imaging: Massive emissions of toxic gas in the Atlantic. Nature 415, 493–494 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Bruchert, V. et al. in Past and Present Water Column Anoxia (ed. Neretin, L. N.) 161–193 (NATO Science Series 40, Springer, 2006)

    Book  Google Scholar 

  12. Berg, P., Risgaard-Petersen, N. & Rysgaard, S. Interpretation of measured concentration profiles in sediment pore water. Limnol. Oceanogr. 43, 1500–1510 (1998)

    Article  ADS  CAS  Google Scholar 

  13. Kuypers, M. M. M. et al. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl Acad. Sci. USA 102, 6478–6483 (2005)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  14. Cardoso, R. B. et al. Sulfide oxidation under chemolithoautotrophic denitrifying conditions. Biotechnol. Bioeng. 95, 1148–1157 (2006)

    Article  CAS  PubMed  Google Scholar 

  15. Peek, A. S., Feldman, R. A., Lutz, R. A. & Vrijenhoek, R. C. Cospeciation of chemoautotrophic bacteria and deep sea clams. Proc. Natl Acad. Sci. USA 95, 9962–9966 (1998)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Newton, I. L. G. et al. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998–1000 (2007)

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Madrid, V. M., Taylor, G. T., Scranton, M. I. & Chistoserdov, A. Y. Phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the Cariaco basin. Appl. Environ. Microbiol. 67, 1663–1674 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sunamura, M., Higashi, Y., Miyako, C., Ishibashi, J. & Maruyama, A. Two bacteria phylotypes are predominant in the Suiyo seamount hydrothermal plume. Appl. Environ. Microbiol. 70, 1190–1198 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Vetter, R. D. Elemental sulfur in the gills of three species of clams containing chemoautotrophic symbiotic bacteria: a possible inorganic energy storage compound. Mar. Biol. 88, 33–42 (1985)

    Article  CAS  Google Scholar 

  20. Campbell, B. J. et al. The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat. Rev. Microbiol. 4, 458–468 (2006)

    Article  CAS  PubMed  Google Scholar 

  21. Wirsen, C. O. et al. Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp that produces filamentous sulphur. Appl. Environ. Microbiol. 68, 316–325 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sievert, S. M. et al. Genome of the Epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans . Appl. Environ. Microbiol. 74, 1145–1156 (2008)

    Article  CAS  PubMed  Google Scholar 

  23. Gevertz, D. et al. Isolation and characterization of strains CVO and FWKO B, two novel nitrate-reducing, sulfide-oxidizing bacteria isolated from oil field brine. Appl. Environ. Microbiol. 66, 2491–2501 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Beman, J. M., Arrigo, K. R. & Matson, P. A. Agricultural runoff fuels large phytoplankton blooms in vulnerable areas of the ocean. Nature 434, 211–214 (2005)

    Article  ADS  Google Scholar 

  25. Grantham, B. A. et al. Upwelling-driven nearshore hypoxia signals ecosystem and oceanographic changes in the northeast Pacific. Nature 429, 749–754 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Sarmiento, J. L. et al. Simulated response of the ocean carbon cycle to anthropogenic climate warming. Nature 393, 245–249 (1998)

    Article  ADS  CAS  Google Scholar 

  27. Paerl, H. W. & Steppe, T. F. Scaling up: the next challenge in environmental microbiology. Environ. Microbiol. 5, 1025–1038 (2003)

    Article  PubMed  Google Scholar 

  28. Ohde, T. et al. Identification and investigation of sulphur plumes along the Namibian coast using the MERIS sensor. Continent. Shelf Res. 27, 744–756 (2007)

    Article  ADS  Google Scholar 

  29. Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Cline, J. D. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol. Oceanogr. 14, 454–458 (1969)

    Article  ADS  CAS  Google Scholar 

  31. Hansen, J. W., Thamdrup, B. & Jorgensen, B. B. Anoxic incubation of sediment in gas-tight plastic bags: a method for biogeochemical process studies. Mar. Ecol. Prog. Ser. 208, 273–282 (2000)

    Article  ADS  Google Scholar 

  32. Thamdrup, B. & Dalsgaard, T. Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl. Environ. Microbiol. 68, 1312–1318 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kallmeyer, J., Ferdelman, T. G., Weber, A., Fossing, H. & Jørgensen, B. B. A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements. Limnol. Oceanogr. Methods 2, 171–180 (2004)

    Article  Google Scholar 

  34. Blazejak, A. et al. Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5′-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (Oligochaeta) from Bermuda and the Bahamas. Appl. Environ. Microbiol. 72, 5527–5536 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kirchman, D. L. et al. Structure of bacterial communities in aquatic systems as revealed by filter PCR. Aquat. Microb. Ecol. 26, 13–22 (2001)

    Article  Google Scholar 

  36. Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Pernthaler, A., Pernthaler, J. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094–3101 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Snaidr, J. et al. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63, 2884–2896 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Gloeckner, F. O. et al. An in situ hybridization protocol for detection and identification of planktonic bacteria. Syst. Appl. Microbiol. 19, 403–406 (1996)

    Article  CAS  Google Scholar 

  40. Fennel, K. & Boss, E. Subsurface maxima of phytoplankton and chlorophyll: Steady-state solutions from a simple model. Limnol. Oceanogr. 48, 1521–1534 (2003)

    Article  ADS  Google Scholar 

Download references


We thank B. Barker Jørgensen, F. Inagaki, C. Hubert, T. Ferdelman and G. Collins for discussions; the Namibian authorities for access to their national waters; the crew of RV Alexander von Humboldt for assistance onboard; S. Krüger for operating the pump-CTD and oceanographic equipment; T. Heene for assistance with the collection of oceanographic data and generating oceanographic plots; and G. Klockgether, J. Sawicka, J. Wulf, S. Lenk, D. Franzke and K. Nkandi for assistance with the analysis. The investigations were supported by the MPG, the BMBF programme Geotechnologien and the project NAMIBGAS, the DFG, BENEFIT and the Namibian Ministry of Fisheries and Natural Resources.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Marcel M. M. Kuypers.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1, a Supplementary Discussion, Supplementary Figures 1- 4 with Legends and Supplementary References. (PDF 318 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Lavik, G., Stührmann, T., Brüchert, V. et al. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457, 581–584 (2009).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing