Skip to main content

Thank you for visiting nature.com. 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.

Shallow breathing: bacterial life at low O2

Key Points

  • Microoxic environments are prevalent in nature, including in aquatic, terrestrial and host-associated environments.

  • Although a subset of bacteria known as microaerophiles grow optimally under microoxic conditions, many bacteria that have traditionally been characterized as aerobes or anaerobes also occupy these environments. All microorganisms that are capable of respiring low levels of O2 are defined as microaerobes.

  • Cytochrome oxidases with a high affinity for O2 are common in phylogenetically diverse bacterial genomes (70% of species surveyed) and provide microaerobes with access to scarce supplies of O2.

  • Analysis of shotgun metagenomes reveals a widespread occurrence of genes encoding high-affinity oxidases, providing intriguing evidence that supports the importance of microaerobic metabolism.

  • Understanding the physiology and ecology of microaerobes in low-O2 environments is integral to advancing our understanding of host-associated microbiomes, for both colonization and pathogen invasion.

  • Advances in both O2-sensing technologies and microoxic cultivation will provide opportunities for the exploration of the local and global impacts of microaerobes.

Abstract

Competition for molecular oxygen (O2) among respiratory microorganisms is intense because O2 is a potent electron acceptor. This competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. Bacteria can harvest O2 present at low, even nanomolar, concentrations using high-affinity terminal oxidases. Here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced bacterial genomes and shotgun metagenomes. The results indicate that bacteria with the potential to respire under microoxic conditions are phylogenetically diverse and intriguingly widespread in nature. We explore the implications of these findings by highlighting the importance of microaerobic metabolism in host-associated bacteria related to health and disease.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: The distribution of terminal oxidases in bacterial genomes linked to physiological groups of microorganisms and their distribution in an O2 gradient.
Figure 2: Distribution of terminal oxidase genes in shotgun metagenomes.
Figure 3: Distribution of high-affinity terminal oxidase genes across terrestrial landscapes following release of the land from agriculture.

References

  1. Brochier-Armanet, C., Talla, E. & Gribaldo, S. The multiple evolutionary histories of dioxygen reductases: implications for the origin and evolution of aerobic respiration. Mol. Biol. Evol. 26, 285–297 (2009). This article includes genomic surveys of terminal oxidase genes and presents a model for the evolutionary origin of aerobic respiration in bacteria and archaea.

    CAS  Article  Google Scholar 

  2. Stolper, D. A., Revsbech, N. P. & Canfield, D. E. Aerobic growth at nanomolar oxygen concentrations. Proc. Natl Acad. Sci. USA 107, 18755–18760 (2010). This study demonstrates aerobic growth of an E. coli strain at nanomolar concentrations of O 2 — concentrations that are orders of magnitude lower than those previously reported.

    CAS  Article  Google Scholar 

  3. Marteyn, B. et al. Modulation of Shigella virulence in response to available oxygen in vivo. Nature 465, 355–358 (2010). This investigation of the effects of O 2 on virulence in Shigella includes the visualization of an oxygenated zone adjacent to the intestinal mucosa.

    CAS  Article  Google Scholar 

  4. Lieberman, T. D. et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nature Genet. 43, 1275–1280 (2011).

    CAS  Article  Google Scholar 

  5. Abreu, I. A., Xavier, A. V., LeGall, J., Cabelli, D. E. & Teixeira, M. Superoxide scavenging by neelaredoxin: dismutation and reduction activities in anaerobes. J. Biol. Inorg. Chem. 7, 668–674 (2002).

    CAS  Article  Google Scholar 

  6. Madigan, M. T., Martinko, J. M., Stahl, D. A. & Clark, D. P. Brock Biology of Microorganisms 13th edn 117–149 (Benjamin Cummings, 2010).

    Google Scholar 

  7. Baughn, A. D. & Malamy, M. H. The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature 427, 441–444 (2004).

    CAS  Article  Google Scholar 

  8. Tiedje, J., Sexstone, A., Parkin, T., Revsbech, N. & Shelton, D. Anaerobic processes in soil. Plant Soils 76, 197–212 (1984).

    CAS  Article  Google Scholar 

  9. Ploug, H., Iversen, M. H. & Fischer, G. Ballast, sinking velocity, and apparent diffusivity within marine snow and zooplankton fecal pellets: implications for substrate turnover by attached bacteria. Limnol. Oceanogr. 53, 1878–1886 (2008).

    Article  Google Scholar 

  10. Alldredge, A. L. & Cohen, Y. Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235, 689–691 (1987).

    CAS  Article  Google Scholar 

  11. Ploug, H. Small-scale oxygen fluxes and remineralization in sinking aggregates. Limnol. Oceanogr. 46, 1624–1631 (2001).

    CAS  Article  Google Scholar 

  12. Stewart, P. S. & Franklin, M. J. Physiological heterogeneity in biofilms. Nature Rev. Microbiol. 6, 199–210 (2008).

    CAS  Article  Google Scholar 

  13. Fenchel, T. & Finlay, B. Oxygen and the spatial structure of microbial communities. Biol. Rev. Camb. Philos. Soc. 83, 553–569 (2008).

    PubMed  Google Scholar 

  14. Kühl, M., Rickelt, L. F. & Thar, R. Combined imaging of bacteria and oxygen in biofilms. Appl. Environ. Microbiol. 73, 6289–6295 (2007).

    Article  Google Scholar 

  15. Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nature Rev. Microbiol. 10, 381–394 (2012).

    CAS  Article  Google Scholar 

  16. Soupène, E., Foussard, M., Boistard, P., Truchet, G. & Batut, J. Oxygen as a key developmental regulator of Rhizobium meliloti N2-fixation gene expression within the alfalfa root nodule. Proc. Natl Acad. Sci. USA 92, 3759–3763 (1995).

    Article  Google Scholar 

  17. Kuzma, M. M., Hunt, S. & Layzell, D. B. Role of oxygen in the limitation and inhibition of nitrogenase activity and respiration rate in individual soybean nodules. Plant Physiol. 101, 161–169 (1993).

    CAS  Article  Google Scholar 

  18. Charrier, M. & Brune, A. The gut microenvironment of helicid snails (Gastropoda: Pulmonata): in-situ profiles of pH, oxygen, and hydrogen determined by microsensors. Can. J. Zool. 81, 928–935 (2003).

    Article  Google Scholar 

  19. Brune, A., Emerson, D. & Breznak, J. A. The termite gut microflora as an oxygen sink: microelectrode determination of oxygen and pH gradients in guts of lower and higher termites. Appl. Environ. Microbiol. 61, 2681–2687 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Van den Abbeele, P., Van de Wiele, T., Verstraete, W. & Possemiers, S. The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiol. Rev. 35, 681–704 (2011).

    CAS  Article  Google Scholar 

  21. Mirza, B. S. & Rodrigues, J. L. Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic conditions. Appl. Environ. Microbiol. 16, 5542–5549 (2012).

    Article  Google Scholar 

  22. Young, V. B. et al. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome (in the press).

  23. Brioukhanov, A. & Netrusov, A. Aerotolerance of strictly anaerobic microorganisms and factors of defense against oxidative stress: a review. Appl. Biochem. Microbiol. 43, 567–582 (2007).

    CAS  Article  Google Scholar 

  24. Hemp, J. et al. Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases. Biochemistry 45, 15405–15410 (2006).

    CAS  Article  Google Scholar 

  25. Calhoun, M. W., Thomas, J. W. & Gennis, R. B. The cytochrome oxidase superfamily of redox-driven proton pumps. Trends Biochem. Sci. 19, 325–330 (1994).

    CAS  Article  Google Scholar 

  26. Pitcher, R. S. & Watmough, N. J. The bacterial cytochrome cbb 3 oxidases. Biochim. Biophys. Acta 1655, 388–399 (2004).

    CAS  Article  Google Scholar 

  27. Brändén, G., Gennis, R. B. & Brzezinski, P. Transmembrane proton translocation by cytochrome c oxidase. Biochim. Biophys. Acta 1757, 1052–1063 (2006).

    Article  Google Scholar 

  28. Puustinen, A., Finel, M., Haltia, T., Gennis, R. B. & Wikström, M. Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30, 3936–3942 (1991).

    CAS  Article  Google Scholar 

  29. Pereira, M. M., Santana, M. & Teixeira, M. A novel scenario for the evolution of haem–copper oxygen reductases. Biochim. Biophys. Acta 1505, 185–208 (2001).

    CAS  Article  Google Scholar 

  30. Han, H. et al. Adaptation of aerobic respiration to low O2 environments. Proc. Natl Acad. Sci. USA 108, 14109–14114 (2011). This report discusses the implications of the adaptation of aerobic respiration to low-O 2 environments.

    CAS  Article  Google Scholar 

  31. Pitcher, R. S., Brittain, T. & Watmough, N. J. Cytochrome cbb3 oxidase and bacterial microaerobic metabolism. Biochem. Soc. Trans. 30, 653–658 (2002).

    CAS  Article  Google Scholar 

  32. Keightley, J. A. et al. Molecular genetic and protein chemical characterization of the cytochrome ba 3 from Thermus thermophilus HB8. J. Biol. Chem. 270, 20345–20358 (1995).

    CAS  Article  Google Scholar 

  33. Rice, C. W. & Hempfling, W. P. Oxygen-limited continuous culture and respiratory energy conservation in Escherichia coli. J. Bacteriol. 134, 115–124 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. D'mello, R., Hill, S. & Poole, R. K. The cytochrome bd quinol oxidase in Escherichia coli has an extremely high oxygen affinity and two oxygen-binding haems: implications for regulation of activity in vivo by oxygen inhibition. Microbiology 142, 755–763 (1996).

    CAS  Article  Google Scholar 

  35. Jackson, R. J. et al. Oxygen reactivity of both respiratory oxidases in Campylobacter jejuni: the cydAB genes encode a cyanide-resistant, low-affinity oxidase that is not of the cytochrome bd type. J. Bacteriol. 189, 1604–1615 (2007).

    CAS  Article  Google Scholar 

  36. Cunningham, L., Pitt, M. & Williams, H. D. The cioAB genes from Pseudomonas aeruginosa code for a novel cyanide-insensitive terminal oxidase related to the cytochrome bd quinol oxidases. Mol. Microbiol. 24, 579–591 (1997).

    CAS  Article  Google Scholar 

  37. Arai, H. Regulation and function of versatile aerobic and anaerobic respiratory metabolism in Pseudomonas aeruginosa. Front. Microbiol. 2, 103 (2011).

    CAS  Article  Google Scholar 

  38. Altschul, S., Gish, W., Miller, W., Myers, E. & Lipman, D. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    CAS  Article  Google Scholar 

  39. Ducluzeau, A. L., Ouchane, S. & Nitschke, W. The cbb 3 oxidases are an ancient innovation of the domain Bacteria. Mol. Biol. Evol. 25, 1158–1166 (2008).

    CAS  Article  Google Scholar 

  40. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997).

    CAS  Article  Google Scholar 

  41. Meyer, F. et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008).

    CAS  Article  Google Scholar 

  42. Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).

    CAS  Article  Google Scholar 

  43. Borisov, V. B. et al. Redox control of fast ligand dissociation from Escherichia coli cytochrome bd. Biochem. Biophys. Res. Commun. 355, 97–102 (2007).

    CAS  Article  Google Scholar 

  44. Reinders, C. A. et al. Rectal nitric oxide and fecal calprotectin in inflammatory bowel disease. Scand. J. Gastroenterol. 42, 1151–1157 (2007).

    CAS  Article  Google Scholar 

  45. Borisov, V. B. et al. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc. Natl Acad. Sci. USA 108, 17320–17324 (2011).

    CAS  Article  Google Scholar 

  46. Wertz, J. T. & Breznak, J. A. Physiological ecology of Stenoxybacter acetivorans, an obligate microaerophile in termite guts. Appl. Environ. Microbiol. 73, 6829–6841 (2007).

    CAS  Article  Google Scholar 

  47. Preisig, O., Zufferey, R., Thöny-Meyer, L., Appleby, C. A. & Hennecke, H. A high-affinity cbb 3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. J. Bacteriol. 178, 1532–1538 (1996).

    CAS  Article  Google Scholar 

  48. Wiles, S., Pickard, K. M., Peng, K., MacDonald, T. T. & Frankel, G. In vivo bioluminescence imaging of the murine pathogen Citrobacter rodentium. Infect. Immun. 74, 5391–5396 (2006).

    CAS  Article  Google Scholar 

  49. Goldman, B. S., Gabbert, K. K. & Kranz, R. G. The temperature-sensitive growth and survival phenotypes of Escherichia coli cydDC and cydAB strains are due to deficiencies in cytochrome bd and are corrected by exogenous catalase and reducing agents. J. Bacteriol. 178, 6348–6351 (1996).

    CAS  Article  Google Scholar 

  50. Jones, S. A. et al. Respiration of Escherichia coli in the mouse intestine. Infect. Immun. 75, 4891–4899 (2007).

    CAS  Article  Google Scholar 

  51. Jones, S. A. et al. Anaerobic respiration of Escherichia coli in the mouse intestine. Infect. Immun. 79, 4218–4226 (2011).

    CAS  Article  Google Scholar 

  52. Weingarten, R. A., Grimes, J. L. & Olson, J. W. Role of Campylobacter jejuni respiratory oxidases and reductases in host colonization. Appl. Environ. Microbiol. 74, 1367–1375 (2008).

    CAS  Article  Google Scholar 

  53. Way, S. S., Sallustio, S., Magliozzo, R. S. & Goldberg, M. B. Impact of either elevated or decreased levels of cytochrome bd expression on Shigella flexneri virulence. J. Bacteriol. 181, 1229–1237 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Alvarez-Ortega, C. & Harwood, C. S. Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration. Mol. Microbiol. 65, 153–165 (2007).

    CAS  Article  Google Scholar 

  55. Shi, L. et al. Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration. Proc. Natl Acad. Sci. USA 102, 15629–15634 (2005).

    CAS  Article  Google Scholar 

  56. Battino, R., Rettich, T. R. & Tominaga, T. The solubility of oxygen and ozone in liquids. J. Phys. Chem. Ref. Data 12, 163–178 (1983).

    CAS  Article  Google Scholar 

  57. Revsbech, N. P., Thamdrup, B., Dalsgaard, T. & Canfield, D. E. Construction of STOX oxygen sensors and their application for determination of O2 concentrations in oxygen minimum zones. Methods Enzymol. 486, 325–341 (2011).

    CAS  Article  Google Scholar 

  58. Klimant, I., Kuhl, M., Glud, R. N. & Holst, G. Optical measurement of oxygen and temperature in micro scale: strategies and biological applications. Sens. Actuators B Chem. 38, 29–37 (1997).

    CAS  Article  Google Scholar 

  59. Grate, J. W., Kelly, R. T., Suter, J. & Anheier, N. C. Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure. Lab Chip 12, 4796–4801 (2012).

    CAS  Article  Google Scholar 

  60. Røy, H. et al. Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science 336, 922–925 (2012).

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank J. Breznak for seminal conversations about the ecological importance of microaerobes; K. D. Noel and C. Waldron for critical reading of this manuscript; T. Teal and B. Klahn for their expert assistance with the genomic and metagenomic analyses; and members of the Schmidt laboratory for many helpful discussions concerning the potential consequences of microaerobes and microoxic environments. This work was supported by grants from the US National Institutes of Health (R01 HG004906 and UH3 DK083993) and the US National Science Foundation (MCB 0731913 and DEB 1027253).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thomas M. Schmidt.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary informtation S1 (table)

Occurrence of high-affinity oxidase genes in bacterial genomes. (PDF 201 kb)

Supplementary informtation S2 (box)

Metagenome Analysis of Terminal Oxidase Genes (PDF 219 kb)

Supplementary informtation S3 (table)

MG-RAST accession numbers for the metagenomes in Figures 2 and 3. (PDF 201 kb)

Related links

Related links

FURTHER INFORMATION

Thomas M. Schmidt's homepage

KBS LTER

MG-RAST

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Morris, R., Schmidt, T. Shallow breathing: bacterial life at low O2. Nat Rev Microbiol 11, 205–212 (2013). https://doi.org/10.1038/nrmicro2970

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro2970

Further reading

Search

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