Quantification of microaerobic growth of Geobacter sulfurreducens

Autoři: Christina Elisabeth Anna Engel aff001;  David Vorländer aff001;  Rebekka Biedendieck aff001;  Rainer Krull aff001;  Katrin Dohnt aff001
Působiště autorů: Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany aff001;  Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany aff002;  Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0215341


Geobacter sulfurreducens was originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate exposure to oxygen but also to use it as terminal electron acceptor. Research performed has so far only revealed the general ability of G. sulfurreducens to reduce oxygen, but the oxygen uptake rate has not been quantified yet, nor has evidence been provided as to how the bacterium achieves oxygen reduction. Therefore, microaerobic growth of G. sulfurreducens was investigated here with better defined operating conditions as previously performed and a transcriptome analysis was performed to elucidate possible metabolic mechanisms important for oxygen reduction in G. sulfurreducens. The investigations revealed that cell growth with oxygen is possible to the same extent as with fumarate if the maximum specific oxygen uptake rate (sOUR) of 95 mgO2 gCDW-1 h-1 is not surpassed. Hereby, the entire amount of introduced oxygen is reduced. When oxygen concentrations are too high, cell growth is completely inhibited and there is no partial oxygen consumption. Transcriptome analysis suggests a menaquinol oxidase to be the enzyme responsible for oxygen reduction. Transcriptome analysis has further revealed three different survival strategies, depending on the oxygen concentration present. When prompted with small amounts of oxygen, G. sulfurreducens will try to escape the microaerobic area; if oxygen concentrations are higher, cells will focus on rapid and complete oxygen reduction coupled to cell growth; and ultimately cells will form protective layers if a complete reduction becomes impossible. The results presented here have important implications for understanding how G. sulfurreducens survives exposure to oxygen.

Klíčová slova:

Cell growth – Dissolved oxygen – Electron acceptors – Gene expression – Oxygen – Pili and fimbriae – Pyruvate – Transcriptome analysis


1. Caccavo F, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol. 1994;60(10):3752–9. 7527204

2. Mehta T, Coppi M V, Childers SE, Lovley DR. Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. Microbiology. 2005;71(12):8634–41.

3. Shelobolina ES, Coppi M V, Korenevsky AA, DiDonato LN, Sullivan SA, Konishi H, et al. Importance of c-type cytochromes for U(VI) reduction by Geobacter sulfurreducens. BMC Microbiol [Internet]. 2007;7(1):16. Available from: http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-7-16

4. Williams KH, Long PE, Davis JA, Wilkins MJ, N’Guessan AL, Steefel CI, et al. Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater. Geomicrobiol J. 2011 Jun;28(5–6):519–39.

5. Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, et al. Geobacter: The Microbe Electric’s Physiology, Ecology, and Practical Applications. Advances in Microbial Physiology. Adv Microb Physiol. 2011;59:1–100. doi: 10.1016/B978-0-12-387661-4.00004-5 22114840

6. Brown DG, Komlos J, Jaffé PR. Simultaneous utilization of acetate and hydrogen by Geobacter sulfurreducens and implications for use of hydrogen as an indicator of redox conditions. Environ Sci Technol. 2005;39(9):3069–76. doi: 10.1021/es048613p 15926554

7. Call DF, Logan BE. Lactate oxidation coupled to iron or electrode reduction by Geobacter sulfurreducens PCA. Appl Environ Microbiol. 2011;77(24):8791–4. doi: 10.1128/AEM.06434-11 22003020

8. Bond DR, Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. Appl Environ Microbiol. 2003;69(3):1548–55. doi: 10.1128/AEM.69.3.1548-1555.2003 12620842

9. Lin WC, Coppi M V, Lovley DR, Lovley DR. Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor. Appl Environ Microbiol. 2004;70(4):2525–8. doi: 10.1128/AEM.70.4.2525-2528.2004 15066854

10. Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, et al. Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments. Science (80-). 2003 Dec 12;302(5652):1967–9.

11. Nunez C, Esteve-Nunez A, Giometti C, Tollaksen S, Khare T, Lin W, et al. DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens. J Bacteriol [Internet]. 2006 Apr 15;188(8):2792–800. Available from: doi: 10.1128/JB.188.8.2792-2800.2006 16585740

12. Nunez C, Esteve-Nunez A, Giometti C, Tollaksen S, Khare T, Lin W, et al. DNA Microarray and Proteomic Analyses of the RpoS Regulon in Geobacter sulfurreducens. J Bacteriol [Internet]. 2006 Apr 15;188(8):2792–800. Available from: doi: 10.1128/JB.188.8.2792-2800.2006 16585740

13. Mouser PJ, Holmes DE, Perpetua LA, DiDonato R, Postier B, Liu A, et al. Quantifying expression of Geobacter spp. oxidative stress genes in pure culture and during in situ uranium bioremediation. ISME J. 2009;3(4):454–65. doi: 10.1038/ismej.2008.126 19129865

14. DiDonato LN, Sullivan SA, Methé BA, Nevin KP, England R, Lovley DR. Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol. 2006;188(24):8469–78. doi: 10.1128/JB.01278-06 17041036

15. Tremblay PL, Lovley DR. Role of the NiFe hydrogenase hya in oxidative stress defense in Geobacter sulfurreducens. J Bacteriol. 2012;194(9):2248–53. doi: 10.1128/JB.00044-12 22366414

16. Lovley DR, Holmes DE, Nevin KP. Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol. 2004;49:219–86. doi: 10.1016/S0065-2911(04)49005-5 15518832

17. Galushko AS, Schink B. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture. Arch Microbiol. 2000;174(5):314–21. doi: 10.1007/s002030000208 11131021

18. Wood PM. The potential diagram for oxygen at pH 7. Biochem J. 1988;253(1):287–9. doi: 10.1042/bj2530287 2844170

19. Butler JE, Glaven RH, Esteve-Núnez A, Nunez C, Shelobolina ES, Bond DR, et al. Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens. Microbiology. 2006;188(2):450–5.

20. Mahadevan R, Bond DR, Butler JE, Coppi V, Palsson BO, Schilling CH, et al. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol. 2006;72(2):1558–68. doi: 10.1128/AEM.72.2.1558-1568.2006 16461711

21. Ramel F, Amrani A, Pieulle L, Lamrabet O, Voordouw G, Seddiki N, et al. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation. Microbiology [Internet]. 2013 Dec 1;159(Pt_12):2663–73. Available from: http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.071282-0. doi: 10.1099/mic.0.071282-0 24085836

22. Altschul S, Madden T, Schäffer A, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res [Internet]. 1997 Sep 1;25(17):3389–402. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/25.17.3389. 9254694

23. Yang K, Borisov VB, Konstantinov AA, Gennis RB. The fully oxidized form of the cytochrome bd quinol oxidase from E. coli does not participate in the catalytic cycle: Direct evidence from rapid kinetics studies. FEBS Lett. 2008 Oct 29;582(25–26):3705–9. doi: 10.1016/j.febslet.2008.09.038 18823983

24. Kabashima Y, Kishikawa JI, Kurokawa T, Sakamoto J. Correlation between proton translocation and growth: Genetic analysis of the respiratory chain of Corynebacterium glutamicum. J Biochem. 2009;146(6):845–55. doi: 10.1093/jb/mvp140 19734178

25. Jenney FE Jr. Anaerobic microbes: Oxygen detoxification without superoxide dismutase. Science (80-). 1999 Oct;286(5438):306–9.

26. Lombard M, Fontecave M, Touati D, Nivière V. Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. J Biol Chem. 2000 Jan 7;275(1):115–21. doi: 10.1074/jbc.275.1.115 10617593

27. Daum B, Gold V. Twitch or swim: Towards the understanding of prokaryotic motion based on the type IV pilus blueprint. Biol Chem. 2018;399(7):799–808. doi: 10.1515/hsz-2018-0157 29894297

28. Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM. Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function. BMC Genomics. 2008;9:1–15. doi: 10.1186/1471-2164-9-1

29. Burrows LL. Pseudomonas aeruginosa Twitching motility: Type IV pili in action. Annu Rev Microbiol. 2012;66(1):493–520.

30. Reguera G. Microbial nanowires and electroactive biofilms. FEMS Microbiol Ecol. 2018 Jul 1;94(7):1–13.

31. Speers AM, Schindler BD, Hwang J, Genc A, Reguera G. Genetic identification of a PilT motor in Geobacter sulfurreducens reveals a role for pilus retraction in extracellular electron transfer. Front Microbiol. 2016;7(OCT):1–17.

32. Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, Lovley DR. Extracellular electron transfer via microbial nanowires. Nature. 2005;435(7045):1098–101. doi: 10.1038/nature03661 15973408

33. Richter L V., Sandler SJ, Weis RM. Two isoforms of Geobacter sulfurreducens PilA have distinct roles in pilus biogenesis, cytochrome localization, extracellular electron transfer, and biofilm formation. J Bacteriol. 2012;194(10):2551–63. doi: 10.1128/JB.06366-11 22408162

34. Steidl RJ, Lampa-Pastirk S, Reguera G. Mechanistic stratification in electroactive biofilms of Geobacter sulfurreducens mediated by pilus nanowires. Nat Commun [Internet]. 2016 Dec 2;7(1):12217. Available from: http://www.nature.com/articles/ncomms12217

35. Sondermann H, Shikuma NJ, Yildiz FH. You’ve come a long way: c-di-GMP signaling. Curr Opin Microbiol. 2012 Apr;15(2):140–6. doi: 10.1016/j.mib.2011.12.008 22226607

36. Boyd CD, O’Toole GA. Second messenger regulation of biofilm formation: Breakthroughs in understanding c-di-GMP effector Systems. Annu Rev Cell Dev Biol. 2012 Nov 10;28(1):439–62.

37. Romling U, Galperin MY, Gomelsky M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev. 2013 Mar 1;77(1):1–52. doi: 10.1128/MMBR.00043-12 23471616

38. Engel C, Schattenberg F, Dohnt K, Schröder U, Müller S, Krull R. Long-Term Behavior of Defined Mixed Cultures of Geobacter sulfurreducens and Shewanella oneidensis in Bioelectrochemical Systems. Front Bioeng Biotechnol. 2019 Mar 27;7:60. doi: 10.3389/fbioe.2019.00060 30972336

39. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev. 1979;43(2):260–96. 390357

40. Kim JR, Min B, Logan BE. Evaluation of procedures to acclimate a microbial fuel cell for electricity production. Appl Microbiol Biotechnol. 2005;68(1):23–30. doi: 10.1007/s00253-004-1845-6 15647935

41. Weisenberger S, Schumpe A. Estimation of gas solublility in salt solution at temperatures from 273 to 363K. AIChE J. 1996;42(1):298–300.

42. Biedendieck R, Borgmeier C, Bunk B, Stammen S, Scherling C, Meinhardt F, et al. Systems biology of recombinant protein production using Bacillus megaterium. 1st ed. Vol. 500, Methods in Enzymology. Oxford: Elsevier Inc.; 2011. 165–195 p.

43. Borgmeier C, Biedendieck R, Hoffmann K, Jahn D, Meinhardt F. Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression. Appl Microbiol Biotechnol. 2011;92(3):583–96. doi: 10.1007/s00253-011-3575-x 21935588

44. Yang Y H, Dudoit S, Luu P, Lin D M, Peng V, Ngai J, Speed T P. Normalization for cDNA microarray data: a robust composite methodaddressing single and multiple slide systematic variation. Nucleic Acids Res. 2002;30(4):e15. doi: 10.1093/nar/30.4.e15 11842121

Článek vyšel v časopise


2020 Číslo 1
Nejčtenější tento týden