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.

Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone

The ISME Journal volume 17, pages 2103–2111 (2023)Cite this article

Subjects

Abstract

Although microbial humus respiration plays a critical role in organic matter decomposition and biogeochemical cycling of elements in diverse anoxic environments, the role of methane-producing species (methanogens) is not well defined. Here we report that a major fraction of humus, humic acid reduction enhanced the growth of Methanosarcina acetivorans above that attributed to methanogenesis when utilizing the energy sources methanol or acetate, results which showed both respiratory and fermentative modes of energy conservation. Growth characteristics with methanol were the same for an identically cultured mutant deleted for the gene encoding a multi-heme cytochrome c (MmcA), results indicating MmcA is not essential for respiratory electron transport to humic acid. Transcriptomic analyses revealed that growth with humic acid promoted the upregulation of genes annotated as cell surface pyrroloquinoline quinone (PQQ)-binding proteins. Furthermore, PQQ isolated from the membrane fraction was more abundant in humic acid-respiring cells, and the addition of PQQ improved efficiency of the extracellular electron transport. Given that the PQQ-binding proteins are widely distributed in methanogens, the findings extend current understanding of microbial humus respiration in the context of global methane dynamics.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Fig. 1: Growth parameters of M. acetivorans grown with or without HA.
Fig. 2: A gene cluster ranged from MA4284 to MA4315 was upregulated in HA-respiring cells compared to nonrespiring cells of M. acetivorans.
Fig. 3: Isolation of PQQ from the membrane fraction of M. acetivorans and analysis by LC–MS.
Fig. 4: Potential roles of PQQ and MP in extracellular electron transport.
Fig. 5: Prevalence of PQQ-binding β-propeller repeat proteins and predicted homologues.

Data availability

Illumina sequence reads have been submitted to the SRA NCBI database under Bioprojects PRJNA859665 and PRJNA862363 including Biosamples SAMN29793682 (SRX16315150 to SRX16315152), SAMN29793683 (SRX16315153 to SRX16315155), SAMN29975242 (SRX16673125 to SRX16673127), and SAMN29975243 (SRX16673128 to SRX16673130).

References

  1. Hayes M. Humus chemistry - genesis, composition, reactions - Stevenson,Fj. Nature. 1983;303:835–6.

    Article  Google Scholar 

  2. Wang SQ, Wang YX, He XS, Lu QH. Degradation or humification: rethinking strategies to attenuate organic pollutants. Trends Biotechnol. 2022;40:1061–72.

    Article  CAS  PubMed  Google Scholar 

  3. Lipczynska-Kochany E. Humic substances, their microbial interactions and effects on biological transformations of organic pollutants in water and soil: a review. Chemosphere. 2018;202:420–37.

    Article  CAS  PubMed  Google Scholar 

  4. Lovley DR, Coates JD, BluntHarris EL, Phillips EJP, Woodward JC. Humic substances as electron acceptors for microbial respiration. Nature. 1996;382:445–8.

    Article  CAS  Google Scholar 

  5. Lovley DR, Fraga JL, Blunt-Harris EL, Hayes LA, Phillips EJP, Coates JD. Humic substances as a mediator for microbially catalyzed metal reduction. Acta Hydroch Hydrob. 1998;26:152–7.

    Article  CAS  Google Scholar 

  6. Scott DT, McKnight DM, Blunt-Harris EL, Kolesar SE, Lovely DR. Quinone moieties act as electron acceptors in the reduction of humic substances by humics-reducing microorganisms. Environ Sci Technol. 1999;32:2984–89.

    Article  Google Scholar 

  7. Shi L, Dong HL, Reguera G, Beyenal H, Lu AH, Liu J, et al. Extracellular electron transfer mechanisms between microorganisms and minerals. Nat Rev Microbiol. 2016;14:651–62.

    Article  CAS  PubMed  Google Scholar 

  8. Roden EE, Kappler A, Bauer I, Jiang J, Paul A, Stoesser R, et al. Extracellular electron transfer through microbial reduction of solid-phase humic substances. Nat Geosci. 2010;3:417–21.

    Article  CAS  Google Scholar 

  9. Klupfel L, Piepenbrock A, Kappler A, Sander M. Humic substances as fully regenerable electron acceptors in recurrently anoxic environments. Nat Geosci. 2014;7:195–200.

    Article  Google Scholar 

  10. Valenzuela EI, Cervantes FJ. The role of humic substances in mitigating greenhouse gases emissions: current knowledge and research gaps. Sci Total Environ. 2021;750:141677.

    Article  CAS  PubMed  Google Scholar 

  11. Ferry JG. How to make a living by exhaling methane. Annu Rev Microbiol. 2010;64:453–73.

    Article  CAS  PubMed  Google Scholar 

  12. Prakash D, Chauhan SS, Ferry JG. Life on the thermodynamic edge: respiratory growth of an acetotrophic methanogen. Sci Adv. 2019;5:eaaw9059.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Yang Z, Lu Y. Coupling methanogenesis with iron reduction by acetotrophic Methanosarcina mazei zm-15. Environ Microbiol Rep. 2022;14:804–11.

    Article  CAS  PubMed  Google Scholar 

  14. Holmes DE, Ueki T, Tang HY, Zhou JJ, Smith JA, Chaput G, et al. A membrane-bound cytochrome enables methanosarcina acetivorans to conserve energy from extracellular electron transfer. mBio. 2019;10:e00789–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Welte C, Deppenmeier U. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. BBA-Bioenerg. 2014;1837:1130–47.

    Article  CAS  Google Scholar 

  16. Ferry JG. Methanosarcina acetivorans: a model for mechanistic understanding of aceticlastic and reverse methanogenesis. Front Microbiol. 2020;11:01806.

    Article  Google Scholar 

  17. Gao KL, Lu YH. Putative extracellular electron transfer in methanogenic archaea. Front Microbiol. 2021;12:611739.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Duine JA, Jongejan JA. Quinoproteins, enzymes with pyrrolo-quinoline quinone as cofactor. Annu Rev Biochem. 1989;58:403–26.

    Article  CAS  PubMed  Google Scholar 

  19. Kobe B, Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struc Biol. 2001;11:725–32.

    Article  CAS  Google Scholar 

  20. Jing H, Takagi J, Liu JH, Lindgren S, Zhang RG, Joachimiak A, et al. Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins. Structure. 2002;10:1453–64.

    Article  CAS  PubMed  Google Scholar 

  21. Jenkins J, Mayans O, Pickersgill R. Structure and evolution of parallel beta-helix proteins. J Struct Biol. 1998;122:236–46.

    Article  CAS  PubMed  Google Scholar 

  22. Takamiya K, Nishimura M. Dual roles of ubiquinone as primary and secondary-electron acceptors in light-induced electron-transfer in chromatophores of chromatiun-D. Plant Cell Physiol. 1975;16:1061–72.

    Article  CAS  Google Scholar 

  23. Ding HG, Robertson DE, Daldal F, Dutton PL. Cytochrome-Bc1 complex [2fe-2s] cluster and its interaction with ubiquinone and ubihydroquinone at the Q0 site - a double-occupancy Q0 site model. Biochemistry. 1992;31:3144–58.

  24. Kato C, Kawai E, Shimizu N, Mikekado T, Kimura F, Miyazawa T, et al. Determination of pyrroloquinoline quinone by enzymatic and LC-MS/MS methods to clarify its levels in foods. Plos One. 2018;13:e0209700.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Noji N, Nakamura T, Kitahata N, Taguchi K, Kudo T, Yoshida S, et al. Simple and sensitive method for pyrroloquinoline quinone (PQQ) analysis in various foods using liquid chromatography/electrospray-lonization tandem mass spectrometry. J Agr Food Chem. 2007;55:7258–63.

    Article  CAS  Google Scholar 

  26. Yan Z, Joshi P, Gorski CA, Ferry JG. A biochemical framework for anaerobic oxidation of methane driven by Fe(III)-dependent respiration. Nat Commun. 2018;9:1642.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Gottschalk G, Thauer RK. The Na+-translocating methyltransferase complex from methanogenic archaea. BBA Bioenerg. 2001;1505:28–36.

    Article  CAS  Google Scholar 

  28. Abken HJ, Tietze M, Brodersen J, Baumer S, Beifuss U, Deppenmeier U. Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei Gol. J Bacteriol. 1998;180:2027–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Yee MO, Rotaru AE. Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes. Sci Rep. 2020;10:372.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Matsutani M, Yakushi T. Pyrroloquinoline quinone-dependent dehydrogenases of acetic acid bacteria. Appl Microbiol Biot. 2018;102:9531–40.

    Article  CAS  Google Scholar 

  31. Qin ZJ, Yu SQ, Chen J, Zhou JW. Dehydrogenases of acetic acid bacteria. Biotechnol Adv. 2022;54:107863.

    Article  CAS  PubMed  Google Scholar 

  32. Anthony C. Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes. Antioxid Redox Sign. 2001;3:757–74.

    Article  CAS  Google Scholar 

  33. Holmes DE, Rotaru AE, Ueki T, Shrestha PM, Ferry JG, Lovley DR. Electron and proton flux for carbon dioxide reduction in methanosarcina barkeri during direct interspecies electron transfer. Front Microbiol. 2018;9:03109.

    Article  Google Scholar 

  34. Huang LY, Liu X, Zhang ZS, Ye J, Rensing C, Zhou SG, et al. Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture. ISME J. 2022;16:370–7.

    Article  CAS  PubMed  Google Scholar 

  35. Evans PN, Boyd JA, Leu AO, Woodcroft B, Parks DH, Hugenholtz P, et al. An evolving view of methane metabolism in the Archaea. Nat Rev Microbiol. 2019;17:219–32.

    Article  CAS  PubMed  Google Scholar 

  36. Sowers KR, Baron SF, Ferry JG. Methanosarcina-acetivorans Sp-Nov, an acetotrophic methane-producing bacterium isolated from marine-sediments. Appl Environ Micro. 1984;47:971–8.

    Article  CAS  Google Scholar 

  37. Tang J, Zhuang L, Ma JL, Tang ZY, Yu Z, Zhou SG. Secondary mineralization of ferrihydrite affects microbial methanogenesis in geobacter-methanosarcina cocultures. Appl Environ Micro. 2016;82:5869–77.

    Article  CAS  Google Scholar 

  38. Li J, Hao XD, van Loosdrecht MCM, Luo YQ, Cao DQ. Effect of humic acids on batch anaerobic digestion of excess sludge. Water Res. 2019;155:431–43.

    Article  CAS  PubMed  Google Scholar 

  39. Song YX, Duan LF, Du KF, Song C, Zhao S, Yuan XZ, et al. Nano zero-valent iron harms methanogenic archaea by interfering with energy conservation and methanogenesis. Environ Sci Nano. 2021;8:3643–54.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Sen Wang from State Key laboratory of Microbial Technology of Shandong University for help and guidance in SEM. The authors thank Wenshan Qi from Biozeron Co., Ltd. for his technical assistance of RNA-Seq in this study. The authors thank Dr. Lovley’s group for providing ∆hpt and ∆hpt∆mmcA of M. acetivorans. This work was supported by National Natural Science Foundation of China (22008142), Natural Science Foundation of Shandong Province (ZR2022YQ31), Natural Science Foundation of Jiangsu Province (BK20200232), and Qilu Youth Talent Program of Shandong University. Prof. Shuguang Wang acknowledges Taishan Scholars project of Shandong Province (NO. tstp20230604).

Author information

Author notes

  1. These authors contributed equally: Yuanxu Song, Rui Huang, Ling Li.

Authors and Affiliations

  1. Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China

    Yuanxu Song, Rui Huang, Kaifeng Du, Fanping Zhu, Chao Song, Xianzheng Yuan, Shuguang Wang & Zhen Yan

  2. State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, 266237, Shandong, China

    Ling Li & Mingyu Wang

  3. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA

    James G. Ferry

  4. Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Shungui Zhou

  5. Suzhou Research Institute, Shandong University, Suzhou, 215123, Jiangsu, China

    Zhen Yan

Authors
  1. Yuanxu Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rui Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ling Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kaifeng Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fanping Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chao Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xianzheng Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Mingyu Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Shuguang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. James G. Ferry
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Shungui Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Zhen Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

ZY and JF conceived and designed the study; YS, KD, LL, RH and FZ performed the experiment and collected the data; ZY, RH, YS, LL and MW wrote the manuscript; ZY, RH, CS, XY, SZ, MW, SW and JF analyzed and interpreted the data; ZY, RH, CS, XY, SZ, MW, SW and JF revised the manuscript.

Corresponding authors

Correspondence to Mingyu Wang, Shuguang Wang or Zhen Yan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Song, Y., Huang, R., Li, L. et al. Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone. ISME J 17, 2103–2111 (2023). https://doi.org/10.1038/s41396-023-01520-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41396-023-01520-y

Search

Advanced search

Quick links