Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species

Abstract

Soil-inhabiting streptomycetes are nature’s medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatiles, molecules that disperse through the soil matrix and may impact other (micro)organisms from a distance. Here, we show that soil- and surface-grown streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile ammonia, dispersing over long distances to inhibit the growth of Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system nullified ammonia biosynthesis and concomitantly air-borne antibiosis. Reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ is used as a resistance strategy by E. coli cells to survive ammonia-mediated antibiosis. Finally, ammonia was shown to enhance the activity of canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis from a distance.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

References

  1. 1.

    Schmidt R, Cordovez V, de Boer W, Raaijmakers J, Garbeva P. Volatile affairs in microbial interactions. ISME J. 2015;9:2329–35.

  2. 2.

    Schulz S, Dickschat JS. Bacterial volatiles: the smell of small organisms. Nat Prod Rep. 2007;24:814–42.

  3. 3.

    Audrain B, Farag MA, Ryu CM, Ghigo JM. Role of bacterial volatile compounds in bacterial biology. FEMS Microbiol Rev. 2015;39:222–33.

  4. 4.

    Kai M, Haustein M, Molina F, Petri A, Scholz B, Piechulla B. Bacterial volatiles and their action potential. Appl Microbiol Biotechnol. 2009;81:1001–12.

  5. 5.

    Kim KS, Lee S, Ryu CM. Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance. Nat Commun. 2013;4:1809.

  6. 6.

    Nijland R, Burgess JG. Bacterial olfaction. Biotechnol J. 2010;5:974–7.

  7. 7.

    Que YA, Hazan R, Strobel B, Maura D, He J, Kesarwani M, et al. A quorum sensing small volatile molecule promotes antibiotic tolerance in bacteria. PLoS ONE. 2013;8:e80140.

  8. 8.

    Schulz-Bohm K, Martín-Sánchez L, Garbeva P. Microbial volatiles: small molecules with an important role in intra- and inter-kingdom interactions. Front Microbiol. 2017;8:2484.

  9. 9.

    Cordovez V, Carrion VJ, Etalo DW, Mumm R, Zhu H, van Wezel GP, et al. Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil. Front Microbiol. 2015;6:1081.

  10. 10.

    Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev. 2016;80:1–43.

  11. 11.

    Hopwood DA. Streptomyces in nature and medicine: the antibiotic makers. New York: Oxford University Press; 2007b.

  12. 12.

    Hopwood DA. Streptomyces in nature and medicine. New York, NY: The Antibiotic Makers. Oxford University Press Inc; 2007a.

  13. 13.

    Berdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot. 2012;65:385–95.

  14. 14.

    Citron CA, Barra L, Wink J, Dickschat JS. Volatiles from nineteen recently genome sequenced actinomycetes. Org Biomol Chem. 2015;13:2673–83.

  15. 15.

    Schöller CEG, Gürtler H, Pedersen R, Molin S, Wilkins K. Volatile metabolites from actinomycetes. J Agric Food Chem. 2002;50:2615–21.

  16. 16.

    Wang C, Wang Z, Qiao X, Li Z, Li F, Chen M, et al. Antifungal activity of volatile organic compounds from Streptomyces alboflavus TD-1. FEMS Microbiol Lett. 2013;341:45–51.

  17. 17.

    Gürtler H, Pedersen R, Anthoni U, Christophersen C, Nielsen PH, Wellington EM, et al. Albaflavenone, a sesquiterpene ketone with a zizaene skeleton produced by a streptomycete with a new rope morphology. J Antibiot. 1994;47:434–9.

  18. 18.

    Davies J. Are antibiotics naturally antibiotics? J Ind Microbiol Biotechnol. 2006;33:496–9.

  19. 19.

    Abrudan MI, Smakman F, Grimbergen AJ, Westhoff S, Miller EL, van Wezel GP, et al. Socially mediated induction and suppression of antibiosis during bacterial coexistence. Proc Natl Acad Sci USA. 2015;112:11054–9.

  20. 20.

    Avalos M, van Wezel GP, Raaijmakers JM, Garbeva P. Healthy scents: microbial volatiles as new frontier in antibiotic research? Curr Opin Microbiol. 2018b;45:84–91.

  21. 21.

    Shatalin K, Shatalina E, Mironov A, Nudler E. H2S: a universal defense against antibiotics in bacteria. Science. 2011;334:986–90.

  22. 22.

    Gusarov I, Nudler E. NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria. Proc Natl Acad Sci USA. 2005;102:13855–60.

  23. 23.

    Shatalin K, Gusarov I, Avetissova E, Shatalina Y, McQuade LE, Lippard SJ, et al. Bacillus anthracis-derived nitric oxide is essential for pathogen virulence and survival in macrophages. Proc Natl Acad Sci USA. 2008;105:1009–13.

  24. 24.

    Gusarov I, Shatalin K, Starodubtseva M, Nudler E. Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science. 2009;325:1380–4.

  25. 25.

    van Sorge NM, Beasley FC, Gusarov I, Gonzalez DJ, von Kockritz-Blickwede M, Anik S, et al. Methicillin-resistant Staphylococcus aureus bacterial nitric-oxide synthase affects antibiotic sensitivity and skin abscess development. J Biol Chem. 2013;288:6417–26.

  26. 26.

    Bernier SP, Letoffe S, Delepierre M, Ghigo JM. Biogenic ammonia modifies antibiotic resistance at a distance in physically separated bacteria. Mol Microbiol. 2011;81:705–16.

  27. 27.

    Fadli M, Chevalier J, Hassani L, Mezrioui NE, Pages JM. Natural extracts stimulate membrane-associated mechanisms of resistance in Gram-negative bacteria. Lett Appl Microbiol. 2014;58:472–7.

  28. 28.

    Yung PY, Grasso LL, Mohidin AF, Acerbi E, Hinks J, Seviour T, et al. Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds. Sci Rep. 2016;6:19899.

  29. 29.

    Liu M, Douthwaite S. Activity of the ketolide telithromycin is refractory to Erm monomethylation of bacterial rRNA. Antimicrob Agents Chemother. 2002;46:1629–33.

  30. 30.

    Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, et al. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology. 2009;155:1758–75.

  31. 31.

    Garbeva P, Hordijk C, Gerards S, de Boer W. Volatile-mediated interactions between phylogenetically different soil bacteria. Front Microbiol. 2014;5:289.

  32. 32.

    Pluskal T, Castillo S, Villar-Briones A, Oresic M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinform. 2010;11:11.

  33. 33.

    Xia J, Sinelnikov IV, Han B, Wishart DS. MetaboAnalyst 3.0-making metabolomics more meaningful. Nucleic Acids Res. 2015;43:W251–W257.

  34. 34.

    Campbell CD, Chapman SJ, Cameron CM, Davidson MS, Potts JM. A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl Environ Microbiol. 2003;69:3593–9.

  35. 35.

    Tezuka T, Ohnishi Y. Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus. J Bacteriol. 2014;196:1369–76.

  36. 36.

    Castric KF, Castric PA. Method for rapid detection of cyanogenic bacteria. Appl Environ Microbiol. 1983;45:701–2.

  37. 37.

    Avalos M, Boetzer M, Pirovano W, Arenas NE, Douthwaite S, van Wezel GP. Complete genome sequence of Escherichia coli AS19, an antibiotic-sensitive variant of E. coli strain B REL606. Genome Announc. 2018a;6:e00385–00318.

  38. 38.

    Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinforma. 2012;13:238.

  39. 39.

    Kitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, Toyonaga H, et al. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 2005;12:291–9.

  40. 40.

    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.

  41. 41.

    Zhu H, Swierstra J, Wu C, Girard G, Choi YH, van Wamel W, et al. Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils. Microbiology. 2014;160:1714–25.

  42. 42.

    Mohan C. Buffers. A guide for the preparation and use of buffers in biological systems, 2006.

  43. 43.

    Gubbens J, Zhu H, Girard G, Song L, Florea BI, Aston P, et al. Natural product proteomining, a quantitative proteomics platform, allows rapid discovery of biosynthetic gene clusters for different classes of natural products. Chem Biol. 2014;21:707–18.

  44. 44.

    Wu C, Kim HK, van Wezel GP, Choi YH. Metabolomics in the natural products field—a gateway to novel antibiotics. Drug Discov Today Technol. 2015;13:11–7.

  45. 45.

    Jones SE, Ho L, Rees CA, Hill JE, Nodwell JR, Elliot MA. Streptomyces exploration is triggered by fungal interactions and volatile signals. Elife. 2017;6:e21738.

  46. 46.

    Letoffe S, Audrain B, Bernier SP, Delepierre M, Ghigo JM. Aerial exposure to the bacterial volatile compound trimethylamine modifies antibiotic resistance of physically separated bacteria by raising culture medium pH. MBio. 2014;5:e00944–00913.

  47. 47.

    Čepl JJPI, Blahůšková A, Cvrčková F, Markoš A. Patterning of mutually interacting bacterial bodies: close contacts and airborne signals.BMC Microbiol. 2010;10:139.

  48. 48.

    Anwar S, Ali B, Sajid I. Screening of rhizospheric actinomycetes for various in-vitro and in-vivo plant growth promoting (PGP) traits and for agroactive compounds. Front Microbiol. 2016;7:1334.

  49. 49.

    Kikuchi G, Motokawa Y, Yoshida T, Hiraga K. Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia. Proc Jpn Acad Ser B. 2008;84:246–63.

  50. 50.

    Zhang L. Identification and characterization of developmental genes in Streptomyces (PhD thesis). Leiden: Leiden University; 2015.

  51. 51.

    Bobille H, Limami AM, Robins RJ, Cukier C, Le Floch G, Fustec J. Evolution of the amino acid fingerprint in the unsterilized rhizosphere of a legume in relation to plant maturity. Soil Biol Biochem. 2016;101:226–36.

  52. 52.

    Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470–80.

  53. 53.

    Conroy MJ, Durand A, Lupo D, Li X-D, Bullough PA, Winkler FK, et al. The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci USA. 2007;104:1213.

  54. 54.

    Wirén Nv, Merrick M. Regulation and function of ammonium carriers in bacteria, fungi, and plants. Molecular mechanisms controlling transmembrane transport. Springer Berlin Heidelberg: Berlin, Heidelberg. 2004;95–120.

  55. 55.

    Nikaido H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev. 2003;67:593–656.

  56. 56.

    Fernandez L, Hancock RE. Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev. 2012;25:661–81.

  57. 57.

    Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA. 2006;103:626–31.

  58. 58.

    Rousk J, Brookes PC, Bååth E. Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization. Appl Environ Microbiol. 2009;75:1589–96.

  59. 59.

    Bárcenas-Moreno G, Rousk J, Bååth E. Fungal and bacterial recolonisation of acid and alkaline forest soils following artificial heat treatments. Soil Biol Biochem. 2011;43:1023–33.

  60. 60.

    Serrano A, Gallego M. Sorption study of 25 volatile organic compounds in several Mediterranean soils using headspace–gas chromatography–mass spectrometry. J Chromatogr A. 2006;1118:261–70.

  61. 61.

    Hughes R, Magee EA, Bingham S. Protein degradation in the large intestine: relevance to colorectal cancer. Curr Issues Intest Microbiol. 2000;1:51–8.

  62. 62.

    Marques APGC, Pires C, Moreira H, Rangel AOSS, Castro PML. Assessment of the plant growth promotion abilities of six bacterial isolates using Zea mays as indicator plant. Soil Biol Biochem. 2010;42:1229–35.

  63. 63.

    Weise T, Kai M, Piechulla B. Bacterial ammonia causes significant plant growth inhibition. PLoS ONE. 2013;8:e63538.

Download references

Acknowledgements

This work was supported by Grant No. 313599 from The Mexican National Council of Science and Technology (CONACYT) to MA, by VIDI grant 864.11.015 from the Netherlands Organization for Scientific Research (NWO) to PG and by grant 14221 from the Netherlands Organization for Scientific Research (NWO) to GPvW. We thank Hans Zweer for technical help with GC/Q-TOF analysis and Lisanne Storm for the help with the volatile antimicrobial screening, Yasuo Ohnishi and Le Zhang for sharing the glycine cleavage system mutants from S. griseus and S. coelicolor respectively, and Stephen Douthwaite for providing E. coli AS19-RlmA.

Author information

Correspondence to Gilles P. van Wezel.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

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

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Avalos, M., Garbeva, P., Raaijmakers, J.M. et al. Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species. ISME J 14, 569–583 (2020). https://doi.org/10.1038/s41396-019-0537-2

Download citation

Further reading