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.

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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.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

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

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  5. 5.

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

    PubMed  Google Scholar 

  6. 6.

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

    CAS  PubMed  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  Google Scholar 

  11. 11.

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

    Google Scholar 

  12. 12.

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

    Google Scholar 

  13. 13.

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

    CAS  PubMed  Google Scholar 

  14. 14.

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

    CAS  PubMed  Google Scholar 

  15. 15.

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

    PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    PubMed  Google Scholar 

  18. 18.

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

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  21. 21.

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

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

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

    PubMed  PubMed Central  Google Scholar 

  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.

    Google Scholar 

  33. 33.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  36. 36.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    PubMed  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    PubMed  PubMed Central  Google Scholar 

  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.

    CAS  Google Scholar 

  50. 50.

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

    Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    Google Scholar 

  55. 55.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

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

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  PubMed Central  Google Scholar 

  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.

    Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  PubMed  Google Scholar 

  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.

    CAS  Google Scholar 

  63. 63.

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

    CAS  PubMed  PubMed Central  Google Scholar 

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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.

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Correspondence to Gilles P. van Wezel.

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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

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