Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens


Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.

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  1. 1.

    Bletz MC, Loudon AH, Becker MH, Bell SC, Woodhams DC, Minbiole KP, Harris RN (2013) Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use. Ecol. Lett. 16:807–820

    Article  PubMed  Google Scholar 

  2. 2.

    Grant EHC, Muths E, Katz RA, Canessa S, Adams MJ, Ballard JR, Berger L, Briggs CJ, Coleman JTH, Gray MJ, Harris MC, Harris RN, Hossack B, Huyvaert KP, Kolby JE, Lips KR, Lovich RE, McCallum HI, Mendelson JI, Nanjappa P, Olson DH, Powers JG, Richgels KLD, Russell RE, Schmidt BR, Spitzen-van der Sluijs A, Watry MK, Woodhams DC, White CL (2017) Even with forewarning, challenges remain in developing a proactive response to emerging diseases. Front Ecol Environ Accepted

  3. 3.

    Brucker RM, Harris RN, Schwantes CR, Gallaher TN, Flaherty DC, Lam BA, Minbiole KP (2008) Amphibian chemical defense: antifungal metabolites of the microsymbiont Janthinobacterium lividum on the salamander Plethodon cinereus. J. Chem. Ecol. 34:1422–1429.

    CAS  Article  PubMed  Google Scholar 

  4. 4.

    Ligon JM, Hill DS, Hammer PE, Torkewitz NR, Hofmann D, Kempf HJ, van Pee KH (2000) Natural products with antifungal activity from Pseudomonas biocontrol bacteria. Pest Manag. Sci. 56:688–695.<688::Aid-Ps186>3.3.Co;2-M

    CAS  Article  Google Scholar 

  5. 5.

    Brucker RM, Baylor CM, Walters RL, Lauer A, Harris RN, Minbiole KPC (2008) The identification of 2,4-diacetylphloroglucinol as an antifungal metabolite produced by cutaneous bacteria of the salamander Plethodon cinereus. J. Chem. Ecol. 34:39–43.

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Lapenda J, Silva P, Vicalvi M, Sena K, Nascimento S (2015) Antimicrobial activity of prodigiosin isolated from Serratia marcescens UFPEDA 398. World J. Microbiol. Biotechnol. 31:399–406

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Shieh WY, Chen YW, Chaw SM, Chiu HH (2003) Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int. J. Syst. Evol. Microbiol. 53:479–484.

    Article  PubMed  Google Scholar 

  8. 8.

    Hejazi A, Falkiner F (1997) Serratia marcescens. J. Med. Microbiol. 46:903–912

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Grimont PA, Grimont F (1978) The genus Serratia. Annu. Rev. Microbiol. 32:221–248.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Schloss PD, Allen HK, Klimowicz AK, Mlot C, Gross JA, Savengsuksa S, McEllin J, Clardy J, Ruess RW, Handelsman J (2010) Psychrotrophic strain of Janthinobacterium lividum from a cold Alaskan soil produces prodigiosin. DNA Cell Biol. 29:533–541.

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Song YX, Liu GF, Li J, Huang HB, Zhang X, Zhang H, Ju JH (2015) Cytotoxic and antibacterial angucycline- and prodigiosin- analogues from the deep-sea derived Streptomyces sp. SCSIO 11594. Marine Drugs 13:1304–1316.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Kumar NR, Nair S (2007) Vibrio rhizosphaerae sp nov., a red-pigmented bacterium that antagonizes phytopathogenic bacteria. Int. J. Syst. Evol. Microbiol. 57:2241–2246.

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Yamamoto C, Takemoto H, Kuno K, Yamamoto D, Tsubura A, Kamata K, Hirata H, Yamamoto A, Kano H, Seki T, Inoue K (1999) Cycloprodigiosin hydrochloride, a new H+/Cl- symporter, induces apoptosis in human and rat hepatocellular cancer cell lines in vitro and inhibits the growth of hepatocellular carcinoma xenografts in nude mice. Hepatology 30:894–902.

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Lee JS, Kim YS, Park S, Kim J, Kang SJ, Lee MH, Ryu S, Choi JM, Oh TK, Yoon JH (2011) Exceptional production of both prodigiosin and cycloprodigiosin as major metabolic constituents by a novel marine bacterium, Zooshikella rubidus S1-1. Appl. Environ. Microbiol. 77:4967–4973.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Sawabe T, Makino H, Tatsumi M, Nakano K, Tajima K, Iqbal MM, Yumoto I, Ezura Y, Christen R (1998) Pseudoalteromonas bacteriolytica sp. nov., a marine bacterium that is the causative agent of red spot disease of Laminaria japonica. Int. J. Syst. Bacteriol. 48:769–774

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Feher D, Barlow RS, Lorenzo PS, Hemscheidt TK (2008) A 2-substituted prodiginine, 2-(p-hydroxybenzyl)prodigiosin, from Pseudoalteromonas rubra. J. Nat. Prod. 71:1970–1972.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Boger DL, Patel M (1988) Total synthesis of prodigiosin, prodigiosene, and desmethoxyprodigiosin: Diels-Alder reactions of heterocyclic azadienes and development of an effective palladium(II)-promoted 2,2′-bipyrrole coupling procedure. J. Org. Chem. 53:1405–1415.

    CAS  Article  Google Scholar 

  18. 18.

    Montaner B, Perez-Tomas R (2003) The prodigiosins: a new family of anticancer drugs. Curr. Cancer Drug Targets 3:57–65

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Castro AJ (1967) Antimalarial activity of prodigiosin. Nature 213:903–904

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Zhang H, Peng Y, Zhang S, Cai G, Li Y, Yang X, Yang K, Chen Z, Zhang J, Wang H, Zheng T, Zheng W (2016) Algicidal effects of prodigiosin on the harmful algae Phaeocystis globosa. Front. Microbiol. 7:602.

    PubMed  PubMed Central  Google Scholar 

  21. 21.

    Han SB, Kim HM, Kim YH, Lee CW, Jang ES, Son KH, Kim SU, Kim YK (1998) T-cell specific immunosuppression by prodigiosin isolated from Serratia marcescens. Int. J. Immunopharmacol. 20:1–13

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Danevčič T, Vezjak MB, Tabor M, Zorec M, Stopar D (2016) Prodigiosin induces autolysins in actively grown Bacillus subtilis cells. Front. Microbiol. 7

  23. 23.

    Danevčič T, Vezjak MB, Zorec M, Stopar D (2016) Prodigiosin—a multifaceted Escherichia coli antimicrobial agent. PLoS One 11:e0162412

    Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Luti K (2015) The role of interspecies interactions in the antibiotic production: a potential approach for producing more effective antibiotics. In: Méndez-Vilas A (ed.) The battle against microbial pathogens: basic science, technological advances and educational programs. Formatex, p 1091–1098

  25. 25.

    Kimyon Ö, Das T, Ibugo AI, Kutty SK, Ho KK, Tebben J, Kumar N, Manefield M (2016) Serratia secondary metabolite prodigiosin inhibits pseudomonas aeruginosa biofilm development by producing reactive oxygen species that damage biological molecules. Front Microbiol 7

  26. 26.

    Alihosseini F, Ju KS, Lango J, Hammock BD, Sun G (2008) Antibacterial colorants: characterization of prodiginines and their applications on textile materials. Biotechnol. Prog. 24:742–747.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Venil CK, Lakshmanaperumalsamy P (2009) An insightful overview on microbial pigment, prodigiosin. Electronic Journal of Biology 5:49–61

    Google Scholar 

  28. 28.

    Bennett J, Bentley R (2000) Seeing red: the story of prodigiosin. Adv. Appl. Microbiol. 47:1–32

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Becker MH, Brucker RM, Schwantes CR, Harris RN, Minbiole KPC (2009) The bacterially produced metabolite violacein is associated with survival of amphibians infected with a lethal fungus. Appl. Environ. Microbiol. 75:6635–6638.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Stotzky G, Schenck S, Papavizas GC (1976) Volatile organic compounds and microorganisms. CRC Crit. Rev. Microbiol. 4:333–382

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Zou C-S, Mo M-H, Gu Y-Q, Zhou J-P, Zhang K-Q (2007) Possible contributions of volatile-producing bacteria to soil fungistasis. Soil Biol. Biochem. 39:2371–2379.

    CAS  Article  Google Scholar 

  32. 32.

    Kerr JR (1999) Bacterial inhibition of fungal growth and pathogenicity. Microb. Ecol. Health Dis. 11:129–142

    Article  Google Scholar 

  33. 33.

    Stahl PD, Parkin TB (1996) Microbial production of volatile organic compounds in soil microcosms. Soil Sci. Soc. Am. J. 60:821–828

    CAS  Article  Google Scholar 

  34. 34.

    Ezra D, Strobel GA (2003) Effect of substrate on the bioactivity of volatile antimicrobials produced by Muscodor albus. Plant Sci. 165:1229–1238.

    CAS  Article  Google Scholar 

  35. 35.

    Fernando WD, Ramarathnam R, Krishnamoorthy AS, Savchuk SC (2005) Identification and use of potential bacterial organic antifungal volatiles in biocontrol. Soil Biol. Biochem. 37:955–964.

    CAS  Article  Google Scholar 

  36. 36.

    Harris RN, Brucker RM, Walke JB, Becker MH, Schwantes CR, Flaherty DC, Lam BA, Woodhams DC, Briggs CJ, Vredenburg VT, Minbiole KP (2009) Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus. ISME J 3:818–824.

    CAS  Article  PubMed  Google Scholar 

  37. 37.

    Woodhams DC, Brandt H, Baumgartner S, Kielgast J, Kupfer E, Tobler U, Davis LR, Schmidt BR, Bel C, Hodel S, Knight R, McKenzie V (2014) Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness. PLoS One 9:e96375.

    Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Loudon AH, Venkataraman A, Van Treuren W, Woodhams DC, Parfrey LW, McKenzie VJ, Knight R, Schmidt TM, Harris RN (2016) Vertebrate hosts as islands: dynamics of selection, immigration, loss, persistence, and potential function of bacteria on salamander skin. Front. Microbiol. 7.

  39. 39.

    Hoyt JR, Cheng TL, Langwig KE, Hee MM, Frick WF, Kilpatrick AM (2015) Bacteria isolated from bats inhibit the growth of Pseudogymnoascus destructans, the causative agent of white-nose syndrome. PLoS One 10:e0121329.

    Article  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Cornelison CT, Gabriel KT, Barlament C, Crow Jr SA (2014) Inhibition of Pseudogymnoascus destructans growth from conidia and mycelial extension by bacterially produced volatile organic compounds. Mycopathologia 177:1–10.

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Becker MH, Walke JB, Murrill L, Woodhams DC, Reinert LK, Rollins-Smith LA, Burzynski EA, Umile TP, Minbiole KPC, Belden LK (2015) Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis. Mol. Ecol. 24:1628–1641.

    Article  PubMed  Google Scholar 

  42. 42.

    Flechas SV, Medina EM, Crawford AJ, Sarmiento C, Cardenas ME, Amezquita A, Restrepo S (2013) Characterization of the first Batrachochytrium dendrobatidis isolate from the Colombian Andes, an amphibian biodiversity hotspot. EcoHealth 10:72–76.

    CAS  Article  PubMed  Google Scholar 

  43. 43.

    Umile TP, McLaughlin PJ, Johnson KR, Honarvar S, Blackman AL, Burzynski EA, Davis RW, Teotonio TL, Hearn GW, Hughey CA, Lagalante AF, Minbiole KPC (2014) Nonlethal amphibian skin swabbing of cutaneous natural products for HPLC fingerprinting. Anal. Methods 6:3277–3284.

    CAS  Article  Google Scholar 

  44. 44.

    Bell SC, Alford RA, Garland S, Padilla G, Thomas AD (2013) Screening bacterial metabolites for inhibitory effects against Batrachochytrium dendrobatidis using a spectrophotometric assay. Dis. Aquat. Org. 103:77–85

    Article  PubMed  Google Scholar 

  45. 45.

    Woodhams DC, Bletz M, Kueneman J, McKenzie V (2016) Managing amphibian disease with skin microbiota. Trends Microbiol. 24:161–164

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ (2014) The amphibian skin-associated microbiome across species, space and life history stages. Mol. Ecol. 23:1238–1250.

    Article  PubMed  Google Scholar 

  47. 47.

    Belden LK, Hughey MC, Rebollar EA, Umile TP, Loftus SC, Burzynski EA, Minbiole K, House LL, Jensen RV, Becker MH (2014) Panamanian frog species host unique skin bacterial communities. Front. Microbiol. 6:1171–1171

    Google Scholar 

  48. 48.

    Sabino-Pinto J, Bletz MC, Islam MM, Shimizu N, Bhuju S, Geffers R, Jarek M, Kurabayashi A, Vences M (2016) Composition of the cutaneous bacterial community in Japanese amphibians: effects of captivity, host species, and body region. Microb. Ecol. 72:460–469.

    Article  PubMed  Google Scholar 

  49. 49.

    Bletz MC, Vences M, Sabino-Pinto J, Taguchi Y, Shimizu N, Nishikawa K, Kurabayashi A (2017) Cutaneous microbiota of the Japanese giant salamander (Andrias japonicus), a representative of an ancient amphibian clade. Hydrobiologia:1–15

  50. 50.

    Perl RB, Gafny S, Malka Y, Renan S, Woodhams DC, Rollins-Smith L, Pask JD, Bletz MC, Geffen E, Vences M (2017) Natural history and conservation of the rediscovered Hula painted frog, Latonia nigriventer. Contrib. Zool. 86:11–37

    Google Scholar 

  51. 51.

    Sanchez E, Bletz MC, Duntsch L, Bhuju S, Geffers R, Jarek M, Dohrmann AB, Tebbe CC, Steinfartz S, Vences M (2017) Cutaneous bacterial communities of a poisonous salamander: a perspective from life stages, body parts and environmental conditions. Microb. Ecol. 73:455–465.

    CAS  Article  PubMed  Google Scholar 

  52. 52.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335–336.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Xu ZZ, Kightley EP, Thompson LR, Hyde ER, Gonzalez A (2017) Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2:e00191–e00116

    PubMed  PubMed Central  Google Scholar 

  54. 54.

    Woodhams DC, Alford RA, Antwis RE, Archer H, Becker MH, Belden LK, Bell SC, Bletz M, Daskin JH, Davis LR, et al. (2015) Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens. Ecology 96:595–595

    Article  Google Scholar 

  55. 55.

    Muletz-Wolz CR, DiRenzo GV, Yarwood SA, Grant EHC, Fleischer RC, Lips KR (2017) Antifungal bacteria on woodland salamander skin exhibit high taxonomic diversity and geographic variability. Appl. Environ. Microbiol. 83:e00186–e00117

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Bresciano JC, Salvador CA, Paz-y-Mino C, Parody-Merino AM, Bosch J, Woodhams DC (2015) Variation in the presence of anti-Batrachochytrium dendrobatidis bacteria of amphibians across life stages and elevations in Ecuador. EcoHealth 12:310–319.

    CAS  Article  PubMed  Google Scholar 

  57. 57.

    Madison JD, Berg EA, Abarca JG, Whitfield SM, Gorbatenko O, Pinto A, Kerby JL (2017) Characterization of Batrachochytrium dendrobatidis inhibiting bacteria from amphibian populations in Costa Rica. Front. Microbiol. 8:290.

    Article  PubMed  PubMed Central  Google Scholar 

  58. 58.

    Witney FR, Failla ML, Weinberg E (1977) Phosphate inhibition of secondary metabolism in Serratia marcescens. Appl. Environ. Microbiol. 33:1042–1046

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455–477.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43:W237–W243.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Chung W-C, Chen L-L, Lo W-S, Kuo P-A, Tu J, Kuo C-H (2013) Complete genome sequence of Serratia marcescens WW4. Genome Announcements 1:e00126–e00113

    Article  PubMed Central  Google Scholar 

  63. 63.

    Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK (2016) Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME J. 10(7):1682–1695.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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We thank An Martel and Frank Pasmans for providing a Bsal culture. We thank Leyla Davis, Holly Archer, and Valerie McKenzie for providing bacterial isolates, Jordan Kueneman for contributing to database curation, and Carly Muletz for discussion of unpublished data. We thank Rebecca Dikow for assistance with genome assembly. Permits were provided by the Autoridad Nacional de Licencias Ambientales (01025).


This study was partly funded by the Dimensions in Biodiversity program DEB-1136662 to KPCM.

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Correspondence to Douglas C. Woodhams or Kevin P. C. Minbiole.

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Woodhams, D.C., LaBumbard, B.C., Barnhart, K.L. et al. Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens. Microb Ecol 75, 1049–1062 (2018).

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  • Skin microbiota
  • Amphibian
  • Disease ecology
  • Chytridiomycosis
  • Secondary metabolites
  • Antifungal