Skip to main content

Advertisement

Log in

Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts

  • Host Microbe Interactions
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Cutaneous bacteria may play an important role in the resistance of amphibians to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Microbial communities resident on hosts’ skin show topographical diversity mapping to skin features, as demonstrated by studies of the human microbiome. We examined skin microbiomes of wild and captive fire-bellied toads (Bombina orientalis) for differences across their body surface. We found that bacterial communities differed between ventral and dorsal skin. Wild toads showed slightly higher bacterial richness and diversity in the dorsal compared to the ventral region. On the other hand, captive toads hosted a higher richness and diversity of bacteria on their ventral than their dorsal skin. Microbial community composition and relative abundance of major bacterial taxonomic groups also differed between ventral and dorsal skin in all populations. Furthermore, microbiome diversity patterns varied as a function of their Bd infection status in wild toads. Bacterial richness and diversity was greater, and microbial community structure more complex, in wild than captive toads. The results suggest that bacterial community structure is influenced by microhabitats associated with skin regions. These local communities may be differentially modified when interacting with environmental bacteria and Bd. A better understanding of microbiome variation across skin regions will be needed to assess how the skin microbiota affects the abilities of amphibian hosts to resist Bd infection, especially in captive breeding programs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

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

Similar content being viewed by others

References

  1. Clarke BT (1997) The natural history of amphibian skin secretions, their normal functioning and potential medical applications. Biol Rev 72:365–379

    Article  PubMed  CAS  Google Scholar 

  2. Woodhams DC, Vredenburg VT, Simon M-A, Billheimer D, Shakhtour B, Shyr Y, Briggs CJ, Rollins-Smith LA, Harris RN (2007) Symbiotic bacteria contribute to innate immune defenses of the threatened mountain yellow-legged frog, Rana muscosa. Biol Cons 138:390–398

    Article  Google Scholar 

  3. Becker MH, Harris RN (2010) Cutaneous bacteria of the redback salamander prevent morbidity associated with a lethal disease. PLoS One 5, e10957

    Article  PubMed Central  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  5. Woodhams DC, Alford RA, Antwis RE, Archer H, Becker MH, Belden LK, Bell SC, Bletz M, Daskin JH, Davis LR, Flechas SV, Lauer A, Gonzalez A, Harris RN, Holden WM, Hughey MC, Ibanez R, Knight R, Kueneman J, Rabemananjara F, Reinert LK, Rollins-Smith LA, Roman-Rodriguez F, Shaw SD, Walke JB, McKenzie V (2015) Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens. Ecology 96:595–595

    Article  Google Scholar 

  6. Rollins-Smith LA, Ramsey JP, Pask JD, Reinert LK, Woodhams DC (2011) Amphibian immune defenses against chytridiomycosis: impacts of changing environments. Integr Comp Biol 51:552–562

    Article  PubMed  CAS  Google Scholar 

  7. Carver S, Bell BD, Waldman B (2010) Does chytridiomycosis disrupt amphibian skin function? Copeia 2010:487–495

    Article  Google Scholar 

  8. Voyles J, Young S, Berger L, Campbell C, Voyles WF, Dinudom A, Cook D, Webb R, Alford RA, Skerratt LF, Speare R (2009) Pathogenesis of chytridiomycosis, a cause of catastrophic amphibian declines. Science 326:582–585

    Article  PubMed  CAS  Google Scholar 

  9. Fisher MC, Garner TWJ, Walker SF (2009) Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu Rev Microbiol 63:291–310

    Article  PubMed  CAS  Google Scholar 

  10. Skerratt L, Berger L, Speare R, Cashins S, McDonald K, Phillott A, Hines H, Kenyon N (2007) Spread of chytridiomycosis has caused the rapid global decline and extinction of frogs. EcoHealth 4:125–134

    Article  Google Scholar 

  11. Bletz MC, Loudon AH, Becker MH, Bell SC, Woodhams DC, Minbiole KPC, 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 

  12. Woodhams D, Bosch J, Briggs C, Cashins S, Davis L, Lauer A, Muths E, Puschendorf R, Schmidt B, Sheafor B, Voyles J (2011) Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis. Front Zool 8:8

    Article  PubMed Central  PubMed  Google Scholar 

  13. Becker M, Harris R, Minbiole K, Schwantes C, Rollins-Smith L, Reinert L, Brucker R, Domangue R, Gratwicke B (2011) Towards a better understanding of the use of probiotics for preventing chytridiomycosis in Panamanian golden frogs. EcoHealth 8:501–506

    Article  PubMed  Google Scholar 

  14. Becker MH, Walke JB, Cikanek S, Savage AE, Mattheus N, Santiago CN, Minbiole KPC, Harris RN, Belden LK, Gratwicke B (2015) Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus. Proc R Soc B 282:20142881

  15. Kung D, Bigler L, Davis LR, Gratwicke B, Griffith E, Woodhams DC (2014) Stability of microbiota facilitated by host immune regulation: informing probiotic strategies to manage amphibian disease. PLoS One 9, e87101

  16. Daskin JH, Bell SC, Schwarzkopf L, Alford RA (2014) Cool temperatures reduce antifungal activity of symbiotic bacteria of threatened amphibians - implications for disease management and patterns of decline. PLoS One 9, e100378

  17. Daskin JH, Alford RA (2012) Context-dependent symbioses and their potential roles in wildlife diseases. Proc R Soc B 279:1457–1465

  18. Jani AJ, Briggs CJ (2014) The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection. Proc Natl Acad Sci U S A 11:5049–5058

    Article  Google Scholar 

  19. McFall-Ngai M, Hadfield MG, Bosch TCG, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229–3236

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  20. Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ (2013) The amphibian skin-associated microbiome across species, space and life history stages. Mol Ecol 23:1238–1250

    Article  PubMed  Google Scholar 

  21. McKenzie VJ, Bowers RM, Fierer N, Knight R, Lauber CL (2011) Co-habiting amphibian species harbor unique skin bacterial communities in wild populations. ISME J 6:588–596

    Article  PubMed Central  PubMed  Google Scholar 

  22. Becker MH, Richards-Zawacki CL, Gratwicke B, Belden LK (2014) The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki). Biol Cons 176:199–206

    Article  Google Scholar 

  23. Loudon AH, Woodhams DC, Parfrey LW, Archer H, Knight R, McKenzie V, Harris RN (2013) Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). ISME J 8:830–840

    Article  PubMed Central  PubMed  Google Scholar 

  24. Grice EA, Segre JA (2011) The skin microbiome. Nat Rev Micro 9:244–253

    Article  CAS  Google Scholar 

  25. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Program NCS, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  26. Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC (2015) Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A 112:E2120–E2129

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  27. Pessier AP, Nichols DK, Longcore JE, Fuller MS (1999) Cutaneous chytridiomycosis in poison dart frogs (Dendrobates spp.) and White’s tree frogs (Litoria caerulea). J Vet Diagn Invest 11:194–199

    Article  PubMed  CAS  Google Scholar 

  28. Hyatt A, Boyle DG, Olsen V, Boyle DB, Berger L, Obendorf D, Dalton A, Kriger K, Heros M, Hines H, Phillott R, Campbell R, Marantelli G, Gleason F, Coiling A (2007) Diagnostic assays and sampling protocols for the detection of Batrachochytrium dendrobatidis. Dis Aquat Organ 73:175–192

    Article  PubMed  CAS  Google Scholar 

  29. Shin J, Bataille A, Kosch TA, Waldman B (2014) Swabbing often fails to detect amphibian chytridiomycosis under conditions of low infection load. PLoS One 9, e111091

    Article  PubMed Central  PubMed  Google Scholar 

  30. Reeder NMM, Pessier AP, Vredenburg VT (2012) A reservoir species for the emerging amphibian pathogen Batrachochytrium dendrobatidis thrives in a landscape decimated by disease. PLoS One 7, e33567

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  31. Goka K, Yokoyama JUN, Une Y, Kuroki T, Suzuki K, Nakahara M, Kobayashi A, Inaba S, Mizutani T, Hyatt AD (2009) Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan. Mol Ecol 18:4757–4774

    Article  PubMed  CAS  Google Scholar 

  32. Bataille A, Fong JJ, Cha M, Wogan GOU, Baek HJ, Lee H, Min M-S, Waldman B (2013) Genetic evidence for a high diversity and wide distribution of endemic strains of the pathogenic chytrid fungus Batrachochytrium dendrobatidis in wild Asian amphibians. Mol Ecol 22:4196–4209

    Article  PubMed  CAS  Google Scholar 

  33. Bai C, Liu X, Fisher MC, Garner TWJ, Li Y (2012) Global and endemic Asian lineages of the emerging pathogenic fungus Batrachochytrium dendrobatidis widely infect amphibians in China. Divers Distrib 18:307–318

  34. Farrer RA, Weinert LA, Bielby J, Garner TWJ, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SLK, Shahar-Golan R, Henk DA, Fisher MC (2011) Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A 108:18732–18736

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  35. Martel A, Blooi M, Adriaensen C, Van Rooij P, Beukema W, Fisher MC, Farrer RA, Schmidt BR, Tobler U, Goka K, Lips KR, Muletz C, Zamudio KR, Bosch J, Lotters S, Wombwell E, Garner TWJ, Cunningham AA, Spitzen-van der Sluijs A, Salvidio S, Ducatelle R, Nishikawa K, Nguyen TT, Kolby JE, Van Bocxlaer I, Bossuyt F, Pasmans F (2014) Recent introduction of a chytrid fungus endangers Western Palearctic salamanders. Science 346:630–631

    Article  PubMed  CAS  Google Scholar 

  36. Masella A, Bartram A, Truszkowki J, Brown D, Neufeld J (2012) PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13:31

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  37. Schloss PD, Westcott SI, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  38. Chun J, Lee H-J, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261

  39. Unterseher M, Jumpponen A, Öpik M, Tedersoo L, Moora M, Dormann CF, Schnittler M (2011) Species abundance distribution and richness estimations in fungal metagenomics - lessons learned from community ecology. Mol Ecol 20:275–285

    Article  PubMed  Google Scholar 

  40. Zhou J, Wu L, Deng Y, Zhi X, Jiang Y-H, Tu Q, Xie J, Van Nostrand JD, He Z, Yang Y (2011) Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5:1303–1313

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  41. Faith DP, Baker AM (2006) Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform 2:121–128

  42. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum-evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  43. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46

  44. R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  45. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300

  46. Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  47. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Res 41:95–98

    CAS  Google Scholar 

  48. Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  49. Jobb G (2011) TREEFINDER version of March 2011. Munich. Germany. Distributed by the author at www.treefinder.de

  50. Barberio C, Delfino G, Mastromei G (1987) A low molecular weight protein with antimicrobial activity in the cutaneous ‘venom’ of the yellow-bellied toad (Bombina variegata pachypus). Toxicon 25:899–909

    Article  PubMed  CAS  Google Scholar 

  51. Mastromei G, Barberio C, Pistolesi S, Delfino G (1991) A bactericidal protein in Bombina variegata pachypus skin venom. Toxicon 29:321–328

    Article  PubMed  CAS  Google Scholar 

  52. Walke JB, Becker MH, Loftus SC, House LL, Cormier G, Jensen RV, Belden LK (2014) Amphibian skin may select for rare environmental microbes. ISME J 8:2207–2217

    Article  PubMed  CAS  Google Scholar 

  53. Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA (2014) Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5:e01371–14

    Article  PubMed Central  PubMed  Google Scholar 

  54. Lam BA, Walke JB, Vredenburg VT, Harris RN (2010) Proportion of individuals with anti-Batrachochytrium dendrobatidis skin bacteria is associated with population persistence in the frog Rana muscosa. Biol Cons 143:529–531

    Article  Google Scholar 

  55. Apprill A, Robbins J, Eren AM, Pack AA, Reveillaud J, Mattila D, Moore M, Niemeyer M, Moore KMT, Mincer TJ (2014) Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? PLoS One 9, e90785

    Article  PubMed Central  PubMed  Google Scholar 

  56. Ruiz-Rodriguez M, Valdivia E, Soler JJ, Martin-Vivaldi M, Martin-Platero AM, Martinez-Bueno M (2009) Symbiotic bacteria living in the hoopoe’s uropygial gland prevent feather degradation. J Exp Biol 212:3621–3626

    Article  PubMed  CAS  Google Scholar 

  57. Lopanik NB (2014) Chemical defensive symbioses in the marine environment. Funct Ecol 28:328–340

    Article  Google Scholar 

  58. Rainey SM, Shah P, Kohl A, Dietrich I (2014) Understanding the Wolbachia-mediated inhibition of arboviruses in mosquitoes: progress and challenges. J Gen Virol 95:517–530

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank Jonathan Fong and Moonsuk Cha for assistance with fieldwork, and Dharmesh Singh for assistance with laboratory work.

Funding

This work was supported by the National Research Foundation of Korea (NRF) (grants 2012K1A2B1A03000496 to B.W., funded by the Ministry of Science, ICT and Future Planning, and 2014063422 to A.B.., funded by the Ministry of Education, government of the Republic of Korea).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Bruce Waldman.

Additional information

Arnaud Bataille and Larisa Lee-Cruz contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 1479 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bataille, A., Lee-Cruz, L., Tripathi, B. et al. Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts. Microb Ecol 71, 221–232 (2016). https://doi.org/10.1007/s00248-015-0653-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-015-0653-0

Keywords

Navigation