Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts

Autoři: Molly C. Bletz aff001;  Boyke Bunk aff003;  Cathrin Spröer aff003;  Peter Biwer aff004;  Silke Reiter aff005;  Falitiana C. E. Rabemananjara aff006;  Stefan Schulz aff004;  Jörg Overmann aff003;  Miguel Vences aff002
Působiště autorů: Department of Biology, University of Massachusetts Boston, Boston, MA, United States of America aff001;  Zoological Institute, Technische Universitt Braunschweig, Braunschweig, Germany aff002;  DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany aff003;  Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany aff004;  Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany aff005;  Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar aff006;  Microbiology Institute, Technische Universität Braunschweig, Braunschweig, Germany aff007
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.

Klíčová slova:

Amphibian genomics – Amphibians – Comparative genomics – Microbiome – Multiple alignment calculation – Phylogenetic analysis – Sequence alignment – Sequence analysis


1. Fisher MC, Garner TW, Walker SF. Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu Rev Microbiol. 2009;63: 291–310. doi: 10.1146/annurev.micro.091208.073435 19575560

2. Stegen G, Pasmans F, Schmidt BR, Rouffaer LO, Van Praet S, Schaub M, et al. Drivers of salamander extirpation mediated by Batrachochytrium salamandrivorans. Nature. Nature Publishing Group; 2017;544: 353–356. doi: 10.1038/nature22059 28425998

3. Bletz MC, Loudon AH, Becker MH, Bell SC, Woodhams DC, Minbiole KPC, et al. Mitigating amphibian chytridiomycosis with bioaugmentation: Characteristics of effective probiotics and strategies for their selection and use. Ecol Lett. 2013;16. doi: 10.1111/ele.12099 23452227

4. Loudon AH, Woodhams DC, Parfrey LW, Archer HM, Knight R, McKenzie V, et al. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). ISME J. Nature Publishing Group; 2014;8: 830–40. doi: 10.1038/ismej.2013.200 24335825

5. Walke JB, Becker MH, Hughey MC, Swartwout M, Jensen R V, Belden LK. Most of the dominant members of amphibian skin bacterial communities can be readily cultured. Appl Environ Microbiol. 2015; doi: 10.1128/AEM.01486-15 26162880

6. Kueneman JG, Bletz MC, Becker CG, Woodhams DC, Vences M. Community richness of amphibian skin bacteria correlates with bioclimate at the global scale. Nat Ecol Evol. 2019;

7. Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ. The amphibian skin-associated microbiome across species, space and life history stages. Mol Ecol. 2014;23: 1238–1250. doi: 10.1111/mec.12510 24171949

8. Bletz MC, Perl RGB, Vences M. Skin microbiota differs drastically between co-occurring frogs and newts. Open Sci. 2017;4: 170107.

9. Jani AJ, Briggs CJ. Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable. Front Microbiol. 2018;9: 1–17. doi: 10.3389/fmicb.2018.00001

10. Sabino-Pinto J, Bletz MC, Islam MM, Shimizu N, Bhuju S, Geffers R, et al. Composition of the cutaneous bacterial community in Japanese amphibians: effects of captivity, host species, and body region. Microb Ecol. Microbial Ecology; 2016; 460–469. doi: 10.1007/s00248-016-0797-6 27278778

11. Bletz MC, Bina Perl RG, Vences M. Skin microbiota differs drastically between co-occurring frogs and newts. R Soc Open Sci. 2017;4. doi: 10.1098/rsos.170107 28484639

12. Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE, Rakotoarison A, et al. Host ecology rather than host phylogeny drives amphibian skin microbial community structure in the biodiversity hotspot of Madagascar. Front Microbiol. 2017;8: Article 1530. doi: 10.3389/fmicb.2017.01530 28861051

13. Belden LK, Hughey MC, Rebollar EA, Umile TP, Loftus SC, Burzynski EA, et al. Panamanian frog species host unique skin bacterial communities. Front Microbiol. 2015;6: 1171. doi: 10.3389/fmicb.2015.01171 26579083

14. Abarca JG, Vargas G, Zuniga I, Whitfield SM, Woodhams DC, Kerby J, et al. Assessment of bacterial communities associated with the skin of costa rican amphibians at la selva biological station. Front Microbiol. 2018;9: 1–12. doi: 10.3389/fmicb.2018.00001

15. Bletz MCMC, Myers J, Woodhams DCDC, Rabemananjara FCEFCE, Rakotonirina A, Weldon C, et al. Estimating herd immunity to amphibian chytridiomycosis in Madagascar based on the defensive function of amphibian skin bacteria. Front Microbiol. 2017;8. doi: 10.3389/fmicb.2017.01751 28959244

16. Blümel S, Mark B, Busse H-J, Kämpfer P, Stolz A. Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. Int J Syst Evol Microbiol. Microbiology Society; 2001;51: 1867–1871. doi: 10.1099/00207713-51-5-1867 11594620

17. Yoon J-H, Kang S-J, Kim W, Oh T-K. Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga. Int J Syst Evol Microbiol. Microbiology Society; 2007;57: 1188–1191. doi: 10.1099/ijs.0.64901-0 17551027

18. Lee J-J, Srinivasan S, Kim MK. Pigmentiphaga soli sp. nov., a bacterium isolated from soil. J Microbiol. Springer; 2011;49: 857–861. doi: 10.1007/s12275-011-1375-8 22068507

19. Lee SD. Pigmentiphaga aceris sp. nov., isolated from tree sap. Int J Syst Evol Microbiol. Microbiology Society; 2017;67: 3198–3202. doi: 10.1099/ijsem.0.002073 28840799

20. Chen Y-G, Zhang Y-Q, Huang K, Tang S-K, Cao Y, Shi J-X, et al. Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment. Int J Syst Evol Microbiol. Microbiology Society; 2009;59: 521–525. doi: 10.1099/ijs.0.002949-0 19244433

21. Proença DN, Grass G, Morais P V. Understanding pine wilt disease: roles of the pine endophytic bacteria and of the bacteria carried by the disease‐causing pinewood nematode. Microbiologyopen. Wiley Online Library; 2017;6: e00415.

22. Bridger N, Drews S, Burdz T, Wiebe D, Pacheco AL, Ng B, et al. Isolation and characterization of Pigmentiphaga-like isolates from human clinical material. J Med Microbiol. Microbiology Society; 2013;62: 708–711. doi: 10.1099/jmm.0.051615-0

23. Bernier A-M, Bernard K. Draft Whole-Genome Sequences for Two Pigmentiphaga Isolates Recovered from Human Clinical Materials. Genome Announc. Am Soc Microbiol; 2017;5: e00726–17. doi: 10.1128/genomeA.00726-17 28774981

24. Huang J, Ling J, Kuang C, Chen J, Xu Y, Li Y. Microbial biodegradation of aniline at low concentrations by Pigmentiphaga daeguensis isolated from textile dyeing sludge. Int Biodeterior Biodegradation. Elsevier; 2018;129: 117–122.

25. Garrido-Sanz D, Manzano J, Martín M, Redondo-Nieto M, Rivilla R. Metagenomic analysis of a biphenyl-degrading soil bacterial consortium reveals the metabolic roles of specific populations. Front Microbiol. Frontiers; 2018;9: 232.

26. Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, et al. Deblur rapidly resolves single-nucleotide community sequence patterns. Gilbert JA, editor. mSystems. 2017;2.

27. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73: 5261–5267. doi: 10.1128/AEM.00062-07 17586664

28. Caporaso JG, Lauber CL, Walters WA, Berg-lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci. 2011;108: 4516–4522. doi: 10.1073/pnas.1000080107 20534432

29. Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006;22: 2971–2972. Available: 17021158

30. Wickham H. ggplot2: Elegant graphics for data analysis. New York: Springer; 2009.

31. Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. Oxford University Press; 2010;26: 589–595. doi: 10.1093/bioinformatics/btp698 20080505

32. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. Cold Spring Harbor Lab; 2012;22: 568–576. doi: 10.1101/gr.129684.111 22300766

33. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. Oxford University Press; 2014;30: 2068–2069. doi: 10.1093/bioinformatics/btu153 24642063

34. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. Oxford University Press; 2016;44: 6614–6624. doi: 10.1093/nar/gkw569 27342282

35. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. Cold Spring Harbor Lab; 2004;14: 1394–1403. doi: 10.1101/gr.2289704 15231754

36. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. Elsevier; 2016;428: 726–731. doi: 10.1016/j.jmb.2015.11.006 26585406

37. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. Oxford University Press; 2017;45: W36–W41. doi: 10.1093/nar/gkx319 28460038

38. Weber T, Rausch C, Lopez P, Hoof I, Gaykova V, Huson DH, et al. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol. Elsevier; 2009;140: 13–17. doi: 10.1016/j.jbiotec.2009.01.007 19297688

39. de Jong A, van Heel AJ, Kok J, Kuipers OP. BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res. Oxford University Press; 2010;38: W647–W651. doi: 10.1093/nar/gkq365 20462861

40. Starcevic A, Zucko J, Simunkovic J, Long PF, Cullum J, Hranueli D. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res. Oxford University Press; 2008;36: 6882–6892. doi: 10.1093/nar/gkn685 18978015

41. Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G. NORINE: a database of nonribosomal peptides. Nucleic Acids Res. Oxford University Press; 2007;36: D326–D331. doi: 10.1093/nar/gkm792 17913739

42. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2017;

43. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33: msw054. doi: 10.1093/molbev/msw054 27004904

44. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics. Oxford University Press; 2008;25: 119–120. doi: 10.1093/bioinformatics/btn578 18990721

45. Crosa JH, Walsh CT. Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev. Am Soc Microbiol; 2002;66: 223–249. doi: 10.1128/MMBR.66.2.223-249.2002 12040125

46. Riley MA, Wertz JE. Bacteriocins: evolution, ecology, and application. Annu Rev Microbiol. Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303–0139, USA; 2002;56: 117–137. doi: 10.1146/annurev.micro.56.012302.161024 12142491

47. Kumariya R, Garsa AK, Rajput YS, Sood SK, Akhtar N, Patel S. Bacteriocins: Classification, synthesis, mechanism of action and resistance development in food spoilage causing bacteria. Microb Pathog. Elsevier; 2019;

48. Cotter PD, Ross RP, Hill C. Bacteriocins—a viable alternative to antibiotics? Nat Rev Microbiol. Nature Publishing Group; 2013;11: 95. doi: 10.1038/nrmicro2937 23268227

49. Robinson SL, Christenson JK, Wackett LP. Biosynthesis and chemical diversity of β-lactone natural products. Nat Prod Rep. Royal Society of Chemistry; 2019;

50. Czech L, Höppner A, Kobus S, Seubert A, Riclea R, Dickschat JS, et al. Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis. Sci Rep. Nature Publishing Group; 2019;9: 364. doi: 10.1038/s41598-018-36247-w 30674920

51. Schulz S, Dickschat JS. Bacterial volatiles: the smell of small organisms. Nat Prod Rep. Royal Society of Chemistry; 2007;24: 814–842. doi: 10.1039/b507392h 17653361

52. Zhang L, Khabbaz SE, Wang A, Li H, Abbasi PA. Detection and characterization of broad-spectrum antipathogen activity of novel rhizobacterial isolates and suppression of Fusarium crown and root rot disease of tomato. J Appl Microbiol. 2015;118: 685–703. doi: 10.1111/jam.12728 25512025

53. Ossowicki A, Jafra S, Garbeva P. The antimicrobial volatile power of the rhizospheric isolate Pseudomonas donghuensis P482. PLoS One. 2017;12: 1–13. doi: 10.1371/journal.pone.0174362 28358818

Článek vyšel v časopise


2019 Číslo 10
Nejčtenější tento týden