Skip to main content

Advertisement

Log in

Microbial Diversity and Chemical Multiplicity of Culturable, Taxonomically Similar Bacterial Symbionts of the Leaf-Cutting Ant Acromyrmex coronatus

  • Invertebrate Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Insects are a highly diverse group, exploit a wide range of habitats, and harbor bacterial symbionts of largely unknown diversity. Insect-associated bacterial symbionts are underexplored but promising sources of bioactive compounds. The community of culturable bacteria associated with the leaf-cutting ant Acromyrmex coronatus (Fabricius) and the diversity of their metabolites produced were investigated. Forty-six phylotypes belonging to Actinobacteria, Firmicutes, and Proteobacteria were identified. The chemical profiles of 65 isolates were further analyzed by LC-MS/MS, and principal components analysis (PCA) was used to group the isolates according to their chemical profiles. Historically, selection of bacterial strains for drug discovery has been based on phenotypic and/or genotypic traits. Use of such traits may well impede the discovery of new compounds; in this study, several indistinguishable phylotypes cultured in identical nutritional and environmental conditions produced completely different chemical profiles. Our data also demonstrated the wide chemical diversity to be explored in insect-associated symbionts.

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

Access this article

Subscribe and save

Springer+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

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
Fig. 8

Similar content being viewed by others

References

  1. Cragg GM, Newman DJ (2013) Natural products: a continuing source of novel drug leads. Biochim Biophys Acta 1830:3670–3695

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Challinor VL, Bode HB (2015) Bioactive natural products from novel microbial sources. Ann N Y Acad Sci 1354:82–97

    Article  PubMed  Google Scholar 

  3. Piel J (2009) Metabolites from symbiotic bacteria. Nat Prod Rep 26(3):338–362

    Article  CAS  PubMed  Google Scholar 

  4. Hou Y, Braun DR, Michel CR, Klassen JL, Adnani N, Wyche TP, Bugni TS (2012) Microbial strain prioritization using metabolomics tools for the discovery of natural products. Anal Chem 84:4277–4283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, O’Hagan S, Knowles JD, Halsall A, HUSERMET Consortium, Wilson ID, Kell DB (2009) Development of a robust and repeatable UPLC−MS method for the long-term metabolomic study of human serum. Anal Chem 81(4):1357–1364

    Article  CAS  PubMed  Google Scholar 

  6. Lin CY, Viant MR, Tjeerdema RS (2006) Metabolomics: methodologies and applications in the environmental sciences. J Pest Sci 31(3):245–251

    Article  CAS  Google Scholar 

  7. Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC, Gerwick L, Gerwick WH (2015) Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. J Nat Prod 78:1671–1682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Mohimani H, Pevzner PA (2016) Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptide genomics to spectral networks. Nat Prod Rep 33:73–86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kellogg JJ, Todd DA, Egan JM, Raja HA, Oberlies NH, Kvalheim OM, Cech NB (2016) Biochemometrics for natural products research: comparison of data analysis approaches and application to identification of bioactive compounds. J Nat Prod 79(2):376–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Boursaux-Eude C, Gross R (2000) New insights into symbiotic associations between ants and bacteria. Res Microbiol 151(7):513–519

    Article  CAS  PubMed  Google Scholar 

  11. Zhang MM, Poulsen M, Currie CR (2007) Symbiont recognition of mutualistic bacteria by Acromyrmex leaf-cutting ants. ISME J 1(4):313–320

    Article  PubMed  Google Scholar 

  12. Abramowski D, Currie CR, Poulsen M (2011) Caste specialization in behavioral defenses against fungus garden parasites in Acromyrmex octospinosus leaf-cutting ants. Insect Soc 58(1):65–75

    Article  Google Scholar 

  13. Little AE, Murakami T, Mueller UG, Currie CR (2006) Defending against parasites: fungus-growing ants combine specialized behaviours and microbial symbionts to protect their fungus gardens. Biol Lett 2(1):12–16

    Article  PubMed  Google Scholar 

  14. Poulsen M, Cafaro M, Boomsma JJ, Currie CR (2005) Specificity of the mutualistic association between actinomycete bacteria and two sympatric species of Acromyrmex leaf-cutting ants. Mol Microbiol 14(11):3597–3604

    CAS  Google Scholar 

  15. Zucchi TD, Guidolin AS, Cônsoli FL (2011) Isolation and characterization of actinobacteria ectosymbionts from Acromyrmex subterraneus brunneus (Hymenoptera, Formicidae). Microbiol Res 166(1):68–76

    Article  CAS  PubMed  Google Scholar 

  16. Mueller UG (2012) Symbiont recruitment versus ant-symbiont co-evolution in the attine ant–microbe symbiosis. Curr Opin Microbiol 15(3):269–277

    Article  PubMed  Google Scholar 

  17. Mueller UG, Dash D, Rabeling C, Rodrigues A (2008) Coevolution between attine ants and actinomycete bacteria: a reevaluation. Evolution 62(11):2894–2912

    Article  CAS  PubMed  Google Scholar 

  18. Samuels RI, Moreira DDO, Mattoso TC (2011) Symbiotic bacteria on the cuticle of the leaf-cutting ant Acromyrmex subterraneus subterraneus protect workers from attack by entomopathogenic fungi. Biol Lett 8(3):461–464

    PubMed  PubMed Central  Google Scholar 

  19. Beemelmanns C, Guo H, Rischer M, Poulsen M (2016) Natural products from microbes associated with insects. Beilstein J Org Chem 12:314–327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM (2016) Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep 33:54–72

    Article  CAS  PubMed  Google Scholar 

  21. Tan GYA, Ward AC, Goodfellow M (2006) Exploration of Amycolatopsis diversity in soil using genus specific primers and novel selective media. Syst Appl Microbiol 29:557–569

    Article  CAS  PubMed  Google Scholar 

  22. Shirling EB, Gottlieb D (1966) Methods for characterizations of Streptomyces species. Int J Syst Evol Microbiol 16:313–340

    Google Scholar 

  23. Hsu SC, Lockwood JL (1975) Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. J Appl Microbiol 29(3):422–426

    CAS  Google Scholar 

  24. Sunnucks P, Hales DF (1996) Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol Biol Evol 13(3):510–524

    Article  CAS  PubMed  Google Scholar 

  25. Gallagher SR, Desjardins PR (2008) Quantitation of DNA and RNA with absorption and fluorescence spectroscopy. Curr Protoc Protein Sci 52:A.4k.1–A.4k.21

  26. Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual3rd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  27. Turner S, Pryer KM, Miao VPW, Palmer JD (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46:327–338

    Article  CAS  PubMed  Google Scholar 

  28. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  30. Sudhir K, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  Google Scholar 

  31. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  32. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791

    Article  PubMed  Google Scholar 

  33. Melo IS, Sanhueza RMV (1995) Métodos de seleção de microrganismos antagônicos a fitopatógenos. Manual técnico, Documentos, 4. Embrapa-CNPMA, Jaguariúna

  34. Kalinovskaya NI, Kuznetsova TA, Ivanova EP, Romanenko LA, Voinov VG, Huth F, Laatsch H (2002) Characterization of surfactin-like cyclic depsipeptides synthesized by Bacillus pumilus from ascidian Halocynthia aurantium. Mar Biotechnol 4(2):179–188

    Article  CAS  Google Scholar 

  35. Pabel CT, Vater J, Wilde C, Franke P, Hofemeister J, Adler B, Bringmann G, Hacker J, Hentschel U (2003) Antimicrobial activities and matrix-assisted laser desorption/ionization mass spectrometry of Bacillus isolates from the marine sponge Aplysina aerophoba. Mar Biotechnol 5(5):424–434

    Article  CAS  Google Scholar 

  36. Xia J, Sinelnikov I, Han B, Wishart DS (2015) MetaboAnalyst 3.0 – making metabolomics more meaningful. Nucleic Acids Res 43(W1):W251–W257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Xia J, Mandal R, Sinelnikov I, Broadhurst D, Wishart DS (2012) MetaboAnalyst 2.0 – a comprehensive server for metabolomic data analysis. Nucleic Acids Res 40:W127–W133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Xia J, Psychogios N, Young N, Wishart DS (2009) MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res 37:W652–W660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sarker SD, Nahar L (2012) An introduction to natural products isolation. Methods Mol Biol 864:1–25

    Article  CAS  PubMed  Google Scholar 

  40. Kasten P, Precetti AA, Precetti CM, Parra JRP (1978) Dados biológicos comparativos de Spodoptera frugiperda (J.E. Smith, 1797) em duas dietas artificias e substrato natural. Rev Agric 53:68–78

    Google Scholar 

  41. Parra JRP (1986) Criação de insetos para estudo com patógenos. In: Alves SB (ed) Controle microbiano de insetos. FEALQ, Piracicaba, pp 348–373

    Google Scholar 

  42. Cafaro MJ, Currie CR (2005) Phylogenetic analysis of mutualistic filamentous bacteria associated with fungus-growing ants. Can J Microbiol 51(6):441–446

    Article  CAS  PubMed  Google Scholar 

  43. Cafaro MJ, Poulsen M, Little AEF, Price SL, Gerardo NM, Wong B, Stuart AE, Larget B, Abbot P, Currie CR (2011) Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria. Proc R Soc B 278:1814–1822

    Article  PubMed  Google Scholar 

  44. Andersen SB, Hansen LH, Sapountzis P, Sorensen SJ, Boomsma JJ (2013) Specificity and stability of the Acromyrmex-Pseudonocardia symbiosis. Mol Ecol 22:4307–4321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Poulsen M, Cafaro MJ, Erhardt DP, Little AEF, Gerardo NM, Tebbets B, Klein BS, Currie CR (2010) Variation in Pseudonocardia antibiotic defence helps govern parasite-induced morbidity in Acromyrmex leaf-cutting ants. Environ Microbiol Rep 2(4):534–540

    Article  CAS  PubMed  Google Scholar 

  46. Seipke RF, Barke J, Brearley C, Hill L, Yu DW, Goss RJM, Hutchings MI (2011) A single Streptomyces symbiont makes multiple antifungals to support the fungus farming ant Acromyrmex octospinosus. PLoS One 6(8):e22028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Barke J, Seipke RF, Grüschow S, Heavens D, Drou N, Bibb MJ, Goss RJM, Yu DW, Hutchings MI (2010) A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC Biol 8:109–118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG (2009) Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants. Proc Natl Acad Sci U S A 106(42):17805–17810

    Article  PubMed  PubMed Central  Google Scholar 

  49. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71(3):495–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Goodfellow M, Fiedler HP (2010) A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie Van Leeuwenhoek 98:119–142

    Article  PubMed  Google Scholar 

  51. Yun JH, Roh SW, Whon TW, Jung MJ, Kim KS, Park DS, Yoon C, Nam YD, Kim YJ, Choi JH, Kim JY, Shin NR, Kim SH, Lee WJ, Bae JW (2014) Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host. Appl Environ Microbiol 80(17):5254–5264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Brachmann AO, Bode HB (2013) Identification and bioanalysis of natural products from insect symbionts and pathogens. Adv Biochem Eng Biotechnol 135:123–155

    CAS  PubMed  Google Scholar 

  53. Crawford JM, Clardy J (2011) Bacterial symbionts and natural products. Chem Commun 47(27):7559–7566

    Article  CAS  Google Scholar 

  54. Poulsen M, Oh DC, Clardy J, Currie CR (2011) Chemical analyses of wasp-associated Streptomyces bacteria reveal a prolific potential for natural products discovery. PLoS One 6(2):e16763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Martinez AFC, Almeida LG, Moraes LAB, Cônsoli FL (2017) Tapping the biotechnological potential of insect microbial symbionts: new insecticidal porphyrins. BMC Microbiol 17:143–152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Waldron C, Madduri K, Crawford K, Merlo DJ, Treadway P, Broughton MC, Baltz RH (2000) A cluster of genes for the biosynthesis of spinosyns, novel macrolide insect control agents produced by Saccharopolyspora spinosa. Antonie Van Leeuwenhoek 78(3–4):385–390

    Article  CAS  PubMed  Google Scholar 

  57. Kirst HA (2010) The spinosyn family of insecticides: realizing the potential of natural products research. J Antibiot 63:101–111

    Article  CAS  Google Scholar 

  58. Sparks TC, Crouse GD, Durst G (2001) Natural products as insecticides: the biology, biochemistry and quantitative structure-activity relationships of spinosyns and spinosoids. Pest Manag Sci 57(10):896–905

    Article  CAS  PubMed  Google Scholar 

  59. Canchaya C, Fournous G, Brüssow H (2004) The impact of prophages on bacterial chromosomes. Mol Microbiol 53:9–18

    Article  CAS  PubMed  Google Scholar 

  60. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6:417–424

    Article  CAS  PubMed  Google Scholar 

  61. Dybvig K (1993) DNA rearrangements and phenotypic switching in prokaryotes. Mol Microbiol 10:465–471

    Article  CAS  PubMed  Google Scholar 

  62. Lorenz MG, Wackemagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58:563–602

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304

    Article  CAS  PubMed  Google Scholar 

  64. Toussaint A, Merlin C (2002) Mobile elements as a combination of functional modules. Plasmid 47:26–35

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Authors are greatly indebted to the two anonymous reviewers who greatly helped improve this manuscript.

Funding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) provided a fellowship to AFCM (Process 2014/21584-3) and a research grant to FLC (Process 2011/50877-0).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Fernando Luís Cônsoli.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Supplementary information is available at the Microbial Ecology website.

ESM 1

(PDF 1157 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Martinez, A.F.C., de Almeida, L.G., Moraes, L.A.B. et al. Microbial Diversity and Chemical Multiplicity of Culturable, Taxonomically Similar Bacterial Symbionts of the Leaf-Cutting Ant Acromyrmex coronatus. Microb Ecol 77, 1067–1081 (2019). https://doi.org/10.1007/s00248-019-01341-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-019-01341-7

Keywords