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Investigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi

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Microbial Environmental Genomics (MEG)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1399))

Abstract

The study of the so-called unculturable bacteria is still considered a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, the identification and characterization of such microbes in complex biological samples is now possible. In this chapter we report how endobacteria thriving inside arbuscular mycorrhizal fungi (AMF), which are themselves obligate biotrophs of plants, can be studied using a combination of in vitro culture, molecular biology, and microscopy techniques.

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References

  1. SchĂ¼ĂŸler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:1413–1421

    Article  Google Scholar 

  2. Bonfante P, Genre A (2008) Plants and arbuscular mycorrhizal fungi: an evolutionary-developmental perspective. Trends Plant Sci 13:492–498

    Article  PubMed  CAS  Google Scholar 

  3. Bonfante P, Anca IA (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383

    Article  PubMed  CAS  Google Scholar 

  4. Bianciotto V, Lumini E, Bonfante P, Vandamme P (2003) ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi. Int J Syst Evol Microbiol 53:121–124

    Article  PubMed  CAS  Google Scholar 

  5. Naumann M, SchĂ¼ĂŸler A, Bonfante P (2010) The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. ISME J 4:862–871

    Article  PubMed  Google Scholar 

  6. Ghignone S, Salvioli A, Anca I, Lumini E, Ortu G, Petiti L, Cruveiller S, Bianciotto V, Piffanelli P, Lanfranco L, Bonfante P (2012) The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. ISME J 6:136–145

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  7. Lumini E, Bianciotto V, Jargeat P, Novero M, Salvioli A, Faccio A, Becard G, Bonfante P (2007) Presymbiotic growth and sporal morphology are affected in the arbuscular mycorrhizal fungus Gigaspora margarita cured of its endobacteria. Cell Microbiol 9:1716–1729

    Google Scholar 

  8. Salvioli A, Ghignone S, Novero M, Navazio L, Venice F, Bagnaresi P, Bonfante P (2015) Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential. ISME J: doi: 10.1038/ismej.2015.91

    Google Scholar 

  9. DesirĂ² A, Salvioli A, Ngonkeu EL, Mondo SJ, Epis S, Faccio A, Kaech A, Pawlowska TE, Bonfante P (2014) Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi. ISME J 8:257–270

    Google Scholar 

  10. Torres-CortĂ©s G, Ghignone S, Bonfante P, SchĂ¼ĂŸler A (2015). Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association. Proc Natl Acad Sci USA 112:7785–7790

    Google Scholar 

  11. Naito M, Morton JB, Pawlowska TE (2015) Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota. Proc Natl Acad Sci USA 112:7791–7796

    Google Scholar 

  12. Engel P, Moran NA (2013) The gut microbiota of insects—diversity in structure and function. FEMS Microbiol Rev 37:699–735

    Google Scholar 

  13. Bianciotto V, Genre A, Jargeat P, Lumini E, Becard G, Bonfante P (2004) Vertical transmission of endobacteria in the arbuscular mycorrhizal fungus Gigaspora margarita through generation of vegetative spores. Appl Environ Microbiol 70:3600–3608

    Google Scholar 

  14. Salvioli A, Lumini E, Anca IA, Bianciotto V, Bonfante P (2008) Simultaneous detection and quantification of the unculturable microbe Candidatus Glomeribacter gigasporarum inside its fungal host Gigaspora margarita. New Phytol 180:248–257

    Google Scholar 

  15. DesirĂ² A, Naumann M, Epis S, Novero M, Bandi C, Genre A, Bonfante P (2013) Mollicutes-related endobacteria thrive inside liverwort-associated arbuscular mycorrhizal fungi. Environ Microbiol 15:822–836

    Article  PubMed  Google Scholar 

  16. Partida-Martinez LP, Hertweck C (2005) Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature 437:884–888

    Article  PubMed  CAS  Google Scholar 

  17. Sato Y, Narisawa K, Tsuruta K, Umezu M, Nishizawa T, Tanaka K, Yamaguchi K, Komatsuzaki M, Ohta H (2010) Detection of betaproteobacteria inside the mycelium of the fungus Mortierella elongata. Microbes Environ 25:321–324

    Article  PubMed  Google Scholar 

  18. DesirĂ² A, Faccio A, Kaech A, Bidartondo MI, Bonfante P (2015) Endogone, one of the oldest plant-associated fungi, host unique Mollicutes-related endobacteria. New Phytol 205:1464–1472

    Article  PubMed  Google Scholar 

  19. Hewitt EJ (1966) Sand and water culture methods used in the study of plant nutrition, 2nd edn. Commonwealth Agricultural Bureau: The Eastern Press, London

    Google Scholar 

  20. Fontaine J, Grandgmougin-Ferjani A, Glorian V, Durand R (2004) 24-Methyl/methylene sterols increase in monoxenic roots after colonization by arbuscular mycorrhizal fungi. New Phytol 163:159–167

    Article  CAS  Google Scholar 

  21. Bécard G, Fortin JA (1988) Early events of vesicular-arbuscular mycorrhiza formation on Ri T-DNA transformed roots. New Phytol 108:211–218

    Article  Google Scholar 

  22. Boisson-Dernier A, Chabaud M, Garcia F, Bécard G, Rosenberg C, Barker DG (2001) Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations. Mol Plant Microbe Interact 14:695–700

    Article  PubMed  CAS  Google Scholar 

  23. Lee J, Lee S, Young JPW (2008) Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 65:339–349

    Google Scholar 

  24. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–11

    Google Scholar 

  25. White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols. Academic Press, San Diego, pp. 315–322

    Google Scholar 

  26. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925

    PubMed  CAS  PubMed Central  Google Scholar 

  27. Koga R, Tsuchida T, Fukatsu T (2003) Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid. Proc R Soc B 270:2543–2550

    Google Scholar 

  28. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:2333

    CAS  PubMed Central  Google Scholar 

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Acknowledgements

The authors wish to thank Mara Novero and Maria Teresa Della Beffa for having provided details on fungal culture conditions. Research in PB laboratory has been funded by the University of Turin (Local project 60 %).

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Correspondence to Alessandro DesirĂ² .

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DesirĂ², A., Salvioli, A., Bonfante, P. (2016). Investigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi. In: Martin, F., Uroz, S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3369-3_2

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  • DOI: https://doi.org/10.1007/978-1-4939-3369-3_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3367-9

  • Online ISBN: 978-1-4939-3369-3

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