Skip to main content
Log in

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm

  • Microbial Ecology and Environmental Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

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.

Institutional subscriptions

Similar content being viewed by others

References

  • Ahern, C.P. and Staff, I.A. 1994. Symbiosis in cycads: The origin and development of coralloid roots in Macrozamia communis (Cycadaceae). Am. J. Bot. 81, 1559–1570.

    Article  Google Scholar 

  • Alford, R.A. and Wilbur, H.M. 1985. Priority effects in experimental pond communities: competition between Bufo and Rana. Ecology 66, 1097–1105.

    Article  Google Scholar 

  • Angelini, P., Rubini, A., Gigante, D., Reale, L., Pagiotti, R., and Venanzoni, R. 2012. The endophytic fungal communities associated with the leaves and roots of the common reed (Phragmites australis) in Lake Trasimeno (Perugia, Italy) in declining and healthy stands. Fungal Ecol. 5, 683–693.

    Article  Google Scholar 

  • Arndt, D., Xia, J., Liu, Y., Zhou, Y., Guo, A.C., Cruz, J.A., Sinelnikov, I., Budwill, K., Nesbø, C.L., and Wishart, D.S. 2012. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 40, W88–W95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baulina, O. and Lobakova, E. 2003. Atypical cell forms overproducing extracellular substances in populations of cycad cyanobionts. Microbiology 72, 701–712.

    Article  CAS  Google Scholar 

  • Bautista, V.V., Monsalud, R.G., and Yokota, A. 2010. Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Wild.) Ohwi. Int. J. Syst. Evol. Microbiol. 60, 627–632.

    Article  CAS  PubMed  Google Scholar 

  • Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P., and Kauserud, H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10, 189.

    Article  PubMed  PubMed Central  Google Scholar 

  • Caiola, M.G. and Canini, A. 1993. Structure and physiology of cycad coralloid roots. Plant Biosyst. 127, 428–445.

    Google Scholar 

  • Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., and Gordon, J.I. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke, K.R. 1993. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117–143.

    Article  Google Scholar 

  • Clarke, K.R., Somerfield, P.J., and Gorley, R.N. 2016. Clustering in non-parametric multivariate analyses. J. Exp. Mar. Biol. Ecol. 483, 147–155.

    Article  Google Scholar 

  • Compant, S., Saikkonen, K., Mitter, B., Campisano, A., and Mercado-Blanco, J. 2016. Editorial special issue: soil, plants and endophytes. Plant Soil 405, 1–11.

    Article  CAS  Google Scholar 

  • Costa, J.L., Romero, E.M., and Lindblad, P. 2004. Sequence based data supports a single Nostoc strain in individual coralloid roots of cycads. FEMS Microbiol. Ecol. 49, 481–487.

    Article  CAS  PubMed  Google Scholar 

  • Cowan, D., Meyer, Q., Stafford, W., Muyanga, S., Cameron, R., and Wittwer, P. 2005. Metagenomic gene discovery: past, present and future. Trends Biotechnol. 23, 321–329.

    Article  CAS  PubMed  Google Scholar 

  • Cox, P.A., Banack, S.A., and Murch, S.J. 2003. Biomagnification of cyanobacterial neurotoxins and neurodegenerative disease among the Chamorro people of Guam. Proc. Natl. Acad. Sci. USA 100, 13380–13383.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cuddy, W.S., Neilan, B.A., and Gehringer, M.M. 2012. Comparative analysis of cyanobacteria in the rhizosphere and as endosymbionts of cycads in drought-affected soils. FEMS Microbiol. Ecol. 80, 204–215.

    Article  CAS  PubMed  Google Scholar 

  • DeLong, E.F., Lory, S., Stackebrandt, E., and Thompson, F.L. 2014. The prokaryotes: alphaproteobacteria and betaproteobacteria. Springer-Verlag, Berlin, Germany.

    Google Scholar 

  • Doyle, J. 1991. DNA protocols for plants. In Hewitt, G.M. (ed.), Molecular techniques in taxonomy. Springer-Verlag, Berlin, Germany.

    Google Scholar 

  • Fisher, J.B. and Vovides, A.P. 2004. Mycorrhizae are present in cycad roots. Bot. Rev. 70, 16–23.

    Article  Google Scholar 

  • Gehringer, M.M., Pengelly, J.J., Cuddy, W.S., Fieker, C., Forster, P.I., and Neilan, B.A. 2010. Host selection of symbiotic cyanobacteria in 31 species of the Australian cycad genus: Macrozamia (Zamiaceae). Mol. Plant Microbe Interact. 23, 811–822.

    Article  CAS  PubMed  Google Scholar 

  • Gehringer, M.M., Adler, L., Roberts, A.A., Moffitt, M.C., Mihali, T.K., Mills, T.J., Fieker, C., and Neilan, B.A. 2012. Nodularin, a cyanobacterial toxin, is synthesized in planta by symbiotic Nostoc sp. ISME J. 6, 1834.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glenn, A., Gold, S., and Bacon, C. 2002. Fdb1 and Fdb2, Fusarium verticillioides loci necessary for detoxification of preformed antimicrobials from corn. Mol. Plant Microbe Interact. 15, 91–101.

    Article  CAS  PubMed  Google Scholar 

  • Glenn, A., Hinton, D., Yates, I., and Bacon, C. 2001. Detoxification of corn antimicrobial compounds as the basis for isolating Fusarium verticillioides and some other Fusarium species from corn. Appl. Environ. Microbiol. 67, 2973–2981.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Halliday, J. and Pate, J. 1976. Symbiotic nitrogen fixation by coralloid roots of the cycad Macrozamia riedlei: physiological characteristics and ecological significance. Funct. Plant Biol. 3, 349–358.

    CAS  Google Scholar 

  • Hardoim, P.R., Van Overbeek, L.S., Berg, G., Pirttilä, A.M., Compant, S., Campisano, A., Döring, M., and Sessitsch, A. 2015. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hill, K.D. 2008. The genus Cycas (Cyeadaceae) in China. Telopea 12, 71–118.

    Article  Google Scholar 

  • Huang, A.H. 2005. Master thesis. The anatomy study of several cycads on nutrition organ. Guangxi University, Guangxi, China.

    Google Scholar 

  • Huang, C.L., Jian, F.Y., Huang, H.J., Chang, W.C., Wu, W.L., Hwang, C.C., Lee, R.H., and Chiang, T.Y. 2014. Deciphering mycorrhizal fungi in cultivated Phalaenopsis microbiome with next-genera tion sequencing of multiple barcodes. Fungal Divers. 66, 77–88.

    Article  Google Scholar 

  • Katz, E. and Demain, A.L. 1977. The peptide antibiotics of Bacillus: chemistry, biogenesis, and possible functions. Bacteriol. Rev. 41, 449–474.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kawaguchi, M. and Minamisawa, K. 2010. Plant-microbe communications for symbiosis. Plant Cell Physiol. 51, 1377–1380.

    Article  CAS  PubMed  Google Scholar 

  • Khan, S.A., Hamayun, M., Yoon, H., Kim, H.Y., Suh, S.J., Hwang, S.K., Kim, J.M., Lee, I.J., Choo, Y.S., and Yoon, U.H. 2008. Plant growth promotion and Penicillium citrinum. BMC Microbiol. 8, 231.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kõljalg, U., Nilsson, R.H., Abarenkov, K., Tedersoo, L., Taylor, A.F., Bahram, M., Bates, S.T., Bruns, T.D., Bengtsson-Palme, J., and Callaghan, T.M. 2013. Towards a unified paradigm for sequencebased identification of fungi. Mol. Ecol. 22, 5271–5277.

    Article  PubMed  Google Scholar 

  • Kuldau, G.A. and Yates, I.E. 2000. Evidence for Fusarium endophytes in cultivated and wild plants, pp. 85–117. In Bacon, C.W. and White, J.F. (eds.), Microbial endophytes. Marcel Dekker, New York, USA.

    Google Scholar 

  • Ladd, B. and Facelli, J.M. 2008. Priority effects produced by plant litter result in non-additive competitive effects. Oecologia 157, 687–696.

    Article  PubMed  Google Scholar 

  • Larsen, E.I., Sly, L.I., and McEwan, A.G. 1999. Manganese (II) adsorption and oxidation by whole cells and a membrane fraction of Pedomicrobium sp. ACM 3067. Arch. Microbiol. 171, 257–264.

    Article  CAS  Google Scholar 

  • Liaimer, A., Jensen, J.B., and Dittmann, E. 2016. A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. Front. Microbiol. 7, 1693.

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu, T., Li, C.M., Han, Y.L., Chiang, T.Y., Chiang, Y.C., and Sung, H.M. 2015. Highly diversified fungi are associated with the achlorophyllous orchid Gastrodia flavilabella. BMC Genomics 16, 185.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lobakova, E., Dubravina, G., and Zagoskina, N. 2004. Formation of phenolic compounds in apogeotropic roots of cycad plants. Russ. J. Plant Phys. 51, 486–493.

    Article  CAS  Google Scholar 

  • Lobakova, E., Orazova, M.K., and Dobrovolskaya, T. 2003. The structure of cyanobacterial communities formed during the degradation of apogeotropic roots of cycads. Microbiology 72, 634–637.

    Article  CAS  Google Scholar 

  • Lu, Y.F. 2006. Master thesis. Studies on root system and fleshy root structure of Cycas. Guangxi University, Guangxi, China.

    Google Scholar 

  • Ludwig, W., Schleifer, K.H., and Whitman, W. 2011. Vol. 3. The Firmicutes. In De Vos, P., Garrity, G.M., Jones, D., Krieg, N.R., Ludwig, W., Rainey, F.A., Schleifer, K.H., and Whitman, W. (eds.), Bergey's Manual of Systematic Bacteriology. Springer Science & Business Media, New York, USA.

    Google Scholar 

  • Meeks, J.C. and Elhai, J. 2002. Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states. Microbiol. Mol. Biol. Rev. 66, 94–121.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nathanielsz, C.P. and Staff, I.A. 1975. A mode of entry of bluegreen algae into the apogeotropic roots of Macrozamia communis. Am. J. Bot. 62, 232–235.

    Article  Google Scholar 

  • Naushad, S., Adeolu, M., Wong, S., Sohail, M., Schellhorn, H.E., and Gupta, R.S. 2015. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 107, 467–485.

    Article  PubMed  Google Scholar 

  • Niu, B., Paulson, J.N., Zheng, X., and Kolter, R. 2017. Simplified and representative bacterial community of maize roots. Proc. Natl. Acad. Sci. USA 114, E2450–E2459.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oliveros, J.C. 2007. VENNY. An interactive tool for comparing lists with Venn Diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html.

    Google Scholar 

  • Pate, J., Lindblad, P., and Atkins, C. 1988. Pathways of assimilation and transfer of fixed nitrogen in coralloid roots of cycad-Nostoc symbioses. Planta 176, 461–471.

    Article  CAS  PubMed  Google Scholar 

  • Rai, A.N., Bergman, B., and Rasmussen, U. 2002. Cyanobacteria in symbiosis. Kluwer Academic Publishers, Dordrecht, the Netherland.

    Book  Google Scholar 

  • Ramirez, K.S., Leff, J.W., Barberán, A., Bates, S.T., Betley, J., Crowther, T.W., Kelly, E.F., Oldfield, E.E., Shaw, E.A., and Steenbock, C. 2014. Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally. P. Roy. Soc. B-Biol. Sci. 281, 20141988.

    Article  Google Scholar 

  • Sasse, J., Martinoia, E., and Northen, T. 2017. Feed your friends: Do plant exudates shape the root microbiome? Trends Plant Sci. 23, 25–41.

    Article  PubMed  Google Scholar 

  • Schulz, B.J.E., Boyle, C.J.C., and Sieber, T.N. 2006. Microbial root endophytes. In Varma, A. (ed.), Soil biology 9. Springer, Berlin, Germany.

  • Shannon, C.E. 1948. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–423.

    Article  Google Scholar 

  • Slepecky, R.A. and Hemphill, H.E. 2006. The genus Bacillus-nonmedical. In Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., and Stackebrandt, E. (eds.), The prokaryotes: A handbook on the biology of bacteria. Vol. 4: Bacteria: Firmicutes, cyanobacteria. Springer Science & Business Media, New York, USA.

    Google Scholar 

  • Stockinger, H., Krüger, M., and Schüβler, A. 2010. DNA barcoding of arbuscular mycorrhizal fungi. New Phytol. 187, 461–474.

    Article  CAS  PubMed  Google Scholar 

  • Tomitani, A., Knoll, A.H., Cavanaugh, C.M., and Ohno, T. 2006. The evolutionary diversification of cyanobacteria: molecularphylogenetic and paleontological perspectives. Proc. Natl. Acad. Sci. USA 103, 5442–5447.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Usher, K.M., Bergman, B., and Raven, J.A. 2007. Exploring cyanobacterial mutualisms. Annu. Rev. Ecol. Syst. 38, 255–273.

    Article  Google Scholar 

  • van der Heijden, M.G. and Schlaeppi, K. 2015. Root surface as a frontier for plant microbiome research. Proc. Natl. Acad. Sci. USA 112, 2299–2300.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vega, F.E., Posada, F., Peterson, S.W., Gianfagna, T.J., and Chaves, F. 2006. Penicillium species endophytic in coffee plants and ochratoxin A production. Mycologia 98, 31–42.

    Article  CAS  PubMed  Google Scholar 

  • Wakelin, S.A., Gupta, V.V., Harvey, P.R., and Ryder, M.H. 2007. The effect of Penicillium fungi on plant growth and phosphorus mobilization in neutral to alkaline soils from southern Australia. Can. J. Microbiol. 53, 106–115.

    Article  CAS  PubMed  Google Scholar 

  • Wei, L.J. 2005. Master thesis. Studies on anatomy structure characteristics of some cycads and adaptation of them and environment. Guangxi University, Guangxi, China.

    Google Scholar 

  • Werner, G.D. and Kiers, E.T. 2015. Order of arrival structures arbuscular mycorrhizal colonization of plants. New Phytol. 205, 1515–1524.

    Article  CAS  PubMed  Google Scholar 

  • White, T.J., Bruns, T., Lee, S., and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, pp. 315–322. In Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.J. (eds.), PCR protocols: a guide to methods and applications. Academic Press, San Diego, USA.

    Google Scholar 

  • Wu, Y.H. 2006. Master thesis. Anatomical studies on vegetative organs of 9 species of Cycads. Guangxi University, Guangxi, China.

    Google Scholar 

  • Xiong, J., Liu, Y., Lin, X., Zhang, H., Zeng, J., Hou, J., Yang, Y., Yao, T., Knight, R., and Chu, H. 2012. Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau. Environ. Microbiol. 14, 2457–2466.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamada, S., Ohkubo, S., Miyashita, H., and Setoguchi, H. 2012. Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae). FEMS Microbiol. Ecol. 81, 696–706.

    Article  CAS  PubMed  Google Scholar 

  • Zhou, J., Zhou, X., Li, Y., and Xing, J. 2015. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing. J. Hazard. Mater. 295, 176–184.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xun Gong.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zheng, Y., Chiang, TY., Huang, CL. et al. Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm. J Microbiol. 56, 337–345 (2018). https://doi.org/10.1007/s12275-018-7438-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-018-7438-3

Keywords

Navigation