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Volume 10, Issue 3

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals Open Access

Abstract

Cycads are known to host symbiotic cyanobacteria, including species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to spp., symbiotic cyanobacteria of the genus were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Aulosira , cyanobiont , cycad coralloid roots , Nostocales , phylometagenomics and symbiosis
Funding
This study was supported by the:
  • SEP-Cinvestav (MX) (Award 103)
    • Principle Award Recipient: AngelicaCibrian-Jaramillo
  • SEP-CINVESTAV (MX) (Award 103)
    • Principle Award Recipient: FranciscoBarona-Gomez
  • Joint Genome Institute (Award 506790)
    • Principle Award Recipient: PaulM D'Agostino
  • Royal Society (Award NAF280631)
    • Principle Award Recipient: FranciscoBarona-Gomez
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals
M Gen 10, 001207 (2024); https://doi.org/10.1099/mgen.0.001207
/content/journal/mgen/10.1099/mgen.0.001207
/content/journal/mgen/10.1099/mgen.0.001207
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