Bonito, G. et al., 2016. Fungal Ecology

Isolating a functionally relevant guild of fungi from the root microbiome of Populus

Gregory Bonito, Khalid Hameed, Rafael Ventura, Jay Krishnan, Christopher W. Schadt, and Rytas Vilgalys
27 may 216,  Fungal Ecology 22: 35-42; doi: 10.1016/j.funeco.2016.04.007


Plant roots interact with a bewilderingly complex community of microbes, including root-associated fungi that are essential for maintaining plant health. To improve understanding of the diversity of fungi in the rhizobiome of Populus deltoides, Populus trichocarpa and co-occurring plant hosts Quercus alba and Pinus taeda, we conducted field and greenhouse studies and sampled, isolated, and characterized the diversity of culturable root-associated fungi on these hosts. Using both general and selective isolation media we obtained more than 1800 fungal isolates from individual surface sterilized root tips. Sequences from the ITS and/or D1– D2 regions of the LSU rDNA were obtained from 1042 of the >1800 pure culture isolates and were compared to accessions in the NCBI nucleotide database and analyzed through phylogenetics for preliminary taxonomic identification. Sequences from these isolates were also compared to 454 sequence datasets obtained directly from the Populus rhizosphere and endosphere. Although most of the ectomycorrhizal taxa known to associate with Populus evaded isolation, many of the abundant sequence types from rhizosphere and endosphere 454 datasets were isolated, including novel species belonging to the Atractiellales. Isolation and identification of key endorrhizal fungi will enable more targeted study of plant-fungal interactions. Genome sequencing is currently underway for a subset of our culture library with the aim of understanding the mechanisms involved in host-endophyte establishment and function. This diverse culture library of fungal root associates will be a valuable resource for metagenomic research, experimentation and further studies on plant-fungal interactions.


•    More than 1800 cultures of fungi were isolated from surface sterilized root tips.
•    ITS and LSU rDNA sequences were generated for the majority of fungal isolates.
•    Identified fungal root endophytes belong to Dikarya and early diverging fungi.
•    Fungal genomes have been sequenced from select Populus isolates presented here.


Bonito GB, Hameed K., Ventura R., Krishnan J., Schadt CW., and Vilgalys R. 2016. Isolating a functionally relevant guild of fungi from the root imcrobiome of Populus. Fungal Ecology 22 (2016)  35-42. doi: 10.1016/j.funeco.2016.04.007

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