Isolating a functionally relevant guild of fungi from the Populus rhizosphere. Public

Gregory Bonito,Khalid Hameed,Rafael Ventura,Jay Krishnan,Christopher W. Schadt,Rytas Vilgalys 2016 April 13 Fungal Ecology 22(2016) 35-42


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 D1e 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.


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