About My Doctoral Research

Plant-fungal-bacterial interactions:

​Elucidating mechanisms of plant growth promotion by fungi in the Mortierellaceae

Microbial promotion of plant growth has great potential to naturally improve agricultural yields while also relieving economic and environmental costs of crop production. Such beneficial microbes can protect host plants against biotic and/or abiotic stresses. One group of plant beneficial microbes is early diverging filamentous fungi. Of these, arbuscular mycorrhizal fungi comprise the most ubiquitous lineage of plant beneficial fungi, but have fastidious growth conditions that make research and manipulation difficult. The Mortierellaceae (Mortierellomycotina) are a closely related lineage of plant associated fungi that are globally ubiquitous, have a broad host range, are easy to culture and manipulate, and some species have demonstrated strong plant growth promotion. Species in the Mortierellaceae present a potential alternative system for research and application of plant growth promoting (PGP) fungi. The objective of this project is to improve characterization of the Mortierellaceae, the extent of their plant growth promotion, and establish Mortierella as a model system for future research of beneficial plant-fungal interactions.

Aim 1
Characterize the diversity and phylogeny of fungi in the Mortierellaceae

This aim will improve global sampling of Mortierellaceae from soils in order to better characterize the diversity and distribution of these fungi. Phylogenetic and phylogenomic approaches will be used to determine how many species are in the this lineage and how they are are related.

Aim 2
Characterize plant associated fungal clades, plant host range, and impact of endofungal bacteria​

This aim will determine how plant growth promoting (PGP) activity is conserved in species across the Mortierellaceae, the range of plant functional guilds that interact with Mortierella elongata, & whether bacterial endosymbionts in the fungi have an impact on the plant-fungal symbiosis.

Aim 3
Elucidate the genetic and metabolic basis of Mortierella-plant association​​​
​

This aim will use transcriptomic analysis of roots from the model plant Arabidopsis thaliana inoculated with M. elongata. This will allow us identify plant genes that are involved in the plant response to the fungus. We expect these to include hormone signaling, nutrient acquisition/starvation, and/or immune response pathways.

Significance

Mortierella is a highly diverse, globally distributed fungal lineage. Some species are known to have PGP activity, which may be impacted by the presence of endosymbiotic bacteria. These fungi have a broad host range, including non-mycorrhizal plants, and are easily cultured, allowing for simplified research design compared to mycorrhizal fungi. M. elongata has been detected on all continents except Antarctica, whereas the current gold-standard PGP fungus Serendipita indica has only been isolated once, limiting the ecological relevance of that model system. If an organism is to be enriched at a large scale, such as an agricultural field, there may be significant advantages to using an organism that is already present, rather than introducing a novel element to the environment. Together, these characteristics make Mortierella an excellent alternative model to the traditional and fastidious arbuscular mycorrhizal fungi for studying tripartite plant-fungal-bacterial interactions. The goal of this project is to initiate characterization of the Mortierella-endobacteria-plant interaction and establish these fungi as a model system for future research into tripartite and PGP symbioses.

Publications

  1. Vandepol N., Liber J, Yocca A, Matlock J, Edger P, Bonito G (2022) Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. PLoS ONE 17(4): e0261908.
  2. Vandepol, N. (2020). Mortierellaceae Phylogenomics and Tripartite Plant-Fungal-Bacterial Symbiosis of Mortierella elongata. Michigan State University - Dissertation.
  3. Vandepol, N., Liber, J., Desirò, A., Na, H., Kennedy, M., Barry, K., ... & Bonito, G. (2020). Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal diversity, 104(1), 267-289.
  4. Du, Z. Y., Zienkiewicz, K., Vandepol, N., Ostrom, N. E., Benning, C., & Bonito, G. M. (2019). Algal-fungal symbiosis leads to photosynthetic mycelium. Elife, 8, e47815.
  5. Hejase, H. A., Vandepol, N., Bonito, G. M., & Liu, K. J. (2018, October). Fastnet: fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data. In RECOMB International conference on Comparative Genomics (pp. 242-259). Springer, Cham.
  6. Hejase, H. A., Vandepol, N., Bonito, G. M., Edger, P. P., & Liu, K. J. (2017, August). Coal-Miner: a statistical method for GWA studies of quantitative traits with complex evolutionary origins. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 107-114).
  7. Gdanetz, K., Benucci, G. M. N., Vandepol, N., & Bonito, G. (2017). CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. BMC bioinformatics, 18(1), 1-9.
  8. Desirò, A., Rimington, W. R., Jacob, A., Vandepol, N., Smith, M. E., Trappe, J. M., ... & Bonito, G. (2017). Multigene phylogeny of Endogonales, an early diverging lineage offungi associated with plants. IMA fungus, 8(2), 245-257.​
  9. Uehling, J., Gryganskyi, A., Hameed, K., Tschaplinski, T., Misztal, P. K., Wu, S., Desirò, A., Vandepol, N., ... & Bonito, G. (2017). Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. Environmental microbiology, 19(8), 2964-2983.

Oral Presentations

* presenting author, † invited speaker
  1. *Benucci N, Vande Pol N, Gdanetz K, Bonito G. Fungal Microbiomes: strategies for improving taxonomic resolution of environmental sequences. UMycoNet Symposium (May 2017) Minneapolis, Minnesota
  2. *†Vande Pol N, Stajich JE, O’Donnell K, Desiro A, Bonito G. Resolving the Mortierellaceae phylogeny through Multi-Locus Sequence Typing (MLST) and phylogenomics. GSA: Fungal Genetics (Mar 2017) Asilomar, California
  3. *Vande Pol N and Bonito G. Beyond rDNA: a multigene phylogenomic approach to resolution of the Mortierellaceae. Mycological Society of America (August 2016) Berkeley, California
  4. *Vande Pol N, O’Donnell K, Stajich J, and Bonito G. Elucidating the mechanisms of Mortierella-plant interactions: a multigene phylogenomic approach to resolution of the Mortierellaceae. Great Lakes - St. Lawrence Mycology Meeting (April 2016) Chaffrey’s Lock, Ontario, Canada

​Poster Presentations

* presenting author
  1. *Vandepol N, Edger P, Bonito G. Differential Arabidopsis thaliana growth effects by soil fungi in the Mortierellaceae. Mycological Society of America (August 2019) Minneapolis, Minnesota
  2. *Bonito G, Vandepol N, Desirò A, Du ZY, Bryson A, ... Genomic diversity of Mortierellomycotina fungi and their symbioses with bacteria and algae. Fungal Genetics (March 2019) Asilomar, CA
  3. *Vandepol N, Stajich JE, O’Donnell K, Desiro A, Bonito G. Resolving the Mortierellaceae phylogeny: A synthesis of Multi-Locus Sequence Typing (MLST) and phylogenomic approaches. International Mycological Congress 11 (July 2018) San Juan, Puerto Rico
  4. *Liber J, Gall E, Vandepol N, Silvia D, Bonito G. Use of Hyphal Image Analysis and Machine Learning to Classify Mucoromycota Soil Fungal Isolates. MSU UUARF Poster Session (April 2018) East Lansing, Michigan​
  5. *Vande Pol N, Stajich JE, O’Donnell K, Desiro A, Bonito G. Resolving the Mortierellaceae phylogeny through Multi-Locus Sequence Typing (MLST) and phylogenomics. Fungal Genetics (March 2017) Asilomar, California
  6. *Bonito G , Desirò A, Uehling  J, Vande Pol N, LaButti  K, Mondo S, Barry K, Grigoriev I. A novel bacterial endosymbiont related to Mycoavidus cysteinexigens inhabits the mycelium of Mortierella minutissima. Fungal Genetics (March 2017) Asilomar, California
  7. *Desirò A, Hao Z, Benucci GMN, Vande Pol N, Chang Y, Barry K, Grigoriev I, Spatafora JW, Bonito G. Mollicutes -related endobacteria in the Mortierellomycotina. Fungal Genetics (March 2017) Asilomar, California
  8. *Benning N, Vande Pol N, Bonito G. Analysis of Mortierella sp. Fatty acid production under varied growth and stress conditions. MSU UUARF Poster Session (April 2016) East Lansing, Michigan
  9. *Desiro A, Hao Z, Vande Pol N, Zienkiewicz K, Zienkiewicz A, Benning N, Cruz TT, Porras-Alfaro A, Bonito G. Endobacterial diversity in the genus Mortierella. European Fungal Genetics Conference (April 2016) Paris, France
  10. *Vande Pol N, Benning N, Poliner E, Desiro A, and Bonito G. Multi-locus sequence typing (MLST) and fatty acid profiles inform the Mortierellaceae phylogeny. Mycological Society of America (August 2015) Edmonton, Alberta, Canada