Biological Sciences, School of


First Advisor

Wayne R. Riekhof

Second Advisor

Steven D. Harris

Date of this Version

Summer 7-14-2022

Document Type



Carr, E.C. (2022). Discovering Novel Polyextremotolerant Fungi, and Determining their Ecological Role Within the Biological Soil Crust Consortium (Publication No. 29318948). [Doctoral Dissertation, University of Nebraska-Lincoln]. ProQuest Dissertations Publishing.


A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Biological Sciences (Genetics, Cellular, and Molecular Biology), Under the Supervision of Professors Wayne R. Riekhof & Steven D. Harris. Lincoln, Nebraska: June, 2022

Copyright © 2022 Erin C. Carr

Chapter 1: "Lichens and Biofilms: Common Collective Growth Imparts Similar Developmental Strategies" is published in: Erin C. Carr, Steven D. Harris, Joshua R. Herr, Wayne R. Riekhof; Lichens and biofilms: Common collective growth imparts similar developmental strategies. Algal Research, 54, 102217.

Chapter 2: "Deciphering the potential niche of two novel black yeast fungi, Exophiala viscosium and Exophiala limosus, from a biological soil crust using their genomes, phenotypes, and melanin regulation" is currently published in: Carr, E.C., Barton, Q., Grambo, S., Sullivan, M., Renfro, C.M., Kuo, A., Pangilinan, J., Lipzen, A., Keymanesh, K., Savage, E., Barry, K., Grigoriev, I.V., Riekhof, W.R., Harris, S.D., 2021. Deciphering the potential niche of novel black yeast fungal isolates in a biological soil crust based on genomes, phenotyping, and melanin regulation. BioRxiv, March 2nd, 2022 doi:10.1101/2021.12.03.471027. But will be published in G3 - Genes, Genomes, Genetics.

Lichens and Biofilms: Common Collective Growth Imparts Similar Developmental Strategies


The ecological niche of polyextremotolerant fungi within oligotrophic ecosystems such as biological soil crusts has not yet been determined. These fungi persist in locations where nutrients are depleted while simultaneously surrounded by autotrophic microbes such as algae and cyanobacteria. Yet it has not been shown that they are engaging in any exchange of nutrients the way lichens do. However, there is seemingly no other way for these fungi to obtain vital nutrients, such as carbon or nitrogen, other than from these microbes. Here we have isolated polyextremotolerant fungi from cold desert biological soil crusts which are a microbial biofilm that form on the surfaces of non-vegetative soils and contain an abundance of autotrophic microbes. The presence of free-living fungi in these biofilms has recently been verified, but only a few fungi have been cultured directly from them, therefore the ecological role of fungi in the biological soil crust remains unknown. With work presented here, we have shown that polyextremotolerant fungi are present within the biological soil crust. Additionally, we have provided potential leads to the ecological niches of these organisms within the biological soil crust. Exophiala viscosium and Exophiala limosus, tentatively named, are two novel species described here, which have been observed to secrete excess amounts of melanin into their media. Since melanin is a carbon-expensive product to make, we believe they are secreting it to protect the biological soil crust from UV and desiccation. Additionally, we have identified what we believe to be a polyextremotolerant fungus with endosymbiotic bacteria, Crusty and its Methylobacterium symbionts Light Pinky and Dark Pinky. While we have not directly confirmed the basis of their endosymbiosis, we believe it is to allow the bacteria to optimally perform aerobic anoxygenic photosynthesis and auxin production, due to the genetic confirmation of the mechanisms required for these processes within the genomes of these bacteria, and the significant increase in active metabolism of Crusty-Pinky when grown in the presence of light. Detailed descriptions of the methods of experiments performed and the results of this study will provide a basis for research in the future on polyextremotolerant fungi, and determine the microbial interactions that allow them to survive oligotrophic conditions.

Advisors: Wayne R. Riekhof & Steven D. Harris

2022-03-11_E_viscosium_Video_1.mp4 (8819 kB)
Video 1; E. viscosium budding

2022-03-11_E_limosus_Video_2.mp4 (10077 kB)
Video 2; E. limosus budding