Date of Award

12-2025

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

School

Biological, Environmental, and Earth Sciences

Committee Chair

Dr. Kevin Kuehn

Committee Chair School

Biological, Environmental, and Earth Sciences

Committee Member 2

Dr. Jacob Schaefer

Committee Member 2 School

Biological, Environmental, and Earth Sciences

Committee Member 3

Dr. Dmitri Mavrodi

Committee Member 3 School

Biological, Environmental, and Earth Sciences

Committee Member 4

Dr. Colin Jackson

Committee Member 5

Dr. Vladislav Gulis

Abstract

A global majority of steams are non-perennial, drying at some point in time and space. Despite the vital roles that fungi and other microbes play in stream ecosystems, most research on stream microbiomes comes from perennial (continuously flowing) streams. The present series of studies addresses this research gap by examining microbial community composition and function in non-perennial streams, with an emphasis on fungi. Chapter I reviews existing scientific literature on the ecological processes that shape microbiome structure and function in non-perennial streams and outlines the varieties of fungi that may live there. Chapter II uses rDNA metabarcoding to survey fungal communities from multiple microhabitats (leaf litter, rock surfaces, and sediments) across a temperate prairie non-perennial stream network, examining relationships between fungal community composition and environmental variables including water permanence, network position, topography, and riparian vegetation. Chapter III replicates this survey approach in a subtropical forest non-perennial stream network, including community metabarcoding of prokaryotes and fungi. Both survey-based approaches found that microbial community composition varies with microhabitat, water permanence, position in the stream network, and riparian vegetation. Both studies suggest that saxicolous freshwater lichens (Verrucariaceae) are bioindicators of water permanence. The latter study suggests that water permanence favors aquatic hyphomycetes, methanogenic Archaea, and photoautotrophic Cyanobacteria, while dry conditions may allow terrestrial soil microbes (e.g., ectomycorrhizal fungi) to access resources in streambed sediments. However, identifying aquatic decomposers remains challenging due to polyphyly, database limitations, and the fact that nominally terrestrial species can contribute to in-stream decomposition. Chapter IV uses a whole-stream flow manipulation experiment to test for flow reduction effects on two substrate types (labile native leaf litter and recalcitrant 95%-cellulose cotton fabric) distributed across two in-stream topographic habitats (deep, slow pools and shallow, fast riffles) and a riparian reference. Results suggest that, while hypoxia in pools did not strongly affect decomposition, decreased flow velocity in riffles following flow reduction impaired decomposition of cotton strips, possibly due to reductions in mechanical abrasion that can contribute to decomposition. Altogether, these studies shed light on microbiome structure and function in non-perennial streams and suggest methodological improvements and directions for future research.

ORCID ID

0000-0001-8890-4714

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