Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Ecology, Evolution, and Organismal Biology


Ecology and Evolutionary Biology

First Advisor

Kirsten S. Hofmockel


Soil microorganisms are the drivers of ecosystem biogeochemistry, but the field of soil ecology lags behind other biological disciplines in understanding habitat constraints driving biodiversity and ecosystem functioning of these microorganisms. One approach to characterizing habitat at the micro-scale is to subset soil into naturally occurring physical associations of particles, organic matter, and microbes called aggregates. However, classic methods of separating soil aggregates can drastically change microbial communities and activities. In this dissertation, a methodological approach to isolating soil aggregates for biological analysis is refined and then applied to evaluating microbial activity and fungal community structure in three ecosystems managed for bioenergy production. Subsequently, aggregate-scale processes are scaled out to contrast ecosystem carbon (C) and nitrogen (N) cycling in the three ecosystems.

Direct contrast of soil extracellular enzyme activities within soil aggregates isolated by traditional slaking means, dry sieving, and optimal moisture found wet sieved large macroaggregates (>2000 µm) had four times greater activity than macroaggregates isolated by the other methods. Very high activity in wet-sieved macroaggregates led to mass-proportional sums of enzyme activities to exceed 100% of whole soil measurements. This indicates the wet-sieving procedure induces enzyme activity not observed in whole soil or in dry and optimal moisture aggregates. Although there were few differences in enzyme activity between dry-sieved and optimal moisture aggregates, the additional care taken in optimal moisture sieving, including rapid partial-drying under sterile conditions at 4°C, may be more important in other metrics of soil biological analysis including DNA-based assays.

Using the optimal moisture approach, I contrasted extracellular enzyme activity and C and N resources within aggregates isolated across two growing seasons from three ecosystems managed for bioenergy feedstock production: row-crop continuous corn agroecosystems and reconstructed tallgrass prairie with and without annual inorganic N fertilizer application. Across aggregate fractions, N-acetyl-glucosaminidase (NAG) activity was greatest in large macroaggregates and cellobiohydrolase activity was greatest in microaggregates (<250 µm). Increased NAG activity in large macroaggregates is likely driven by greater total C and N within that fraction. Increased cellobiohydrolase activity in microaggregates may indicate enzymes are largely stabilized on the outside of microaggregates, interacting with substrates in the surrounding pore networks rather than intra-aggregate organic matter. Aggregate turn-over was detected across the two growing seasons and disintegration of large macroaggregates corresponded with peaks in enzyme activity. Release of organic matter with aggregate turn-over may be a driver of these spikes in enzyme activity.

Fungi are major components of soil microbial communities and perform several important decomposition functions. However, there has been less research dedicated to fungal communities and the forces structuring them compared with soil bacteria. I utilized the optimal moisture aggregate isolation approach to evaluate soil fungal communities within soil aggregates from the aforementioned bioenergy cropping systems. Fungal richness was much greater in microaggregates compared with large macroaggregates and proportional sums of aggregate-level richness indicate whole soil sampling approaches are underestimating fungal richness two-fold. However, fungal community structure was affected by ecosystem to greater extent than aggregation. Unfertilized prairies supported greater abundance of members of the Basidiomycota family Strophariaceae, and genus Limonomyces, which were not present in corn or fertilized prairie systems, but were highly abundant in prairie systems. Fertilized prairies contained greater abundance of fungi from the Basidiomycota family Psathyrellaceae and genus Thanatephours as well as Ascomycota family Orbiliaceae and Trichoderma citrinoviride. Corn communities were distinguished with greater abundance of unknown Basidiomycota and arbuscular mycorrhizal fungi from the order Glomerales.

Aggregate-scale differences in extracellular enzyme activity and fungal communities contributed to ecosystem-scale differences in C and N cycling between the unfertilized prairie, fertilized prairie, and corn systems. Whole soil analysis showed fertilized prairies accrued more soil C and N than unfertilized prairies and corn systems, driven by increased microbial biomass, enzyme activity, and aggregation in fertilized prairie systems. Fertilized prairies had greater C-inputs in the form of roots than corn systems and greater inorganic N inputs, in the form of fertilizer, than unfertilized prairies. Thus, coupling of C and N inputs in fertilized prairies facilitated microbial growth and activity, which in turn enhanced soil aggregation, protection of microbially-processed organic matter, and total soil C and N pools.

In summary, this dissertation provides a replicable method for soil aggregate isolation that can be used to test hypotheses about soil habitat influences on microbial communities and activities. It was determined that soil enzyme activity varied between aggregate fractions similarly in three managed ecosystems, reflecting consistent aggregate-level controls on enzyme activities. Fungal community structure was also influenced by aggregate fraction, but the ecosystem-level response was much greater. Together, differences in aggregate habitat, in concert with plant inputs and management regime, influenced C and N cycling in corn, unfertilized and fertilized prairie ecosystems. Thus, knowledge of microbial responses at the soil aggregate scale can refine and improve scientific understanding of terrestrial ecosystem biogeochemistry.

Copyright Owner

Elizabeth Marie Bach



File Format


File Size

147 pages