Response of Soil Microbially Mediated Nutrient Cycling and Community Structure to Timber Harvest in the Pacific Northwest

approved: ______________________________________________________ David D. Myrold Forest harvest persists as one of the most globally important industries, and crucially provides raw wood products for both building and fuel materials. Mechanistically complex abiotic and biotic processes curb ecosystem recovery following timber harvest and it is of great importance to understand the effects of this practice on biogeochemical cycling and ecosystem function to determine the potential for long-term sustainability. This thesis was motivated by a lack of comprehensive understanding as to the consistency of preexisting and post-harvest microbially mediated process rates and community composition across a large region of the same dominant vegetation type. I sought to determine how timber harvest across the Pacific Northwest impacts microbial biogeochemical cycling activity and community structure of both prokaryotic and fungal communities in response to harvest. At nine managed Douglas-fir forests, samples were collected from exact locations within sites one year prior to and twelve to fifteen months following clear-cut harvesting. The objective of the first study was to determine the degree of variability in microbially mediated process rates and pools of C and N, and generalized trends that are evident across sites one year following harvest. Samples were analyzed for various C and N pools, and the potential activities of biogeochemically important extracellular enzymes were measured. Soil incubations were performed to determine respiration rate and N production over time. Soil DNA isolates were used to quantify 16S rRNA and ITS gene copy numbers using qPCR, and all measurements were statistically compared between preand post-harvest samples. Total soil C and N did not change significantly following harvest, but the C: N ratio of dissolved components decreased consistently and biomass C: N ratios generally increased. Activities of β–glucosidase and cellobiohydrolase increased significantly whereas activities of phenol oxidase and peroxidase decreased significantly. Cumulative respiration over the incubation period declined substantially, and total N pools changed from primarily DON pre-harvest, to primarily NO3 post-harvest. Changes in activity rates and pool sizes following harvest were generally related to C to N balances. Pre-harvest measurements suggested communities may be co-limited by C and N, while the emergence of strong C limitation was evident post-harvest. The generalized trends identified from this study can be used in future research as reference points for ecosystem status during forest succession, and for correlation with an investigation of changes in microbial community composition and structure. The objective of the second study was to determine the factors shaping soil microbial communities of Douglas-fir forests in the Pacific Northwest, and to identify generalized shortterm effects of timber harvest on the richness, diversity, and structureof these communities. DNA was extracted from soils and sequenced using the Illumina® Miseq platform to determine differences in prokaryotic and fungal communities. When communities were considered separately preand post-harvest, pH most consistently explained community dissimilarity among sites. Although community dispersion did not vary between preand post-harvest samples, OTU richness was consistently and significantly higher following tree removal. Both prokaryotic and fungal community structures were significantly different in postcompared to pre-harvest soils, even when just OTUs representing the top 50% of sequences were considered. Relative abundance of the dominant three bacterial phyla (Proteobacteria, Acidobacteria, and Verrucomicrobia) did not change significantly following harvest, but some less-represented phyla decreased (Actinobacteria) or increased (Bacteroidetes) significantly in relative abundance. Basidiomycota abundance decreased significantly whereas Ascomycota and Zygomycota abundance increased. Ectomycorrhizal fungi were enriched across pre-harvest samples, whereas many known saprotrophic species were enriched post-harvest. In conclusion, general alterations in fungal communities, as well as select bacterial and archaeal taxa, may serve as appropriate indicators of disturbance and ecosystem status across this region. ©Copyright by Rachel E. Danielson September 11, 2015 All Rights Reserved Response of Soil Microbially Mediated Nutrient Cycling and Community Structure to Timber Harvest in the Pacific Northwest. by Rachel E. Danielson