Date of Award


Date Available to Non-EWU Users

December 2016

Document Type


Degree Name

Master of Science (MS) in Biology




"Although sediment microbes play key roles in decomposition and nitrogen (N) cycling, responses of microbial communities to N additions within watersheds is not well understood. Agriculture contributes excess N into stream systems, predominantly as ammonia, which is transformed through nitrification into nitrate by prokaryotes that produce the ammonia monooxygenase enzyme (AMO). The Latah Creek watershed in WA State (USA) drains approximately 1178 km², of which half is agricultural. Because the tributary streams reside in forested, agricultural and mixed use drainages, samples from these stream sediments capture microbial communities at different spatial gradients of land use. My research aimed to answer: to what extent does the percentage of agriculture within a drainage affect microbial community compositions?, and more specifically, how does it affect the abundance of nitrifying bacteria? Water and sediment samples were collected from ten locations along the watershed in spring and fall 2012. Two PCR techniques were used on the extracted sediment and pore-water DNA: terminal restriction fragment length polymorphism (T-RFLP) on the small ribosomal subunit 16S rRNA assessed microbial diversity; and quantitative PCR (qPCR) on amoA, a subunit of the nitrifying gene ammonia monooxygenase, measured nitrifier abundance. A geographic information system (ArcGIS) was used to determine the percentage of agricultural land within each of the ten sampled tributary drainages; these percentages ranged from 0% at the headwaters to 96% along the Palouse. pH, temperature, conductivity and dissolved oxygen were measured in situ. Water samples were tested for nitrite, nitrate, ammonia, dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP). The General Linear Model was used to assess relationships between physical and chemical variables, with and without molecular data. Season had a significant effect on SRP, temperature, pH, # of taxa, and % taxa dominance. Watershed area had a significant effect on % taxa dominance. % agriculture had a significant effect on conductivity and nitrifier abundance. Across the watershed, the abundance of nitrifying bacteria was positively correlated with an increase in agriculture. This study helps to better relate microbial communities and nitrification to patterns of land use and water quality"--Leaf iv.

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