Term of Award

Spring 2017

Degree Name

Master of Science in Biology (M.S.)

Document Type and Release Option

Thesis (open access)

Copyright Statement / License for Reuse

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.


Department of Biology

Committee Chair

Subhrajit Saha

Committee Member 1

John Schenk

Committee Member 2

Tiehang Wu


Worldwide chemical fertilizer use has increased by four times during the last 50 years. Conventional agricultural systems have a high nitrifying nature, resulting in a loss of nearly 70% of overall nitrogen (N) fertilizer inputs, an estimated economic loss of $81 billion. Over application of fertilizer is rampant in tropical developing nations in Central America, where coffee is major crop. Agroforestry offers ecologically sustainable land management strategies that promote the provision of ecosystem services such as, protection of biodiversity, climate change mitigation, and water and soil regulation. When legume trees are incorporated as the shade tree in coffee production, direct inputs of nitrogen can occur. The specific objectives of this study were, (1) to quantify the effects of inorganic fertilizer and shade treatments on soil organic carbon (SOC), (2) measure and quantify the mineralization rates under inorganic fertilizer and shade treatments, (3) determine if the spatial abundance of ammonia oxidizing bacteria (AOB) is affected by varying shade management, or by inorganic fertilizer treatment, and 4) measure the effects of inorganic fertilizer application on the transfer of biologically fixed N by Erythrina poeppigiana to Coffea arabica in agroforestry systems in the region. The field study was conducted in Aquiares, Costa Rica. Chemical fertilizer was applied between four treatments at the rate of 0, 110, 170, and 230 kg N ha-1 yr-1 and coupled with three shade treatments (no shade, managed shade, full shade) defined by the management strategies of the legume tree E. poeppigiana. Analyses showed no significant difference in total SOC by fertilizer and shade treatments. Measured NH4+ µmol/L NH4+ and NO2- + NO3- µmol/L NO3- concentrations differed significantly by the shade treatment, but net nitrogen mineralization rates were not significantly different by fertilizer or shade treatment. A significant difference in dsDNA copy number of AOB per soil g-1 was determined by shade treatment. Finally, fertilizer treatment demonstrated a significant effect on the potential for biologically fixed nitrogen from E. poeppigiana to be transferred to coffee planted in association. Coffee agroforestry systems with full shade E. poeppigiana legume trees offered additional inputs of nitrogen to mitigate the use of chemical fertilizers.

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Research Data and Supplementary Material