Hybrid-poplar tree plantations provide a source for biofuel and biomass, but they also increase forest isoprene emissions. The consequences of increased isoprene emissions include higher rates of tropospheric ozone production, increases in the lifetime of methane, and increases in atmospheric aerosol production, all of which affect the global energy budget and/or lead to the degradation of air quality. Using RNA interference (RNAi) to suppress isoprene emission, we show that this trait, which is thought to be required for the tolerance of abiotic stress, is not required for high rates of photosynthesis and woody biomass production in the agroforest plantation environment, even in areas with high levels of climatic stress. Biomass production over 4 y in plantations in Arizona and Oregon was similar among genetic lines that emitted or did not emit significant amounts of isoprene. Lines that had substantially reduced isoprene emission rates also showed decreases in flavonol pigments, which reduce oxidative damage during extremes of abiotic stress, a pattern that would be expected to amplify metabolic dysfunction in the absence of isoprene production in stress-prone climate regimes. However, compensatory increases in the expression of other proteomic components, especially those associated with the production of protective compounds, such as carotenoids and terpenoids, and the fact that most biomass is produced prior to the hottest and driest part of the growing season explain the observed pattern of high biomass production with low isoprene emission. Our results show that it is possible to reduce the deleterious influences of isoprene on the atmosphere, while sustaining woody biomass production in temperate agroforest plantations.

Despite a critical need to evaluate effectiveness of forest treatments in improving stand health, practitioners lack quantitative, repeatable metrics to assess tree vigor and stand health. We evaluated canopy and whole tree attributes of ponderosa pine (Pinus ponderosa Dougl. Ex Laws) related to carbon balance, water balance, and susceptibility to insects and pathogens in dry, pine-dominated forest stands during a multi-year drought, an environmental challenge to stand resilience. Metrics of trees in two unmanaged, and seven treated forested stands, in both uplands and lowlands to develop the quantitative approach. Whole tree and crown attributes including needle length and color, branchlet length and diameter, needle retention (needle ages and retention within ages), and frequency of insects, fungi, and abiotic needle damage were statistically selected to assess tree vigor. Cluster analysis of vigor attributes revealed that trees responded or persisted independently within a forest treatment; forest treatments did not necessarily yield similar tree responses within a stand. A rapid, qualitative assessment was developed to rank trees as low, average, and above-average vigor. To demonstrate an application of our approach, trees were ranked annually over six years in most stands, as well as in a stand where the prescription was adjusted due to the evaluation. The proportion of trees in the three tree vigor ranks differed, suggesting differing levels of stand health. Quantitative metrics and qualitative ranking of tree vigor could assist in selecting trees to be retained to meet specific management objectives, to evaluate treatment implementation, and to monitor post-treatment changes in stand health.

Drought, ozone (O3), and nitrogen deposition (N) alter foliar pigments and tree crown structure that may be remotely detectable. Remote sensing tools are needed that pre-emptively identify trees susceptible to environmental stresses could inform forest managers in advance of tree mortality risk. Jeffrey pine, a component of the economically important and widespread western yellow pine in North America was investigated in the southern Sierra Nevada. Transpiration of mature trees differed by 20% between microsites with adequate (mesic (M)) vs. limited (xeric (X)) water availability as described in a previous study. In this study, in-the-crown morphological traits (needle chlorosis, branchlet diameter, and frequency of needle defoliators and dwarf mistletoe) were significantly correlated with aerially detected, sub-crown spectral traits (upper crown NDVI, high resolution (R), near-infrared (NIR) Scalar (inverse of NDVI) and THERM Δ, and the difference between upper and mid crown temperature). A classification tree model sorted trees into X and M microsites with THERM Δ alone (20% error), which was partially validated at a second site with only mesic trees (2% error). Random forest separated M and X site trees with additional spectra (17% error). Imagery taken once, from an aerial platform with sub-crown resolution, under the challenge of drought stress, was effective in identifying droughted trees within the context of other environmental stresses.

This thesis is dedicated to my family: my wife Julie and our daughter Scarlet. You guys are my motivation and my refuge. Thank you for your patience, love and encouragement. You both put up with my exhaustion, irritability and lack of housework as I completed this thesis. Thank you. v Table of Contents: i Abstract iii Acknowledgements vii List of Figures 1 Chapter 1: Introduction 1 Background 4 VOCs and chemical ecology 5 Environmental impacts of VOCs 10 Isoprene 15 Arundo donax 17 Goals of this thesis 19 Chapter 2: Materials and Methods 19 Hermiston field campaign, 2012 23 Hermiston field campaign, 2013 24 Gas exchange measurements 24 Differences between 2012 and 2013 Hermiston field campaigns 27 EPA Chamber Experiments, 2013 29 Isoprene emission across canopy height survey 30 Isoprene emission response to light level survey 31 Statistical analysis of data 33 Chapter 3: Results 33 3.A: Effect of fertilizer, water management and temperature on leaf chlorophyll content in A. donax 39 3.B: Effect of fertilizer and water management on leaf photosynthesis in A. donax 45 3.C: Effect of fertilizer, water management and temperature on leaf stomatal conductance in A. donax vi 53 3.D: Effect of fertilizer, water management and temperature on leaf water use efficiency in A. donax 59 3.E: Effect of fertilizer, water management and temperature on specific leaf mass in in A. donax 64 3.F: Effect of fertilizer, water management, temperature, canopy height and light level on isoprene emission in A. donax 75 3.G: Effect of nitrogen amendment and temperature on gas exchange in A. donax 78 Chapter 4: Discussion 78 4.A: Biofuels, air quality and Arundo donax 81 4.B: Arundo donax physiology 90 4.C: Isoprene emission in Arundo donax 100 4.D: Gas exchange measurements 101 4.E: Conclusions and future directions 105 References 113 Appendix-Supplemental data 113 Table 1. Fertilizers added to each individual plant by treatment group 113 Table 2. lbs acre-1 fertilizer usage for each treatment 114 Table 3. Mean values and standard deviations for physiological attributes of Arundo donax Recent bioenergy research has focused on improving a few crops such as Miscanthus, poplars, Arundo donax, sugar cane and corn, as well as developing models to predict how various bioenergy sources will impact or mitigate global climate change (Searchinger, 2008). These models have increased in complexity as they attempt to account for the footprints of bioenergy 'from seed to wheel' in order to answer the question-what is the true cost of bioenergy production? Sophisticated models now account for the water, fertilizers and pesticides used on biofuel crops, the fuels used for planting, harvesting, transportation and refining, and LUC impacts, such as adjustments in the amount of carbon the land sequesters. Additionally, recent models have begun to include impacts from indirect land use change (ILUC), such as deforestation that may occur thousands of miles away from biofuel production in response to the market effects of replacing food crops with energy crops (...

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