The effects of a changing climate on root respiration of woody plants in sugar maple forests and northern peatlands

Global climate change might significantly impact future ecosystems. The purpose of this thesis was to investigate potential changes in woody plant fine root respiration in response to a changing climate. In a sugar maple dominated northern hardwood forest, the soil was experimentally warmed (+4 °C) to determine if the tree roots could metabolically acclimate to warmer soil conditions. After one and a half years of soil warming, there was an indication of slight acclimation in the fine roots of sugar maple, helping the ecosystem avoid excessive C loss to the atmosphere. In a poor fen northern peatland in northern Michigan, the impacts of water level changes on woody plant fine root respiration were investigated. In areas of increased and also decreased water levels, there were increases in the CO2 efflux from ecosystem fine root respiration. These studies show the importance of investigating further the impacts climate change may have on C balance in northern ecosystems.

Variation in carbon content of tropical tree species from Ghana

Most research on carbon content of trees has focused on temperate tree species with little information existing on the carbon content of tropical tree species. This study investigated the variation in carbon content of selected tropical tree species and compared carbon content of Khaya spp from two ecozones in Ghana. Allometric equations developed for mixed-plantation stands for wet evergreen forest verified the expected strong relationship between tree volumes and dbh (r2>0.93) and volume and dbh2×height (r2>0.97). Carbon concentration, wood density and carbon content differed significantly among species. Volume at age 12 ranged from 0.01 to 1.04 m3 per tree, and wood density was highly variable among species, ranging from 0.27 to 0.76 g cm-3. This suggests that species specific density data is critical for accurate conversion of volumes derived from allometric relationships into carbon contents. Significant differences in density of Khaya spp existed between the wet and moist semi-deciduous ecozones. The baseline species-level information from this study will be useful for carbon accounting and development of carbon sequestration strategies in Ghana and other tropical African countries.

The long-term effects of whole-tree harvest at final felling on soil properties in a Norway Spruce (Picea Abies (L) Karst.) Stand

Increased demand for forest-derived biomass has resulted in changes in harvest intensities in Finland. Conventional stem-only harvest (CH) has to some extent been replaced with whole-tree harvest (WTH). The latter involves a greater removal of nutrients from the forest ecosystem, as all the above ground biomass is exported from the site. This has raised concerns that WTH could result in large changes in the nutrient dynamics of a forest stand and could eventually lower its site productivity. Little empirical data exists to support this assumption as only a limited number of studies have been conducted on the topic. A majority of these discuss the short-term effects, thus the long-term consequences remain unknown. The objective of this study was to compare differences in soil properties after CH and WTH in a fertile Norway spruce (Picea abies (L) Karst.) stand in Southern Finland. The site was clear-felled in August 2000 and spruce seedlings were planted in the following summer. Soil sampling in the form of systematic randomized sampling was carried out in May 2011. Changes in base saturation, cation exchange capacity, elemental pools (total and exchangeable) and acidity were studied in both organic and mineral horizons. The results indicate that WTH lowered effective cation exchange capacity and base saturation particularly in the humus layer. The pools of exchangeable Al and Fe were increased in the humus layer, whereas the amount of exchangeable Ca decreased in both layers. WTH also resulted in lower Ca/Al-ratios across the sampled layers. Treatment did not have a significant effect on pH, total pools of elements or on the C/N-ratio of the soil. The results suggest that although the stand possesses significant pools of nutrients at present, WTH, if continued, could have long-term effects on site productivity.

Regulation of woody plant development by gibberellin catabolic and signaling genes

Gibberellin (GA) is a growth promoting hormone implicated in regulating a diversity of plant processes. This dissertation examines the role of GA metabolic and signaling genes in woody plant growth and development. Transgenic modifications, expression analysis, physiological/biochemical assays, biometric measurements and histological analysis were used to understand the regulatory roles these genes play in the model woody plant, Populus. Our results highlight the importance of GA regulatory genes in woody perennial growth, including: phenology, wood formation, phenotypic plasticity, and growth/survival under field conditions. We characterize two putative Populus orthologs of the SHORT INTERNODES (SHI) gene from Arabidopsis, a negative regulator of GA signaling. RNAi-mediated suppression of Populus SHI-like genes increased several growth-related traits, including extent of xylem proliferation, in a dose-dependent manner. Three Populus genes, sharing sequence homology to the positive regulator of GA signaling gene PHOTOPERIOD-RESPONSIVE 1 (PHOR1) from Solanum, are up-regulated in GA-deficient and insensitive plants suggesting a conserved role in GA signaling. We demonstrate that Populus PHOR1-like genes have overlapping and divergent function(s). Two PHOR1-like genes are highly expressed in roots, predominantly affect root growth (e.g., morphology, starch quantity and gravitropism), and induced by short-days (SD). The other PHOR1-like gene is ubiquitously expressed with a generalized function in root and shoot development. The effects of GA catabolic and signaling genes on important traits (e.g., adaptive and productivity traits) were studied in a multi-year field trial. Transgenics overexpressing GA 2-oxidase (GA2ox) and DELLA genes showed tremendous variation in growth, form, foliage, and phenology (i.e., vegetative and reproductive). Observed gradients in trait modifications were correlated to transgene expression levels, in a manner suggesting a dose-dependent relationship. We explore GA2ox and DELLA genes involvement in mediating growth responses to immediate short-term drought stress, and SD photoperiods, signaling prolonged periods of stress (e.g., winter bud dormancy). GA2ox and DELLA genes show substantial up-regulation in response to drought and SDs. Transgenics overexpressing homologs of these genes subjected to drought and SD photoperiods show hypersensitive growth restraint and increased stress resistances. These results suggest growth cessation (i.e., dormancy) in response to adverse conditions is mediated by GA regulatory genes.

Regulation of woody plant development by auxin and polar auxin transport

Auxin is a key regulator in plant growth and development. This dissertation examines the role of auxin and polar auxin transport in woody growth and development. Strategies of promoter reporter system, microarray expression analysis, transgenic modification, physiological assays, anatomical analysis, and histochemical/biochemical assays were employed to improve our understanding of auxin study in Populus. The results demonstrate various aspects of auxin regulation on shoot growth, root development, wood formation, and gravitropism in woody tissues. We describe the behavior of the DR5 reporter system for measuring auxin concentrations and response in stably transformed Populus trees. Our study shows that DR5 reporter system can be efficiently used in Populus to study auxin biology at a cellular resolution. We investigated the global gene expression in responding to auxin in Populus root. The results revealed groups of IBA up- and down- regulated genes involved in various biological processes including cell wall modification, root growth and lateral root formation, transporter activity and hormone crosstalk. We also verify two of the identified genes' function by transgenic modification in Populus, which encode auxin efflux carrier PtPIN9 and transcription factor PtERF72. We investigated the role of PtPIN9 in woody growth and development, especially in wood formation and gravitropic response in woody stem. We found that overexpressing PtPIN9 enhanced several growth parameters while suppression of PtPIN9 has inhibited tension wood formation. Our results show that PIN9 and other members from PIN family could be possible useful tools for increasing biomass productivity, wood quality, or in modifying plant form.

UNDERSTANDING FARMERS’ PERCEPTIONS AND THE EFFECTS OF SHEA TREE Vitellaria paradoxa DISTRIBUTION IN AGROFORESTRY PARKLANDS OF THE UPPER WEST REGION, GHANA

Agroforestry parklands represent a vast majority of the agricultural landscape under subsistent-oriented farming in semi-arid West Africa. Parklands are characterized by the growth of well- maintained trees (e.g., shea) on cultivated fields as a result of both environmental and human influences. Shea (Vitellaria paradoxa) provides a cultural and economic benefit to the local people of Ghana, especially women. Periods between traditional fallow rotation systems have reduced recently due to agricultural development and a demand for higher production. As a result, shea trees, which regenerate during fallow periods, has decreased over the landscape. The aim of this study was to determine beneficial spatial distributions of V. paradoxa to maintain high yields of staple crops, and how management of V. paradoxa will differ between male and female farmers as a result of farmer based needs and use of shea. Vegetation growth and grain yield of maize (Zea mays) associated with individual trees, clumped trees, and open fields were measured. Soil moisture and light availability were also measured to determine how V. paradoxa affected resource availability of maize in either clumped or scattered distributions of V. paradoxa. As expected, light availability increased as measurement locations moved farther away from all trees. However, soil moisture was actually greater under trees in clumps than under individual trees. Maize stalk height and cob length showed no difference between clumped and single trees at each measurement location. Grain yield per plot and per cob increased as measurement locations moved farther from single trees, but was actually greater near clumped trees that in the open field subplots. Cob length and maize stalk height increased with greater light availability, but grain yield per cob or per plot showed no relationship with light, but were not affected by soil moisture. Conversely, grain yield increased with increasing soil moisture, but had no relationship with light availability. Initial farming capital is the largest constraint to female farmers; therefore the collection of shea can help provide women with added income that could meet their specific farming needs. Our data indicate that overall effects of maintaining clumped distributions of V. paradoxa provided beneficial microclimates for staple crops when compared to single trees. It is recommended that male and female farmers allow shea to grow in clumped spatial distributions rather than maintaining scattered, individual trees.

Retention of canopy trees as biological legacies for balancing woody biomass production and biodiversity in managed aspen forests of the Great Lakes Region

Green-tree retention under the conceptual framework of ecological forestry has the potential to provide both biomass feedstock for industry and maintain quality wildlife habitat. I examined the effects of retained canopy trees as biological legacies (“legacy trees”) in aspen (Populus spp.) forests on above-ground live woody biomass, understory plant floristic quality, and bird diversity. Additionally, I evaluated habitat quality for a high conservation priority species, the Golden-winged Warbler (Vermivora chrysoptera). I selected 27 aspen-dominated forest stands in northern Wisconsin with nine stands in each of three legacy tree retention treatments (conifer retention, hardwood retention, and clearcuts or no retention) across a chronosequence (4-36 years post-harvest). Conifer retention stands had greater legacy tree and all tree species biomass but lower regenerating tree biomass than clearcuts. Coniferous but not hardwood legacy trees appeared to suppress regenerating tree biomass. I evaluated the floristic quality of the understory plant assemblage by estimating the mean coefficient of conservatism (C). Mean C was lower in young stands than in middle-age or old stands; there was a marginally significant (p=0.058) interaction effect between legacy tree retention treatment and stand age. Late-seral plant species were positively associated with stand age and legacy tree diameter or age revealing an important relationship between legacy tree retention and stand development. Bird species richness was greatest in stands with hardwood retention particularly early in stand development. Six conservation priority bird species were indicators of legacy tree retention or clearcuts. Retention of legacy trees in aspen stands provided higher quality nest habitat for the Golden-winged Warbler than clearcuts based on high pairing success and nesting activity. Retention of hardwoods, particularly northern red oak (Quercus rubra), yielded the most consistent positive effects in this study with the highest bird species richness and the highest quality habitat for the Golden-winged Warbler. This treatment maintained stand biomass comparable to clearcuts and did not suppress regenerating tree biomass. In conclusion, legacy tree retention can enhance even-aged management techniques to produce a win-win scenario for the conservation of declining bird species and late-seral understory plants and for production of woody biomass feedstock from naturally regenerating aspen forests.

Effects of elevated atmospheric CO2 and O3 on wood density, antomical proerties and decomposition of Northern Hardwoods

Anthropogenic activities continue to drive atmospheric CO2 and O3 concentrations to levels higher than during the pre-industrial era. Accumulating evidence indicates that both elevated CO2 and elevated O3 could modify the quantity and biochemistry of woody plant biomass. Anatomical properties of woody plants are largely influenced by the activity of the cambium and the growth characteristics of wood cells, which are in turn influenced by a range of environmental factors. Hence, alterations in the concentrations of atmospheric CO2 and / or O3 could also impact wood anatomical properties. Many fungi derive their metabolic resources for growth from plant litter, including woody tissue, and therefore modifications in the quantity, biochemistry and anatomical properties of woody plants in response to elevated CO2 and / or O3 could impact the community of wood-decaying fungi and rates of wood decomposition. Consequently carbon and nutrient cycling and productivity of terrestrial ecosystem could also be impacted. Alterations in wood structure and biochemistry of woody plants could also impact wood density and subsequently impact wood quality. This dissertation examined the long term effects of elevated CO2 and / or O3 on wood anatomical properties, wood density, wood-decaying fungi and wood decomposition of northern hardwood tree species at the Aspen Free-Air CO2 and O3 Enrichment (Aspen FACE) project, near Rhinelander, WI, USA. Anatomical properties of wood varied significantly with species and aspen genotypes and radial position within the stem. Elevated CO2 did not have significant effects on wood anatomical properties in trembling aspen, paper birch or sugar maple, except for marginally increasing (P < 0.1) the number of vessels per square millimeter. Elevated O3 marginally or significantly altered vessel lumen diameter, cell wall area and vessel lumen area proportions depending on species and radial position. In line with the modifications in the anatomical properties, elevated CO2 and O3, alone, significantly modified wood density but effects were species and / or genotype specific. However, the effects of elevated CO2 and O3, alone, on wood anatomical properties and density were ameliorated when in combination. Wood species had a much greater impact on the wood-decaying fungal community and initial wood decomposition rate than did growth or decomposition of wood in elevated CO2 and / or O3. Polyporales, Agaricales, and Russulales were the dominant orders of fungi isolated. Based on the current results, future higher levels of CO2 and O3 may have moderate effects on wood quality of northern hardwoods, but for utilization purposes these may not be considered significant. However, wood-decaying fungal community composition and decomposition of northern hardwoods may be altered via shifts in species and / or genotype composition under future higher levels of CO2 and O3.

Assessing success of forest restoration efforts in degraded montane cloud forests in southern Mexico

Montane cloud forests are home to great biodiversity. However, non-sustainable anthropogenic activities have led to the loss of forest cover in southern Mexico. Increasing conservation, restoration and sustainable use of forest resources prevents the loss of cloud forests. In this study, success of forest restoration was evaluated in a degraded forest of Highlands Chiapas. The goal of this study was to assess the structure and composition of native tree species. We evaluated vegetation composition at three sites that had undergone enrichment plantings. Floristic composition and structure of the herbaceous, seedling, sapling, and overstory layers were measured. A total of sixty-six native tree species were recorded. Enrichment planting was found to have increased tree diversity. Moreover, 54% of the planted species were found in the understory, indicating that they were successfully recruiting. In conclusion, enrichment planting can aid in the conservation of forest cover in degraded areas.

Towards greater accuracy in individual-tree mortality regression

Background mortality is an essential component of any forest growth and yield model. Forecasts of mortality contribute largely to the variability and accuracy of model predictions at the tree, stand and forest level. In the present study, I implement and evaluate state-of-the-art techniques to increase the accuracy of individual tree mortality models, similar to those used in many of the current variants of the Forest Vegetation Simulator, using data from North Idaho and Montana. The first technique addresses methods to correct for bias induced by measurement error typically present in competition variables. The second implements survival regression and evaluates its performance against the traditional logistic regression approach. I selected the regression calibration (RC) algorithm as a good candidate for addressing the measurement error problem. Two logistic regression models for each species were fitted, one ignoring the measurement error, which is the “naïve” approach, and the other applying RC. The models fitted with RC outperformed the naïve models in terms of discrimination when the competition variable was found to be statistically significant. The effect of RC was more obvious where measurement error variance was large and for more shade-intolerant species. The process of model fitting and variable selection revealed that past emphasis on DBH as a predictor variable for mortality, while producing models with strong metrics of fit, may make models less generalizable. The evaluation of the error variance estimator developed by Stage and Wykoff (1998), and core to the implementation of RC, in different spatial patterns and diameter distributions, revealed that the Stage and Wykoff estimate notably overestimated the true variance in all simulated stands, but those that are clustered. Results show a systematic bias even when all the assumptions made by the authors are guaranteed. I argue that this is the result of the Poisson-based estimate ignoring the overlapping area of potential plots around a tree. Effects, especially in the application phase, of the variance estimate justify suggested future efforts of improving the accuracy of the variance estimate. The second technique implemented and evaluated is a survival regression model that accounts for the time dependent nature of variables, such as diameter and competition variables, and the interval-censored nature of data collected from remeasured plots. The performance of the model is compared with the traditional logistic regression model as a tool to predict individual tree mortality. Validation of both approaches shows that the survival regression approach discriminates better between dead and alive trees for all species. In conclusion, I showed that the proposed techniques do increase the accuracy of individual tree mortality models, and are a promising first step towards the next generation of background mortality models. I have also identified the next steps to undertake in order to advance mortality models further.

Automated design of self-stabilization

Self-stabilization is a property of a distributed system such that, regardless of the legitimacy of its current state, the system behavior shall eventually reach a legitimate state and shall remain legitimate thereafter. The elegance of self-stabilization stems from the fact that it distinguishes distributed systems by a strong fault tolerance property against arbitrary state perturbations. The difficulty of designing and reasoning about self-stabilization has been witnessed by many researchers; most of the existing techniques for the verification and design of self-stabilization are either brute-force, or adopt manual approaches non-amenable to automation. In this dissertation, we first investigate the possibility of automatically designing self-stabilization through global state space exploration. In particular, we develop a set of heuristics for automating the addition of recovery actions to distributed protocols on various network topologies. Our heuristics equally exploit the computational power of a single workstation and the available parallelism on computer clusters. We obtain existing and new stabilizing solutions for classical protocols like maximal matching, ring coloring, mutual exclusion, leader election and agreement. Second, we consider a foundation for local reasoning about self-stabilization; i.e., study the global behavior of the distributed system by exploring the state space of just one of its components. It turns out that local reasoning about deadlocks and livelocks is possible for an interesting class of protocols whose proof of stabilization is otherwise complex. In particular, we provide necessary and sufficient conditions – verifiable in the local state space of every process – for global deadlock- and livelock-freedom of protocols on ring topologies. Local reasoning potentially circumvents two fundamental problems that complicate the automated design and verification of distributed protocols: (1) state explosion and (2) partial state information. Moreover, local proofs of convergence are independent of the number of processes in the network, thereby enabling our assertions about deadlocks and livelocks to apply on rings of arbitrary sizes without worrying about state explosion.

Small-scale timber stand management techniques : a case study of woodlots in Isangati, Tanzania

Small-scale village woodlots of less than 0.5ha are the preferred use of land for local farmers with extra land in the village of Isangati, a small community located in the southern highlands of Tanzania. Farmers view woodlots as lucrative investments that do not involve intensive labor or time. The climate is ideal for the types of trees grown and the risks are minimal with no serious threats from insects, fires, thieves, or grazing livestock. It was hypothesized that small-scale village woodlot owners were not maximizing timber outputs with their current timber stand management and harvesting techniques. Personal interviews were conducted over a five month period and field data was collected at each farmer’s woodlots over a seven month period. Woodlot field data included woodlot size, number of trees, tree species, tree height, dbh, age, and spacing. The results indicated that the lack of proper woodlot management techniques results in failure to fully capitalize on the investment of woodlots. While farmers should continue with their current harvesting rotations, some of the reasons for not maximizing tree growth include close spacing (2m x 2m), no tree thinning, extreme pruning (60% of tree), and little to no weeding. Through education and hands-on woodlot management workshops, the farmers could increase their timber output and value of woodlots.

Development of an optimization model for biofuel facility size and location and a simulation model for design of a biofuel supply chain

To mitigate greenhouse gas (GHG) emissions and reduce U.S. dependence on imported oil, the United States (U.S.) is pursuing several options to create biofuels from renewable woody biomass (hereafter referred to as “biomass”). Because of the distributed nature of biomass feedstock, the cost and complexity of biomass recovery operations has significant challenges that hinder increased biomass utilization for energy production. To facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization and tapping unused forest residues, it is proposed to develop biofuel supply chain models based on optimization and simulation approaches. The biofuel supply chain is structured around four components: biofuel facility locations and sizes, biomass harvesting/forwarding, transportation, and storage. A Geographic Information System (GIS) based approach is proposed as a first step for selecting potential facility locations for biofuel production from forest biomass based on a set of evaluation criteria, such as accessibility to biomass, railway/road transportation network, water body and workforce. The development of optimization and simulation models is also proposed. The results of the models will be used to determine (1) the number, location, and size of the biofuel facilities, and (2) the amounts of biomass to be transported between the harvesting areas and the biofuel facilities over a 20-year timeframe. The multi-criteria objective is to minimize the weighted sum of the delivered feedstock cost, energy consumption, and GHG emissions simultaneously. Finally, a series of sensitivity analyses will be conducted to identify the sensitivity of the decisions, such as the optimal site selected for the biofuel facility, to changes in influential parameters, such as biomass availability and transportation fuel price. Intellectual Merit The proposed research will facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization in the renewable biofuel industry. The GIS-based facility location analysis considers a series of factors which have not been considered simultaneously in previous research. Location analysis is critical to the financial success of producing biofuel. The modeling of woody biomass supply chains using both optimization and simulation, combing with the GIS-based approach as a precursor, have not been done to date. The optimization and simulation models can help to ensure the economic and environmental viability and sustainability of the entire biofuel supply chain at both the strategic design level and the operational planning level. Broader Impacts The proposed models for biorefineries can be applied to other types of manufacturing or processing operations using biomass. This is because the biomass feedstock supply chain is similar, if not the same, for biorefineries, biomass fired or co-fired power plants, or torrefaction/pelletization operations. Additionally, the research results of this research will continue to be disseminated internationally through publications in journals, such as Biomass and Bioenergy, and Renewable Energy, and presentations at conferences, such as the 2011 Industrial Engineering Research Conference. For example, part of the research work related to biofuel facility identification has been published: Zhang, Johnson and Sutherland [2011] (see Appendix A). There will also be opportunities for the Michigan Tech campus community to learn about the research through the Sustainable Future Institute.

Life cycle assessment of biofuels produced by the new integrated hydropyrolysis-hydroconversion (IH2) process

Biofuels are alternative fuels that have the promise of reducing reliance on imported fossil fuels and decreasing emission of greenhouse gases from energy consumption. This thesis analyses the environmental impacts focusing on the greenhouse gas (GHG) emissions associated with the production and delivery of biofuel using the new Integrated Hydropyrolysis and Hydroconversion (IH2) process. The IH2 process is an innovative process for the conversion of woody biomass into hydrocarbon liquid transportation fuels in the range of gasoline and diesel. A cradle-to-grave life cycle assessment (LCA) was used to calculate the greenhouse gas emissions associated with diverse feedstocks production systems and delivery to the IH2 facility plus producing and using these new renewable liquid fuels. The biomass feedstocks analyzed include algae (microalgae), bagasse from a sugar cane-producing locations such as Brazil or extreme southern US, corn stover from Midwest US locations, and forest feedstocks from a northern Wisconsin location. The life cycle greenhouse gas (GHG) emissions savings of 58%–98% were calculated for IH2 gasoline and diesel production and combustion use in vehicles compared to fossil fuels. The range of savings is due to different biomass feedstocks and transportation modes and distances. Different scenarios were conducted to understand the uncertainties in certain input data to the LCA model, particularly in the feedstock production section, the IH2 biofuel production section, and transportation sections.

PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.