The SUCEST-FUN regulatory network database: Designing an energy grass

Modern sugarcane cultivars are complex hybrids resulting from crosses among several Saccharum species. Traditional breeding methods have been employed extensively in different countries over the past decades to develop varieties with increased sucrose yield and resistance to pests and diseases. Conventional variety improvement, however, may be limited by the narrow pool of suitable genes. Thus, molecular genetics is seen as a promising tool to assist in the process of developing improved varieties. The SUCEST-FUN Project (http://sucest-fun.org) aims to associate function with sugarcane genes using a variety of tools, in particular those that enable the study of the sugarcane transcriptome. An extensive analysis has been conducted to characterise, phenotypically, sugarcane genotypes with regard to their sucrose content, biomass and drought responses. Through the analysis of different cultivars, genes associated with sucrose content, yield, lignin and drought have been identified. Currently, tools are being developed to determine signalling and regulatory networks in grasses, and to sequence the sugarcane genome, as well as to identify sugarcane promoters. This is being implemented through the SUCEST-FUN (http://sucest-fun.org) and GRASSIUS databases (http://grassius.org), the cloning of sugarcane promoters, the identification of cis-regulatory elements (CRE) using Chromatin Immunoprecipitation-sequencing (ChIP-Seq) and the generation of a comprehensive Signal Transduction and Transcription gene catalogue (SUCAST Catalogue).

Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as "molecular domestication", by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.

Factors controlling water-column respiration in rivers of the central and southwestern Amazon Basin

We examined the factors controlling the variability in water-column respiration rates in Amazonian rivers. Our objectives were to determine the relationship between respiration rates and the in situ concentrations of the size classes of organic carbon (OC), and the biological source (C-3 and C-4 plants and phytoplankton) of organic matter (OM) supporting respiration. Respiration was measured along with OC size fractions and dissolved oxygen isotopes (delta O-18-O-2) in rivers of the central and southwestern Amazon Basin. Rates ranged from 0.034 mu mol O-2 L-1 h(-1) to 1.78 mu mol O-2 L-1 h(-1), and were four-fold higher in rivers with evidence of photosynthetic production (demonstrated by delta O-18-O-2<24.2 parts per thousand) as compared to rivers lacking such evidence (delta O-18-O-2>24.2 parts per thousand; 1.35 +/- 0.22 vs. 0.30 +/- 0.29 mu mol L-1 h(-1)). Rates were likely elevated in the former rivers, which were all sampled during low water, due to the stimulation of heterotrophic respiration via the supply of a labile, algal-derived substrate and/or the occurrence of autotrophic respiration. The organic composition of fine particulate OM (FPOM) of these rivers is consistent with a phytoplankton origin. Multiple linear regression analysis indicates that [FPOC], C:N-FPOC ratios, and [O-2] account for a high amount of the variability in respiration rates (r(2) = 0.80). Accordingly, FPOC derived from algal sources is associated with elevated respiration rates. The delta C-13 of respiration-derived CO2 indicates that the role of phytoplankton, C-3 plants, and C-4 grasses in supporting respiration is temporally and spatially variable. Future scaling work is needed to evaluate the significance of phytoplankton production to basin-wide carbon cycling.

Viability of recently harvested and stored Xylopia aromatica (Lam.) Mart. (Annonaceae) seeds

Xylopia aromatica is a native species from Brazil's "Cerrado", recommended for restoration ecology and also as a medicine. Its seeds have embryos with morphophysiological dormancy, making nursery propagation difficult. The objective of this study was to verify the efficiency of X-ray and tetrazolium tests for evaluating the viability of three seed lots, stored for different periods. All seeds were X-rayed (13 kV, 350 seconds) and samples used for tetrazolium and germination tests. In the tetrazolium test, seeds were submitted to six treatments at two temperatures (25 and 30 °C) with imbibition in distilled water and immersion in three concentrations of tetrazolium solution (0.5, 0.75 and 1%) at the two imbibition temperatures. Seeds for the germination test were placed for imbibition in distilled water and a 500 ppm Promalin® (6-Benzyladenine + GA4 + GA7) solution and later sown in sterilized sand. The embryo could not be observed with the X-ray test. However, those seeds observed with an undamaged endosperm did not differ in the percentages of seeds with firm and stained endosperms observed in the tetrazolium test for all the lots. The tetrazolium test is efficient for evaluating seed viability, principally if imbibed at 30 °C and immersed in a 0.5% solution at 30 °C.

Il monitoraggio suolo-pianta per la valutazione dell'inquinamento da metalli pesanti nell'ambiente urbano

Il lavoro di tesi è incentrato sulla valutazione del degrado del suolo dovuto a fenomeni di inquinamento da metalli pesanti aerodispersi, ovvero apportati al suolo mediante deposizioni atmosferiche secche ed umide, in ambiente urbano. Lo scopo della ricerca è legato principalmente alla valutazione dell’efficienza del metodo di monitoraggio ideato che affianca al campionamento e all’analisi pedologica l’utilizzo di bioindicatori indigeni, quali il muschio, il cotico erboso, le foglie di piante arboree e il materiale pulverulento depositatosi su di esse. Una semplice analisi pedologica infatti non permette di discriminare la natura dei contaminanti in esso ritrovati. I metalli pesanti possono raggiungere il suolo attraverso diverse vie. In primo luogo questi elementi in traccia si trovano naturalmente nei suoi; ma numerose sono le fonti antropiche: attività industriali, traffico veicolare, incenerimento dei rifiuti, impianti di riscaldamento domestico, pratiche agricole, utilizzo di acque con bassi requisiti di qualità, ecc. Questo fa capire come una semplice analisi del contenuto totale o pseudo - totale di metalli pesanti nel suolo non riesca a rispondere alla domanda su quale si la fonte di provenienza di queste sostanze. Il metodo di monitoraggio integrato suolo- pianta è stato applicato a due diversi casi di studio. Il primo denominato “Progetto per il monitoraggio e valutazione delle concentrazioni in metalli pesanti e micro elementi sul sistema suolo - pianta in aree urbane adibite a verde pubblico dell’Emilia – Romagna” ha permesso di valutare l’insorgenza di una diminuzione della qualità dell’ecosistema parco urbano causata dalla ricaduta di metalli pesanti aerotrasportati, in tre differenti realtà urbane dell’Emilia Romagna: le città di Bologna, Ferrara e Cesena. Le città presentano caratteristiche pedologiche, ambientali ed economico-sociali molto diverse tra loro. Questo ha permesso di studiare l’efficienza del metodo su campioni di suolo e di vegetali molto diversi per quanto riguarda le aliquote di metalli pesanti riscontrate. Il secondo caso di studio il “Monitoraggio relativo al contenuto in metalli pesanti e microelementi nel sistema acqua-suolo-pianta delle aree circostanti l’impianto di termovalorizzazione e di incenerimento del Frullo (Granarolo dell’Emilia - BO)” è stato invece incentrato sulla valutazione della qualità ambientale delle aree circostanti l’inceneritore. Qui lo scenario si presentava più omogeneo dal punto di vista pedologico rispetto al caso di studio precedente, ma molto più complesso l’ecosistema di riferimento (urbano, extra-urbano ed agricolo). Seppure il metodo suolo-pianta abbia permesso di valutare gli apporti di metalli pesanti introdotti per via atmosferica, non è stato possibile imputarne l’origine alle sole emissioni prodotte dall’inceneritore.

Emissions of volatile organic compounds from tropical savanna vegetation and biomass burning

This dissertation focuses on characterizing the emissions of volatile organic compounds (VOCs) from grasses and young trees, and the burning of biomass mainly from Africa and Indonesia. The measurements were performed with a proton-transfer-reaction mass spectrometer (PTR-MS). The biogenic emissions of tropical savanna vegetation were studied in Calabozo (Venezuela). Two field campaigns were carried out, the first during the wet season (1999) and the second during the dry season (2000). Three grass species were studied: T. plumosus, H. rufa and A. canescens, and the tree species B. crassifolia, C. americana and C. vitifolium. The emission rates were determined with a dynamic plant enclosure system. In general, the emissions increased exponentially with increasing temperature and solar radiation. Therefore, the emission rates showed high variability. Consequently, the data were normalized to a standard temperature of 30°C, and standard emission rates thus determined allowed for interspecific and seasonal comparisons. The range of average daytime (10:00-16:00) emission rates of total VOCs measured from green (mature and young) grasses was between 510-960 ngC/g/h. Methanol was the primary emission (140-360 ngC/g/h), followed by acetaldehyde, butene and butanol and acetone with emission rates between 70-200 ngC/g/h. The emissions of propene and methyl ethyl ketone (MEK) were <80 ngC/g/h, and those of isoprene and C5-alcohols were between 10-130 ngC/g/h. The oxygenated species represented 70-75% of the total. The emission of VOCs was found to vary by up to a factor of three between plants of the same species, and by up to a factor of two between the different species. The annual source of methanol from savanna grasses worldwide estimated in this work was 3 to 4.4 TgC, which could represent up to 12% of the current estimated global emission from terrestrial vegetation. Two of the studied tree species, were isoprene emitters, and isoprene was also their primary emission (which accounted for 70-94% of the total carbon emitted) followed by methanol and butene + butanol. The daytime average emission rate of isoprene measured in the wet season was 27 mgC/g/h for B. crassifolia, and 123 mgC/g/h for C. vitifolium. The daytime emissions of methanol and butene + butanol were between 0.3 and 2 mgC/g/h. The total sum of VOCs emission measured during the day in the wet season was between 30 and 130 mgC/g/h. In the dry season, in contrast, the methanol emissions from C. vitifolium saplings –whose leaves were still developing– were an order of magnitude higher than in the wet season (15 mgC/g/h). The isoprene emission from B. crassifolia in the dry season was comparable to the emission in the wet season, whereas isoprene emission from C. vitifolium was about a factor of three lower (~43 mgC/g/h). Biogenic emission inventories show that isoprenoids are the most prominent and best-studied compounds. The standard emission rates of isoprene and monoterpenes of the measured savanna trees were in the lower end of the range found in the literature. The emission of other biogenic VOCs has been sparsely investigated, but in general, the standard emissions from trees studied here were within the range observed in previous investigations. The biomass burning study comprised the measurement of VOCs and other trace-gas emissions of 44 fires from 15 different fuel types, primarily from Africa and Indonesia, in a combustion laboratory. The average sum of emissions (excluding CO2, CO and NO) from African fuels was ~18 g(VOC)/kg. Six of the ten most important emissions were oxygenated VOCs. Acetic acid was the major emission, followed by methanol and formaldehyde. The emission of methane was of the same order as the methanol emission (~5 g/kg), and that of nitrogen-containing compounds was ~1 g/kg. An estimate of the VOC source from biomass burning of savannas and grasslands worldwide suggests that the sum of emissions is about 56 Tg/yr, of which 34 Tg correspond to oxygenated VOCs, 14 Tg to unsaturated and aromatic compounds, 5 Tg to methane and 3 Tg to N-compounds. The estimated emissions of CO, CO2 and NO are 216, 5117 and 9.4 Tg/yr, respectively. The emission factors reported here for Indonesian fuels are the first results of laboratory fires using Indonesian fuels. Acetic acid was the highest organic emission, followed by acetol, a compound not previously reported in smoke, methane, mass 97 (tentatively identified as furfural, dimethylfuran and ethylfuran), and methanol. The sum of total emissions of Indonesian fuels was 91 g/kg, which is 5 times higher than the emissions from African fuels. The results of this study reinforces the importance of oxygenated compounds. Due to the vast area covered by tropical savannas worldwide, the biogenic and biomass burning emission of methanol and other oxygenated compounds may be important for the regional and even global tropospheric chemistry.

Palynologie und Sedimentologie der Interglazialprofile Döttingen, Bonstorf, Munster und Bilshausen

Palynologie und Sedimentologie der Interglazialprofile Döttingen, Bonstorf, Munster und Bilshausen Zusammenfassung In der vorliegenden Dissertation wurden vier dem Holstein-Interglazial zugehörige Bohrkerne sowie ein rhumezeitlicher Bohrkern palynologisch und sedimentologisch bearbeitet. Die holsteinzeitlichen Bohrkerne stammen aus Kieselgurlagerstätten der Lüneburger Heide (Bonstorf und Munster) und aus einem Trockenmaar (Döttingen) in der Eifel. Der rhumezeitliche Kern stammt aus der Typlokalität Bilshausen im Harzvorland. Neben Prozentwertdiagrammen werden Pollendichte- und wenn möglich Polleninfluxwerte vorgestellt, die insbesondere für die Lokalitäten Hetendorf/Bonstorf und Munster/Breloh bisher nicht verfügbar waren. Mit dem Profil Döttingen konnte erstmals eine sowohl vollständige als auch nicht innerhalb des klassischen Aufkommens holsteinzeitlicher Fundstellen im norddeutschen Tiefland positionierte Holsteinsequenz aus dem deutschen Mittelgebirge dokumentiert werden. Das erhaltene Pollendiagramm bestätigt die aus den norddeutschen Profilen bekannte holsteintypische Vegetationsabfolge, durch die das Holstein gegenüber anderen Interglazialen wie Holozän, Eem oder Rhume palynologisch definiert ist. Neben der grundsätzlichen Übereinstimmung der Pollensequenz unterscheidet sich das Profil Döttingen aber deutlich im prozentualen Aufkommen der beteiligten Taxa von den norddeutschen Profilen. So wird eine hohe Alnus-Präsenz als Merkmal deutscher Holsteinprofile bestätigt, jedoch ist die, in den norddeutschen Lokalitäten durchhaltend hohe oder dominante Beteiligung von Pinus im deutschen Mittelgebirge nicht vorhanden und muss daher auf die Standortbedingungen Norddeutschlands zurückgeführt werden. Abies dagegen ist im Holstein der Mittelgebirge wesentlich präsenter als im norddeutschen Flachland. Im Profil Döttingen wurden insgesamt 10 Tephralagen gefunden. Auf eine dieser Tephren folgt ein „Birken-Kiefern-Gräser Vorstoß“, der palynostratigraphisch dem älteren „Birken-Kiefern Vorstoß“ in Munster/Breloh entspricht. Als eine Typologie des Holstein kann das in den Profilen Döttingen und Munster bestätigte intraholsteinzeitliche Carpinus-Minimum verstanden werden. An Hand sedimentologischer und palynologischer Befunde aus dem Bohrkern MU 2 muss die Existenz zweier, in der Literatur postulierter, postholsteinzeitlicher, „Nachschwankungen“ in Munster/Breloh in Frage gestellt, wenn nicht abgelehnt werden. In Kern MU 2 fallen palynostratigraphische Grenzen häufig mit Sandeinschaltungen zusammen. Eine dieser Sandeinschaltungen, nämlich unmittelbar vor dem älteren „Birken-Kiefern-Vorstoß“, korreliert in ihrer stratigraphischen Position mit der den „Birken-Kiefern-Gräser-Vorstoß“ im Profil Döttingen einleitenden Tephralage. Es gelang die Dauer des intraholsteinzeitlichen Carpinus Minimums auf etwa 1500±100 Jahre zu bestimmen und eine interne Zweigliederung zu dokumentieren. Im rhumezeitlichen Kern von Bilshausen (BI 1) konnten zahlreiche Störungen nachgewiesen werden. Insbesondere im Teufenbereich des Bilshausener „Birken-Kiefern-Vorstoßes“ deuten diese auf eine möglicherweise verfälschte Überlieferung. Der palynologisch markante „Lindenfall“ von Bilshausen liegt im Bereich einer isoklinalen Schichtenverfaltung. Die in der Literatur im Horizont des „Lindenfalls“ beschriebene „Bilshausentephra“ wurde nicht gefunden. Warvenzählungen an den Kernen MU 1, MU 2 und BI 1 ermöglichten Pollenzonendauern in Holstein- und Rhume-Interglazial zu bestimmen. Dabei wurde mittels den Warvenzählungen, unter zu Hilfenahme von Literaturdaten und von Schätzwerten eine Dauer für das Holstein-Interglazial sensu stricto (Pollenzonen I-XIV) von 15400-17800 Jahren und für das Rhume-Interglazial von wahrscheinlich 22000 Jahren bis maximal 26000 Jahren ermittelt.

LCA-GIS Integrated approach for a Sustainable Land Use Under Energy Crops

In genere, negli studi di vocazionalità delle colture, vengono presi in considerazione solo variabili ambientali pedo-climatiche. La coltivazione di una coltura comporta anche un impatto ambientale derivante dalle pratiche agronomiche ed il territorio può essere più o meno sensibile a questi impatti in base alla sua vulnerabilità. In questo studio si vuole sviluppare una metodologia per relazionare spazialmente l’impatto delle colture con le caratteristiche sito specifiche del territorio in modo da considerare anche questo aspetto nell’allocazione negli studi di vocazionalità. LCA è stato utilizzato per quantificare diversi impatti di alcune colture erbacee alimentari e da energia, relazionati a mappe di vulnerabilità costruite con l’utilizzo di GIS, attraverso il calcolo di coefficienti di rischio di allocazione per ogni combinazione coltura-area vulnerabile. Le colture energetiche sono state considerate come un uso alternativo del suolo per diminuire l’impatto ambientale. Il caso studio ha mostrato che l’allocazione delle colture può essere diversa in base al tipo e al numero di impatti considerati. Il risultato sono delle mappe in cui sono riportate le distribuzioni ottimali delle colture al fine di minimizzare gli impatti, rispetto a mais e grano, due colture alimentari importanti nell’area di studio. Le colture con l’impatto più alto dovrebbero essere coltivate nelle aree a vulnerabilità bassa, e viceversa. Se il rischio ambientale è la priorità, mais, colza, grano, girasole, e sorgo da fibra dovrebbero essere coltivate solo nelle aree a vulnerabilità bassa o moderata, mentre, le colture energetiche erbacee perenni, come il panico, potrebbero essere coltivate anche nelle aree a vulnerabilità alta, rappresentando cosi una opportunità per aumentare la sostenibilità di uso del suolo rurale. Lo strumento LCA-GIS inoltre, integrato con mappe di uso attuale del suolo, può aiutare a valutarne il suo grado di sostenibilità ambientale.

Evaluation of the photosynthetic efficiency of sweet sorghum under drought and cold conditions

Sweet sorghum, a C4 crop of tropical origin, is gaining momentum as a multipurpose feedstock to tackle the growing environmental, food and energy security demands. Under temperate climates sweet sorghum is considered as a potential bioethanol feedstock, however, being a relatively new crop in such areas its physiological and metabolic adaptability has to be evaluated; especially to the more frequent and severe drought spells occurring throughout the growing season and to the cold temperatures during the establishment period of the crop. The objective of this thesis was to evaluate some adaptive photosynthetic traits of sweet sorghum to drought and cold stress, both under field and controlled conditions. To meet such goal, a series of experiments were carried out. A new cold-tolerant sweet sorghum genotype was sown in rhizotrons of 1 m3 in order to evaluate its tolerance to progressive drought until plant death at young and mature stages. Young plants were able to retain high photosynthetic rate for 10 days longer than mature plants. Such response was associated to the efficient PSII down-regulation capacity mediated by light energy dissipation, closure of reaction centers (JIP-test parameters), and accumulation of glucose and sucrose. On the other hand, when sweet sorghum plants went into blooming stage, neither energy dissipation nor sugar accumulation counteracted the negative effect of drought. Two hybrids with contrastable cold tolerance, selected from an early sowing field trial were subjected to chilling temperatures under controlled growth conditions to evaluate in deep their physiological and metabolic cold adaptation mechanisms. The hybrid which poorly performed under field conditions (ICSSH31), showed earlier metabolic changes (Chl a + b, xanthophyll cycle) and greater inhibition of enzymatic activity (Rubisco and PEPcase activity) than the cold tolerant hybrid (Bulldozer). Important insights on the potential adaptability of sweet sorghum to temperate climates are given.

Mechanical Properties of Plant Underground Storage Organs and Implications for Dietary Models of Early Hominins

The diet of early human ancestors has received renewed theoretical interest since the discovery of elevated d13C values in the enamel of Australopithecus africanus and Paranthropus robustus. As a result, the hominin diet is hypothesized to have included C4 grass or the tissues of animals which themselves consumed C4 grass. On mechanical grounds, such a diet is incompatible with the dental morphology and dental microwear of early hominins. Most inferences, particularly for Paranthropus, favor a diet of hard or mechanically resistant foods. This discrepancy has invigorated the longstanding hypothesis that hominins consumed plant underground storage organs (USOs). Plant USOs are attractive candidate foods because many bulbous grasses and cormous sedges use C4 photosynthesis. Yet mechanical data for USOs—or any putative hominin food—are scarcely known. To fill this empirical void we measured the mechanical properties of USOs from 98 plant species from across sub-Saharan Africa. We found that rhizomes were the most resistant to deformation and fracture, followed by tubers, corms, and bulbs. An important result of this study is that corms exhibited low toughness values (mean = 265.0 J m-2) and relatively high Young’s modulus values (mean = 4.9 MPa). This combination of properties fits many descriptions of the hominin diet as consisting of hard-brittle objects. When compared to corms, bulbs are tougher (mean = 325.0 J m-2) and less stiff (mean = 2.5 MPa). Again, this combination of traits resembles dietary inferences, especially for Australopithecus, which is predicted to have consumed soft-tough foods. Lastly, we observed the roasting behavior of Hadza hunter-gatherers and measured the effects of roasting on the toughness on undomesticated tubers. Our results support assumptions that roasting lessens the work of mastication, and, by inference, the cost of digestion. Together these findings provide the first mechanical basis for discussing the adaptive advantages of roasting tubers and the plausibility of USOs in the diet of early hominins.

Golden-winged Warbler habitat model validation for northern Wisconsin and central Minnesota

Between 1966 and 2003, the Golden-winged Warbler (Vermivora chrysoptera) experienced declines of 3.4% per year in large parts of the breeding range and has been identified by Partners in Flight as one of 28 land birds requiring expedient action to prevent its continued decline. It is currently being considered for listing under the Endangered Species Act. A major step in advancing our understanding of the status and habitat preferences of Golden-winged Warbler populations in the Upper Midwest was initiated by the publication of new predictive spatially explicit Golden-winged Warbler habitat models for the northern Midwest. Here, I use original data on observed Golden-winged Warbler abundances in Wisconsin and Minnesota to compare two population models: the hierarchical spatial count (HSC) model with the Habitat Suitability Index (HSI) model. I assessed how well the field data compared to the model predictions and found that within Wisconsin, the HSC model performed slightly better than the HSI model whereas both models performed relatively equally in Minnesota. For the HSC model, I found a 10% error of commission in Wisconsin and a 24.2% error of commission for Minnesota. Similarly, the HSI model has a 23% error of commission in Minnesota; in Wisconsin due to limited areas where the HSI model predicted absences, there was incomplete data and I was unable to determine the error of commission for the HSI model. These are sites where the model predicted presences and the Golden-winged Warbler did not occur. To compare predicted abundance from the two models, a 3x3 contingency table was used. I found that when overlapped, the models do not complement one another in identifying Golden-winged Warbler presences. To calculate discrepancy between the models, the error of commission shows that the HSI model has only a 6.8% chance of correctly classifying absences in the HSC model. The HSC model has only 3.3% chance of correctly classifying absences in the HSI model. These findings highlight the importance of grasses for nesting, shrubs used for cover and foraging, and trees for song perches and foraging as key habitat characteristics for breeding territory occupancy by singing males.

Effects of conifer sawdust, hardwood sawdust, and peat on soil properties and a barefoot conifer seedling development

Organic amendments are commonly used to improve tree nursery soil conditions for increased seedling growth. However, few studies compare organic amendments effects on soil conditions, and fewer compare subsequent effects on seedling growth. The effects of three organic amendments on soil properties and seedling growth were investigated at the USDA Forest Service J.W. Toumey Nursery in Watersmeet, MI. Pine sawdust (red pine, Pinus resinosa), hardwood sawdust (maple, Acer spp. and aspen, Populus spp.), and peat were individually incorporated into a loamy sand nursery soil in August, 2006, and soil properties were sampled periodically for the next 14 months. Jack (Pinus banksiana), red, and white pine (Pinus strobus) were sown into test plots in June, 2007 and sampled for growth responses at the end of the growing season. It is hypothesized; pine sawdust and peat can be used as a satisfactory soil amendment to improve soil conditions and produce high quality seedlings, when compared to hardwood sawdust in bareroot nursery soils. This study has the potential to reduce nursery costs while broadening soil amendment options. The addition of peat and pine sawdust increased soil organic matter above control soil conditions after 14 months. However, hardwood sawdust-amended soils did not differ from control soils after same time period. High N concentrations in peat increased total soil N over the other treatments. Similarly, the addition of peat increased soil matric potential and available water over all other treatments. Seedlings grew tallest with the largest stem diameter, and had the largest biomass in both control soil and soil amended with peat, compared to either sawdust treatment. Seedlings grown in peat-amended soils had higher N concentrations than those grown in soils treated with pine sawdust, though neither was different from seedlings grown in control or hardwood sawdust-amended soils. Overall, peat is a well suited organic soil amendment for the enhancement of soil properties, but no amendments were able to increase one-year seedling growth over control soils.

Effects of management on native and exotic plant communities in Pictured Rocks National Lakeshore in the Upper Peninsula of Michigan

Ecological disturbances may be caused by a range of biotic and abiotic factors. Among these are disturbances that result from human activities such as the introduction of exotic plants and land management activities. This dissertation addresses both of these types of disturbance in ecosystems in the Upper Peninsula of Michigan. Invasive plants are a significant cause of disturbance at Pictured Rocks Natural Lakeshore. Management of invasive plants is dependent on understanding what areas are at risk of being invaded, what the consequences of an invasion are on native plant communities and how effective different tools are for managing the invasive species. A series of risk models are described that predict three stages of invasion (introduction, establishment and spread) for eight invasive plant species at Pictured Rocks National Lakeshore. These models are specific to this location and include species for which models have not previously been produced. The models were tested by collecting point data throughout the park to demonstrate their effectiveness for future detection of invasive plants in the park. Work to describe the impacts and management of invasive plants focused on spotted knapweed in the sensitive Grand Sable Dunes area of Pictured Rocks National Lakeshore. Impacts of spotted knapweed were assessed by comparing vegetation communities in areas with varying amounts of spotted knapweed. This work showed significant increases in species diversity in areas invaded by knapweed, apparently as a result of the presence of a number of non-dune species that have become established in spotted knapweed invaded areas. An experiment was carried out to compare annual spot application of two herbicides, Milestone® and Transline® to target spotted knapweed. This included an assessment of impacts of this type of treatment on non-target species. There was no difference in the effectiveness of the two herbicides, and both significantly reduced the density of spotted knapweed during the course of the study. Areas treated with herbicide developed a higher percent cover of grasses during the study, and suffered limited negative impacts on some sensitive dune species such as beach pea and dune stitchwort, and on some other non-dune species such as hawkweed. The use of these herbicides to reduce the density of spotted knapweed appears to be feasible over large scales.

Extracellular matrix of the charophycean green algae

A comprehensive knowledge of cell wallstructure and function throughout the plant kingdom is essential to understanding cell wall evolution. The fundamental understanding of the charophycean green algal cell wall is broadening. The similarities and differences that exist between land plant and algal cell walls provide opportunities to understand plant evolution. A variety of polymers previously associated with higher plants were discovered in the charophycean green algae (CGA), including homogalacturonans, cross-linking glycans, arabinogalactan protein, β-glucans, and cellulose. The cellulose content of CGA cell walls ranged from 6% to 43%, with the higher valuescomparable to that found in the primary cell wall of land plants (20-30%). (1,3)β-glucans were found in the unicellular Chlorokybus atmophyticus, Penium margaritaceum, and Cosmarium turpini, the unbranched filamentous Klebsormidium flaccidum, and the multicellular Chara corallina. The discovery of homogalacturonan in Penium margaritaceum representsthe first confirmation of land plant-type pectinsin desmids and the second rigorous characterization of a pectin polymer from the charophycean algae. Homogalacturonan was also indicated from the basal species Chlorokybus atmophyticus and Klebsormidium flaccidum. There is evidence of branched pectins in Cosmarium turpini and linkage analysis suggests the presence of type I rhamnogalacturonan (RGI). Cross-linking β-glucans are associated with cellulose microfibrils during land plant cell growth, and were found in the cell wall of CGA. The evidence of mixed-linkage glucan (MLG) in the 11 charophytesis both suprising and significant given that MLG was once thought to be specific to some grasses. The organization and structure of Cosmarium turpini and Chara corallina MLG was found to be similar to that of Equisetumspp., whereas the basal species of the CGA, Chlorokybus atmophyticus and Klebsormidium flaccidum, have unique organization of alternating of 3- and 4-linkages. The significance of this result on the evolution of the MLG synthetic pathway has yet to be determined. The extracellular matrix (ECM) of Chlorokybus atmophyticus, Klebsormidium flaccidum, and Spirogyra spp. exhibits significant biochemical diversity, ranging from distinct “land plant” polymers to polysaccharides unique to these algae. The neutral sugar composition of Chlorokybus atmophyticus hot water extract and Spirogyra extracellular polymeric substance (EPS), combined with antibody labeling results, revealed the distinct possibility of an arabinogalactan protein in these organisms. Polysaccharide analysis of Zygnematales (desmid) EPS, indicated a probable range of different EPS backbones and substitution patterns upon the core portions of the molecules. Desmid EPS is predominately composed of a complex matrix of branched, uronic acid containing polysaccharides with ester sulfate substitutions and, as such, has an almost infinite capacity for various hydrogen bonding, hydrophobic interaction and ionic cross-bridging motifs, which characterize their unique function in biofilms. My observations support the hypothesis that members of the CGA represent the phylogenetic line that gave rise to vascular plants and that the primary cell wall of vascular plants many have evolved directly from structures typical of the cell wall of filamentous green algae found in the charophycean green algae.

Biochemical Conversions of Lignocellulosic Biomass for Sustainable Fuel-Ethanol Production in the Upper Midwest

Biofuels are an increasingly important component of worldwide energy supply. This research aims to understand the pathways and impacts of biofuels production, and to improve these processes to make them more efficient. In Chapter 2, a life cycle assessment (LCA) is presented for cellulosic ethanol production from five potential feedstocks of regional importance to the upper Midwest - hybrid poplar, hybrid willow, switchgrass, diverse prairie grasses, and logging residues - according to the requirements of Renewable Fuel Standard (RFS). Direct land use change emissions are included for the conversion of abandoned agricultural land to feedstock production, and computer models of the conversion process are used in order to determine the effect of varying biomass composition on overall life cycle impacts. All scenarios analyzed here result in greater than 60% reduction in greenhouse gas emissions relative to petroleum gasoline. Land use change effects were found to contribute significantly to the overall emissions for the first 20 years after plantation establishment. Chapter 3 is an investigation of the effects of biomass mixtures on overall sugar recovery from the combined processes of dilute acid pretreatment and enzymatic hydrolysis. Biomass mixtures studied were aspen, a hardwood species well suited to biochemical processing; balsam, a high-lignin softwood species, and switchgrass, an herbaceous energy crop with high ash content. A matrix of three different dilute acid pretreatment severities and three different enzyme loading levels was used to characterize interactions between pretreatment and enzymatic hydrolysis. Maximum glucose yield for any species was 70% oftheoretical for switchgrass, and maximum xylose yield was 99.7% of theoretical for aspen. Supplemental β-glucosidase increased glucose yield from enzymatic hydrolysis by an average of 15%, and total sugar recoveries for mixtures could be predicted to within 4% by linear interpolation of the pure species results. Chapter 4 is an evaluation of the potential for producing Trichoderma reesei cellulose hydrolases in the Kluyveromyces lactis yeast expression system. The exoglucanases Cel6A and Cel7A, and the endoglucanase Cel7B were inserted separately into the K. lactis and the enzymes were analyzed for activity on various substrates. Recombinant Cel7B was found to be active on carboxymethyl cellulose and Avicel powdered cellulose substrates. Recombinant Cel6A was also found to be active on Avicel. Recombinant Cel7A was produced, but no enzymatic activity was detected on any substrate. Chapter 5 presents a new method for enzyme improvement studies using enzyme co-expression and yeast growth rate measurements as a potential high-throughput expression and screening system in K. lactis yeast. Two different K. lactis strains were evaluated for their usefulness in growth screening studies, one wild-type strain and one strain which has had the main galactose metabolic pathway disabled. Sequential transformation and co-expression of the exoglucanase Cel6A and endoglucanase Cel7B was performed, and improved hydrolysis rates on Avicel were detectable in the cell culture supernatant. Future work should focus on hydrolysis of natural substrates, developing the growth screening method, and utilizing the K. lactis expression system for directed evolution of enzymes.