ANALYSIS OF POPULUS TREMULOIDES CLONAL VARIATION AND DELINEATION IN THE OTTAWA NATIONAL FOREST

The technique of delineating Populus tremuloides (Michx.) clonal colonies based on morphology and phenology has been utilized in many studies and forestry applications since the 1950s. Recently, the availability and robustness of molecular markers has challenged the validity of such approaches for accurate clonal identification. However, genetically sampling an entire stand is largely impractical or impossible. For that reason, it is often necessary to delineate putative genet boundaries for a more selective approach when genetically analyzing a clonal population. Here I re-evaluated the usefulness of phenotypic delineation by: (1) genetically identifying clonal colonies using nuclear microsatellite markers, (2) assessing phenotypic inter- and intraclonal agreement, and (3) determining the accuracy of visible characters to correctly assign ramets to their respective genets. The long-term soil productivity study plot 28 was chosen for analysis and is located in the Ottawa National Forest, MI (46° 37'60.0" N, 89° 12'42.7" W). In total, 32 genets were identified from 181 stems using seven microsatellite markers. The average genet size was 5.5 ramets and six of the largest were selected for phenotypic analyses. Phenotypic analyses included budbreak timing, DBH, bark thickness, bark color or brightness, leaf senescence, leaf serrations, and leaf length ratio. All phenotypic characters, except for DBH, were useful for the analysis of inter- and intraclonal variation and phenotypic delineation. Generally, phenotypic expression was related to genotype with multiple response permutation procedure (MRPP) intraclonal distance values ranging from 0.148 and 0.427 and an observed MRPP delta value=0.221 when the expected delta=0.5. The phenotypic traits, though, overlapped significantly among some clones. When stems were assigned into phenotypic groups, six phenotypic groups were identified with each group containing a dominant genotype or clonal colony. All phenotypic groups contained stems from at least two clonal colonies and no clonal colony was entirely contained within one phenotypic group. These results demonstrate that phenotype varies with genotype and stand clonality can be determined using phenotypic characters, but phenotypic delineation is less precise. I therefore recommend that some genetic identification follow any phenotypic delineation. The amount of genetic identification required for clonal confirmation is likely to vary based on stand and environmental conditions. Further analysis, however, is needed to test these findings in other forest stands and populations.

An Analysis of the Potential Risk Exposure to Lead (Pb) through Urban Community Gardens

Community gardening in cities is increasing, driven by social interaction and food security. City soils are sinks for heavy metals; including neurotoxic lead (Pb). Exposure routes are primarily through inhalation/ingestion of soil, or second by ingestion of plants that have accumulated Pb. This research evaluates soil at three Liberty City, Florida sites estimating risk of Pb exposure through primary and secondary pathways. Soil cores were collected from Liberty City, and red Malabar spinach (Basella rubra) was grown in Pb soil treatments in a greenhouse. Total soil Pb levels and plant tissues were measured after acid digestion, by ICP-OES. In Liberty City, two sites had hotspots with areas of elevated soil Pb levels. Plants grown on Pb contaminated soil all accumulated statistically significant Pb concentrations. Therefore, there is a potential risk of Pb exposure to residents in Liberty City by exposure in hotspot sites through both the primary and secondary pathways.

Influence of Soil Biogeochemical Properties on the Invasiveness of Old World Climbing Fern (Lygodium microphyllum)

The state of Florida has one of the most severe exotic species invasion problems in the United States, but little is known about their influence on soil biogeochemistry. My dissertation research includes a cross-continental field study in Australia, Florida, and greenhouse and growth chamber experiments, focused on the soil-plant interactions of one of the most problematic weeds introduced in south Florida, Lygodium microphyllum (Old World climbing fern). Analysis of field samples from the ferns introduced and their native range indicate that L microphyllum is highly dependent on arbuscular mycorrhizal fungi (AMF) for phosphorus uptake and biomass accumulation. Relationship with AMF is stronger in relatively dry conditions, which are commonly found in some Florida sites, compared to more common wet sites where the fern is found in its native Australia. In the field, L. microphyllum is found to thrive in a wide range of soil pH, texture, and nutrient conditions, with strongly acidic soils in Australia and slightly acidic soils in Florida. Soils with pH 5.5 - 6.5 provide the most optimal growth conditions for L. microphyllum, and the growth declines significantly at soil pH 8.0, indicating that further reduction could happen in more alkaline soils. Comparison of invaded and uninvaded soil characteristics demonstrates that L. microphyllum can change the belowground soil environment, with more conspicuous impact on nutrient-poor sandy soils, to its own benefit by enhancing the soil nutrient status. Additionally, the nitrogen concentration in the leaves, which has a significant influence in the relative growth rate and photosynthesis, was significantly higher in Florida plants compared to Australian plants. Given that L. microphyllum allocates up to 40% of the total biomass to rhizomes, which aid in rapid regeneration after burning, cutting or chemical spray, hence management techniques targeting the rhizomes look promising. Over all, my results reveal for the first time that soil pH, texture, and AMF are major factors facilitating the invasive success of L. mcirophyllum. Finally, herbicide treatments targeting rhizomes will most likely become the widely used technique to control invasiveness of L. microphyllum in the future. However, a complete understanding of the soil ecosystem is necessary before adding any chemicals to the soil to achieve a successful long-term invasive species management strategy.

Singularity and multifractal characterization of signals with wavelets. Application to clay soil images

In the field of multiscale analysis of signals, including images, the wavelet transform is one of the most attractive and powerful tool due to its ability to focus on signals structures at different scales. Wavelet Transform at different scales is successfully applied to image characterization (which can be applied to a watermarking scheme) and multiscale singularity detection and processing. In this work we show further research of computation of multifractals properties such as the multifractal spectrum (D(alpha)) applied to dye stained images of natural terrain. This can be useful for statically describing preferential flow path geometry.

Integrated soil fertility management in eastern and western Africa: The role of knowledge and innovation systems, its adoption and impact

The rise in population growth, as well as nutrient mining, has contributed to low agricultural productivity in Sub-Saharan Africa (SSA). A plethora of technologies to boost agricultural production have been developed but the dissemination of these agricultural innovations and subsequent uptake by smallholder farmers has remained a challenge. Scientists and philanthropists have adopted the Integrated Soil Fertility Management (ISFM) paradigm as a means to promote sustainable intensification of African farming systems. This comparative study aimed: 1) To assess the efficacy of Agricultural Knowledge and Innovation Systems (AKIS) in East (Kenya) and West (Ghana) Africa in the communication and dissemination of ISFM (Study I); 2) To investigate how specifically soil quality, and more broadly socio-economic status and institutional factors, influence farmer adoption of ISFM (Study II); and 3) To assess the effect of ISFM on maize yield and total household income of smallholder farmers (Study III). To address these aims, a mixed methodology approach was employed for study I. AKIS actors were subjected to social network analysis methods and in-depth interviews. Structured questionnaires were administered to 285 farming households in Tamale and 300 households in Kakamega selected using a stratified random sampling approach. There was a positive relationship between complete ISFM awareness among farmers and weak knowledge ties to both formal and informal actors at both research locations. The Kakamega AKIS revealed a relationship between complete ISFM awareness among farmers and them having strong knowledge ties to formal actors implying that further integration of formal actors with farmers’ local knowledge is crucial for the agricultural development progress. The structured questionnaire was also utilized to answer the query pertaining to study II. Soil samples (0-20 cm depth) were drawn from 322 (Tamale, Ghana) and 459 (Kakamega, Kenya) maize plots and analysed non-destructively for various soil fertility indicators. Ordinal regression modeling was applied to assess the cumulative adoption of ISFM. According to model estimates, soil carbon seemed to preclude farmers from intensifying input use in Tamale, whereas in Kakamega it spurred complete adoption. This varied response by farmers to soil quality conditions is multifaceted. From the Tamale perspective, it is consistent with farmers’ tendency to judiciously allocate scarce resources. Viewed from the Kakamega perspective, it points to a need for farmers here to intensify agricultural production in order to foster food security. In Kakamega, farmers with more acidic soils were more likely to adopt ISFM. Other household and farm-level factors necessary for ISFM adoption included off-farm income, livestock ownership, farmer associations, and market inter-linkages. Finally, in study III a counterfactual model was used to calculate the difference in outcomes (yield and household income) of the treatment (ISFM adoption) in order to estimate causal effects of ISFM adoption. Adoption of ISFM contributed to a yield increase of 16% in both Tamale and Kakamega. The innovation affected total household income only in Tamale, where ISFM adopters had an income gain of 20%. This may be attributable to the different policy contexts under which the two sets of farmers operate. The main recommendations underscored the need to: (1) improve the functioning of AKIS, (2) enhance farmer access to hybrid maize seed and credit, (3) and conduct additional multi-locational studies as farmers operate under varying contexts.

Spatial variability of satured soil hydraulic conductivity in the region of Araguaia River - Brazil.

This study evaluates the spatial variability of saturated hydraulic conductivity in the soil in an area of 51,850 ha at the headwaters of the Araguaia River MT/GO. This area is highly vulnerable because it is a location of recharging through natural water infiltration of the Guarani Aquifer System and an area of intense increases in agriculture since its adoption by growers in the last 30 years. Soil samples were collected at 383 points, geographically located by GPS. The samples were collected from depths of 0 - 20 cm and 60 - 80 cm. Exploratory statistics and box-plot were used in the descriptive analysis and semivariogram were constructed to determine the spatial model. The exploratory analysis showed that the mean hydraulic conductivity in the superficial layer was less than at the level of 60-80 cm; however, the greatest variability evaluated with a coefficient of variation also was from this layer. Data tended towards a normal distribution. These results can be explained by the greater soil compaction in the superficial layer. The semivariogram models, adjusted for the two layers, were exponential and demonstrated moderate and strong dependence, with ranges of 5000 and 3000 utm respectively. It was concluded that soil use is influencing the spatial distribution model of the hydraulic conductivity in the region.

Soil management systems for sustainable melon cropping in the Submedian of the São Francisco Valley.

Changes in soils management systems, including the application of green manure, are able to increase crop productivity. The aim of this study was to propose a soil management system with the use of green manure to improve the nutritional status and melon productivity in the submedian of the São Francisco Valley. The experiment was installed in Typic Plinthustalf and conducted in split plot. There were two soil tillage systems, tillage (T) and no tillage (NT), and three types of green manure (two vegetal cocktails: VC1- 75% legumes (L) + 25% non-legumes (NL); VC2- 25% L+ 75% NL and spontaneous vegetation (SV)). The experimental design was a randomised block with four replications. Fourteen species of legumes, grasses and oilseeds were used for the composition of the plant cocktails. We evaluated production of the dry shoot and root biomass and carbon and nutrient accumulation by green manures and melon plant. Data were subjected to analysis of variance and the treatment means were compared by Tukey´s test (P<0.05). Shoot biomass production and carbon and nutrient accumulation were higher in plant mixtures compared to spontaneous vegetation. The root system of the plant cocktails added larger quantities of biomass and nutrients to the soil to a depth of 0.60 m when compared to the spontaneous vegetation. The cultivation of plant cocktails with soil tillage, regardless of their composition, is a viable alternative for adding biomass and nutrients to the soil in melon crops in semi-arid conditions, providing productivity increases.

Biplot analysis of strawberry genotypes recommended for the State of Espírito Santo.

Most strawberry genotypes grown commercially in Brazil originate from breeding programs in the United States, and are therefore not adapted to the various soil and climatic conditions found in Brazil. Thus, quantifying the magnitude of genotype x environment (GE) interactions serves as a primary means for increasing average Brazilian strawberry yields, and helps provide specific recommendations for farmers on which genotypes meet high yield and phenotypic stability thresholds. The aim of this study was to use AMMI (additive main effects and multiplicative interaction) and GGE biplot (genotype main effects + genotype x environment interaction) analyses to identify high-yield, stable strawberry genotypes grown at three locations in Espírito Santo for two agricultural years. We evaluated seven strawberry genotypes (Dover, Camino Real, Ventana, Camarosa, Seascape, Diamante, and Aromas) at three locations (Domingos Martins, Iúna, and Muniz Freire) in agricultural years 2006 and 2007, totaling six study environments. Joint analysis of variance was calculated using yield data (t/ha), and AMMI and GGE biplot analysis was conducted following the detection of a significant genotypes x agricultural years x locations (G x A x L) interaction. During the two agricultural years, evaluated locations were allocated to different regions on biplot graphics using both methods, indicating distinctions among them. Based on the results obtained from the two methods used in this study to investigate the G x A x L interaction, we recommend growing the Camarosa genotype for production at the three locations assessed due to the high frequency of favorable alleles, which were expressed in all localities evaluated regardless of the agricultural year.

Effect of residual vanadyl ions on the spectroscopic analysis of humic acids: a multivariate approach.

In a study of the vanadyl (VO2þ)-humic acids system, the residual vanadyl ion suppressed fluorescence and specific electron paramagnetic resonance (EPR) and NMR signals. In the case of NMR, the proton rotating frame relaxation times (T1qH) indicate that this suppression is due to an inefficient H-C cross polarization, which is a consequence of a shortening of T1qH. Principal components analysis (PCA) facilitated the isolation of the effect of the VO2þ ion and indicated that the organic free radical signal was due to at least two paramagnetic centres and that the VO2þ ion preferentially suppressed the species whose electronic density is delocalized over O atoms (greater g-factor). additionally, the newly obtained variables (principal components ? PC) indicated that, as the result of the more intense tillage a relative increase occurred in the accumulation of: (i) recalcitrant structures; (ii) lignin and long-chain alkyl structures; and (iii) organic free radicals with smaller g-factors.

Assessment of heavy metals in soils of a vineyard region with the use of principal component analysis.

Agricultural management with chemicals may contaminate the soil with heavy metals. The objective of this study was to apply Principal Component Analysis and geoprocessing techniques to identify the origin of the metals Cu, Fe, Mn, Zn, Ni, Pb, Cr and Cd as potential contaminants of agricultural soils. The study was developed in an area of vineyard cultivation in the State of São Paulo, Brazil. Soil samples were collected and GPS located under different uses and coverings. The metal concentrations in the soils were determined using the DTPA method. The Cu and Zn content was considered high in most of the samples, and was larger in the areas cultivated with vineyards that had been under the application of fungicides for several decades. The concentrations of Cu and Zn were correlated. The geoprocessing techniques and the Principal Component Analysis confirmed the enrichment of the soil with Cu and Zn because of the use and management of the vineyards with chemicals in the preceding decades.

Biomarker analysis in soils of the Amazon rainforest after vegetation fire.

The objective of this study was to determine the origin of organic matter incorporated in Amazon forest soils subjected to vegetation fire by analyzing the aliphatic biomarkers (n-alkanes) present in lipid extracts of soil samples.

Combined effects of soil biotic and abiotic factors, influenced by sewage sludge incorporation, on the incidence of corn stalk rot.

Abstract: The objectives of this study were to evaluate the combined effects of soil bioticand abiotic factors on the incidence of Fusarium corn stalk rot, during four annual incorporations of two typesofsewagesludge intosoil ina 5-years field assay under tropical conditions and topredict the effectsof these variables on the disease. For each type of sewage sludge, the following treatments were included: control with mineral fertilization recommended for corn; control without fertilization; sewage sludge based on the nitrogen concentration that provided the same amount of nitrogen as in the mineral fertilizer treatment; and sewage sludge that provided two, four and eight times the nitrogen concentration recommended for corn. Increasing dosages of both types of sewage sludge incorporated into soil resulted in increased corn stalk rot incidence, being negatively correlated with corn yield. A global analysis highlighted the effect of the year of the experiment, followed by the sewage sludge dosages. The type of sewage sludge did not affect the disease incidence. Amultiple logistic model using a stepwise procedure was fitted based on the selection of a model that included the three explanatory parameters for disease incidence: electrical conductivity, magnesium and Fusarium population. In the selected model, the probability of higher disease incidence increased with an increase of these three explanatory parameters. When the explanatory parameters were compared, electrical conductivity presented a dominant effect and was the main variable to predict the probability distribution curves of Fusarium corn stalk rot, after sewage sludge application into the soil.

A methodological approach for the performance optimization of transient seepage models through inverse analysis

The topic of the Ph.D project focuses on the modelling of the soil-water dynamics inside an instrumented embankment section along Secchia River (Cavezzo (MO)) in the period from 2017 to 2018 and the quantification of the performance of the direct and indirect simulations . The commercial code Hydrus2D by Pc-Progress has been chosen to run the direct simulations. Different soil-hydraulic models have been adopted and compared. The parameters of the different hydraulic models are calibrated using a local optimization method based on the Levenberg - Marquardt algorithm implemented in the Hydrus package. The calibration program is carried out using different types of dataset of observation points, different weighting distributions, different combinations of optimized parameters and different initial sets of parameters. The final goal is an in-depth study of the potentialities and limits of the inverse analysis when applied to a complex geotechnical problem as the case study. The second part of the research focuses on the effects of plant roots and soil-vegetation-atmosphere interaction on the spatial and temporal distribution of pore water pressure in soil. The investigated soil belongs to the West Charlestown Bypass embankment, Newcastle, Australia, that showed in the past years shallow instabilities and the use of long stem planting is intended to stabilize the slope. The chosen plant species is the Malaleuca Styphelioides, native of eastern Australia. The research activity included the design and realization of a specific large scale apparatus for laboratory experiments. Local suction measurements at certain intervals of depth and radial distances from the root bulb are recorded within the vegetated soil mass under controlled boundary conditions. The experiments are then reproduced numerically using the commercial code Hydrus 2D. Laboratory data are used to calibrate the RWU parameters and the parameters of the hydraulic model.

Gwas analysis for the identification of molecular basis responsible for yield related traits and disease resistance in durum wheat

The PhD thesis was developed in the framework of Innovar H2020 project. This project aimed at using genomics, transcriptomics and phenotyping techniques to update varietal registration procedure used in Europe for Value of Cultivation and Use (VCU) and Distinctiness Uniformity and Stability (DUS) protocols. The phenotypic and genotypic diversity of a durum wheat panel were assessed for different agronomic traits, connected with wheat development, disease resistance and spike fertility. A panel of 253 durum wheat varieties was characterized for VCU and DUS traits and genotyped with Illumina 90K SNP Chip array (Wang et al., 2014). GWAS analysis was performed, detecting strong QTLs confirmed also by literature review. Candidate genes were identified for each trait and molecular markers will be developed to be used for marker assisted selection in breeding programs. As for disease resistance, the panel was evaluated for resistance to Soil-Borne-Cereal-Mosaic-Virus (SBCMV). A major QTL, sbm2, was detected on chromosome 2B responsible for durum wheat resistance (Maccaferri et al., 2011). The sbm2 interval was explored by fine mapping on segregant population using KASP markers and by RNASeq analysis, detecting candidate genes involved in plant-pathogen reaction. As regards yield related traits, detailed analysis was performed on the GNI-2A QTL (Milner et al., 2016), responsible for increased number spike fertility. Fine mapping analysis was performed on durum panel identifying hox2 a strong candidate gene, codifying for transcription factor protein. The gene is paralogue of GNI-1 (Sakuma et al., 2019), and it has a 4 kbp deletion responsible for increased number of florets per spikelet. To conclude, the herein reported thesis shows a complete characterization of agronomic and disease resistance traits in modern durum wheat varieties. The results obtained will augment available information for each variety, identifying informative molecular markers for breeding purposes and QTLs/candidate genes responsible for different agronomic traits.

Soil quality in an experimental vineyard treated with biochar and compost

In order to increase fertility of agricultural soils, in the framework of circular economy, the use of soil amendments such as biochar, compost, and mixtures of the two, has been implemented in recent years. Although it has been demonstrated that their use can improve the physico-chemical characteristics of soil and plant yield, few studies investigated the effect of these amendments on the soil fauna, and consequently the biological quality of soils. This study aimed to provide information on soil fauna, in particular microarthropods , in plots of an experimental vineyard treated with different soil amendments (biochar, compost, and CB mix, i.e. a mixture of biochar and compost) compared to untreated plots. What emerged from this study is that taxa abundances are significantly increased in compost-treated soil samples compared to untreated and CB mix ones. The value of the QBS-ar index obtained in soil samples treated with CB mix is lower than in samples treated with compost, biochar, and untreated, although the difference was not statistically significant. The physico-chemical soil characteristics are, in general, significantly more favorable in samples treated with CB mix than in the control, although the soil fauna seems to be partially negatively influenced by the treatment with CB mix. In fact, the number of taxa, in particular the number of taxa most adapted to edaphic life, are significantly negatively affected by the application of the CB mix. Concluding, improved physico-chemical characteristics induced by soil amendments do not always correspond to a positive response of the soil fauna, at least with respect to the QBS-ar approach.