ISA - Teses de Doutoramento
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The Doctoral Theses is the collection of academic works produced to obtain the PhD degree at the School of Agriculture.
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- Potential effect of retrotransposons as determinant factors in the genetic variability and virulence of Hemileia vastatrixPublication . Laureano, Alexandre Miguel Ribeiro; Castro, Dora Cristina Vicente Batista Lyon de; Talhinhas, Pedro Manuel VieiraCoffee leaf rust is a devastating disease caused by Hemileia vastatrix Berkeley & Broome, leading to huge losses in coffee production. Hemileia vastatrix is an obligate biotrophic pathogen from the Pucciniales family, with the urediniosporic life cycle as the only one known in field. Coffee plant breeding strategies have increasingly become a viable alternative for mitigating coffee rust, although the adaptative capacity of the fungus have been overcoming the duration of the coffee restistant genotipes. There are over 55 races/pathotypes of Hemileia vastatrix, therefore it is of great importance to comprehend how genetic variation is promoted, as well as the regulator mechanisms of the differentiated pathogen virulence profiles. Retrotransposons are associated with genome structural variations and gene expression regulation in plant pathogens. These features may be associated to their capacity to rapidly evolve virulence. In this work, the genome size estimation and the genetic variability, concerning nucleotide sequence and copy number, of three selected retrotransposons (R190, R1057 and R2407), as well as the relative expression profiles along the course of the infection process, were investigated among Hemileia vastatrix contrasting pathotypes to assess their putative association with virulence profiles. The measured genome size (789 Mbp) and its intraspecific variation (166 Mbp) suggests a strong genomic dynamic of expansion/contraction episodes. Moreover, the analysis of the retrotransposons DNA sequences and the construction of median-joining haplotype networks revealed a high level of polymorphism and divergence, both between isolates and within the same isolate. The apparent remarkable activity and mutational rate of the retrotransposons studied may represent a determining mechanism for the generation of genetic diversity in a supposedly asexual pathogen such as H. vastatrix. Moreover, the qPCR analysis of two compatible interactions (Hv1427; race II [v5] and Hv70; race XXIV [v2,4,5]), throughout the infection process (compatible interaction with Coffea arabica var. Caturra 19/1 [SH5] and H152/3 [SH2,4,5], respectively).
- Evaluating the effectiveness of postfire restoration in Portugal with a focus on deciduous oak forestsPublication . Lopes, Luís Filipe Azevedo Curto Sousa; Acácio, Vanda Cristina de Carvalho; Fernandes, Paulo Alexandre MartinsFire has long been a natural element of forest dynamics. However, changes in fire regimes in recent decades in Europe (e.g., more frequent and severe fires) have led to negative ecological, social, and economic impacts. Portugal, situated in Mediterranean Europe, exemplifies this scenario as a region highly susceptible to wildfires and presently undergoing shifts in fire regimes. Here, deciduous oak forest ecosystems, which have an important role in biodiversity conservation, soil and water provision, and climate regulation, are today reduced to small, fragmented areas and present a high fire incidence. Following fire events, postfire management strategies can be employed to reduce the negative fire effects, although such actions may also have consequences on the recovery of soil and vegetation. As such, the objective of this thesis was to examine the effectiveness of various public environmental measures employed in postfire restoration in Portugal over recent decades, with a focus on deciduous oak forests. In this thesis, I identified three main factors within the public funding process that have been limiting the efficacy of postfire emergency stabilization in Portugal: the financing model, an oversimplified approach to eligible interventions, and slow decision-making and execution. I also observed a small positive impact of postfire interventions on the recovery of deciduous oak forests. Conversely, I found a negative impact of postfire drought events and frequent fires on this recovery. Finally, the quantification of multiple ecosystem services highlighted the existence of trade-offs due to management choices, indicating the necessity to outline long-term objectives for the burned area, since different postfire management approaches may favour distinct ecosystem services. Further studies are required to enhance the effectiveness (and consequently the efficacy) of the multiple stages of postfire restoration in Portugal.
- Exploring the links between farming systems, biodiversity and ecosystem services at the landscape scalePublication . Silva, João Pedro Ferreira da; Santos, José Manuel Osório de Barros de Lima e; Magalhães, Maria Manuela Raposo; Moreira, Francisco Manuel Ribeiro FerrariaAgricultural landscapes in Europe are very diverse, ranging from traditional landscapes, characterized, for example, by low-intensity grazing in mountain areas, to landscapes dominated by intensive and specialized systems, characterized by little diversified production of plant products and/or animals and dependent on large amounts of inputs (e.g. agrochemicals, energy, water). This gradient of landscape patterns corresponds to different impacts on biodiversity and ecosystem services (BES). The diversity of agricultural landscapes has attracted the interest of multiple investigations over time, but the complexity behind the decisions of multiple farmers across a landscape gives rise to many research questions. This thesis uses a systems approach and aims to be innovative in bringing together farmers' decisions, taken at the farm-level, and BES outcomes, produced at the landscape-level. Through this approach, it also aims to deepen knowledge about the biophysical and socioeconomic factors that influence farmers' decisions. A better understanding of the role played by these factors in the genesis and dynamics of agricultural landscapes can help to increase knowledge about human/environment interactions, thus allowing for anticipating management decisions taken by farmers and, consequently, supporting the planning of more multifunctional landscapes and policy design focused on the provision of ecosystem services by agriculture. This thesis consists of five chapters, the first of which corresponds to the general introduction and the fifth to the general discussion and conclusion. Between Chapter 1 and Chapter 5, three main chapters are developed in a scientific paper format, in which the aforementioned topics are investigated. The research presented in this thesis was carried out at various scales, from regional (Peneda-Gerês mountains and Alentejo) to national (Mainland Portugal).
- Os cicadelídeos e outros hemípteros (Cicadomorpha e Fulgoromorpha) como pragas emergentes e potenciais vetores de Xylella fastidiosa (Wells et al.) em citrinos, na região do AlgarvePublication . Bigolin, Mauricio; Silva, José Carlos Franco Santos; Simões, Manuela Rodrigues BrancoO presente trabalho constitui o primeiro estudo sobre os Auchenorrhyncha associados a citrinos, no Algarve. Atenção particular foi dada ao cicadelídeo Penthimiola bella, praga exótica detetada em 2012. Teve como objetivos: 1) Determinar a dispersão e níveis populacionais de P. bella, no Algarve; 2) Estudar o padrão de distribuição espacial de P. bella ao nível da árvore, bem como o seu ritmo circadiano; 3) Identificar e caracterizar as espécies de Auchenorrhyncha que surgem associadas aos citrinos, no Algarve, e potenciais vetores de Xylella fastidiosa, bem como estudar a dinâmica sazonal da espécie dominante, P. bella. Foi evidenciada a expansão de P. bella no Algarve. Relativamente à distribuição espacial ao nível da árvore, verificou-se efeito da exposição da armadilha nas capturas, com valores mais elevados no quadrante noroeste, não se tendo observado influência da altura da armadilha. Padrão distinto foi observado quando se consideraram separadamente as capturas de machos e fêmeas, com maior proporção de machos, nas armadilhas a 1,6m do solo e maior proporção de fêmeas a 2,6m. Penthimiola bella mostrou ter atividade diurna, com comportamento bimodal, no verão, e unimodal, no outono. Os resultados sugerem que o intervalo de temperaturas ótimas e a temperatura mínima para a sua atividade se deverão situar entre 24ºC e 31ºC, e entre 18,8ºC e 21,2ºC, respetivamente. As populações de P. bella, em citrinos, no Algarve, estão principalmente ativas entre maio e novembro, estimando-se 3 a 4 gerações anuais. A dinâmica sazonal é claramente influenciada pela temperatura, sugerindo um paralelismo com a evolução fenológica dos citrinos. As comunidades de Auchenorrhyncha evidenciaram elevada diversidade, com 53 espécies e morfoespécies identificadas. Apenas uma, Philaenus sp., provavelmente P. tesselatus foi considerada potencial vetor de X. fastidiosa. Os cicadelídeos Penthimiola bella, Sophonia orientalis, Asymmetrasca decedens e Hebata decipiens foram referenciados como potenciais pragas dos citrinos, no Algarve.
- Climate variability effects on productivity of a cork oak woodlandPublication . Bicho, Maria Catarina Gomes Pedro; Costa e Silva, Filipe Miguel de Carvalho; Correia, Alexandra Cristina Pires; David, Jorge SoaresTrees, herbs and shrubs are the “engines” of the cork oak ecosystem productivity. Although climate have an impact on each compartment productivity, the system is intrinsically linked with human presence and management practices which interfere with the ecosystem responses to environmental stresses. Herbaceous layer and shrubs are very well adapted and responsive to these variations, but trees productivity is strongly associated with the amount of leaves produced which results from a complex interaction between climate, phenology and accumulated reserves. Long-term monitoring sites located in representative areas allows to consolidate the knowledge on these processes because they offer the opportunity to understand the cycles of decline and recovery after disturbance. This knowledge is essential to support management decisions that must be adaptive under a paradigmatic economic and climate change scenario. This work was carried out in a cork oak forest in the central region, where continuous data was collected over nine years and in two vegetation strata: herbs and trees. Herbaceous production in the monitored improved pasture was 8 times higher than in the natural pasture, due to initial fertilization and legume-rich seed mixtures used. The accumulated rainfall from February to May was determinant in both systems. Drought increased the proportion of grasses and reduced the legumes with the natural pasture showing a higher drought resilient tendency. The pattern of production and fall of leaves, flowers, acorns and radial growth of trees was assessed in contrasting years. Leaf production decreased with reduced accumulated rainfall from autumn/winter prior to budburst but the acorn mast years were determinant in this reduction suggesting a competitive interaction between reproductive and vegetative growth. Dry winters/springs led to an anticipation of the maximum seasonal cork growth rate by approximately 2 months compared to wet years. Dry years strongly reduced phellogen activity and radial growth.
- Phytosanitary problems of maize, peanuts and cassava flakes (tapioca) stored by smallholder farmers in Southern MozambiquePublication . Sitoe, Márcio Daniel; Mexia, António Maria Marques; Magro, Ana Maria Da Costa Aldir; Mondjana, Ana Maria Da GraçaIn this study, the phytosanitary problems of maize, peanuts and cassava flakes (tapioca) stored by smallholder farmers in southern Mozambique were analyzed. Specifically, it aimed to (i) evaluate the contamination by fungi and aflatoxins in maize, peanuts and cassava flakes stored by smallholder farmers, and (ii) assess farmer´s perception of maize and peanuts contamination by insects, fungi, and mycotoxins and their possible relationship with the occurrence of diseases in the family. To study the health status of maize grains, peanuts and cassava flakes, samples were obtained from rural properties. The perception study regarding the occurrence of diseases related to the ingestion of mycotoxins was based on interviews with 384 smallholder farmers. The fungi isolated were Aspergillus flavus, Aspergillus niger, Fusarium sp., Penicillium citrinum, Penicillium paxilli, Rhizophus sp., and Trichoderma sp., in maize grains, Aspergillus sp., A. flavus, A. niger, Fusarium sp., Penicillium sp., and P. citrinum, in peanut grains and, Aspergillus sp., Aspergillus candidus, Aspergillus clavatus, A. flavus, A. niger, Aspergillus terreus, Chaetomium sp., Eurotium sp., Eurotium chevalieri, Eurotium proliferans, Eurotium repens, Penicillium sp., P. citrinum, Penicillium funiculosum, and Penicillium variable in cassava flakes. In addition to A. flavus known as aflatoxin producer, the isolated fungi, namely, A. candidus, A. terreus and P. citrinum, are related to citrinin production, A. clavatus and A. terreus to patulin, A. niger to citrinin and ochratoxin A, and P. paxilli to paxilline. The occurrence of P. citrinum, P. paxilli and Trichoderma sp., from maize, P. citrinum from peanuts and A. candidus, A. terreus, Chaetomium sp., E. chevalieri, E. proliferans, E. repens, P. citrinum, P. funiculosum and P. variable from cassava flakes, is reported for the first time in Mozambique. In the tested samples, the level of aflatoxin contamination was higher than the 4 μg/kg allowed by the European Union in all the samples, while contamination higher than the 10 μg/kg allowed by the Codex Alimentarius was observed in 66.66% of the samples. The farmers associate images of food contaminated by mycotoxins with fungi occurrence, but do not recognize the ingestion of such foods as a cause of disease. Therefore, the results suggest that rural Mozambican families are exposed to risks related to the consumption of food contaminated by mycotoxins.
- Resilience of alder in response to global change stressorsPublication . Marques, Inês Catarina Gomes; González, Patricia María Rodríguez; David, Teresa Soares; Solla Hach, Alejandro; Garbelotto, MatteoAlders (Alnus spp.) are riparian tree species frequently used in restoration actions due to their contribution to the health of fluvial ecosystems and to their pioneer role in ecological succession. Alder decline induced by global change stressors such as heat, drought and invasive pathogens, including Phytophthora spp., intensifies the need for a better understanding of alder resilience, which in turn inform best management practices in riparian corridors. Additionally, the recent taxonomic differentiation between the pan-European Alnus glutinosa and the Iberian-North African A. lusitanica prompts for the investigation of traits and responses to decline that differentiate both species. This thesis aims to (1) assess the genotypic and phenotypic variation in A. glutinosa and A. lusitanica populations across their latitudinal range (from Northern Africa to Scandinavia), (2) assess alders’ resilience to individual and combined abiotic and biotic stressors and (3) supply a tool for managers and stakeholders to support ecosystem management decisions in riparian corridors experiencing alder decline. This thesis identified morphological and biochemical differences between A. glutinosa and A. lusitanica. The southern populations of A. lusitanica showed higher genetic diversity than A. glutinosa populations and possibly adaptation advantages to lower water availability and heat. Alders’ response to the combination of drought or heat with Phytophthora spp. was dependent on species, genetic groups and ecological preferences. The decision-support tool ADnet pinpointed some key factors favouring Phytophthora alni survival and determining disease incidence, based on expert knowledge from several scientific backgrounds, bibliographic information and an original dataset. First and foremost, this thesis contributes new knowledge regarding the restoration and management of riparian corridors by supplying a screening of specific alder traits and genetic groups possibly correlated with adaptation potential to abiotic and biotic stressors. Additionally, it provides a tool to support management decisions and knowledge transfer to specifically address P. ×alni-induced alder decline.
- Autochthonous biological resources: the potential of the mirid Dicyphus cerastii for biological control in protected cropsPublication . Duarte, Gonçalo Nuno Abraços Henriques Gomes; Figueiredo, Elisabete; Silva, Elsa Maria Borges daDicyphine mirids (Hemiptera: Miridae: Bryocorinae: Dicyphini) are important biological control agents (BCAs) in protected crops. Despite this, only two species are commercially available in Europe, Macrolophus pygmaeus and Nesidiocoris tenuis. The former establishes slowly, and the latter can cause damage to tomato crops. Dicyphus cerastii occurs along the Mediterranean basin and spontaneously colonizes protected tomato crops in Portugal, where it often co-occurs with N. tenuis. Dicyphus cerastii has been previously observed feeding on several tomato pests. However, many aspects of its biology and ecology remain poorly studied. This thesis intended to better understand the role of D. cerastii as BCA, and whether it can be an alternative or a complement to N. tenuis, by gathering information on its biological traits, predatory interactions, and phytophagous behaviour. Our results indicate that D. cerastii may be a valuable predator in tomato crops since it showed high voracity on important pests even when compared to other dicyphines. Moreover, we observed that, despite being able to damage fruit and cause flower abortion, the impact of D. cerastii on the tomato plant is less severe than N. tenuis. Though mirids only engaged in intraguild predation in absence of extraguild prey, D. cerastii preyed more often on N. tenuis than otherwise. We also found that D. cerastii had a longer developmental period, higher mortality, and lower reproductive rate than N. tenuis, particularly above 20 °C, which could be the main reason behind the apparent seasonal competitive displacement by N. tenuis. Overall, this thesis contributed to increase the knowledge on the dicyphine complex of protected crops by understanding the services and disservices provided by D. cerastii. Given its better performance at lower temperatures and high voracity, D. cerastii may complement N. tenuis in spring conditions in Portugal, which further evidences the importance of conservation of autochthonous biological resources.
- Status of mangrove ecosystem conservation in Mozambique: contribution to minimising the effects of climate changePublication . Cuamba, Ezídio da Lúcia; Madeira, Manuel Armando Valeriano; Carvalho, Ana Paula Soares Marques de; Bandeira, Salomão OlindaMangrove forests provide diversified ecosystem services, supporting plants, animals, microorganisms and community livelihood for subsistence. Mangroves and other blue carbon ecosystems sequester great quantities of carbon, becoming of relevant value to climate change adaptation and mitigation strategies. This study describes the mangrove forest structure, trees biomass pools and carbon stocks in different soil depth of Pemba Bay, in Northern Mozambique. We used a stratified random design, where the inventory considered three different mangrove strata: overstory, understory and dead trees, including soils, in five nested sub-plots in a 0,74 ha square plot. Biomass was calculated using allometric equations and carbon stock as a sum of the carbon per unit area of considered layers. All of the mangrove species reported to occur in Mozambique were found and measured in Pemba Bay. Understory, overstory, and dead standing trees, respectively dominated the stocking densities of mangrove forest. For the understory, the stocking densities were variable among the plots, averaging 6741 trees ha-1, and ranging from 477 to 24192 trees ha-1. The overstory stocking densities average was 695 trees ha-1, and ranging from 299 to 1156 trees ha-1, whereas, the dead standing trees averaged 126 trees ha-1, and ranging from 13 to 325 trees ha-1. The average soil carbon content (depth 0-150 cm) was estimated as 224.3 Mg ha-1. The total carbon accumulated in mangrove system was of 309.11 Mg ha-1, very high in the soil (71.4%); aboveground biomass contributes with 28.6% (overstory, understory and dead trees pools).
- Sludge treatment by Earthworm-Enhanced reed beds towards smart-citiesPublication . Gholipour, Amir; Duarte, Elizabeth Fernandes de Almeida; Fragoso, Rita do Amaral; Galvão, Ana FonsecaThis study explored an innovative approach for sewage sludge management using sludge treatment reed bed (STRB) enhanced with earthworms (W-STRB). To the authors’ knowledge, it was the first evaluation of STRB with earthworms under temperate climate (Portugal). The research included experiments in Beirolas wastewater treatment plant (pilot-scale) and Horto greenhouse at ISA (bench-scale). Beirolas pilot-scale was assessed for one year of feeding (24 cycles, mean sludge loading rate (SLR): 43.59 ± 14.49 kg of dry solids (DS) per m2.year) and 132 days of final resting. Four types of units were tested including planted unit with earthworms (WP), planted unit without earthworms (P), without plant with earthworms (W) and control unit without plants and earthworms (C), all replicated. In Beirolas pilot-scale, the plant species was Arundo donax and the earthworm was Eisenia fetida. In Horto bench-scale, two plant species were tested, Arundo donax and Phragmites australis. Planted units included Eisenia fetida earthworms and an additional unit without plants or earthworms was used as control. The bench-scale was studied for six months of feeding (50, 60, and 70 kg.DS.m-2.year-1) and two months of resting. Beirolas experiment showed that DS of all units were over 70 % while volatile solid content (VS) reached the minimum content at 53 % in the WP unit indicating higher stabilization in the presence of earthworms. A synergistic impact of earthworms could also increase plant biomass production by 30 % in the WP unit compared to the P unit. The WP unit showed significant reduction in the release mass (g) of pollutants in the drained water. The WP unit reduced 10 % the mass of heavy metal in the residual sludge compared to the P unit. The study emphasized earthworms’ positive role in STRB, and potential reuse of the residual sludge contributing to circular economy in smart cities.