Une mauvaise connaissance des propriétés des sols et de leur fonctionnement peut avoir de nombreuses conséquences néfastes sur le rendement et la qualité des récoltes, sur la dégradation des sols et sur une pollution de l’environnement. En raison de l’importance des pratiques agricoles, notre étude s’est focalisée sur leur impact sur la qualité et la santé des sols. La recherche s’est effectuée de novembre 2003 à octobre 2007 sur des vergers de pommiers implantés sur des collines dans le nord-est de la Slovénie. Deux pratiques agricoles fréquentes dans cette région ont été suivies : (i) une irrigation localisée au goutte à goutte sur des Calcaric Cambisol (CALCOSOL) développés sur marnes, et ses effets sur la stabilité structurale des sols et leur biomasse microbienne à la Station expérimentale de Gačnik et (ii) la combinaison d’un engrais organique (Compo guano) et d’un amendement calcaire dans un verger conduit en agriculture biologique à Pohorski dvor sur un District Cambisol (ALOCRISOL) développé sur schistes. La présence de microbes pathogènes fécaux dans le sol, dus à l’irrigation ou à l’apport d’engrais organiques animaux a aussi été recherchée sur les deux sites. Le régime hydrique du sol a été suivi durant deux étés par des relevés tensiométriques hebdomadaires sur les deux sites. A la station expérimentale de Gačnik, un rang irrigué a été comparé à un rang non irrigué. La teneur en matière organique totale, son fractionnement granulométrique et la signature isotopique des différentes fractions permettant de discuter de leur origine et leur turn over ont été mesurés. La biomasse microbienne et son activité ont été caractérisées au printemps et à l’automne en 2004 et 2005. La stabilité structurale a été mesurée selon la méthode de Bartoli à l’automne 2004 et au printemps 2005. Sur le verger conduit en agriculture biologique à Pohorski dvor seul le pH et les paramètres microbiologiques ont été suivis selon la même périodicité en comparant les différents traitements dans une expérimentation par blocs. Enfin, sur les deux sites, une quantification des champignons, des bactéries (aérobies, anaérobies, coliformes fécaux) et des virus présents dans le sol a été réalisée. Incidence de l’irrigation par goutte à goutte sur la qualité du sol sur le site de Gačnik sur la qualité physique du sol- Les sols de ce verger, argilo-limoneux et carbonatés, varient fortement de l’amont à l’aval de la parcelle située sur une pente de 15%. le sol est peu épais à l’amont, la marne altérée apparaissant dès 60 cm tandis qu’à mi-pente et à l’aval le sol est épais >1 m et la marne plus fortement altérée. L’observation des profils pédologiques et l’historique de la parcelle montrent que le sol a été fortement remanié sur les 60 premiers centimètres préalablement à la plantation du verger. Le passage d’une plantation en terrasses à une plantation dans le sens de la pente a conduit à l’effacement des terrasses suivi d’un labour profond dont en voit encore la trace à 60 cm de profondeur à l’aval de la parcelle (Fig. 3.3 & Tab. 3.9). Un échantillonnage systématique de la teneur en carbone organique de l’horizon de surface, selon un pas de 6 m, montre un accroissement selon la pente suivant une forme en zig-zag reflétant la trace des anciennes terrasses (Fig. 3.19). Dans les 30 premiers centimètres la teneur en matières organiques, le rapport C/N et la capacité d’échange cationique augmentent de l’amont vers l’aval tandis la teneur en carbonates de calcium décroît (Fig. 3.15). Le pH reste stable entre 8 et 8, 4. A la surface du sol dans les rangs de plantation traités par désherbage chimique, une croûte alguaire se forme sur le côté ombragé du rang... / Underestimation of soil properties and poor understanding of soil conditions can have many negative consequences, which results in quality or quantity of yield, soil degradation or even environmental pollution. According to importance of agricultural practices, our study focused on their impact on soil quality and health. The research took place from November 2003 to October 2007 in apple orchards in north-eastern Slovenia where two frequent agricultural practices were investigated: (i) drip irrigation on Calcaric Cambisol and its effects on structural stability and microbial biomass at Gačnik experimental station and (ii) combination of organic fertiliser (Campo guano) and liming in organic farming to enhance microbial biomass and nitrogen nutrition at Pohorshi dvor on Dystric Cambisol. The presence of faecal pathogens in the soil due to irrigation or organic fertilizer was also investigated. Water potential was measured during two seasons in both locations. Structural stability according Bartoli method, organic mater characteristics (including grain size organic matter fractionation and isotopic signature of organic carbon origin), and microbiological parameters were analysed as potential indicators of soil quality in irrigation practice comparing an irrigated (IR) to a non-irrigated (NIR) row. In organic farming, mainly pH and microbiological parameters were followed according treatments on an experimental blocks comparison. According to hilly terrain and land levelling in Gačnik, we were dealing with two groups of soil differing in thickness, organic matter, and calcium carbonate contents: one at upslope and another at mid and downslope. Considering soil characteristics, slope effect was more expressed than irrigation effect. According to slope, water gravimetric content (W), organic matter (OM), microbial biomass (MB), and respiration (R) increased towards downslope while total carbonates (Ca) and structural stability (SS) decreased. According to irrigation, W, OM, and SS contents decreased, while MB and R increased from NIR to IR rows. No difference was observed for Ca between treatments. According to slope, higher carbonate content was as an important factor for higher structural stability as organic matter pool. According to irrigation, lower W in IRR row could be explained by modification in root distribution due to drip irrigation. Irrigation leads to an increase of soil microbial biomass and its activity (as a short-time effect) and decrease of OM (as a long-term effect); moreover, a decrease of OM originating from the marl bedrock was observed in IRR row and attributed to microbial mineralization. Lower SS of IRR row is related to the OM reduction. Seasonal variations of structural stability show complex trends resulting from the combination of climatic conditions and biological activity. In organic fertilising study, the interaction of Compo guano and lime together was not clear, but in long term this is probably the best solution because it had positive consequences on both soil pH and available nitrogen, while preserving fair levels of MB and labile organic matter (LOM). Irrigation water and Compo guano were considered as eventual sources of faecal coliforms which remains in soils. From our study it was concluded that OM, MB, R and faecal coliforms can be treated as general useful indicators in assessing soil quality. According to agricultural practice, SS should be emphasized as an important quality indicator in irrigation practice and pH in organic farming.

PhD (Zoology) / Department of Zoology / An ever growing human population and accelerating land use change is associated with the loss of species and their ecosystem services. Agricultural intensification has led to a worldwide threat of extinction to about one quarter of all bat species, despite the valuable ecosystem service of pest control provided by bats. The decline in bat populations is mainly attributed to the loss or fragmentation of habitats, roost sites and feeding opportunities related to agricultural intensification and land use change. Therefore, proactive management of bat communities in agricultural landscapes is essential. South Africa is the world’s largest producer of macadamias and the industry continues to grow. This study gains insight into the habitat use and foraging behaviour of insectivorous bat species on a temporal and spatial scale, in and around macadamia orchards in order to advise management strategies on how to increase bat activity and, possibly, pest control. It also focuses on the preferences of artificial roost sites used by insectivorous bats in macadamia orchards. The diet of insectivorous bat species is especially difficult to study and the least invasive tool to gain information is the study of bat faecal pellets. In order to provide evidence for the consumption of pest insect species by bats and thus incentive to farmers for a more integrated pest management approach (IPM), this study explored molecular approach to insectivorous bat diet analyses using fragment analysis of bat faecal pellets with fluorescent-labelled species-specific primers (designed for the CO I gene). This study was conducted in the subtropical fruit growing area of Levubu, Limpopo province, South Africa between the towns Thohoyandou (22°59'03.7 S, 30°27'12.8 E) and Makhado/Louis Trichardt (23°03'03.6 S, 29°55'12.7 E). Levubu also accounts for the second highest production of macadamia in South Africa. An introduction to the order Chiroptera and into the relevance of insectivorous bat species to agriculture as well as the importance of a more integrated pest management approach (IPM) focusing on bats is provided in Chapter One. Bats were acoustically monitored and light traps were used to catch arthropods during one annual cycle. I sampled five macadamia orchards once a month from September 2015 to August 2016 and used GIS and R to analyse both the general bat activity and foraging bat activity of the two main foraging guilds (open-air/clutter edge guild) in different land use types as well as total bat activity with respect to arthropod abundances. As reported in Chapter Two, results show that the overall clutter edge guild activity (number of passes) decreased with macadamia and orchard (all other fruit) cover in the macadamia high season (December to end of May) and increased with bush cover and distance to settlements (potential roosts) in the macadamia low season (June to end of November). Open-air guild activity increased with fallow cover (uncultivated grassland with scattered trees and shrubs) in the high season. Foraging activity (feeding buzzes) of the clutter edge guild increased with bush cover over the whole year. Total activity (both guilds) increased with abundance of true bugs (Hemiptera), including the main macadamia pests, and bush cover. Macadamia cover has a negative effect on the activity of the clutter edge guild in the high season, with low activity in the orchard center (high cover), and activity increasing in a linear way with decreasing orchard cover at the orchard edge (low cover). These results suggest that the clutter edge guild prefers foraging close to the edges of the orchards rather than in the center, while the open-air guild prefers semi-natural habitats (fallow). When numbers of pest arthropods drop in the macadamia orchards, the natural land use type, bush, becomes a more important foraging habitat and thereby increased the activity of the clutter edge guild. From June 2016 to July 2017, I scanned 31 bat houses, mounted on poles on six macadamia orchards, for bats or any other occupants such as wasps, birds and bees. Twenty-one multichambered bat houses of three slightly different chamber designs were erected on poles, in sets of three. Additionally, five bat houses of the type ‘Rocket box’, four bat houses in sets of two (black and white) and one colony bat house were erected. Bats were counted and visually identified to family or species level. From December 2016 to end of March 2017, three IButtons were installed to record temperature variation between one set of three bat houses. As reported in Chapter Three, results show that the central bat house in the set of three and the black bat house in the set of two had a significantly positive effect on bat house occupancy. There was a significant difference in the mean temperature between the houses in the set of three, with a significant difference in temperature of 0.46°C between the central and the first bat house. The three bat houses erected in sets varied slightly in their chamber design, with the central bathouse having the most chambers (six), while the bat houses to either side had less chambers (four), set at an angle or straight. This and the insulation to either side by the other bat houses is assumingly what caused the central bat house to be on average warmer. The Yellow-bellied house bat (Scotophilus dinganii) was by far the most recorded and the only species observed to co-habitat a bat house with another animal species, in particular honeybees. The study might confirm assumptions in that the microclimate of bat houses, respectively their insulation, sun exposure and color appear to be important factors influencing bat house occupancy. The two preferred bat houses in our study were the black, in the set of black and white, as well as the central, and on average warmest bat house, in the set of three. I collected bat faecal pellets with two different methods between July 2015 and April 2017 to determine the prevalence of pest insects in faecal pellets. Eighteen of the bat houses (in sets of three) on three different farms and two Egyptian slit-faced bat (Nycteris thebaica) roosts were fitted with trays in order to collect pellets from those occupied by bats. I noted occupancy of bat houses to species or family level to keep disturbance minimal. Additionally, I collected pellets from individuals captured by means of mist nets and harp traps. Four of the main pest-insects; the two-spotted stinkbug (Pentatomidae: Bathycoelia distincta), the green vegetable bug (Pentatomidae: Nezara viridula), the macadamia nut borer (Tortricidae: Thaumatotibia batrachopa) and the litchi moth (Tortricidae: Cryptophlebia peltastica), were collected from pheromone traps or after scouting for primer development and optimisation. After extracting DNA from the bat faecal samples the target regions were amplified in a multiplex PCR and fluorescently labelled PCR amplicons were analysed and interpreted. In order to verify multiplex analyses results, all samples were amplified with all four sets of primers in plates and those that produced amplicons were purified and sequenced. As reported in Chapter Four, results show that fragment analyses yielded a total of 63 out of 103 samples tested positive for pest insect species (61%) with a total of 92 positive fragments. Primer specificity could be confirmed to 100% for the sequences obtained for Bathycoelia distincta (26/26) and Nezara viridula (12/12) primers but not for all sequences obtained fot Cryptophlebia peltastica (18/30) and Thaumatotibia batrachopa (1/14) primers. One sample showed no positive fragments but contained a positive sequence for N. viridula. Three samples tested positive for one pest-species fragment but contained a positive sequence for a second pest-species (B. distincta, T. batrachopa and C. peltastica). Adding four positive fragments and one additional positive sequence to the data. This means that sequences of pest insect species were obtained from 54 out of the 103 samples (55.6%) with a total of 73 pest insect sequences. For the high season (December to end of May) a total of 37 positive fragments for the four pest insect species and 24 negative samples were yielded and for the a low season (June to end of November) a total of 36 positive fragments and 15 negative samples. Looking at the pest consumption of the different bat species or families, our results show that all of them foraged on pest insect species. Whereas, all species and families except Myotis bocagii and Rhinolophus simulator (for which N<2) foraged on both the Lepidopteran and Hemipteran pest species. Therefore, all families of bats of which faecal pellets were analysed for this study (Molossidae, Nycteridae, Rhinolophidae and Vespertilionidae) foraged on one or more of the four pest insect species. In summary, Chapter Five concludes that natural and semi-natural vegetation promote bat activity in macadamia orchards, and potentially bats' provision of the ecosystem service of pest control. In times of accelerating land use change, remnants of natural vegetation are important refuges and need to be maintained or restored to conserve bat species and promote their ecosystem services. The study also shows that bat activity might be improved by adding roosting opportunities to orchards. Warm and well-insulated bat houses mounted freestanding on poles and in sets appeared to work best in northern South Africa. Further research on co-habitation of bat houses and displacement behaviour as well as the potential importance of altitude and distance to water is needed. All of the species or families of bats from which faecal pellets were collected have been confirmed to forage on at least one of the four pest insects and the bat species have shown to be much more generalist and presumably opportunistic feeders than previously assumed. Thus, this study provides incentive and advice to farmers for a more integrated pest management approach (IPM). / NRF

The aim of this study was to propose a non-destructive method for measuring Pinus sylvestris seedlings, to determine whether water stress would be evident in laboratory spectra of pines, to compare whether the response of pines would differ by ecotype, and to investigate whether two ecotypes of Pinus sylvestris could be distinguished using laboratory and image spectroscopy. For these purposes, hyperspectral images of seed orchards from August 2020 were processed and a three-month laboratory experiment was conducted, in which stress from water deficit was induced in two-year-old pine seedlings from the upland and hilly ecotypes. Spectral data were analysed using mixed statistical models, analysis of variance, principal component analysis, training of supervised pixel classifiers, vegetation indices, and linear regression. Based on the analyses, it was found that water stress can be detected in severely stressed Pinus sylvestris seedlings. The most sensitive spectral bands to water content were observed in the region between 1000-2500 nm. The initial response to water stress did not differ by ecotype, but a faster recovery was observed at the upland ecotype after the period of draught. The two Pinus sylvestris ecotypes were distinguished with high accuracy from both laboratory and image spectral...

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