Browsing by Subject "West Africa"
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(2023)While the effects of agricultural land use on biodiversity are beginning to unravel in Europe and North America, Africa remains poorly studied. Biodiversity in a broad sense provides ecosystem functioning and services, whose importance has become obvious to humankind in the quickly changing modern world. In Ghana, the practice of mango farming continues to grow in popularity due to suitable climate and potential source of livelihood. With increased demand and production of mango, natural habitats, namely savannahs, are being converted to plantations. The effects of such habitat conversion on local biodiversity are unknown for most taxa, thus providing an interesting study system for biodiversity research. Given the direct relation between functional diversity and ecosystem services, in this work I compare the taxonomic and functional diversity of ground-living spiders between mango orchards and savannah. I chose spiders (Arthropoda; Araneae) as model organisms as they critically contribute to several ecosystem services, such as biological pest control and nitrogen cycling, while being ubiquitous and abundant, thus easy to collect in the field. Spiders were captured with pitfall traps from six mango and four savannah areas in the Northern region of Ghana. A total of 424 individuals and 53 (morpho)species were identified and counted. Additionally, six morphological and four ecological traits were quantified for each (morpho)species. With these data, I calculated taxonomic richness and evenness, functional richness, dispersion, and evenness, and beta diversity of the different assemblages in the R environment. These metrics were then compared between spiders collected from mango orchards and savannah. Mango orchards showed lower taxonomic and functional evenness than savannah, contrary to all other alpha diversity measures. The two habitat types share many of the same diversity of ground-living spiders, but species and traits are distributed less evenly in mango orchards due to incomplete niche differentiation between species. Both taxonomic and functional beta diversity were significantly different between habitat types indicating that mango orchards sustain a similar richness of species as savannah, but the species composition is different. In conclusion, mango orchards have the potential to conserve some aspects of the original diversity, but species composition and the way species interact are substantially different. We should strive to find the best practices to produce mango without radically changing the natural biodiversity patterns.
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(2020)Constantly increasing level of bacteria becoming resistant to clinically relevant antibiotics challenges the modern medical achievements made over the past century. In global scale, one of the most significant information gaps concerning the occurrence of resistant bacteria is located in West African countries. Klebsiella pneumoniae and Escherichia coli strains resistant to 3rd generation cephalosporins and carbapenems are a major risk to public health through infections with limited or no available treatment options. The resistance to these antibiotics among Enterobacteriaceae is mainly mediated by hydrolyzing enzymes such as extended-spectrum beta-lactamases (ESBL). The focus of this thesis is to study the genes encoding these enzymes and other resistance factors found in K. pneumoniae and E. coli isolated from human stool and waste water samples in Burkina Faso and Mali. Tree Enterobacteriaceae isolates were selected for whole genome sequence (WGS) analysis based on their phenotypic resistance profiles defined by disk diffusion method. Reads were assembled to draft genomes and the genomes were studied for their antibiotic resistance genes, virulence genes and their associations to mobile genetic elements found in these isolates’ genomes. Additionally a pan-genome was created to investigate species specific features of K. pneumoniae and their role in heavy load of antibiotic resistance genes among these isolates. Pan-genome consisted of two genomes sequenced in this study and 12 genomes from the publically available database. 16-month old Burkinabe child was a carrier of one ESBL-producing K. pneumoniae (isolate Burkina_1) and one ESBL-positive E. coli along with the resistance to multiple other antibiotics. With genome wide analysis the K. pneumoniae strain could be described as sequence type (ST) 45 representing, multidrug resistant and ESBL-gene CTX-M-15 carrying strain with highly similar virulence gene profile to strains previously described as pathogenic K. pneumoniae causing neonatal sepsis. K. pneumoniae isolated from the stool sample of an adult living in Burkina Faso was found to be multidrug resistant, though non-ESBL-producer strain (isolate Burkina_2). The isolate showed no similarity to any previously described sequence type. CTX-M-15 encoding E. coli of ST38 (isolate Mali_1) carried by Malian child showed resistance to five different classes of antibiotics in addition to the 3rd generation cephalosporins. At the same time the isolate showed hybrid virulence gene profile with virulence genes associated to many different E. coli pathotypes including neonatal meningitis causing E. coli (NMEC). The exceptional plasticity of K. pneumoniae genome could be recognized as one of the putative explanations for the high number of resistance genes found among the isolates studied in this work. Antibiotic resistance genes were found to be associated to mobile genetic elements (MGE) and as the genetic plasticity is caused by the acquisition of external genetic material via MGEs such as plasmids, this can lead to indirect accumulation of resistance genes in these genomes. The results in this thesis work show alarming examples of pathogens that potentially cause severe infections, have extremely narrow or no treatment options and are carried by infants. These findings are in line with the few data about the level of faecal carriage of ESBL-producing strains by people in Burkina Faso and Mali reported previously.
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(2023)Land-use change stands behind the current biodiversity crisis and all it entails in terms of ecosystem services. Guinea-Bissau, in West Africa, is originally characterized by a forest- savanna mosaic biome. However, while savannas have long been planted with rice, both rice paddies and forest remnants are now being converted into cashew monocultures – the only cash crop in the country – at unprecedented rates. The ecological impact of such rapid change is largely unknown. To help fill this gap, we examined how three diversity metrics – rarefied species richness, abundance and composition – varied across forest remnants, cashew orchards and rice paddies for amphibians and reptiles in northern Guinea-Bissau. To do so, visual encounter surveys were carried across 21 sampling sites, seven of each habitat type. A total of 703 amphibian and 266 reptile encounters was recorded from nine and 14 taxa, respectively. The results show class-specific responses to habitat type. Amphibians’ diversity in forest remnants and cashew orchards was similar across all metrics, but rice paddies had a higher abundance and unique composition compared to forest remnants. Reptiles’ abundance was highest in cashew orchards and this habitat had a distinct composition, when compared to forest remnants. Rice paddies sustained both lower reptile richness and abundance. Overall, our results are not in agreement with the expected detrimental impacts of cashew expansion, which might be due to the still high heterogeneity of habitat types within the landscape. Rice paddies proved particularly important for amphibians, and for open-habitat reptiles, boosting overall species diversity. In face of the eminent habitat conversion, maintaining heterogeneous landscapes, including the persistence of both forest remnants and rice paddies, will allow minimizing biodiversity loss in West Africa.
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