Nghalipo, Elise Ndatulumukwa Ndahafa2025-12-112025-12-112024-11Nghalipo, E.N.N. (2024). Plant influences on taxonomic and functional diversity of soil microbial communities and soil biogeochemistry in a hyper-arid desert [unpublished doctoral dissertation]. Namibia university of science and technology.http://hdl.handle.net/10628/1101Dryland ecosystems are characterised by extreme environmental conditions, including large temperature fluxes, infrequent and highly variable rainfall patterns, and soil deficiency in organic matter. Consequently, vegetation in these regions is sparse and unevenly distributed, which creates unique microhabitats that harbor distinct microbial assemblages. In hyper-arid desert ecosystems, vegetation plays a pivotal role in shaping the taxonomic and functional diversity of soil microbial communities, thereby influencing soil biogeochemical processes. Generally, vegetation can play a significant role in regulating the temporal and spatial variation of soil microbial activities within the vegetation canopy by influencing various abiotic factors, such as soil moisture, solar radiation and temperature fluctuations, therefore creating specific niches that support diverse microbial communities. While previous studies have investigated soil microbiomes in the Namib Desert, these studies primarily focused on the central gravel plains, leaving the Skeleton Coast National Park, part of the northern Namib Desert, largely unexplored; thus, there is limited understanding of the soil microbiomes in this hyper-arid coastal region. This thesis aimed to provide insights into the influence of vegetation on the taxonomic and functional diversity of soil microbial communities and the associated biogeochemical processes by amplicon-based analyses and litterbag techniques, respectively, in this hyper-arid desert. Chapter 2: Total environmental DNA was extracted to evaluate the microbial communities associated with plant hummocks in the Skeleton Coast National Park. The V3-V4 region of the bacterial (and archaeal) 16S rRNA gene and the ITS-1 and ITS-2 regions of the fungal internal transcribed spacer (ITS) rRNA regions were amplified and sequenced to assess bacterial and fungal communities associated with plant hummocks and determine how soil microbial communities compare between plant hummock soils and bare soils (unvegetated: windward slope and gravel plain). The findings revealed that vegetated hummocks and their surrounding soils of the Skeleton Coast National Park possess qualitatively distinct soil microbiomes. Notably, vegetated hummock soils harbored a significantly higher number of observed species relative to bare soils. This suggests that vegetation plays a crucial role in enhancing microbial diversity in this hyper-arid environment. Such diversity is vital, as soil 2 microbial communities are integral to ecosystem functions, including nutrient cycling and organic matter decomposition. Chapter 3: The functional capacity of bacterial communities was predicted based on whole-shotgun metagenomic datasets to evaluate the microbial functional potential in three sampling locations: vegetated hummock, unvegetated windward slope, and gravel plains. Additionally, these datasets were used to investigate metabolic strategies that underlie the ability of these soil microbes to thrive and perform ecosystem functions in this hyper-arid ecosystem. The metagenomic analyses identified functions related to carbon fixation, carbon degradation, ammonium oxidation, methane metabolism, and sulfur assimilation. Vegetated hummock soils had higher enrichment of functional capacity relative to bare soils, suggesting that vegetation patches significantly influence microbial functional potential. Moreover, diverse taxa with the potential to utilise unique metabolic strategies were identified, enabling them to thrive and perform essential ecosystem functions in this hyper-arid ecosystem. For instance, the detection of marker genes such as NiFe hydrogenase Hyd-1 and norBC suggests metabolic pathways involved in atmospheric hydrogen oxidation to fix CO₂ and adaptations to environmental stress in hyper-arid environments. Chapter 4: The study employed the litterbag technique to evaluate the influence of vegetation patches on litter decomposition rates. It compared the decomposition of two contrasting litter types (shrub and grass) under both vegetated and unvegetated patches. Additionally, the study examined how litter chemical composition, including nitrogen and carbon content, as well as the C: N ratio, affects decomposition rates. The results indicated that litter decayed more rapidly in unvegetated patches than in vegetated ones, with shrub litterbags retaining less mass than grass litterbags, regardless of the patch type. Moreover, shrub litter, which had higher nitrogen content, lower carbon and a lower C: N ratio than grass litter, decomposed at a faster rate. These findings provide insights into the mechanisms driving litter decay rates in drylands, which are crucial for predicting litter decay in hyper-arid ecosystems. This work highlights that vegetation in hyper-arid deserts is a key determinant of soil microbial diversity and function. Through its influence on microbial communities, vegetation drives 3 essential biogeochemical processes that sustain ecosystem productivity. Understanding the interactions between vegetation and soil microbes in these ecosystems is essential for comprehending biogeochemistry and the functioning and dynamics of dryland ecosystems. Findings from this study contribute to the literature on how hyper-arid deserts such as the Namib Desert are microbially mediated and how the various edaphic communities adapt to extreme conditions in these regions. Furthermore, this study enhances our understanding of how different decomposition mechanisms influence litter decay rates and will ultimately aid in predicting litter decay rates in hyper-arid ecosystems.enSoil biogeochemistryHyper-arid desertSoil microbial communitiesMicrobial diversityPlant-soil interactionsThesis