Microbes are the life support system of the biosphere. Their metabolic activities have been tightly linked to establishing and maintaining core ecosystem processes around the globe, including the polar deserts of terrestrial Antarctica. Shaped by the continent’s extreme abiotic constraints and physical isolation, core ecosystem processes such as primary production and geochemical cycling often involve unique taxa with novel functional traits thus emphasizing the high conservational value of endemic microbiota. Up till now, microorganisms were rarely considered in Antarctic conservation frameworks despite growing concerns about complex environmental change and our anthropogenic footprint. Major gaps in biodiversity surveys and a general lack of understanding in the basic ecological concepts (niche and neutral) underlying the assemblage of Antarctic soil microbial communities has led to their poor protection status and regional sampling bias. Systematic retrieval of baseline data across the continent is therefore much needed, especially in Eastern Antarctica. In support of bridging this gap, we combined a comprehensive amplicon survey (>700 soil samples) with multivariate analyses and high-end modelling approaches to discern biogeographic patterns of polar soil bacteria, micro-eukarya and archaea throughout two coastal regions in Eastern Antarctica – the Windmill Islands and hyperarid Vestfold Hills. This thesis entails three simple but important mission statements: (1) to unveil the diversity of East Antarctic soil microbiota using a multi-domain approach; (2) to identify key edaphic drivers and threshold tipping points by advancing methods for quantifying multispecies responses to change along environmental gradients; and (3) to explore the influence of wind-driven dispersal as a new initiative for monitoring ecosystem change using a combination of dust samples and particulate trajectory modelling with historical climate data. Soil biodiversity profiles and co-occurrence networks found bacteria, micro-eukarya and archaea likely to be jointly responsible for molding the microbial backbone of Antarctic polar desert ecosystems. Species co-existence is proposed to be linked to tradeoffs between niche (environmental filtering and competition) and neutral (dispersal, speciation and drift) processes. However, the scales weighing these processes are heavily tipped in favor of strong niche-partitioning, which is expected given the harsh abiotic constraints. Bacteria (average Chao1 = 1427.57), the most strongly niche-driven (wPLN = 1.000, wNB = <0.001), were found to be inherently more diverse than micro-eukarya (average Chao1 = 92.93) and archaea (average Chao1 = 45.60) in the same environments where they co-occurred. In comparison, neutrality played a larger role in the assemblage of micro-eukaryotic (wPLN = <0.001, wNB = 1.000) and archaeal (wPLN = 0.960, wNB = 0.040) communities – especially at the Vestfold Hills, which were identified as a potentially sensitive sink location for local windblown particles travelling westward from the Windmill Islands. Employment of a modified Gradient Forest model enabled us to explore non-linear relationships between biodiversity (>17, 000 sequence variants) and the environment (79 physiochemical variables), for the first time, on the hyperarid Vestfold Hills soil microbiome. Moisture availability was primarily responsible for shaping the regional microbiome. Highest rates of compositional turnover were observed for rarer lineages of bacteria and micro-eukarya within the 10 – 12 % moisture range. Often the most responsive were taxa with phototrophic or nutrient-cycling capacities such as Cyanobacteria, Chlorophyta and Ochrophyta, which were detected in relatively high amounts within soil at Old Wallow (OW) and Rookery Lake (RL). High dispersal propensity of Chlorophyta (>75 %), based on dust biodiversity profiles (n = 25), generated some insight on the potential implications of wind-driven dispersal upon current ecosystem dynamics as Antarctica warms up. In theory, habitat expansion for micro-algal blooms via aeolian processes may lead to increased phototrophic capacity thereby resulting in potential competition for dominance between primary production strategies across Eastern Antarctica. Cascading events from this hypothetical scenario would be especially pertinent if aeolian deposition occurred within the vicinity of bird and seal colonies, like those found at OW and RL in the Vestfold Hills. When also taking into account the distinctive soil micro-eukaryotic and bacterial components at these two East Antarctic sites, OW and RL were recommended as conservation targets for further sampling and protection. Escalation of consequences from climate change and human activities are major threats to Antarctica’s unique biodiversity. In the coming century, strengthening of links between science and governance will be key towards forming a solid basis for future conservation planning and management across Antarctica. Integration of microbial data has been identified as crucial to this action. This thesis tackles one part of the equation by bringing attention to the vastly understudied coastal regions of Eastern Antarctica. More baseline surveys and research, however, are needed to capture the full scope of biodiversity offered by the Antarctic soil microbiome. This enormous effort would require sustained funding, increased international cooperation and greater year-round access to all regions.