This thesis explores the diversity of the microbial biosphere using sequencing data in environmental genomics. It focuses on analyzing microbial diversity through community profiling, which involves targeting specific marker genes, such as the small subunit ribosomal RNA (SSU rRNA), to study microbial community structure. The work highlights the importance of taxonomic classification, diversity estimation, and comparison of community composition across different samples. It also addresses the challenges and limitations of sequencing technologies, including random and systematic errors, and proposes methods to compensate for these. The thesis discusses the impact of sequencing technologies on the study of microbial communities, emphasizing the need for improved methodologies to accurately assess microbial diversity and ecology. It also explores the concept of the "rare biosphere," which refers to the relatively small but significant portion of microbial life that is difficult to detect due to its low abundance. The thesis provides insights into the diversity of microbial communities in extreme environments, such as alkaline soda lakes, and highlights the importance of understanding microbial biogeography and the factors that influence community structure. The work also emphasizes the need for interdisciplinary approaches, combining biology, informatics, and mathematics, to advance the field of environmental genomics. The thesis concludes that evaluating and optimizing the methodologies used in environmental genomics is essential for accurately interpreting ecological questions, such as the rare biosphere and microbial biogeography.This thesis explores the diversity of the microbial biosphere using sequencing data in environmental genomics. It focuses on analyzing microbial diversity through community profiling, which involves targeting specific marker genes, such as the small subunit ribosomal RNA (SSU rRNA), to study microbial community structure. The work highlights the importance of taxonomic classification, diversity estimation, and comparison of community composition across different samples. It also addresses the challenges and limitations of sequencing technologies, including random and systematic errors, and proposes methods to compensate for these. The thesis discusses the impact of sequencing technologies on the study of microbial communities, emphasizing the need for improved methodologies to accurately assess microbial diversity and ecology. It also explores the concept of the "rare biosphere," which refers to the relatively small but significant portion of microbial life that is difficult to detect due to its low abundance. The thesis provides insights into the diversity of microbial communities in extreme environments, such as alkaline soda lakes, and highlights the importance of understanding microbial biogeography and the factors that influence community structure. The work also emphasizes the need for interdisciplinary approaches, combining biology, informatics, and mathematics, to advance the field of environmental genomics. The thesis concludes that evaluating and optimizing the methodologies used in environmental genomics is essential for accurately interpreting ecological questions, such as the rare biosphere and microbial biogeography.