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Metagenomics targets the total genomic information encoded by microbial communities. DNA recovered from an environment of interest is used directly for next-generation sequencing (NGS) without prior isolation of single community members, ultimately to reconstruct genes and genomes with dedicated bioinformatic tools. Since most microbes fail to grow in the laboratory as pure cultures, metagenomics and NGS have recently revolutionized the field of microbiology by giving the first insights into this so-called “microbial dark matter”. In this dissertation, the reader takes a dive into the rich biodiversity of the hypersaline soda lakes located in south-western Siberia (Russia). A soda lake is a special type of salt lake with an extremely high salinity and a strongly alkaline pH buffered by carbonate/bi-carbonate salts. Despite being a very harsh environment for multi-cellular life, many specialized prokaryotes, i.e. Bacteria and Archaea, grow preferably under the double-extreme conditions in soda lakes and are therefore called haloalkaliphiles. Taxonomic and functional groups that were unknown prior to this work were identified using a combination of metagenomics, metatranscriptomics (RNA), 16S rRNA gene amplicon sequencing and biogeochemical profiling. More than thousand novel genomes were reconstructed from both the brines and sediments of Siberian soda lakes. A selection of newly discovered prokaryotes, including several members from the enigmatic taxonomic groups Candidate Phyla Radiation (CPR) and DPANN Archaea, was further studied with special attention to their natural abundance, potential survival mechanisms and their possible role in the biogeochemical cycling of carbon, nitrogen and sulfur compounds.