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The microbial diversity in oligotrophic isolated crystalline FennoscandianShield bedrock fracture groundwaters is high, but the core community has notbeen identified. Here we characterized the bacterial and archaeal communitiesin 12 water conductive fractures situated at depths between 296 and 798 m byhigh throughput amplicon sequencing using the Illumina HiSeq platform.Between 1.7  ×  10<sup>4</sup> and 1.2  ×  10<sup>6</sup> bacterial orarchaeal sequence reads per sample were obtained. These sequences revealedthat up to 95 and 99 % of the bacterial and archaeal sequences obtainedfrom the 12 samples, respectively, belonged to only a few common species,i.e. the core microbiome. However, the remaining rare microbiome containedover 3- and 6-fold more bacterial and archaeal taxa. The metabolic propertiesof the microbial communities were predicted using PICRUSt. The approximateestimation showed that the metabolic pathways commonly included fermentation,fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation,and methanogenesis/anaerobic methane oxidation, but carbon fixation throughthe Calvin cycle, reductive TCA cycle, and the Wood–Ljungdahl pathway wasalso predicted. The rare microbiome is an unlimited source of genomicfunctionality in all ecosystems. It may consist of remnants of microbialcommunities prevailing in earlier environmental conditions, but could also beinduced again if changes in their living conditions occur

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland