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

Malin Bomberg, Tiina Lamminmäki, Merja Itävaara

Research output: Contribution to journalArticleScientificpeer-review

9 Citations (Scopus)

Abstract

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798g m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7g * g 104 and 1.2g * g 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99g % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e.The core microbiome. However, the remaining rare microbiome contained over 3-and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.
Original languageEnglish
Pages (from-to)6031-6047
JournalBiogeosciences
Volume13
Issue number21
DOIs
Publication statusPublished - 2016
MoE publication typeA1 Journal article-refereed

Fingerprint

bedrock
Finland
microbial communities
microbial community
groundwater
Calvin cycle
oxidation
carbon fixation
methanogenesis
fermentation
shield
genomics
beta oxidation
fatty acid
oxidative phosphorylation
gluconeogenesis
tricarboxylic acid cycle
methane
environmental conditions
glycolysis

Keywords

  • archaea
  • bacteria (microorganisms)

Cite this

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title = "Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland",
abstract = "The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798g m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7g * g 104 and 1.2g * g 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99g {\%} of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e.The core microbiome. However, the remaining rare microbiome contained over 3-and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.",
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Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland. / Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja.

In: Biogeosciences, Vol. 13, No. 21, 2016, p. 6031-6047.

Research output: Contribution to journalArticleScientificpeer-review

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N2 - The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798g m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7g * g 104 and 1.2g * g 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99g % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e.The core microbiome. However, the remaining rare microbiome contained over 3-and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

AB - The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798g m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7g * g 104 and 1.2g * g 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99g % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e.The core microbiome. However, the remaining rare microbiome contained over 3-and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

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