Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids

Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse M. Ahonen, Ilmo T. Kukkonen, Merja Itävaara

Research output: Contribution to journalArticleScientificpeer-review

25 Citations (Scopus)

Abstract

The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300g m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.
Original languageEnglish
Pages (from-to)3091-3108
JournalBiogeosciences
Volume13
Issue number10
DOIs
Publication statusPublished - 2016
MoE publication typeA1 Journal article-refereed

Fingerprint

bedrock
microbial communities
microbial community
Precambrian
fluid
fracture zone
Methanobacteriaceae
Burkholderiales
Comamonadaceae
Pseudomonadaceae
Clostridiales
amino sugars
serpentinization
carbon fixation
methanogens
network analysis
carbon
energy
bacterial communities
hydrogen

Keywords

  • archaea
  • bacteria (microorganisms)
  • burkholderiales
  • clostridiales
  • comamonadaceae
  • methanobacteriaceae
  • otus
  • pseudomonadaceae

Cite this

Purkamo, L., Bomberg, M., Kietäväinen, R., Salavirta, H., Nyyssönen, M., Nuppunen-Puputti, M., ... Itävaara, M. (2016). Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids. Biogeosciences, 13(10), 3091-3108. https://doi.org/10.5194/bg-13-3091-2016
Purkamo, Lotta ; Bomberg, Malin ; Kietäväinen, Riikka ; Salavirta, Heikki ; Nyyssönen, Mari ; Nuppunen-Puputti, Maija ; Ahonen, Lasse M. ; Kukkonen, Ilmo T. ; Itävaara, Merja. / Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids. In: Biogeosciences. 2016 ; Vol. 13, No. 10. pp. 3091-3108.
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abstract = "The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300g m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible {"}keystone{"} genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.",
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Purkamo, L, Bomberg, M, Kietäväinen, R, Salavirta, H, Nyyssönen, M, Nuppunen-Puputti, M, Ahonen, LM, Kukkonen, IT & Itävaara, M 2016, 'Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids', Biogeosciences, vol. 13, no. 10, pp. 3091-3108. https://doi.org/10.5194/bg-13-3091-2016

Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids. / Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka; Salavirta, Heikki; Nyyssönen, Mari; Nuppunen-Puputti, Maija; Ahonen, Lasse M.; Kukkonen, Ilmo T.; Itävaara, Merja.

In: Biogeosciences, Vol. 13, No. 10, 2016, p. 3091-3108.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Purkamo, Lotta

AU - Bomberg, Malin

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AU - Itävaara, Merja

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N2 - The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300g m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.

AB - The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300g m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.

KW - archaea

KW - bacteria (microorganisms)

KW - burkholderiales

KW - clostridiales

KW - comamonadaceae

KW - methanobacteriaceae

KW - otus

KW - pseudomonadaceae

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DO - 10.5194/bg-13-3091-2016

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