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Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2016 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 5, 1192-1203 p.Article in journal (Refereed) Published
Abstract [en]

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 mu m filter. Such cells of <0.22 mu m would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 mu m populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Place, publisher, year, edition, pages
2016. Vol. 10, no 5, 1192-1203 p.
National Category
URN: urn:nbn:se:uu:diva-264125DOI: 10.1038/ismej.2015.185ISI: 000374377200016PubMedID: 26484735OAI: diva2:859097
Swedish Research Council, 621-2014-4398Swedish Research Council, 2012-3892The Crafoord Foundation, 20130557

Supplementary information available for this article at

Available from: 2015-10-06 Created: 2015-10-06 Last updated: 2016-06-22Bibliographically approved
In thesis
1. Exposing the Dark Microbial Biosphere
Open this publication in new window or tab >>Exposing the Dark Microbial Biosphere
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Dark biosphere research has been widely neglected, although by volume this biome comprises the lion’s share of habitats on our planet. In these systems the main metabolic strategies are of chemotrophic nature, leading to gradual depletion of redox gradients essential for sustaining life. Thus these environments are regarded more or less close to chemical equilibrium.

Here, we use sequence data of whole community metagenomes and taxonomic marker approaches to study the ecology of environments close to the thermodynamic limit: deep terrestrial aquifers and aphotic systems impacted by petroleum- derived products. We show that these systems select for individuals with reduced genomes and cell sizes, likely as a mode to save energy. Due to genome reduction, these so called “streamlined” cells are reduced in the number of genes and metabolic pathways. This loss has led to community members sharing the metabolic burden of synthesizing in particular energy costly metabolites, creating tight interdependencies between the community members, as a consequence. In addition, we propose that cells scavenging anabolic products derived from detrital biomass and intermediate fermentation products are equally important in these systems. Hence, life at the thermodynamic limit involves a much more complex biological system than previously shown, that goes beyond traditionally described electron- and intermediate metabolite-transfer dependencies.

This thesis furthermore includes ecological implications, demonstrating how species diversity and community metabolism are shaped by redox gradients and dispersal potential in the deep biosphere and contaminated sediments. This research is also relevant from a practical point of view, as it pinpoints new opportunities for enhanced bioremediation through metabolite additions in order to raise the efficiency of degradation processes.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2015. 45 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1301
National Category
urn:nbn:se:uu:diva-264115 (URN)978-91-554-9363-9 (ISBN)
Public defence
2015-11-20, Friessalen, Evolutionary Biology Centre (EBC), Norbyvägen 14, Uppsala, 09:00 (English)
Available from: 2015-10-29 Created: 2015-10-05 Last updated: 2016-03-07Bibliographically approved

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Hubalek, ValerieBertilsson, Stefan
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