Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

Abstract

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 μm filter. Such cells of <0.22 μm 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 μm 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.

Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth

“…The Fennoscandian deep biosphere contains highly diverse microbial communities with rather low cell counts [20,50,[61][62][63]. Although the community compositions have been extensively studied and found to contain a multitude of metabolic potential, only few studies exist to date that show the utilization of specific carbon sources by the deep subsurface community.…”

“…SIP targeting the acetate-assimilating communities revealed the suitability of the modified filter-concentration C-SIP method for saline, low biomass subsurface fluids. However, this method could have underestimated the role of small-sized subsurface cells passing the 0.22 µm pore size filters [61,89]. The SIP method relies on the ability of the microorganisms to actively metabolize these, given heavy isotope-labelled substrates.…”

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

“…In some cases, this sporadic distribution of the immobilized microorganisms could lead to erroneous interpretation of subsurface community compositions judged by singular or irregularly repeated molecular fingerprints. To date, only a few research projects have concentrated on the long-term dynamics of deep subsurface communities (e.g., Wu et al, 2016). …”

Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition

“…The loss of essential biosynthesis function in various taxonomic groups has previously been associated with energy-and nutrient-limitation selecting for small cells with reduced genomes such as found in the open ocean and deep biosphere 33,34 .…”