Special Issue "Terra Incognita—Microbial Processes and Interactions in the Deep Biosphere"

A special issue of Geosciences (ISSN 2076-3263). This special issue belongs to the section "Biogeosciences".

Deadline for manuscript submissions: closed (30 November 2018)

Special Issue Editors

Guest Editor
Dr. Malin Bomberg

VTT Technical Research Centre of Finland, 02044 Espoo, Finland
Website 1 | Website 2 | E-Mail
Interests: terrestrial deep biosphere; nitrogen cycling; sulfur metabolism; methane; Fennoscandian Shield; microbial ecology; microbial metabolism; fungi; archaea; mines; bioleaching
Guest Editor
Dr. Lotta Purkamo

University of St Andrews, St Andrews, KY16 9AL Fife, UK
Website | E-Mail
Interests: microbial ecology; microbial metabolism; deep biosphere; astrobiology; limits of life; carbon cycling

Special Issue Information

Dear Colleagues,

Microorganisms inhabit almost all locations on Earth, including the deep subsurface. Although the prerequisites for life, such as the presence of water, nutrients and energy sources, and space, can be found from the deep subsurface, it also presents challenges for the microbial life. The lack of oxygen and light, the depth related increasing pressure and heat, and the scarcity of substrates set demands on the microbial metabolic activities in the deep subsurface, and may force the microorganisms to collaborate for synergistic benefits. So far, the subsurface microbial communities have been shown to possess a great variety of different metabolic properties, ranging from chemolithoautotrophy to fermentation and hydrocarbon degradation. At the same time, the deep subsurface microorganisms may have smaller genomes compared to surface microorganisms. Many novel microbial taxa, such as the Woesearchaea or Parcubacteria, that lack laboratory-grown representatives, have been shown by metagenomic sequencing methods to have genomes lacking even the fundamental genes for a self-sufficient lifestyle. This indicates that these groups are either parasites or symbionts. This may be a general feature for oligotrophic environments, as these microbacteria and -archaea are abundant in the deep subsurface, and this lifestyle may be especially useful in deep environments by bringing a greater metabolic repertoire for the host organism. Nevertheless, the deep subsurface has also been shown to sustain heterotrophic prokaryotic and eukaryotic microorganisms, those able to recycle organic matter for the benefit of the rest of the community. It was recently shown that certain fungi and sulphate reducing bacteria form synergistic relationships in the deep subsurface where the SRB benefit from the metabolic activities of the fungi, and vice versa. In addition, the relationship between autotrophic and heterotrophic microorganisms in deep subsurface environments and the effects of secreted metabolites in these environments are still largely unknown.

For this special issue we invite research papers, short communications and reviews covering microbial metabolisms and/or microbial interactions and networks in deep subsurface environments. We hope to learn more about how e.g. carbon and nitrogen flow between different microbial groups and how one microbe’s waste may be another microbe’s food. Can ancient carbon or carbonate in fracture fillings in rocks be used as carbon source? How do viruses or fungi contribute to the nutrient cycling in the deep subsurface? Does the high microbial diversity seen in many oligotrophic deep subsurface environment also mean a high, albeit dormant, metabolic diversity that can be put to use when environmental parameters change, e.g. due to tectonic activities? How does the phosphorus, sulphur or iron cycles work in the deep subsurface? The deep biosphere still presents many open questions on issues, which ultimately may have influence on global concerns, such as climate change scenarios, and may also present new theories for the possibility of life on other planetary bodies.

Dr. Malin Bomberg
Dr. Lotta Purkamo
Guest Editors

Manuscript Submission Information

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Keywords

  • Deep biosphere
  • Metabolic networks
  • Geobiology
  • Nutrient cycling
  • Autotroph
  • Lithotroph
  • Anaerobic community
  • Heterotroph

Published Papers (4 papers)

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Research

Open AccessArticle
Microbial and Geochemical Investigation down to 2000 m Deep Triassic Rock (Meuse/Haute Marne, France)
Received: 31 August 2018 / Revised: 7 December 2018 / Accepted: 13 December 2018 / Published: 20 December 2018
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Abstract
In 2008, as part of a feasibility study for radioactive waste disposal in deep geological formations, the French National Radioactive Waste Management Agency (ANDRA) drilled several boreholes in the transposition zone in order to define the potential variations in the properties of the [...] Read more.
In 2008, as part of a feasibility study for radioactive waste disposal in deep geological formations, the French National Radioactive Waste Management Agency (ANDRA) drilled several boreholes in the transposition zone in order to define the potential variations in the properties of the Callovo–Oxfordian claystone formation. This consisted of a rare opportunity to investigate the deep continental biosphere that is still poorly known. Four rock cores, from 1709, 1804, 1865, and 1935 m below land surface, were collected from Lower and Middle Triassic formations in the Paris Basin (France) to investigate their microbial and geochemical composition. Rock leachates showed high salinities ranging from 100 to 365 g·L−1 NaCl, current temperatures averaging 65 °C, no detectable organic matter, and very fine porosity. Microbial composition was studied using a dual cultural and molecular approach. While the broad-spectrum cultural media that was used to activate microbial communities was unsuccessful, the genetic investigation of the dominant 16S rRNA gene sequences revealed eight bacterial genera considered as truly indigenous to the Triassic cores. Retrieved taxa were affiliated to aerobic and facultative anaerobic taxon, mostly unknown to grow in very saline media, except for one taxon related to Halomonas. They included Firmicutes and α-, β-, and γ-Proteobacteria members that are known from many subsurface environments and deep terrestrial and marine ecosystems. As suggested by geochemical analyses of rocks and rock leachates, part of the indigenous bacterial community may originate from a cold paleo-recharge of the Trias aquifer with water originating from ice melting. Thus, retrieved DNA would be fossil DNA. As previously put forward to explain the lack of evidence of microbial life in deep sandstone, another hypothesis is a possible paleo-sterilisation that is based on the poly-extremophilic character of the confined Triassic sandstones, which present high salinity and temperature. Full article
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Open AccessArticle
Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth
Geosciences 2018, 8(11), 418; https://doi.org/10.3390/geosciences8110418
Received: 8 September 2018 / Revised: 27 October 2018 / Accepted: 8 November 2018 / Published: 13 November 2018
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Abstract
The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the [...] Read more.
The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited. Full article
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Open AccessArticle
Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland
Geosciences 2018, 8(11), 399; https://doi.org/10.3390/geosciences8110399
Received: 14 September 2018 / Revised: 17 October 2018 / Accepted: 30 October 2018 / Published: 1 November 2018
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Abstract
Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities [...] Read more.
Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities. Full article
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Open AccessArticle
Ancient Microbial Activity in Deep Hydraulically Conductive Fracture Zones within the Forsmark Target Area for Geological Nuclear Waste Disposal, Sweden
Geosciences 2018, 8(6), 211; https://doi.org/10.3390/geosciences8060211
Received: 24 April 2018 / Revised: 4 June 2018 / Accepted: 7 June 2018 / Published: 11 June 2018
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Abstract
Recent studies reveal that organisms from all three domains of life—Archaea, Bacteria, and even Eukarya—can thrive under energy-poor, dark, and anoxic conditions at large depths in the fractured crystalline continental crust. There is a need for an increased understanding of the processes and [...] Read more.
Recent studies reveal that organisms from all three domains of life—Archaea, Bacteria, and even Eukarya—can thrive under energy-poor, dark, and anoxic conditions at large depths in the fractured crystalline continental crust. There is a need for an increased understanding of the processes and lifeforms in this vast realm, for example, regarding the spatiotemporal extent and variability of the different processes in the crust. Here, we present a study that set out to detect signs of ancient microbial life in the Forsmark area—the target area for deep geological nuclear waste disposal in Sweden. Stable isotope compositions were determined with high spatial resolution analyses within mineral coatings, and mineralized remains of putative microorganisms were studied in several deep water-conducting fracture zones (down to 663 m depth), from which hydrochemical and gas data exist. Large isotopic variabilities of δ13Ccalcite (−36.2 to +20.2‰ V-PDB) and δ34Spyrite (−11.7 to +37.8‰ V-CDT) disclose discrete periods of methanogenesis, and potentially, anaerobic oxidation of methane and related microbial sulfate reduction at several depth intervals. Dominant calcite–water disequilibrium of δ18O and 87Sr/86Sr precludes abundant recent precipitation. Instead, the mineral coatings largely reflect an ancient archive of episodic microbial processes in the fracture system, which, according to our microscale Rb–Sr dating of co-genetic adularia and calcite, date back to the mid-Paleozoic. Potential Quaternary precipitation exists mainly at ~400 m depth in one of the boreholes, where mineral–water compositions corresponded. Full article
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