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As part of the International Continental Drilling Program deep lake drilling project Paleo Van, we investigated sulfate reduction (SR) in deep sediment cores of the saline, alkaline (salinity 21.4%0, alkalinity 155 m mEq-1, pH 9.81) Lake Van, Turkey. The cores were retrieved in the Northern Basin (NB) and at Ahlat Ridge (AR) and reached a maximum depth of 220 m. Additionally, 65-75 cm long gravity cores were taken at both sites. SR rates (SRR) were low (<22 nmol cm-3 day-1) compared to lakes with higher salinity and alkalinity, indicating that salinity and alkalinity are not limiting SR in Lake Van. Both sites differ significantly in rates and depth distribution of SR. In NB, SRR are up to 10 times higher than at AR. SR could be detected down to 19 mblf (meters below lake floor) at NB and down to 13 mblf at AR. Although SRR were lower at AR than at NB, organic matter (OM) concentrations were higher. In contrast, dissolved OM in the pore water at AR contained more macromolecular OM and less low molecular weight OM.VVe thus suggest, that OM content alone cannot be used to infer microbial activity at Lake Van but that quality of OM has an important impact as well. These differences suggest that biogeochemical processes in lacustrine sediments are reacting very sensitively to small variations in geological, physical, or chemical parameters over relatively short distances.
The new in situ geodynamic laboratory established in the framework of the ICDP Eger project aims to develop the most modern, comprehensive, multiparameter laboratory at depth for studying earthquake swarms, crustal fluid flow, mantle-derived CO2 and helium degassing, and processes of the deep biosphere. In order to reach a new level of high-frequency, near-source and multiparameter observation of earthquake swarms and related phenomena, such a laboratory comprises a set of shallow boreholes with high-frequency 3-D seismic arrays as well as modern continuous real-time fluid monitoring at depth and the study of the deep biosphere.
This laboratory is located in the western part of the Eger Rift at the border of the Czech Republic and Germany (in the West Bohemia–Vogtland geodynamic region) and comprises a set of five boreholes around the seismoactive zone. To date, all monitoring boreholes have been drilled. This includes the seismic monitoring boreholes S1, S2 and S3 in the crystalline units north and east of the major Nový Kostel seismogenic zone, borehole F3 in the Hartoušov mofette field and borehole S4 in the newly discovered Bažina maar near Libá. Supplementary borehole P1 is being prepared in the Neualbenreuth maar for paleoclimate and biological research. At each of these sites, a borehole broadband seismometer will be installed, and sites S1, S2 and S3 will also host a 3-D seismic array composed of a vertical geophone chain and surface seismic array. Seismic instrumenting has been completed in the S1 borehole and is in preparation in the remaining four monitoring boreholes. The continuous fluid monitoring site of Hartoušov includes three boreholes, F1, F2 and F3, and a pilot monitoring phase is underway. The laboratory also enables one to analyze microbial activity at CO2 mofettes and maar structures in the context of changes in habitats. The drillings into the maar volcanoes contribute to a better understanding of the Quaternary paleoclimate and volcanic activity.
The new in situ geodynamic laboratory established in the framework of the ICDP Eger project aims to develop the most modern, comprehensive, multiparameter laboratory at depth for studying earthquake swarms, crustal fluid flow, mantle-derived CO2 and helium degassing, and processes of the deep biosphere. In order to reach a new level of high-frequency, near-source and multiparameter observation of earthquake swarms and related phenomena, such a laboratory comprises a set of shallow boreholes with high-frequency 3-D seismic arrays as well as modern continuous real-time fluid monitoring at depth and the study of the deep biosphere.
This laboratory is located in the western part of the Eger Rift at the border of the Czech Republic and Germany (in the West Bohemia-Vogtland geodynamic region) and comprises a set of five boreholes around the seismoactive zone. To date, all monitoring boreholes have been drilled. This includes the seismic monitoring boreholes S1, S2 and S3 in the crystalline units north and east of the major Novy Kostel seismogenic zone, borehole F3 in the Hartousov mofette field and borehole S4 in the newly discovered Bazina maar near Liba. Supplementary borehole P1 is being prepared in the Neualbenreuth maar for paleoclimate and biological research. At each of these sites, a borehole broadband seismometer will be installed, and sites S1, S2 and S3 will also host a 3-D seismic array composed of a vertical geophone chain and surface seismic array. Seismic instrumenting has been completed in the S1 borehole and is in preparation in the remaining four monitoring boreholes. The continuous fluid monitoring site of Hartousov includes three boreholes, F1, F2 and F3, and a pilot monitoring phase is underway. The laboratory also enables one to analyze microbial activity at CO2 mofettes and maar structures in the context of changes in habitats. The drillings into the maar volcanoes contribute to a better understanding of the Quaternary paleoclimate and volcanic activity.
The low-productivity South Pacific Gyre (SPG) is Earth's largest oceanic province. Its sediment accumulates extraordinarily slowly (0.1-1 m per million years). This sediment contains a living community that is characterized by very low biomass and very low metabolic activity. At every depth in cored SPG sediment, mean cell abundances are 3 to 4 orders of magnitude lower than at the same depths in all previously explored subseafloor communities. The net rate of respiration by the subseafloor sedimentary community at each SPG site is 1 to 3 orders of magnitude lower than the rates at previously explored sites. Because of the low respiration rates and the thinness of the sediment, interstitial waters are oxic throughout the sediment column in most of this region. Consequently, the sedimentary community of the SPG is predominantly aerobic, unlike previously explored subseafloor communities. Generation of H-2 by radiolysis of water is a significant electron-donor source for this community. The per-cell respiration rates of this community are about 2 orders of magnitude higher (in oxidation/reduction equivalents) than in previously explored anaerobic subseafloor communities. Respiration rates and cell concentrations in subseafloor sediment throughout almost half of the world ocean may approach those in SPG sediment.
Although a large fraction of the world's biomass resides in the subsurface, there has been no study of the effects of catastrophic disturbance on the deep biosphere and the rate of its subsequent recovery. We carried out an investigation of the microbiology of a 1.76 km drill core obtained from the similar to 35 million-year-old Chesapeake Bay impact structure, USA, with robust contamination control. Microbial enumerations displayed a logarithmic downward decline, but the different gradient, when compared to previously studied sites, and the scatter of the data are consistent with a rnicrobiota influenced by the geological disturbances caused by the impact. Microbial abundance is low in buried crater-fill, ocean-resurge, and avalanche deposits despite the presence of redox couples for growth. Coupled with the low hydraulic conductivity, the data suggest the microbial community has not yet recovered from the impact similar to 35 million years ago. Microbial enumerations, molecular analysis of microbial enrichment cultures, and geochemical analysis showed recolonization of a deep region of impact-fractured rock that was heated to above the upper temperature limit for life at the time of impact. These results show how, by fracturing subsurface rocks, impacts can extend the depth of the biosphere. This phenomenon would have provided deep refugia for life on the more heavily bombarded early Earth, and it shows that the deeply fractured regions of impact craters are promising targets to study the past and present habitability of Mars.
An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG) and Halobacteria) within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence analyses (CCA) showed that the availability of electron acceptors and the quality of electron donors (indicated by age) strongly influenced the community structure. In contrast, within the Gulf of Lion core, characterized by a homogeneous lithological structure of upper-slope environment, most detected groups were Bacteroidetes and, to a lesser extent, Betaproteobacteria. At both site, the detection of Betaproteobacteria coincided with increased terrestrial inputs, as confirmed by the geochemical measurements (Si, Sr, Ti and Ca). In the Gulf of Lion, geochemical parameters were also found to drive microbial community composition. Taken together, our data suggest that the palaeoenvironmental history of erosion and deposition recorded in the Western Mediterranean Sea sediments has left its imprint on the sedimentological context for microbial habitability, and then indirectly on structure and composition of the microbial communities during the late Quaternary.
Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Previous studies suggested that eDNA plays an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Previous methods for eDNA extraction were either not suitable for oligotrophic sediments or only allowed quantification but no genetic analyses. Our procedure is based on cell detachment and eDNA liberation from sediment particles by sequential washing with an alkaline sodium phosphate buffer followed by a separation of cells and eDNA. The separated eDNA is then bound onto silica particles and purified, whereas the intracellular DNA from the separated cells is extracted using a commercial kit. The method provides extra- and intracellular DNA of high purity that is suitable for downstream applications like PCR. Extracellular DNA was extracted from organic-rich shallow sediment of the Baltic Sea, glacially influenced sediment of the Barents Sea and from the oligotrophic South Pacific Gyre. The eDNA concentration in these samples varied from 23 to 626 ng g(-1) wet weight sediment. A number of experiments were performed to verify each processing step. Although extraction efficiency is higher than other published methods, it is not fully quantitative. (C) 2014 Elsevier B.V. All rights reserved.
The subsurface harbors a large fraction of Earth's living biomass, forming complex microbial ecosystems. Without a profound knowledge of the ongoing biologically mediated processes and their reaction to anthropogenic changes it is difficult to assess the long-term stability and feasibility of any type of geotechnical utilization, as these influence subsurface ecosystems. Despite recent advances in many areas of subsurface microbiology, the direct quantification of turnover processes is still in its infancy, mainly due to the extremely low cell abundances. We provide an overview of the currently available techniques for the quantification of microbial turnover processes and discuss their specific strengths and limitations. Most techniques employed so far have focused on specific processes, e.g. sulfate reduction or methanogenesis. Recent studies show that processes that were previously thought to exclude each other can occur simultaneously, albeit at very low rates. Without the identification of the respective processes it is impossible to quantify total microbial activity. Even in cases where all simultaneously occurring processes can be identified, the typically very low rates prevent quantification. In many cases a simple measure of total microbial activity would be a better and more robust measure than assays for several specific processes. Enzyme or molecular assays provide a more general approach as they target key metabolic compounds. Depending on the compound targeted a broader spectrum of microbial processes can be quantified. The two most promising compounds are ATP and hydrogenase, as both are ubiquitous in microbes. Technical constraints limit the applicability of currently available ATP-assays for subsurface samples. A recently developed hydrogenase radiotracer assay has the potential to become a key tool for the quantification of subsurface microbial activity.
Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H(2)ases to successively higher concentrations of H-2 in successively deeper zones.
Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H(2)ases to successively higher concentrations of H-2 in successively deeper zones.