TY  - JOUR
A1  - Ciobanu, M. -C.
A1  - Rabineau, M.
A1  - Droz, L.
A1  - Revillon, S.
A1  - Ghiglione, J. -F.
A1  - Dennielou, B.
A1  - Jorry, S. -J.
A1  - Kallmeyer, Jens
A1  - Etoubleau, J.
A1  - Pignet, P.
A1  - Crassous, P.
A1  - Vandenabeele-Trambouze, O.
A1  - Laugier, J.
A1  - Guegan, M.
A1  - Godfroy, A.
A1  - Alain, K.
T1  - Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments
JF  - Biogeosciences
N2  - 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.
Y1  - 2012
U6  - https://doi.org/10.5194/bg-9-3491-2012
SN  - 1726-4170
VL  - 9
IS  - 9
SP  - 3491
EP  - 3512
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Kallmeyer, Jens
A1  - Grewe, Sina
A1  - Glombitza, Clemens
A1  - Kitte, J. Axel
T1  - Microbial abundance in lacustrine sediments: a case study from Lake Van, Turkey
JF  - International journal of earth sciences
N2  - The ICDP "PaleoVan" drilling campaign at Lake Van, Turkey, provided a long (> 100 m) record of lacustrine subsurface sedimentary microbial cell abundance. After the ICDP campaign at Potrok Aike, Argentina, this is only the second time deep lacustrine cell counts have been documented. Two sites were cored and revealed a strikingly similar cell distribution despite differences in organic matter content and microbial activity. Although shifted towards higher values, cell counts from Lake Potrok Aike, Argentina, reveal very similar distribution patterns with depth. The lacustrine cell count data are significantly different from published marine records; the most probable cause is differences in sedimentary organic matter composition with marine sediments containing a higher fraction of labile organic matter. Previous studies showed that microbial activity and abundance increase centimetres to metres around geologic interfaces. The finely laminated Lake Van sediment allowed studying this phenomenon on the microscale. We sampled at the scale of individual laminae, and in some depth intervals, we found large differences in microbial abundance between the different laminae. This small-scale heterogeneity is normally overlooked due to much larger sampling intervals that integrate over several centimetres. However, not all laminated intervals exhibit such large differences in microbial abundance, and some non-laminated horizons show large variability on the millimetre scale as well. The reasons for such contrasting observations remain elusive, but indicate that heterogeneity of microbial abundance in subsurface sediments has not been taken into account sufficiently. These findings have implications not just for microbiological studies but for geochemistry as well, as the large differences in microbial abundance clearly show that there are distinct microhabitats that deviate considerably from the surrounding layers.
KW  - Subsurface biosphere
KW  - Deep biosphere
KW  - Lake Van
KW  - Cell counts
KW  - Lacustrine sediment
Y1  - 2015
U6  - https://doi.org/10.1007/s00531-015-1219-6
SN  - 1437-3254
SN  - 1437-3262
VL  - 104
IS  - 6
SP  - 1667
EP  - 1677
PB  - Springer
CY  - New York
ER  - 
TY  - JOUR
A1  - Green-Saxena, A.
A1  - Feyzullayev, A.
A1  - Hubert, C. R. J.
A1  - Kallmeyer, Jens
A1  - Krueger, M.
A1  - Sauer, P.
A1  - Schulz, Hans-Martin
A1  - Orphan, V. J.
T1  - Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan
JF  - Environmental microbiology
N2  - Terrestrial mud volcanoes (TMVs) represent geochemically diverse habitats with varying sulfur sources and yet sulfur cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in four TMVs in Azerbaijan. A combination of geochemical analyses, biological rate measurements and molecular diversity surveys (targeting metabolic genes aprA and dsrA and SSU ribosomal RNA) supported the presence of active sulfur-oxidizing and sulfate-reducing guilds in all four TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. The TMVs varied in potential sulfate reduction rates (SRR) by up to four orders of magnitude with highest SRR observed in sediments where in situ sulfate concentrations were highest. Maximum temperatures at which SRR were measured was 60 degrees C in two TMVs. Corresponding with these trends in SRR, members of the potentially thermophilic, spore-forming, Desulfotomaculum were detected in these TMVs by targeted 16S rRNA analysis. Additional sulfate-reducing bacterial lineages included members of the Desulfobacteraceae and Desulfobulbaceae detected by aprA and dsrA analyses and likely contributing to the mesophilic SRR measured. Phylotypes affiliated with sulfide-oxidizing Gamma- and Betaproteobacteria were abundant in aprA libraries from low sulfate TMVs, while the highest sulfate TMV harboured 16S rRNA phylotypes associated with sulfur-oxidizing Epsilonproteobacteria. Altogether, the biogeochemical and microbiological data indicate these unique terrestrial habitats support diverse active sulfur-cycling microorganisms reflecting the in situ geochemical environment.
Y1  - 2012
U6  - https://doi.org/10.1111/1462-2920.12015
SN  - 1462-2912
VL  - 14
IS  - 12
SP  - 3271
EP  - 3286
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kallmeyer, Jens
A1  - Pockalny, Robert
A1  - Adhikari, Rishi Ram
A1  - Smith, David C.
A1  - D'Hondt, Steven
T1  - Global distribution of microbial abundance and biomass in subseafloor sediment
JF  - Proceedings of the National Academy of Sciences of the United States of America
N2  - The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9 center dot 10(29) cells [corresponding to 4.1 petagram (Pg) C and similar to 0.6% of Earth's total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth's total number of microbes and total living biomass to be, respectively, 50-78% and 10-45% lower than previous estimates.
KW  - deep biosphere
KW  - cell enumeration
KW  - global microbial biomass
KW  - subsurface life
Y1  - 2012
U6  - https://doi.org/10.1073/pnas.1203849109
SN  - 0027-8424
VL  - 109
IS  - 40
SP  - 16213
EP  - 16216
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Lappe, Michael
A1  - Kallmeyer, Jens
T1  - A cell extraction method for oily sediments
JF  - Frontiers in microbiology
N2  - Hydrocarbons can be found in many different habitats and represent an important carbon source for microbes. As fossil fuels, they are also an important economical resource and through natural seepage or accidental release they can be major pollutants. DNA-specific stains and molecular probes bind to hydrocarbons, causing massive background fluorescence, thereby hampering cell enumeration. The cell extraction procedure of Kallmeyer et al. (2008) separates the cells from the sediment matrix. In principle, this technique can also be used to separate cells from oily sediments, but it was not originally optimized for this application. Here we present a modified extraction method in which the hydrocarbons are removed prior to cell extraction. Due to the reduced background fluorescence the microscopic image becomes clearer, making cell identification, and enumeration much easier. Consequently, the resulting cell counts from oily samples treated according to our new protocol are significantly higher than those treated according to Kallmeyer et al. (2008). We tested different amounts of a variety of solvents for their ability to remove hydrocarbons and found that n-hexane and in samples containing more mature oils methanol, delivered the best results. However, as solvents also tend to lyse cells, it was important to find the optimum solvent to sample ratio, at which hydrocarbon extraction is maximized and cell lysis minimized. A volumetric ratio of 1:2-1:5 between a formalin-fixed sediment slurry and solvent delivered highest cell counts. Extraction efficiency was around 30-50% and was checked on both oily samples spiked with known amounts of E. coli cells and oil-free samples amended with fresh and biodegraded oil. The method provided reproducible results on samples containing very different kinds of oils with regard to their degree of biodegradation. For strongly biodegraded oil MeOH turned out to be the most appropriate solvent, whereas for less biodegraded samples n-hexane delivered best results.
KW  - cell enumeration
KW  - hydrocarbons
KW  - cell separation
KW  - subsurface microbiology
Y1  - 2011
U6  - https://doi.org/10.3389/fmicb.2011.00233
SN  - 1664-302X
VL  - 2
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Sauer, Patrick
A1  - Glombitza, Clemens
A1  - Kallmeyer, Jens
T1  - A system for incubations at high gas partial pressure
JF  - Frontiers in microbiology
N2  - High-pressure is a key feature of deep subsurface environments. High partial pressure of dissolved gasses plays an important role in microbial metabolism, because thermodynamic feasibility of many reactions depends on the concentration of reactants. For gases, this is controlled by their partial pressure, which can exceed 1 MPa at in situ conditions. Therefore, high hydrostatic pressure alone is not sufficient to recreate true deep subsurface in situ conditions, but the partial pressure of dissolved gasses has to be controlled as well. We developed an incubation system that allows for incubations at hydrostatic pressure up to 60 MPa, temperatures up to 120 degrees C, and at high gas partial pressure. The composition and partial pressure of gasses can be manipulated during the experiment. To keep costs low, the system is mainly made from off-the-shelf components with only very few custommade parts. A flexible and inert PVDF (polyvinylidene fluoride) incubator sleeve, which is almost impermeable for gases, holds the sample and separates it from the pressure fluid. The flexibility of the incubator sleeve allows for sub-sampling of the medium without loss of pressure. Experiments can be run in both static and flow-through mode. The incubation system described here is usable for versatile purposes, not only the incubation of microorganisms and determination of growth rates, but also for chemical degradation or extraction experiments under high gas saturation, e.g., fluid-gas-rock-interactions in relation to carbon dioxide sequestration. As an application of the system we extracted organic compounds from sub-bituminous coal using H2O as well as a H2O-CO2 mixture at elevated temperature (90 degrees C) and pressure (5 MPa). Subsamples were taken at different time points during the incubation and analyzed by ion chromatography. Furthermore we demonstrated the applicability of the system for studies of microbial activity, using samples from the Isis mud volcano. We could detect an increase in sulfate reduction rate upon the addition of methane to the sample.
KW  - high-pressure incubation system
KW  - gas partial pressure
KW  - sub-sampling
KW  - carbon dioxide
KW  - low molecular weight organic acids
Y1  - 2012
U6  - https://doi.org/10.3389/fmicb.2012.00025
SN  - 1664-302X
VL  - 3
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Alawi, Mashal
A1  - Schneider, Beate
A1  - Kallmeyer, Jens
T1  - A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample
JF  - Journal of microbiological methods
N2  - 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.
KW  - Extracellular DNA
KW  - eDNA
KW  - Intracellular DNA
KW  - South Pacific Gyre
KW  - Ancient DNA
KW  - Fossil DNA
Y1  - 2014
U6  - https://doi.org/10.1016/j.mimet.2014.06.009
SN  - 0167-7012
SN  - 1872-8359
VL  - 104
SP  - 36
EP  - 42
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Adhikari, Rishi Ram
A1  - Glombitza, Clemens
A1  - Nickel, Julia C.
A1  - Anderson, Chloe H.
A1  - Dunlea, Ann G.
A1  - Spivack, Arthur J.
A1  - Murray, Richard W.
A1  - Kallmeyer, Jens
T1  - Hydrogen Utilization Potential in Subsurface Sediments
JF  - Frontiers in microbiology
N2  - 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.
KW  - hydrogenase
KW  - tritium assay
KW  - deep biosphere
KW  - microbial activity
KW  - Lake Van
KW  - Barents Sea
KW  - Equatorial Pacific
KW  - Gulf of Mexico
Y1  - 2016
U6  - https://doi.org/10.3389/fmicb.2016.00008
SN  - 1664-302X
VL  - 7
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Nickel, Julia C.
A1  - di Primio, Rolando
A1  - Mangelsdorf, Kai
A1  - Stoddart, Daniel
A1  - Kallmeyer, Jens
T1  - Characterization of microbial activity in pockmark fields of the SW-Barents Sea
JF  - Marine geology : international journal of marine geology, geochemistry and geophysics
N2  - Multibeam bathymetry revealed the occurrence of numerous craterlike depressions, so-called pockmarks, on the sea floor of the Hammerfest Basin and the Loppa High, south-western Barents Sea. To investigate whether these pockmarks are related to ongoing gas seepage, microbial processes associated with methane metabolism were analyzed using geochemical, biogeochemical and microbiological techniques. Gravity cores were collected along transects crossing individual pockmarks, allowing a direct comparison between different locations inside (assumed activity center), on the rim, and outside of a pockmark (reference sites). Concentrations of hydrocarbons in the sediment, particularly methane, were measured as headspace (free) gas, and in the occluded and adsorbed gas fraction. Down to a depth of 2.6 m below sea floor (mbsf) sulfate reduction rates were quantified by radiotracer incubations. Concentrations of dissolved sulfate in the porewater were determined as well. Neither the sulfate profiles nor the gas measurements show any evidence of microbial activity or active fluid venting. Methane concentrations and sulfate reduction rates were extremely low or even below the detection limit. The results show that the observed sediment structures are most likely paleo-pockmarks, their formation probably occurred during the last deglaciation.
KW  - pockmark
KW  - Barents Sea
KW  - sulfate reduction
KW  - microbial activity
KW  - Loppa High
Y1  - 2012
U6  - https://doi.org/10.1016/j.margeo.2012.02.002
SN  - 0025-3227
VL  - 332
IS  - 12
SP  - 152
EP  - 162
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Nomosatryo, Sulung
A1  - Tjallingii, Rik
A1  - Henny, Cynthia
A1  - Ridwansyah, Iwan
A1  - Wagner, Dirk
A1  - Tomás, Sara
A1  - Kallmeyer, Jens
T1  - Surface sediment composition and depositional environments in tropical Lake Sentani, Papua Province, Indonesia
JF  - Journal of Paleolimnology
N2  - Tropical Lake Sentani in the Indonesian Province Papua consists of four separate basins and is surrounded by a catchment with a very diverse geology. We characterized the surface sediment (upper 5 cm) of the lake's four sub-basins based on multivariate statistical analyses (principal component analysis, hierarchical clustering) of major element compositions obtained by X-ray fluorescence scanning. Three types of sediment are identified based on distinct compositional differences between rivers, shallow/proximal and deep/distal lake sediments. The different sediment types are mainly characterized by the correlation of elements associated with redox processes (S, Mn, Fe), carbonates (Ca), and detrital input (Ti, Al, Si, K) derived by river discharge. The relatively coarse-grained river sediments mainly derive form the mafic catchment geology and contribution of the limestone catchment geology is only limited. Correlation of redox sensitive and detrital elements are used to reveal oxidation conditions, and indicate oxic conditions in river samples and reducing conditions for lake sediments. Organic carbon (TOC) generally correlates with redox sensitive elements, although a correlation between TOC and individual elements change strongly between the three sediment types. Pyrite is the quantitatively dominant reduced sulfur mineral, monosulfides only reach appreciable concentrations in samples from rivers draining mafic and ultramafic catchments. Our study shows large spatial heterogeneity within the lake's sub-basins that is mainly caused by catchment geology and topography, river runoff as well as the bathymetry and the depth of the oxycline. We show that knowledge about lateral heterogeneity is crucial for understanding the geochemical and sedimentological variations recorded by these sediments. The highly variable conditions make Lake Sentani a natural laboratory, with its different sub-basins representing different depositional environments under identical tropical climate conditions.
KW  - Tropical lake
KW  - Lacustrine sediment
KW  - XRF analysis
KW  - Multivariate
KW  - statistics
Y1  - 2022
U6  - https://doi.org/10.1007/s10933-022-00259-4
SN  - 0921-2728
SN  - 1573-0417
PB  - Springer
CY  - Dordrecht
ER  -