TY - JOUR A1 - Roy, Hans A1 - Kallmeyer, Jens A1 - Adhikari, Rishi Ram A1 - Pockalny, Robert A1 - Jorgensen, Bo Barker A1 - D'Hondt, Steven T1 - Aerobic microbial respiration in 86-million-year-old deep-sea red clay JF - Science N2 - Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O-2 liter(-1) year(-1) near the sediment-water interface to 0.001 micromoles of O-2 liter(-1) year(-1) at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10(-3) femtomoles of O-2 cell(-1) day(-1) 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux. Y1 - 2012 U6 - https://doi.org/10.1126/science.1219424 SN - 0036-8075 VL - 336 IS - 6083 SP - 922 EP - 925 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Noah, Mareike A1 - Lappe, Michael A1 - Schneider, Beate A1 - Vieth-Hillebrand, Andrea A1 - Wilkes, Heinz A1 - Kallmeyer, Jens T1 - Tracing biogeochemical and microbial variability over a complete oil sand mining and recultivation process JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Recultivation of disturbed oil sand mining areas is an issue of increasing importance. Nevertheless only little is known about the fate of organic matter, cell abundances and microbial community structures during oil sand processing, tailings management and initial soil development on reclamation sites. Thus the focus of this work is on biogeochemical changes of mined oil sands through the entire process chain until its use as substratum for newly developing soils on reclamation sites. Therefore, oil sand, mature fine tailings (MFTs) from tailings ponds and drying cells and tailings sand covered with peat-mineral mix (PMM) as part of land reclamation were analyzed. The sample set was selected to address the question whether changes in the above-mentioned biogeochemical parameters can be related to oil sand processing or biological processes and how these changes influence microbial activities and soil development. GC-MS analyses of oil-derived biomarkers reveal that these compounds remain unaffected by oil sand processing and biological activity. In contrast, changes in polycyclic aromatic hydrocarbon (PAH) abundance and pattern can be observed along the process chain. Especially naphthalenes, phenanthrenes and chrysenes are altered or absent on reclamation sites, Furthermore, root-bearing horizons on reclamation sites exhibit cell abundances at least ten times higher (10(8) to 10(9) cells g(-1)) than in oil sand and MFF samples (10(7) cells g(-1)) and show a higher diversity in their microbial community structure. Nitrate in the pore water and roots derived from the PMM seem to be the most important stimulants for microbial growth. The combined data show that the observed compositional changes are mostly related to biological activity and the addition of exogenous organic components (PMM), whereas oil extraction, tailings dewatering and compaction do not have significant influences on the evaluated compounds. Microbial community composition remains relatively stable through the entire process chain. (C) 2014 Elsevier B.V. All rights reserved. KW - Oil sands KW - Tailings ponds KW - Reclamation KW - PAN KW - Biomarker KW - Microbial community analysis Y1 - 2014 U6 - https://doi.org/10.1016/j.scitotenv.2014.08.020 SN - 0048-9697 SN - 1879-1026 VL - 499 SP - 297 EP - 310 PB - Elsevier CY - Amsterdam ER - 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 - Kallmeyer, Jens ED - Laskin, AI ED - Sariaslani, S ED - Gadd, GM T1 - Detection and quantification of microbial cells in subsurface sediments JF - Advances in applied microbiology JF - Advances in Applied Microbiology N2 - Quantification of total cell abundance is one of the most fundamental parameters in the exploration of subsurface life. Despite all recent advances in molecular techniques, this parameter is usually determined by fluorescence microscopy. In order to obtain reliable and reproducible results, it is important not just to focus on the actual cell enumeration but also to consider the entire chain of processing. Starting with the retrieval of the sample, over subsampling and sample processing to the final step of fluorescence microscopy, there are many potential sources of contamination that have to be assessed and, if possible, avoided. Because some degree of sample contamination will always occur, it is necessary to employ some form of contamination control. Different tracers are available, each one with its specific advantages and drawbacks. In many cases, the problems arise not after the sample has arrived in a well-equipped laboratory with highly trained personnel, but much earlier at the drill site or in a field camp. In this review, I discuss the different aspects of cell enumeration in subsurface sediment, evaluating every step in the long process chain. Y1 - 2011 SN - 978-0-12-387048-3 U6 - https://doi.org/10.1016/B978-0-12-387048-3.00003-9 SN - 0065-2164 VL - 76 SP - 79 EP - 103 PB - Elsevier CY - San Diego 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 -