@misc{VuilleminFrieseAlawietal.2016,
  author    = {Vuillemin, Aur{\`e}le and Friese, Andr{\´e} and Alawi, Mashal and Henny, Cynthia and Nomosatryo, Sulung and Wagner, Dirk and Crowe, Sean A. and Kallmeyer, Jens},
  title     = {Geomicrobiological features of ferruginous sediments from Lake Towuti, Indonesia},
  series = {Frontiers in microbiology},
  journal   = {Frontiers in microbiology},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407312},
  pages     = {16},
  year      = {2016},
  abstract  = {Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae. Chloroflexi, and Therrnoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanornicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.},
  language  = {en}
}
@article{VuilleminHornFrieseetal.2018,
  author    = {Vuillemin, Aurele and Horn, Fabian and Friese, Andre and Winkel, Matthias and Alawi, Mashal and Wagner, Dirk and Henny, Cynthia and Orsi, William D. and Crowe, Sean A. and Kallmeyer, Jens},
  title     = {Metabolic potential of microbial communities from ferruginous sediments},
  series = {Environmental microbiology},
  volume    = {20},
  journal   = {Environmental microbiology},
  number    = {12},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1462-2912},
  doi       = {10.1111/1462-2920.14343},
  pages     = {4297 -- 4313},
  year      = {2018},
  abstract  = {Ferruginous (Fe-rich, SO4-poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.},
  language  = {en}
}
@article{SauerGlombitzaKallmeyer2012,
  author    = {Sauer, Patrick and Glombitza, Clemens and Kallmeyer, Jens},
  title     = {A system for incubations at high gas partial pressure},
  series = {Frontiers in microbiology},
  volume    = {3},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2012.00025},
  pages     = {9},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{RoyKallmeyerAdhikarietal.2012,
  author    = {Roy, Hans and Kallmeyer, Jens and Adhikari, Rishi Ram and Pockalny, Robert and Jorgensen, Bo Barker and D'Hondt, Steven},
  title     = {Aerobic microbial respiration in 86-million-year-old deep-sea red clay},
  series = {Science},
  volume    = {336},
  journal   = {Science},
  number    = {6083},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.1219424},
  pages     = {922 -- 925},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{NomosatryoTjallingiiHennyetal.2022,
  author    = {Nomosatryo, Sulung and Tjallingii, Rik and Henny, Cynthia and Ridwansyah, Iwan and Wagner, Dirk and Tom{\´a}s, Sara and Kallmeyer, Jens},
  title     = {Surface sediment composition and depositional environments in tropical Lake Sentani, Papua Province, Indonesia},
  series = {Journal of Paleolimnology},
  journal   = {Journal of Paleolimnology},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-022-00259-4},
  pages     = {20},
  year      = {2022},
  abstract  = {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.},
  language  = {en}
}
@article{NoahLappeSchneideretal.2014,
  author    = {Noah, Mareike and Lappe, Michael and Schneider, Beate and Vieth-Hillebrand, Andrea and Wilkes, Heinz and Kallmeyer, Jens},
  title     = {Tracing biogeochemical and microbial variability over a complete oil sand mining and recultivation process},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {499},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2014.08.020},
  pages     = {297 -- 310},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{NickeldiPrimioMangelsdorfetal.2012,
  author    = {Nickel, Julia C. and di Primio, Rolando and Mangelsdorf, Kai and Stoddart, Daniel and Kallmeyer, Jens},
  title     = {Characterization of microbial activity in pockmark fields of the SW-Barents Sea},
  series = {Marine geology : international journal of marine geology, geochemistry and geophysics},
  volume    = {332},
  journal   = {Marine geology : international journal of marine geology, geochemistry and geophysics},
  number    = {12},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0025-3227},
  doi       = {10.1016/j.margeo.2012.02.002},
  pages     = {152 -- 162},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{NagakuraSchubertWagneretal.2022,
  author    = {Nagakura, Toshiki and Schubert, Florian and Wagner, Dirk and Kallmeyer, Jens},
  title     = {Biological sulfate reduction in deep subseafloor sediment of Guaymas Basin},
  series = {Frontiers in microbiology},
  volume    = {13},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  organization    = {IODP Exp 385 Shipboard Sci Party},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2022.845250},
  pages     = {12},
  year      = {2022},
  abstract  = {Sulfate reduction is the quantitatively most important process to degrade organic matter in anoxic marine sediment and has been studied intensively in a variety of settings. Guaymas Basin, a young marginal ocean basin, offers the unique opportunity to study sulfate reduction in an environment characterized by organic-rich sediment, high sedimentation rates, and high geothermal gradients (100-958 degrees C km(-1)). We measured sulfate reduction rates (SRR) in samples taken during the International Ocean Discovery Program (IODP) Expedition 385 using incubation experiments with radiolabeled (SO42-)-S-35 carried out at in situ pressure and temperature. The highest SRR (387 nmol cm(-3) d(-1)) was recorded in near-surface sediments from Site U1548C, which had the steepest geothermal gradient (958 degrees C km(-1)). At this site, SRR were generally over an order of magnitude higher than at similar depths at other sites (e.g., 387-157 nmol cm(-3) d(-1) at 1.9 mbsf from Site U1548C vs. 46-1.0 nmol cm(-3) d(-1) at 2.1 mbsf from Site U1552B). Site U1546D is characterized by a sill intrusion, but it had already reached thermal equilibrium and SRR were in the same range as nearby Site U1545C, which is minimally affected by sills. The wide temperature range observed at each drill site suggests major shifts in microbial community composition with very different temperature optima but awaits confirmation by molecular biological analyses. At the transition between the mesophilic and thermophilic range around 40 degrees C-60 degrees C, sulfate-reducing activity appears to be decreased, particularly in more oligotrophic settings, but shows a slight recovery at higher temperatures.},
  language  = {en}
}
@article{MrlinaKaempfKroneretal.2009,
  author    = {Mrlina, Jan and K{\"a}mpf, Horst and Kroner, Corinna and Mingram, Jens and Stebich, Martina and Brauer, Achim and Geissler, Wolfram H. and Kallmeyer, Jens and Matthes, Heidrun and Seidl, Michal},
  title     = {Discovery of the first Quaternary maar in the Bohemian Massif, Central Europe, based on combined geophysical and geological surveys},
  issn      = {0377-0273},
  doi       = {10.1016/j.jvolgeores.2009.01.027},
  year      = {2009},
  abstract  = {Based on results of previous investigations of tephra-tuff volcaniclastic deposits and a geophysical survey in the surroundings of the Zelezna hurka Quaternary volcano, West Bohemia, we performed detailed geophysical Surveys using gravimetry, magnetometry and electrical conductivity techniques. Striking anomalies were revealed in a morphological depression near Mytina, West Bohemia, as a strong evidence of the assumed maar-diatreme structure. The sharp isometric gravity low of -2.30 mGal, as well as the corresponding positive magnetic anomaly of 200 nT with a negative rim on its northern side indicate a steeply clipping geological body of low density and containing magnetic rocks/minerals. Magnetic survey also showed pronounced local anomalies outside the depression that can reflect relicts of the tephra rim of the maar. This geophysical evidence was then proven by an exploratory drilling near the centre of the gravity anomaly. Macroscopic on-site evaluation of the core, and more detailed sedimentological, petrochemical, palynological and microbiological laboratory analyses further confirmed the existence of a maar structure filled by 84 m of lake sediments reflecting a Succession of several warm and cold climatic periods. Results Of palynological analyses confirm the presence of a continuous palaeoclimate archive, with at least three successive warmer periods of most probably interstadial character from the upper Quaternary Saalian complex. Therefore. the recovered sediment sequence holds strong potential for in-depth palaeoclimate reconstruction and deep biosphere studies. At the bottom of the Mytina-1 (MY- 1) borehole (84-85.5 M), Country rock debris Was found, containing also volcanic bombs and lapilli. The discovered volcanic Structure is considered to be the first known Quaternary maar-diatreme volcano on the territory of the Bohemian Massif. Because of hidden active magmatic processes in combination with earthquake swarm seismicity ca. 20-30 km north of the Mytina maar, reconstruction of the palaeovolcanological evolution is important for evaluation of hazard potential of the NE and E Part of the Cheb Basin.},
  language  = {en}
}
@article{MitzscherlingHornWinterfeldetal.2019,
  author    = {Mitzscherling, Julia and Horn, Fabian and Winterfeld, Maria and Mahler, Linda and Kallmeyer, Jens and Overduin, Pier Paul and Schirrmeister, Lutz and Winkel, Matthias and Grigoriev, Mikhail N. and Wagner, Dirk and Liebner, Susanne},
  title     = {Microbial community composition and abundance after millennia of submarine permafrost warming},
  series = {Biogeosciences},
  volume    = {16},
  journal   = {Biogeosciences},
  number    = {19},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-16-3941-2019},
  pages     = {3941 -- 3958},
  year      = {2019},
  abstract  = {Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 degrees C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore-offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 degrees C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes delta O-18 and delta D, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 degrees C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.},
  language  = {en}
}
@article{LappeKallmeyer2011,
  author    = {Lappe, Michael and Kallmeyer, Jens},
  title     = {A cell extraction method for oily sediments},
  series = {Frontiers in microbiology},
  volume    = {2},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2011.00233},
  pages     = {11},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@article{KallmeyerSmith2009,
  author    = {Kallmeyer, Jens and Smith, David C.},
  title     = {An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts},
  issn      = {0168-6496},
  doi       = {10.1111/j.1574-6941.2009.00684.x},
  year      = {2009},
  abstract  = {We present a method for the rapid and simple extraction of DNA from marine sediments using electroelution. It effectively separates DNA from compounds, including humic substances, that interfere with subsequent DNA quantification and amplification. After extraction of the DNA from the sediment into an aqueous solution, the crude sample is encased in 2\% agarose gel and exposed to an electrical current, which draws the DNA out of the gel into a centrifugal filter vial. After electroelution, the sample is centrifuged to remove contaminants <= 100 000 Da. Recovery of DNA using this method is quantitative and does not discriminate on the basis of size, as determined using DNA standards and DNA extracts from environmental samples. Amplification of DNA is considerably improved due to removal of PCR inhibitors. For Archaea, only these purified extracts yielded PCR products. This method allows for the use of relatively large volumes of sediment and is particularly useful for sediments containing low biomass such as deeply buried marine sediments. It works with both organic-rich and -poor sediment, as well as with sediment where calcium carbonate is abundant and sediment where it is limited; consequently, adjustment of protocols is unnecessary for samples with very different organic and mineral contents.},
  language  = {en}
}
@article{KallmeyerPockalnyAdhikarietal.2012,
  author    = {Kallmeyer, Jens and Pockalny, Robert and Adhikari, Rishi Ram and Smith, David C. and D'Hondt, Steven},
  title     = {Global distribution of microbial abundance and biomass in subseafloor sediment},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {109},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {40},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1203849109},
  pages     = {16213 -- 16216},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@article{KallmeyerPockalnyD'Hondt2009,
  author    = {Kallmeyer, Jens and Pockalny, Rob and D'Hondt, Steven},
  title     = {Quantifying global subseafloor microbial abundance : method and implications},
  issn      = {0016-7037},
  doi       = {10.1016/j.gca.2009.05.009},
  year      = {2009},
  language  = {en}
}
@article{KallmeyerGreweGlombitzaetal.2015,
  author    = {Kallmeyer, Jens and Grewe, Sina and Glombitza, Clemens and Kitte, J. Axel},
  title     = {Microbial abundance in lacustrine sediments: a case study from Lake Van, Turkey},
  series = {International journal of earth sciences},
  volume    = {104},
  journal   = {International journal of earth sciences},
  number    = {6},
  publisher = {Springer},
  address   = {New York},
  issn      = {1437-3254},
  doi       = {10.1007/s00531-015-1219-6},
  pages     = {1667 -- 1677},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@misc{KallmeyerGreweGlombitzaetal.2015,
  author    = {Kallmeyer, Jens and Grewe, Sina and Glombitza, Clemens and Kitte, J. Axel},
  title     = {Microbial abundance in lacustrine sediments},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {723},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42982},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429828},
  pages     = {1667 -- 1677},
  year      = {2015},
  abstract  = {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.},
  language  = {en}
}
@misc{Kallmeyer2011,
  author    = {Kallmeyer, Jens},
  title     = {Detection and quantification of microbial cells in subsurface sediments},
  series = {Advances in applied microbiology},
  volume    = {76},
  journal   = {Advances in applied microbiology},
  editor    = {Laskin, AI and Sariaslani, S and Gadd, GM},
  publisher = {Elsevier},
  address   = {San Diego},
  isbn      = {978-0-12-387048-3},
  issn      = {0065-2164},
  doi       = {10.1016/B978-0-12-387048-3.00003-9},
  pages     = {79 -- 103},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{IjiriInagakiKuboetal.2018,
  author    = {Ijiri, Akira and Inagaki, Fumio and Kubo, Yusuke and Adhikari, Rishi Ram and Hattori, Shohei and Hoshino, Tatsuhiko and Imachi, Hiroyuki and Kawagucci, Shinsuke and Morono, Yuki and Ohtomo, Yoko and Ono, Shuhei and Sakai, Sanae and Takai, Ken and Toki, Tomohiro and Wang, David T. and Yoshinaga, Marcos Y. and Arnold, Gail L. and Ashi, Juichiro and Case, David H. and Feseker, Tomas and Hinrichs, Kai-Uwe and Ikegawa, Yojiro and Ikehara, Minoru and Kallmeyer, Jens and Kumagai, Hidenori and Lever, Mark Alexander and Morita, Sumito and Nakamura, Ko-ichi and Nakamura, Yuki and Nishizawa, Manabu and Orphan, Victoria J. and R{\o}y, Hans and Schmidt, Frauke and Tani, Atsushi and Tanikawa, Wataru and Terada, Takeshi and Tomaru, Hitoshi and Tsuji, Takeshi and Tsunogai, Urumu and Yamaguchi, Yasuhiko T. and Yoshida, Naohiro},
  title     = {Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {802},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42700},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427002},
  pages     = {16},
  year      = {2018},
  abstract  = {Microbial life inhabiting subseafloor sediments plays an important role in Earth's carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90\% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (10 2 to 10 3 cells cm -3 ) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated.},
  language  = {en}
}
@article{IjiriInagakiKuboetal.2018,
  author    = {Ijiri, Akira and Inagaki, Fumio and Kubo, Yusuke and Adhikari, Rishi Ram and Hattori, Shohei and Hoshino, Tatsuhiko and Imachi, Hiroyuki and Kawagucci, Shinsuke and Morono, Yuki and Ohtomo, Yoko and Ono, Shuhei and Sakai, Sanae and Takai, Ken and Toki, Tomohiro and Wang, David T. and Yoshinaga, Marcos Y. and Arnold, Gail L. and Ashi, Juichiro and Case, David H. and Feseker, Tomas and Hinrichs, Kai-Uwe and Ikegawa, Yojiro and Ikehara, Minoru and Kallmeyer, Jens and Kumagai, Hidenori and Lever, Mark Alexander and Morita, Sumito and Nakamura, Ko-ichi and Nakamura, Yuki and Nishizawa, Manabu and Orphan, Victoria J. and Roy, Hans and Schmidt, Frauke and Tani, Atsushi and Tanikawa, Wataru and Terada, Takeshi and Tomaru, Hitoshi and Tsuji, Takeshi and Tsunogai, Urumu and Yamaguchi, Yasuhiko T. and Yoshida, Naohiro},
  title     = {Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex},
  series = {Science Advances},
  volume    = {4},
  journal   = {Science Advances},
  number    = {6},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {2375-2548},
  doi       = {10.1126/sciadv.aao4631},
  pages     = {15},
  year      = {2018},
  language  = {en}
}
@article{GreenSaxenaFeyzullayevHubertetal.2012,
  author    = {Green-Saxena, A. and Feyzullayev, A. and Hubert, C. R. J. and Kallmeyer, Jens and Krueger, M. and Sauer, P. and Schulz, Hans-Martin and Orphan, V. J.},
  title     = {Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan},
  series = {Environmental microbiology},
  volume    = {14},
  journal   = {Environmental microbiology},
  number    = {12},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {1462-2912},
  doi       = {10.1111/1462-2920.12015},
  pages     = {3271 -- 3286},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}