TY - JOUR A1 - Lipus, Daniel A1 - Jia, Zeyu A1 - Bartholomäus, Alexander A1 - Burckhardt, Oliver A1 - Sondermann, Megan A1 - Wagner, Dirk A1 - Kallmeyer, Jens T1 - Circular metagenome-assembled genome of Methanobacterium sp. strain ERen5, a putative methanogenic, H2-utilizing terrestrial subsurface archaeon JF - Microbiology Resource Announcements N2 - A circular, single-contig Methanobacterium sp. metagenome-assembled genome (MAG) was recovered from high-CO2 enrichments inoculated with drill core material from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered MAG highlighted putative methanogenesis genes, providing valuable information on archaeal activity in the deep biosphere. Y1 - 2022 U6 - https://doi.org/10.1128/mra.00676-22 SN - 2576-098X VL - 11 IS - 10 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Jia, Zeyu A1 - Lipus, Daniel A1 - Bartholomaeus, Alexander A1 - Burckhardt, Oliver A1 - Sondermann, Megan A1 - Wagner, Dirk A1 - Kallmeyer, Jens T1 - Metagenome-assembled genome of a putative methanogenic Methanosarcina sp. strain enriched from terrestrial high-CO2 subsurface sediments JF - Microbiology Resource Announcements N2 - A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H-2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere. A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H-2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere. Y1 - 2022 U6 - https://doi.org/10.1128/mra.01039-22 SN - 2576-098X VL - 11 IS - 12 PB - American Society for Microbiology CY - Washington 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 - TY - JOUR A1 - Fischer, Tomáš A1 - Hrubcova, Pavla A1 - Dahm, Torsten A1 - Woith, Heiko A1 - Vylita, Tomáš A1 - Ohrnberger, Matthias A1 - Vlček, Josef A1 - Horalek, Josef A1 - Dedecek, Petr A1 - Zimmer, Martin A1 - Lipus, Martin P. A1 - Pierdominici, Simona A1 - Kallmeyer, Jens A1 - Krüger, Frank A1 - Hannemann, Katrin A1 - Korn, Michael A1 - Kaempf, Horst A1 - Reinsch, Thomas A1 - Klicpera, Jakub A1 - Vollmer, Daniel A1 - Daskalopoulou, Kyriaki T1 - ICDP drilling of the Eger Rift observatory BT - magmatic fluids driving the earthquake swarms and deep biosphere JF - Scientific drilling : reports on deep earth sampling and monitoring N2 - 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. Y1 - 2022 U6 - https://doi.org/10.5194/sd-31-31-2022 SN - 1816-8957 SN - 1816-3459 VL - 31 SP - 31 EP - 49 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Fischer, Tomas A1 - Hrubcova, Pavla A1 - Dahm, Torsten A1 - Woith, Heiko A1 - Vylita, Tomas A1 - Ohrnberger, Matthias A1 - Vlcek, Josef A1 - Horalek, Josef A1 - Dedecek, Petr A1 - Zimmer, Martin A1 - Lipus, Martin P. A1 - Pierdominici, Simona A1 - Kallmeyer, Jens A1 - Krüger, Frank A1 - Hannemann, Katrin A1 - Korn, Michael A1 - Kämpf, Horst A1 - Reinsch, Thomas A1 - Klicpera, Jakub A1 - Vollmer, Daniel A1 - Daskalopoulou, Kyriaki T1 - ICDP drilling of the Eger Rift observatory BT - magmatic fluids driving the earthquake swarms and deep biosphere JF - Scientific Drilling N2 - 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. Y1 - 2022 U6 - https://doi.org/10.5194/sd-31-31-2022 SN - 1816-8957 SN - 1816-3459 VL - 31 SP - 31 EP - 49 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Nagakura, Toshiki A1 - Schubert, Florian A1 - Wagner, Dirk A1 - Kallmeyer, Jens T1 - Biological sulfate reduction in deep subseafloor sediment of Guaymas Basin JF - Frontiers in microbiology N2 - 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. KW - sulfate reduction KW - subsurface life KW - deep biosphere KW - thermophiles; KW - Guaymas Basin Y1 - 2022 U6 - https://doi.org/10.3389/fmicb.2022.845250 SN - 1664-302X VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Ijiri, Akira A1 - Inagaki, Fumio A1 - Kubo, Yusuke A1 - Adhikari, Rishi Ram A1 - Hattori, Shohei A1 - Hoshino, Tatsuhiko A1 - Imachi, Hiroyuki A1 - Kawagucci, Shinsuke A1 - Morono, Yuki A1 - Ohtomo, Yoko A1 - Ono, Shuhei A1 - Sakai, Sanae A1 - Takai, Ken A1 - Toki, Tomohiro A1 - Wang, David T. A1 - Yoshinaga, Marcos Y. A1 - Arnold, Gail L. A1 - Ashi, Juichiro A1 - Case, David H. A1 - Feseker, Tomas A1 - Hinrichs, Kai-Uwe A1 - Ikegawa, Yojiro A1 - Ikehara, Minoru A1 - Kallmeyer, Jens A1 - Kumagai, Hidenori A1 - Lever, Mark Alexander A1 - Morita, Sumito A1 - Nakamura, Ko-ichi A1 - Nakamura, Yuki A1 - Nishizawa, Manabu A1 - Orphan, Victoria J. A1 - Roy, Hans A1 - Schmidt, Frauke A1 - Tani, Atsushi A1 - Tanikawa, Wataru A1 - Terada, Takeshi A1 - Tomaru, Hitoshi A1 - Tsuji, Takeshi A1 - Tsunogai, Urumu A1 - Yamaguchi, Yasuhiko T. A1 - Yoshida, Naohiro T1 - Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex JF - Science Advances Y1 - 2018 U6 - https://doi.org/10.1126/sciadv.aao4631 SN - 2375-2548 VL - 4 IS - 6 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Vuillemin, Aurele A1 - Horn, Fabian A1 - Friese, Andre A1 - Winkel, Matthias A1 - Alawi, Mashal A1 - Wagner, Dirk A1 - Henny, Cynthia A1 - Orsi, William D. A1 - Crowe, Sean A. A1 - Kallmeyer, Jens T1 - Metabolic potential of microbial communities from ferruginous sediments JF - Environmental microbiology N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1111/1462-2920.14343 SN - 1462-2912 SN - 1462-2920 VL - 20 IS - 12 SP - 4297 EP - 4313 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Mitzscherling, Julia A1 - Horn, Fabian A1 - Winterfeld, Maria A1 - Mahler, Linda A1 - Kallmeyer, Jens A1 - Overduin, Pier Paul A1 - Schirrmeister, Lutz A1 - Winkel, Matthias A1 - Grigoriev, Mikhail N. A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Microbial community composition and abundance after millennia of submarine permafrost warming JF - Biogeosciences N2 - 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. Y1 - 2019 U6 - https://doi.org/10.5194/bg-16-3941-2019 SN - 1726-4170 SN - 1726-4189 VL - 16 IS - 19 SP - 3941 EP - 3958 PB - Copernicus CY - Göttingen 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 -