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 - GEN A1 - Vuillemin, Aurèle A1 - Friese, André A1 - Alawi, Mashal A1 - Henny, Cynthia A1 - Nomosatryo, Sulung A1 - Wagner, Dirk A1 - Crowe, Sean A. A1 - Kallmeyer, Jens T1 - Geomicrobiological features of ferruginous sediments from Lake Towuti, Indonesia T2 - Frontiers in microbiology N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 440 KW - bottom waters KW - iron-rich sediment KW - sedimentary microbes KW - extracellular DNA KW - sulfate reduction KW - iron reduction KW - Lake Towuti Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407312 ER - TY - JOUR A1 - Krauze, Patryk A1 - Kämpf, Horst A1 - Horn, Fabian A1 - Liu, Qi A1 - Voropaev, Andrey A1 - Wagner, Dirk A1 - Alawi, Mashal T1 - Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic JF - Frontiers in microbiology N2 - The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments. KW - elevated CO2 concentration KW - microbial ecology KW - deep biosphere KW - Eger Rift KW - paleo-sediment KW - Sulfuricurvum KW - Gallionella KW - Sideroxydans Y1 - 2017 U6 - https://doi.org/10.3389/fmicb.2017.02446 SN - 1664-302X VL - 8 PB - Frontiers Research Foundation CY - Lausanne 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 - GEN A1 - Liu, Qi A1 - Kämpf, Horst A1 - Bussert, Robert A1 - Krauze, Patryk A1 - Horn, Fabian A1 - Nickschick, Tobias A1 - Plessen, Birgit A1 - Wagner, Dirk A1 - Alawi, Mashal T1 - Influence of CO2 degassing on the microbial community in a dry mofette field in Hartoušov, Czech Republic (Western Eger Rift) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartousov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km(2) and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumine MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1100 KW - geo-bio interaction KW - elevated CO2 concentration KW - paleo-sediment KW - deep biosphere KW - acidophilic microorganisms KW - Acidobactetiaceae KW - Acidithiobacillus KW - Acidothermus Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-471153 SN - 1866-8372 IS - 1100 ER - TY - GEN A1 - Genderjahn, Steffi A1 - Alawi, Mashal A1 - Mangelsdorf, Kai A1 - Horn, Fabian A1 - Wagner, Dirk T1 - Desiccation- and saline-tolerant bacteria and archaea in Kalahari pan sediments T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 993 KW - saline pan KW - Kalahari KW - Halobacteria KW - Gemmatimonadetes KW - Firmicutes Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459154 SN - 1866-8372 IS - 993 ER - TY - JOUR A1 - Genderjahn, Steffi A1 - Alawi, Mashal A1 - Mangelsdorf, Kai A1 - Horn, Fabian A1 - Wagner, Dirk T1 - Desiccation- and saline-solerant bacteria and archaea in kalahari an sediments JF - Frontiers in microbiology N2 - More than 41% of the Earth’s land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan. KW - saline pan KW - Kalahari KW - Halobacteria KW - Gemmatimonadetes KW - Firmicutes Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.02082 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Liu, Qi A1 - Kämpf, Horst A1 - Bussert, Robert A1 - Krauze, Patryk A1 - Horn, Fabian A1 - Nickschick, Tobias A1 - Plessen, Birgit A1 - Wagner, Dirk A1 - Alawi, Mashal T1 - Influence of CO2 degassing on the microbial community in a dry mofette field in Hartoušov, Czech Republic (Western Eger Rift) JF - Frontiers in Microbiology N2 - The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartousov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km(2) and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumine MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites. KW - geo–bio interaction KW - elevated CO2 KW - concentration KW - paleo-sediment KW - deep biosphere KW - acidophilic microorganisms KW - Acidobacteriaceae KW - Acidithiobacillus KW - Acidothermus Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.02787 SN - 1664-302X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Genderjahn, Steffi A1 - Alawi, Mashal A1 - Wagner, Dirk A1 - Schueller, I. A1 - Wanke, A. A1 - Mangelsdorf, Kai T1 - Microbial community responses to modern environmental and Past Climatic Conditions in Omongwa Pan, Western Kalahari BT - a paired 16S rRNA Gene profiling and lipid biomarker approach JF - Journal of geophysical research : Biogeosciences N2 - Due to a lack of well-preserved terrestrial climate archives, paleoclimate studies are sparse in southwestern Africa. Because there are no perennial lacustrine systems in this region, this study relies on a saline pan as an archive for climate information in the western Kalahari (Namibia). Molecular biological and biogeochemical analyses were combined to examine the response of indigenous microbial communities to modern and past climate-induced environmental conditions. The 16S rRNA gene high-throughput sequencing was applied to sediment samples from Omongwa pan to characterize the modern microbial diversity. Highest diversity of microorganisms, dominated by the extreme halophilic archaeon Halobacteria and by the bacterial phylum Gemmatimonadetes, was detected in the near-surface sediments of Omongwa pan. In deeper sections abundance and diversity significantly decreases and Bacillus, known to form spores, become dominant. Lipid biomarkers for living and past microbial life were analyzed to track the influence of climate variation on the abundance of microbial communities from the Last Glacial Maximum to Holocene time. Since water is an inevitable requirement for microbial life, in this dry region the abundance of past microbial biomarkers was evaluated to conclude on periods of increased paleoprecipitation in the past. The data point to a period of increased humidity in the western Kalahari during the Last Glacial to Holocene transition indicating a southward shift of the Intertropical Convergence Zone during this period. Comparison with results from a southwestern Kalahari pan suggests complex displacements of the regional atmospheric systems since the Last Glacial Maximum. Y1 - 2018 U6 - https://doi.org/10.1002/2017JG004098 SN - 2169-8953 SN - 2169-8961 VL - 123 IS - 4 SP - 1333 EP - 1351 PB - American Geophysical Union CY - Washington ER - TY - JOUR A1 - Serrano, Paloma A1 - Alawi, Mashal A1 - de Vera, Jean-Pierre Paul A1 - Wagner, Dirk T1 - Response of Methanogenic Archaea from Siberian Permafrost and Non-permafrost Environments to Simulated Mars-like Desiccation and the Presence of Perchlorate JF - Astrobiology N2 - Numerous preflight investigations were necessary prior to the exposure experiment BIOMEX on the International Space Station to test the basic potential of selected microorganisms to resist or even to be active under Mars-like conditions. In this study, methanogenic archaea, which are anaerobic chemolithotrophic microorganisms whose lifestyle would allow metabolism under the conditions on early and recent Mars, were analyzed. Some strains from Siberian permafrost environments have shown a particular resistance. In this investigation, we analyzed the response of three permafrost strains (Methanosarcina soligelidi SMA-21, Candidatus Methanosarcina SMA-17, Candidatus Methanobacterium SMA-27) and two related strains from non-permafrost environments (Methanosarcina mazei, Methanosarcina barkeri) to desiccation conditions (-80 degrees C for 315 days, martian regolith analog simulants S-MRS and P-MRS, a 128-day period of simulated Mars-like atmosphere). Exposure of the different methanogenic strains to increasing concentrations of magnesium perchlorate allowed for the study of their metabolic shutdown in a Mars-relevant perchlorate environment. Survival and metabolic recovery were analyzed by quantitative PCR, gas chromatography, and a new DNA-extraction method from viable cells embedded in S-MRS and P-MRS. All strains survived the two Mars-like desiccating scenarios and recovered to different extents. The permafrost strain SMA-27 showed an increased methanogenic activity by at least 10-fold after deep-freezing conditions. The methanogenic rates of all strains did not decrease significantly after 128 days S-MRS exposure, except for SMA-27, which decreased 10-fold. The activity of strains SMA-17 and SMA-27 decreased after 16 and 60 days P-MRS exposure. Non-permafrost strains showed constant survival and methane production when exposed to both desiccating scenarios. All strains showed unaltered methane production when exposed to the perchlorate concentration reported at the Phoenix landing site (2.4 mM) or even higher concentrations. We conclude that methanogens from (non-)permafrost environments are suitable candidates for potential life in the martian subsurface and therefore are worthy of study after space exposure experiments that approach Mars-like surface conditions. KW - Methanogenic archaea KW - Simulated Mars-like conditions KW - Subfreezing temperatures KW - Martian regolith analogs KW - Perchlorate KW - Permafrost Y1 - 2019 U6 - https://doi.org/10.1089/ast.2018.1877 SN - 1531-1074 SN - 1557-8070 VL - 19 IS - 2 SP - 197 EP - 208 PB - Liebert CY - New Rochelle ER -