Publications by authors named "Clemens Glombitza"

18 Publications

  • Page 1 of 1

Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment.

Commun Biol 2021 08 25;4(1):1006. Epub 2021 Aug 25.

Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.

Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below.
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http://dx.doi.org/10.1038/s42003-021-02507-1DOI Listing
August 2021

Response to substrate limitation by a marine sulfate-reducing bacterium.

ISME J 2021 Jul 20. Epub 2021 Jul 20.

Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark.

Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (K) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the K for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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http://dx.doi.org/10.1038/s41396-021-01061-2DOI Listing
July 2021

Organic matter mineralization in modern and ancient ferruginous sediments.

Nat Commun 2021 04 13;12(1):2216. Epub 2021 Apr 13.

GFZ German Research Centre for Geosciences, Potsdam, Germany.

Deposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite highly abundant reactive ferric iron phases like goethite that persist throughout the sediment. Ferric iron can thus be buried over geologic timescales even in the presence of labile organic carbon. Coexistence of ferric iron with millimolar concentrations of methane further demonstrates lack of iron-dependent methane oxidation. With negligible methane oxidation, methane diffuses from the sediment into overlying waters where it can be oxidized with oxygen or escape to the atmosphere. In low-oxygen ferruginous Archaean and Proterozoic oceans, therefore, sedimentary methane production was likely favored with strong potential to influence Earth's early climate.
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http://dx.doi.org/10.1038/s41467-021-22453-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044167PMC
April 2021

Temperature limits to deep subseafloor life in the Nankai Trough subduction zone.

Science 2020 12;370(6521):1230-1234

Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.
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http://dx.doi.org/10.1126/science.abd7934DOI Listing
December 2020

Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment.

ISME J 2021 03 18;15(3):833-847. Epub 2020 Nov 18.

Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.

Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.
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http://dx.doi.org/10.1038/s41396-020-00817-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027456PMC
March 2021

Macrofaunal control of microbial community structure in continental margin sediments.

Proc Natl Acad Sci U S A 2020 07 23;117(27):15911-15922. Epub 2020 Jun 23.

Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule Zürich, 8092 Zürich, Switzerland;

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.
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http://dx.doi.org/10.1073/pnas.1917494117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376573PMC
July 2020

Origin of Short-Chain Organic Acids in Serpentinite Mud Volcanoes of the Mariana Convergent Margin.

Front Microbiol 2019 26;10:1729. Epub 2019 Jul 26.

Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland.

Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H), methane (CH), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δC-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.
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http://dx.doi.org/10.3389/fmicb.2019.01729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677109PMC
July 2019

Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and Geochemistry.

Appl Environ Microbiol 2019 02 6;85(4). Epub 2019 Feb 6.

Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, Texas, USA

Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities. Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.
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http://dx.doi.org/10.1128/AEM.02164-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365825PMC
February 2019

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment.

Environ Microbiol 2018 08 3;20(8):2927-2940. Epub 2018 Sep 3.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria.

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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http://dx.doi.org/10.1111/1462-2920.14297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175234PMC
August 2018

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

Front Microbiol 2018 15;9:967. Epub 2018 May 15.

Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 10 to 10 cells cm within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 10 cells cm throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %TC (percentage of total organic carbon present as amino acid carbon), %TN (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.
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http://dx.doi.org/10.3389/fmicb.2018.00967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963217PMC
May 2018

Microbially Mediated Coupling of Fe and N Cycles by Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Littoral Freshwater Sediments.

Appl Environ Microbiol 2018 01 2;84(2). Epub 2018 Jan 2.

Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Germany

Nitrate-reducing iron(II)-oxidizing bacteria have been known for approximately 20 years. There has been much debate as to what extent the reduction of nitrate and the oxidation of ferrous iron are coupled via enzymatic pathways or via abiotic processes induced by nitrite formed by heterotrophic denitrification. The aim of the present study was to assess the coupling of nitrate reduction and iron(II) oxidation by monitoring changes in substrate concentrations, as well as in the activity of nitrate-reducing bacteria in natural littoral freshwater sediment, in response to stimulation with nitrate and iron(II). In substrate-amended microcosms, we found that the biotic oxidation of ferrous iron depended on the simultaneous microbial reduction of nitrate. Additionally, the abiotic oxidation of ferrous iron by nitrite in sterilized sediment was not fast enough to explain the iron oxidation rates observed in microbially active sediment. Furthermore, the expression levels of genes coding for enzymes crucial for nitrate reduction were in some setups stimulated by the presence of ferrous iron. These results indicate that there is a direct influence of ferrous iron on bacterial denitrification and support the hypothesis that microbial nitrate reduction is stimulated by biotic iron(II) oxidation. The coupling of nitrate reduction and Fe(II) oxidation affects the environment at a local scale, e.g., by changing nutrient or heavy metal mobility in soils due to the formation of Fe(III) minerals, as well as at a global scale, e.g., by the formation of the primary greenhouse gas nitrous oxide. Although the coupling of nitrate reduction and Fe(II) oxidation was reported 20 years ago and has been studied intensively since then, the underlying mechanisms still remain unknown. One of the main knowledge gaps is the extent of enzymatic Fe(II) oxidation coupled to nitrate reduction, which has frequently been questioned in the literature. In the present study, we provide evidence for microbially mediated nitrate-reducing Fe(II) oxidation in freshwater sediments. This evidence is based on the rates of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and on the effect of iron on the expression of genes required for denitrification.
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http://dx.doi.org/10.1128/AEM.02013-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5752864PMC
January 2018

Microbial Sulfate Reduction Potential in Coal-Bearing Sediments Down to ~2.5 km below the Seafloor off Shimokita Peninsula, Japan.

Front Microbiol 2016 5;7:1576. Epub 2016 Oct 5.

Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and TechnologyKochi, Japan; Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and TechnologyYokohama, Japan; Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan.

Sulfate reduction is the predominant anaerobic microbial process of organic matter mineralization in marine sediments, with recent studies revealing that sulfate reduction not only occurs in sulfate-rich sediments, but even extends to deeper, methanogenic sediments at very low background concentrations of sulfate. Using samples retrieved off the Shimokita Peninsula, Japan, during the Integrated Ocean Drilling Program (IODP) Expedition 337, we measured potential sulfate reduction rates by slurry incubations with S-labeled sulfate in deep methanogenic sediments between 1276.75 and 2456.75 meters below the seafloor. Potential sulfate reduction rates were generally extremely low (mostly below 0.1 pmol cm d) but showed elevated values (up to 1.8 pmol cm d) in a coal-bearing interval (Unit III). A measured increase in hydrogenase activity in the coal-bearing horizons coincided with this local increase in potential sulfate reduction rates. This paired enzymatic response suggests that hydrogen is a potentially important electron donor for sulfate reduction in the deep coalbed biosphere. By contrast, no stimulation of sulfate reduction rates was observed in treatments where methane was added as an electron donor. In the deep coalbeds, small amounts of sulfate might be provided by a cryptic sulfur cycle. The isotopically very heavy pyrites (δS = +43‰) found in this horizon is consistent with its formation via microbial sulfate reduction that has been continuously utilizing a small, increasingly S-enriched sulfate reservoir over geologic time scales. Although our results do not represent activity, and the sulfate reducers might only have persisted in a dormant, spore-like state, our findings show that organisms capable of sulfate reduction have survived in deep methanogenic sediments over more than 20 Ma. This highlights the ability of sulfate-reducers to persist over geological timespans even in sulfate-depleted environments. Our study moreover represents the deepest evidence of a potential for sulfate reduction in marine sediments to date.
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http://dx.doi.org/10.3389/fmicb.2016.01576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051215PMC
October 2016

Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content.

Environ Microbiol 2016 09 27;18(9):3159-74. Epub 2016 Jun 27.

Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Tuebingen, Germany.

Coastal marine sediments contain varying concentrations of iron, oxygen, nitrate and organic carbon. It is unknown how organic carbon content influences the activity of nitrate-reducing and phototrophic Fe(II)-oxidizers and microbial Fe-redox cycling in such sediments. Therefore, microcosms were prepared with two coastal marine sediments (Kalø Vig and Norsminde Fjord at Aarhus Bay, Denmark) varying in TOC from 0.4 to 3.0 wt%. The microcosms were incubated under light/dark conditions with/without addition of nitrate and/or Fe(II). Although most probable number (MPN) counts of phototrophic Fe(II)-oxidizers were five times lower in the low-TOC sediment, phototrophic Fe(II) oxidation rates were higher compared with the high-TOC sediment. Fe(III)-amended microcosms showed that this lower net Fe(II) oxidation in the high-TOC sediment is caused by concurrent bacterial Fe(III) reduction. In contrast, MPN counts of nitrate-reducing Fe(II)-oxidizers and net rates of nitrate-reducing Fe(II) oxidation were comparable in low- and high-TOC sediments. However, the ratio of nitratereduced :iron(II)oxidized was higher in the high-TOC sediment, suggesting that a part of the nitrate was reduced by mixotrophic nitrate-reducing Fe(II)-oxidizers and chemoorganoheterotrophic nitrate-reducers. Our results demonstrate that dynamic microbial Fe cycling occurs in these sediments and that the extent of Fe cycling is dependent on organic carbon content.
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http://dx.doi.org/10.1111/1462-2920.13387DOI Listing
September 2016

Hydrogen Utilization Potential in Subsurface Sediments.

Front Microbiol 2016 26;7. Epub 2016 Jan 26.

Geomicrobiology Group, Institute of Earth and Environmental Science, University of PotsdamPotsdam, Germany; Helmholtz-Centre Potsdam - GFZ German Research Centre for GeosciencesPotsdam, Germany.

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 H2ases to successively higher concentrations of H2 in successively deeper zones.
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http://dx.doi.org/10.3389/fmicb.2016.00008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726784PMC
February 2016

Formate, acetate, and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland.

Front Microbiol 2015 24;6:846. Epub 2015 Aug 24.

Department of Bioscience, Center for Geomicrobiology, Aarhus University Aarhus, Denmark.

Volatile fatty acids (VFAs) are key intermediates in the anaerobic mineralization of organic matter in marine sediments. We studied the role of VFAs in the carbon and energy turnover in the sulfate reduction zone of sediments from the sub-arctic Godthåbsfjord (SW Greenland) and the adjacent continental shelf in the NE Labrador Sea. VFA porewater concentrations were measured by a new two-dimensional ion chromatography-mass spectrometry method that enabled the direct analysis of VFAs without sample pretreatment. VFA concentrations were low and surprisingly constant (4-6 μmol L(-1) for formate and acetate, and 0.5 μmol L(-1) for propionate) throughout the sulfate reduction zone. Hence, VFAs are turned over while maintaining a stable concentration that is suggested to be under a strong microbial control. Estimated mean diffusion times of acetate between neighboring cells were <1 s, whereas VFA turnover times increased from several hours at the sediment surface to several years at the bottom of the sulfate reduction zone. Thus, diffusion was not limiting the VFA turnover. Despite constant VFA concentrations, the Gibbs energies (ΔGr) of VFA-dependent sulfate reduction decreased downcore, from -28 to -16 kJ (mol formate)(-1), -68 to -31 kJ (mol acetate)(-1), and -124 to -65 kJ (mol propionate)(-1). Thus, ΔGr is apparently not determining the in-situ VFA concentrations directly. However, at the bottom of the sulfate zone of the shelf station, acetoclastic sulfate reduction might operate at its energetic limit at ~ -30 kJ (mol acetate)(-1). It is not clear what controls VFA concentrations in the porewater but cell physiological constraints such as energetic costs of VFA activation or uptake could be important. We suggest that such constraints control the substrate turnover and result in a minimum ΔGr that depends on cell physiology and is different for individual substrates.
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http://dx.doi.org/10.3389/fmicb.2015.00846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547046PMC
September 2015

Sulfate reduction controlled by organic matter availability in deep sediment cores from the saline, alkaline Lake Van (Eastern Anatolia, Turkey).

Front Microbiol 2013 29;4:209. Epub 2013 Jul 29.

Geomicrobiology Group, Institute of Earth and Environmental Sciences, University of Potsdam Potsdam, Germany.

As part of the International Continental Drilling Program deep lake drilling project PaleoVan, we investigated sulfate reduction (SR) in deep sediment cores of the saline, alkaline (salinity 21.4‰, alkalinity 155 m mEq(-1), pH 9.81) Lake Van, Turkey. The cores were retrieved in the Northern Basin (NB) and at Ahlat Ridge (AR) and reached a maximum depth of 220 m. Additionally, 65-75 cm long gravity cores were taken at both sites. SR rates (SRR) were low (≤22 nmol cm(-3) day(-1)) compared to lakes with higher salinity and alkalinity, indicating that salinity and alkalinity are not limiting SR in Lake Van. Both sites differ significantly in rates and depth distribution of SR. In NB, SRR are up to 10 times higher than at AR. SR could be detected down to 19 mblf (meters below lake floor) at NB and down to 13 mblf at AR. Although SRR were lower at AR than at NB, organic matter (OM) concentrations were higher. In contrast, dissolved OM in the pore water at AR contained more macromolecular OM and less low molecular weight OM. We thus suggest, that OM content alone cannot be used to infer microbial activity at Lake Van but that quality of OM has an important impact as well. These differences suggest that biogeochemical processes in lacustrine sediments are reacting very sensitively to small variations in geological, physical, or chemical parameters over relatively short distances.
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http://dx.doi.org/10.3389/fmicb.2013.00209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725400PMC
August 2013

A system for incubations at high gas partial pressure.

Front Microbiol 2012 3;3:25. Epub 2012 Feb 3.

Geomicrobiology Group, Institute for Earth and Environmental Sciences, University of Potsdam Potsdam, Germany.

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°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 custom-made 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 H(2)O as well as a H(2)O-CO(2) mixture at elevated temperature (90°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.
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http://dx.doi.org/10.3389/fmicb.2012.00025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271276PMC
October 2012

Photochemical preparation of highly functionalized 1-indanones.

J Org Chem 2004 Oct;69(22):7582-91

Institut für Chemie, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany.

A series of o-alkylphenyl alkyl ketones 1 were synthesized by different methods. The presence of a leaving group X adjacent to the carbonyl group is the special peculiarity of these ketones. Upon irradiation the keto carbonyl group of these compounds undergoes an n-pi* excitation followed by a 1,5-hydrogen migration from the o-alkyl substituent to the carbonyl oxygen atom. The thus formed 1,4-diradicals are subject to a very rapid elimination of acid HX, giving 1,5-diradicals. We called this process spin center shift. After intersystem crossing these diradicals cyclize to 1-indanones 20 in good yields. Depending on the solvent and on substituents, o-alkoxyalkyl ketones 22 or benzo[c]furanes 21 are obtained as byproducts. The mechanism of the cyclization was elucidated by quantum chemical calculations and kinetic measurements.
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http://dx.doi.org/10.1021/jo040173xDOI Listing
October 2004
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