Clemens Glombitza

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Glombitza

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Clemens

ORCID

0000-0002-0938-2952

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Publications 1 - 10 of 14

Temperature limits to deep subseafloor life in the Nankai Trough subduction zone
Heuer, Verena B.; Inagaki, Fumio; Morono, Yuki; et al. (2020)
Science
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.
Methanogenesis by CO₂ reduction dominates lake sediments with different organic matter compositions
Su, Guangyi; Tolu, Julie; Glombitza, Clemens; et al. (2025)
Biogeosciences
Microbial methane production is a key reaction involved in the terminal step of anaerobic degradation of organic matter. The energy substrates of methane-producing microorganisms are largely generated during the breakdown of larger organic molecules by fermentative microorganisms, wherein the products of fermentation may vary with the chemical compositions of these larger molecules. Due to differences in energy substrates among methane-producing microorganisms, it is thus possible that organic matter compositional variations select for different communities of methane producers Here, we investigate the sources and compositions of OC in sediments of Lake Geneva and how both are potentially linked to methane production. Differences in dominant long-chain fatty acid abundances and carbon isotopic compositions suggest the predominance of diagenetically altered phytoplankton-derived OC at a profundal site (PS) and temporally highly variable sources of both aquatic and terrestrial OC in a deltaic location. Despite these differences, radiotracer-based methanogenesis rate measurements and stable isotopic signatures of methane indicate significant methane production that is dominated by CO₂ reduction (>95% of total methanogenesis) in both locations. Matching this interpretation, members of well-known CO₂-reducing Methanoregula sp. dominate both sites. Similarly, no clear effect of OC source on methane production rates was evident. Our data demonstrate that OC of diverse sources and diagenetic states supports microbial methane production, but the data do not indicate a clear impact of the OC source on the dominant methanogenic pathway or the community structure of methanogenic microorganisms in lacustrine sediments.
Active microbial sulfate reduction in fluids of serpentinizing peridotites of the continental subsurface
Glombitza, Clemens; Putman, Lindsay I.; Rempfert, Kaitlin R.; et al. (2021)
Communications Earth & Environment
Serpentinization of peridotites in Earth’s mantle is associated with the generation of hydrogen and low molecular weight organics that could support subsurface life. Studies of microbial metabolisms in peridotite-hosted environments have focused primarily on methanogenesis, yet DNA sequences, isotopic composition of sulfides and thermodynamic calculations suggest there is potential for microbial sulfate reduction too. Here, we use a sulfate radiotracer-based method to quantify microbial sulfate reduction rates in serpentinization fluids recovered from boreholes in the Samail Ophiolite, Oman and the California Coast Range Ophiolite, USA. We find that low levels of sulfate reduction occur at pH up to 12.3. These low levels could not be stimulated by addition of hydrogen, methane or small organic acids, which indicates that this metabolism is limited by factors other than substrate availability. Cellular activity drops at pH > 10.5 which suggests that high fluid pH exerts a strong control on sulfate-reducing organisms in peridotites.
Response to substrate limitation by a marine sulfate-reducing bacterium
Marietou, Angeliki; Kjeldsen, Kasper U.; Glombitza, Clemens; et al. (2022)
The ISME Journal
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 (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km 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−1 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.
Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment
Lagostina, Lorenzo; Frandsen, Søs; MacGregor, Barbara J.; et al. (2021)
Communications Biology
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.
A one-million-year isotope record from siderites formed in modern ferruginous sediments
Kallmeyer, Jens; Vuillemin, Aurèle; Mayr, Christoph; et al. (2023)
GSA Bulletin
Ancient iron formations hold important re-cords of environmental conditions during the Precambrian eons. Reconstructions of past oceanic systems require investigation of mod-ern ferruginous analogs to disentangle water column and diagenetic signals recorded in iron-bearing minerals. We analyzed oxy-gen, iron, and carbon isotopes in siderite, a ferrous carbonate phase commonly used as an environmental proxy, from a 100-m-long record spanning a 1 Ma depositional his-tory in ferruginous Lake Towuti, Indonesia. Combining bulk sediment and pore water geochemistry, we traced processes control-ling siderite isotope signatures. We show that siderite oxygen isotope compositions (delta 18O) reflect in-lake hydrological and depositional conditions. Low iron isotope values (delta 56Fe) record water column oxygenation events over geological timescales, with minor diage-netic partitioning of Fe isotopes by microbial iron reduction after deposition. The carbon isotope compositions (delta 13C) reflect the incor-poration of biogenic HCO3-, which is consis-tent with sediment organic matter reminer-alization lasting over ca. 200 ka after burial. Positive delta 13C excursions indicate an increased production of biogenic methane that escaped the sediment during low lake levels. Diffusion across the sediment-water interface during initial formation of siderites tends to align the isotope signatures of bottom waters to those of pore waters. As microbial reduction of ferric iron and oxidation of organic matter proceed and saturate pore water conditions with respect to siderite, overgrowth on nu-clei partially mutes the environmental signal inherited from past bottom waters over ca. 1 Ma. Because high depositional fluxes of fer-ric iron and organic matter in early oceans would have promoted similar microbial pro-cesses in ferruginous deposits prior to lithifi- cation, the environmental record contained in siderite grains can successively integrate depositional and early diagenetic signals over short geological timescales.
Accessing the subsurface biosphere within rocks undergoing active low‐temperature serpentinization in the Samail ophiolite (Oman Drilling Project)
Templeton, Alexis S.; Ellison, Eric T.; Glombitza, Clemens; et al. (2021)
Journal of Geophysical Research: Biogeosciences
The Oman Drilling Project established an “Active Alteration” multi-borehole observatory in peridotites undergoing low-temperature serpentinization in the Samail Ophiolite. The highly serpentinized rocks are in contact with strongly reducing fluids. Distinct hydrological regimes, governed by differences in rock porosity and fracture density, give rise to steep redox (Eh +200 to −750 mV) and pH (pH range 8.5–11.2) gradients within the 300–400 m deep boreholes. The serpentinites and fluids host an active subsurface ecosystem. Microbial cell abundances in serpentinite vary at least six orders of magnitude, from ≤3.5 × 101 to 2.9 × 107 cells/g. Low levels of biological sulfate reduction (2–1,000 fmol/cm3/day) can be detected in rock cores, particularly in rocks in contact with reduced groundwaters with pH < 10.5. Thermodesulfovibrio is the predominant sulfate reducer identified via metagenomic sequencing of adjacent groundwater communities. We infer that transport and reaction of microbially generated sulfide with the serpentine and brucite assemblages gives rise to optical darkening and sulfide overprinting, including the formation of tochilinite-vallerite group minerals, potentially serving as an indicator that this system is inhabited by microbial life. Olivine mesh-cores replaced with ferroan brucite and minor awaruite, abundant veins containing hydroandradite garnet and polyhedral serpentine, and late-stage carbonate veins are suggested as targets for future spatially resolved life-detection investigations. The high-quality whole-round core samples that have been preserved can be further probed to define how life distributes itself and functions within a system where chemical disequilibria are sustained by low-temperature water/rock interaction, and how biosignatures of in situ microbial activity are generated.
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment
Pelikan, Claus; Wasmund, Kenneth; Glombitza, Clemens; et al. (2021)
The ISME Journal
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 13C-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 13C-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.
Rapid metabolism fosters microbial survival in the deep, hot subseafloor biosphere
Beulig, Felix; Schubert, Florian; Adhikari, Rishi R.; et al. (2022)
Nature Communications
A fourth of the global seabed sediment volume is buried at depths where temperatures exceed 80 °C, a previously proposed thermal barrier for life in the subsurface. Here, we demonstrate, utilizing an extensive suite of radiotracer experiments, the prevalence of active methanogenic and sulfate-reducing populations in deeply buried marine sediment from the Nankai Trough subduction zone, heated to extreme temperature (up to ~120 °C). The small microbial community subsisted with high potential cell-specific rates of energy metabolism, which approach the rates of active surface sediments and laboratory cultures. Our discovery is in stark contrast to the extremely low metabolic rates otherwise observed in the deep subseafloor. As cells appear to invest most of their energy to repair thermal cell damage in the hot sediment, they are forced to balance delicately between subsistence near the upper temperature limit for life and a rich supply of substrates and energy from thermally driven reactions of the sedimentary organic matter.
Drivers of methane-cycling archaeal abundances, community structure, and catabolic pathways in continental margin sediments
Deng, Longhui; Bölsterli, Damian; Glombitza, Clemens; et al. (2025)
Frontiers in Microbiology
Marine sediments contain Earth's largest reservoir of methane, with most of this methane being produced and consumed in situ by methane-cycling archaea. While numerous studies have investigated communities of methane-cycling archaea in hydrocarbon seeps and sulfate-methane transition zones, less is known about how these archaea change from the seafloor downward throughout diffusion-dominated marine sediments. Focusing on four continental margin sites of the North Sea-Baltic Sea transition, we here investigate the in situ drivers of methane-cycling archaeal community structure and metabolism based on geochemical and stable carbon-isotopic gradients, functional gene (mcrA) copy numbers and phylogenetic compositions, and thermodynamic calculations. We observe major changes in community structure that largely follow vertical gradients in sulfate concentrations and lateral gradients in organic carbon reactivity and content. While methane-cycling archaeal communities in bioturbated and sulfatic zones are dominated by known methyl-disproportionating Methanosarcinaceae and putatively CO2-reducing Methanomicrobiaceae, the communities change toward dominance of methane-oxidizing taxa (ANME-2a-b, ANME-2c, ANME-1a-b) in sulfate-methane transition zones (SMTZs). By contrast, the underlying methanogenesis zones are dominated by the physiologically uncharacterized ANME-1d, new genus-level groups of putatively CO2-reducing Methanomicrobiaceae, and methyl-reducing Methanomassiliicoccales. Notably, mcrA copy numbers of several major taxa increase by 2 to 4 orders of magnitude from the sulfatic zone into the SMTZ or methanic zone, providing evidence of net population growth in subsurface sediment. We propose that burial-related geochemical changes cause methane-cycling archaea in continental margin sediments to go through three successional stages (sulfatic, SMTZ, methanic). Herein, the onset of each new successional stage is characterized by a period of growth- and mortality-driven turnover in the dominant taxa.

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Clemens Glombitza

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