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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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2
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Riva A, Rasoulimehrabani H, Cruz-Rubio JM, Schnorr SL, von Baeckmann C, Inan D, Nikolov G, Herbold CW, Hausmann B, Pjevac P, Schintlmeister A, Spittler A, Palatinszky M, Kadunic A, Hieger N, Del Favero G, von Bergen M, Jehmlich N, Watzka M, Lee KS, Wiesenbauer J, Khadem S, Viernstein H, Stocker R, Wagner M, Kaiser C, Richter A, Kleitz F, Berry D. Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting. Nat Commun 2023; 14:8210. [PMID: 38097563 PMCID: PMC10721620 DOI: 10.1038/s41467-023-43448-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.
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Affiliation(s)
- Alessandra Riva
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Hamid Rasoulimehrabani
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - José Manuel Cruz-Rubio
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Stephanie L Schnorr
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cornelia von Baeckmann
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Deniz Inan
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Georgi Nikolov
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, Medical University of Vienna, Vienna, Austria
| | - Márton Palatinszky
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Aida Kadunic
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Norbert Hieger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Kang Soo Lee
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Julia Wiesenbauer
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Sanaz Khadem
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Helmut Viernstein
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Freddy Kleitz
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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3
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Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Boettcher T, Cheng JX, Wagner M. The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration. bioRxiv 2023:2023.11.12.566429. [PMID: 38014294 PMCID: PMC10680583 DOI: 10.1101/2023.11.12.566429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.
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4
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Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. New Phytol 2023; 240:439-451. [PMID: 37381111 PMCID: PMC10962543 DOI: 10.1111/nph.19112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
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Affiliation(s)
- Hannes Schmidt
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Doctoral School in Microbiology and Environmental ScienceUniversity of ViennaVienna1030Austria
| | - David Seki
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
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5
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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. ISME J 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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6
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Gegenbauer C, Bellaire A, Schintlmeister A, Schmid MC, Kubicek M, Voglmayr H, Zotz G, Richter A, Mayer VE. Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue. New Phytol 2023; 238:2210-2223. [PMID: 36683444 PMCID: PMC10962571 DOI: 10.1111/nph.18761] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/05/2023] [Indexed: 05/04/2023]
Abstract
The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients. Uptake was analysed with a 15 N labelling experiment, subsequent isotope ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS). We encountered two hyphae types: a thick melanized type assigned to 'black fungi' (Chaetothyriales, Cladosporiales, and Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers, both hyphae types co-occurred. 15 N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types results in a synergism in terms of nutrient uptake. Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect-derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.
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Affiliation(s)
- Christian Gegenbauer
- Division of Structural and Functional Botany, Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 141030WienAustria
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Ecosystem ScienceUniversity of ViennaDjerassiplatz 11030WienAustria
| | - Anke Bellaire
- Division of Structural and Functional Botany, Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 141030WienAustria
| | - Arno Schintlmeister
- Division of Microbial Ecology and Large‐Instrument Facility of Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaDjerassiplatz 11030ViennaAustria
| | - Markus C. Schmid
- Division of Microbial Ecology and Large‐Instrument Facility of Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaDjerassiplatz 11030ViennaAustria
| | - Markus Kubicek
- Institute of Chemical Technologies and Analytics, TU WienGetreidemarkt 9/1641060ViennaAustria
| | - Hermann Voglmayr
- Mycology Research Group, Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 141030WienAustria
- Institute of Forest Entomology, Forest Pathology and Forest ProtectionUniversity of Natural Resources and Life Sciences, Vienna (BOKU)Peter‐Jordan‐Strasse 821190WienAustria
| | - Gerhard Zotz
- Institute for Biology and Environmental SciencesCarl von Ossietzky University OldenburgOldenburgGermany
- Smithsonian Tropical Research InstituteApdo 2072BalboaPanama
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Ecosystem ScienceUniversity of ViennaDjerassiplatz 11030WienAustria
| | - Veronika E. Mayer
- Division of Structural and Functional Botany, Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 141030WienAustria
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7
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Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
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8
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Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C. Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica. New Phytol 2021; 232:2457-2474. [PMID: 34196001 PMCID: PMC9291818 DOI: 10.1111/nph.17591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 05/04/2023]
Abstract
Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided 15 N-labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a 13 CO2 atmosphere. We analysed the short-term distribution of 13 C and 15 N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more 13 C to root parts that received more 15 N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of 13 C and 15 N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungus-delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale.
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Affiliation(s)
- Werner Mayerhofer
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass SpectrometryUniversity of ViennaViennaA‐1030Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Julia Wiesenbauer
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Raphael Gabriel
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaA‐1030Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure ResearchUniversity of ViennaViennaA‐1030Austria
| | - Peta Clode
- Centre for Microscopy, Characterisation & AnalysisUniversity of Western AustraliaPerthWA6009Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass SpectrometryUniversity of ViennaViennaA‐1030Austria
- Department of Chemistry and BioscienceAalborg UniversityAalborgDK‐9220Denmark
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaA‐1030Austria
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9
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Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C. Recently photoassimilated carbon and fungus-delivered nitrogen are spatially correlated in the ectomycorrhizal tissue of Fagus sylvatica. New Phytol 2021; 232:2457-2474. [PMID: 34196001 DOI: 10.5281/zenodo.5035482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 05/21/2023]
Abstract
Ectomycorrhizal plants trade plant-assimilated carbon for soil nutrients with their fungal partners. The underlying mechanisms, however, are not fully understood. Here we investigate the exchange of carbon for nitrogen in the ectomycorrhizal symbiosis of Fagus sylvatica across different spatial scales from the root system to the cellular level. We provided 15 N-labelled nitrogen to mycorrhizal hyphae associated with one half of the root system of young beech trees, while exposing plants to a 13 CO2 atmosphere. We analysed the short-term distribution of 13 C and 15 N in the root system with isotope-ratio mass spectrometry, and at the cellular scale within a mycorrhizal root tip with nanoscale secondary ion mass spectrometry (NanoSIMS). At the root system scale, plants did not allocate more 13 C to root parts that received more 15 N. Nanoscale secondary ion mass spectrometry imaging, however, revealed a highly heterogenous, and spatially significantly correlated distribution of 13 C and 15 N at the cellular scale. Our results indicate that, on a coarse scale, plants do not allocate a larger proportion of photoassimilated C to root parts associated with N-delivering ectomycorrhizal fungi. Within the ectomycorrhizal tissue, however, recently plant-assimilated C and fungus-delivered N were spatially strongly coupled. Here, NanoSIMS visualisation provides an initial insight into the regulation of ectomycorrhizal C and N exchange at the microscale.
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Affiliation(s)
- Werner Mayerhofer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna, Vienna, A-1030, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Julia Wiesenbauer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Raphael Gabriel
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, A-1030, Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, A-1030, Austria
| | - Peta Clode
- Centre for Microscopy, Characterisation & Analysis, University of Western Australia, Perth, WA, 6009, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna, Vienna, A-1030, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, DK-9220, Denmark
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, A-1030, Austria
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10
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Schueffl H, Theiner S, Hermann G, Mayr J, Fronik P, Groza D, van Schonhooven S, Galvez L, Sommerfeld NS, Schintlmeister A, Reipert S, Wagner M, Mader RM, Koellensperger G, Keppler BK, Berger W, Kowol CR, Legin A, Heffeter P. Albumin-targeting of an oxaliplatin-releasing platinum(iv) prodrug results in pronounced anticancer activity due to endocytotic drug uptake in vivo. Chem Sci 2021; 12:12587-12599. [PMID: 34703544 PMCID: PMC8494022 DOI: 10.1039/d1sc03311e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022] Open
Abstract
Oxaliplatin is a very potent platinum(ii) drug which is frequently used in poly-chemotherapy schemes against advanced colorectal cancer. However, its benefit is limited by severe adverse effects as well as resistance development. Based on their higher tolerability, platinum(iv) prodrugs came into focus of interest. However, comparable to their platinum(ii) counterparts they lack tumor specificity and are frequently prematurely activated in the blood circulation. With the aim to exploit the enhanced albumin consumption and accumulation in the malignant tissue, we have recently developed a new albumin-targeted prodrug, which supposed to release oxaliplatin in a highly tumor-specific manner. In more detail, we designed a platinum(iv) complex containing two maleimide moieties in the axial position (KP2156), which allows selective binding to the cysteine 34. In the present study, diverse cell biological and analytical tools such as laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS), isotope labeling, and nano-scale secondary ion mass spectrometry (NanoSIMS) were employed to better understand the in vivo distribution and activation process of KP2156 (in comparison to free oxaliplatin and a non-albumin-binding succinimide analogue). KP2156 forms very stable albumin adducts in the bloodstream resulting in a superior pharmacological profile, such as distinctly prolonged terminal excretion half-life and enhanced effective platinum dose (measured by ICP-MS). The albumin-bound drug is accumulating in the malignant tissue, where it enters the cancer cells via clathrin- and caveolin-dependent endocytosis, and is activated by reduction to release oxaliplatin. This results in profound, long-lasting anticancer activity of KP2156 against CT26 colon cancer tumors in vivo based on cell cycle arrest and apoptotic cell death. Summarizing, albumin-binding of platinum(iv) complexes potently enhances the efficacy of oxaliplatin therapy and should be further developed towards clinical phase I trials.
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Affiliation(s)
- Hemma Schueffl
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna Borschkegasse 8a A-1090 Vienna Austria +43-1-40160-957555 +43-1-40160-57594
| | - Sarah Theiner
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 38 A-1090 Vienna Austria
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 38 A-1090 Vienna Austria
| | - Josef Mayr
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
| | - Philipp Fronik
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
| | - Diana Groza
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna Borschkegasse 8a A-1090 Vienna Austria +43-1-40160-957555 +43-1-40160-57594
| | - Sushilla van Schonhooven
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna Borschkegasse 8a A-1090 Vienna Austria +43-1-40160-957555 +43-1-40160-57594
| | - Luis Galvez
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 38 A-1090 Vienna Austria
| | - Nadine S Sommerfeld
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology and Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna Djerassiplatz 1 A-1030 Vienna Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, University Biology Building (UBB) Djerassiplatz 1 A-1030 Vienna Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology and Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, University of Vienna Djerassiplatz 1 A-1030 Vienna Austria
| | - Robert M Mader
- Department of Medicine I and Comprehensive Cancer Center, Medical University of Vienna Waehringer Guertel 18-20 1090 Vienna Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 38 A-1090 Vienna Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
- Research Cluster "Translational Cancer Therapy Research", University of Vienna, Medical University of Vienna Vienna Austria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna Borschkegasse 8a A-1090 Vienna Austria +43-1-40160-957555 +43-1-40160-57594
- Department of Medicine I and Comprehensive Cancer Center, Medical University of Vienna Waehringer Guertel 18-20 1090 Vienna Austria
| | - Christian R Kowol
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
- Department of Medicine I and Comprehensive Cancer Center, Medical University of Vienna Waehringer Guertel 18-20 1090 Vienna Austria
| | - Anton Legin
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria +43-1-4277-852601 +43-1-4277-9526 +43-1-4277-52610 +43-1-4277-52611
| | - Petra Heffeter
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna Borschkegasse 8a A-1090 Vienna Austria +43-1-40160-957555 +43-1-40160-57594
- Department of Medicine I and Comprehensive Cancer Center, Medical University of Vienna Waehringer Guertel 18-20 1090 Vienna Austria
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11
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Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L. Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces. mSystems 2021; 6:e0118620. [PMID: 34058098 PMCID: PMC8269255 DOI: 10.1128/msystems.01186-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.
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Affiliation(s)
- Gabriela F. Paredes
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Tobias Viehboeck
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Raymond Lee
- Washington State University, School of Biological Sciences, Pullman, Washington, USA
| | - Marton Palatinszky
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela A. Mausz
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Siegfried Reipert
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Vienna, Austria
| | - Arno Schintlmeister
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Vienna, Austria
| | - Andreas Maier
- University of Vienna, Faculty of Geosciences, Geography, and Astronomy, Department of Geography and Regional Research, Geoecology, Vienna, Austria
| | - Jean-Marie Volland
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Claudia Hirschfeld
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Michael Wagner
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Aalborg University, Department of Chemistry and Bioscience, Aalborg, Denmark
| | - David Berry
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Stephanie Markert
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Silvia Bulgheresi
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Lena König
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
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12
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Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar S, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A. Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Nat Microbiol 2021; 6:885-898. [PMID: 34127845 PMCID: PMC8289736 DOI: 10.1038/s41564-021-00917-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse ‘Candidatus Izemoplasma’, Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse ‘Candidatus Izemoplasmatales’ (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed. Using microcosms, stable isotope probing, genome-resolved metagenomics and NanoSIMS, the authors identify diverse bacterial taxa that can degrade extracellular DNA in marine sediments, including ‘Candidatus Izemoplasma’, which encode numerous extracellular nucleases.
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Affiliation(s)
- Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Austrian Polar Research Institute, Vienna, Austria. .,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Arno Schintlmeister
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Austrian Polar Research Institute, Vienna, Austria.,Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Amy Noel
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Casey R J Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thilo Hofmann
- Division of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria.,Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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13
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Neuditschko B, Legin AA, Baier D, Schintlmeister A, Reipert S, Wagner M, Keppler BK, Berger W, Meier‐Menches SM, Gerner C. Die Wechselwirkung mit ribosomalen Proteinen begleitet die Stressinduktion des Wirkstoffkandidaten BOLD-100/KP1339 im endoplasmatischen Retikulum. Angew Chem Weinheim Bergstr Ger 2021; 133:5121-5126. [PMID: 38505777 PMCID: PMC10947255 DOI: 10.1002/ange.202015962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 11/09/2022]
Abstract
AbstractDer metallhaltige Wirkstoff BOLD‐100/KP1339 zeigte bereits vielversprechende Resultate in verschiedenen In vitro‐ und In vivo‐Tumormodellen sowie in klinischen Studien. Der detaillierte Wirkmechanismus wurde jedoch noch nicht komplett aufgeklärt. Als entscheidende Wirkstoffeffekte kristallisierten sich kürzlich die Stressinduktion im endoplasmatischen Retikulum (ER) und die damit einhergehende Modulierung von HSPA5 (GRP78) heraus. Das spontane und stabile Addukt zwischen BOLD‐100 und menschlichem Serumalbumin wurde als Immobilisierungsstrategie ausgewählt, um einen chemoproteomischen Ansatz auszuführen, der die ribosomalen Proteine RPL10, RPL24 und den Transkriptionsfaktor GTF2I als potentielle Interaktoren dieser Ru(III)‐Verbindung identifizierten. Dieses Ergebnis wurde mit proteomischen und transkriptomischen Profiling‐Experimenten kombiniert, was die Interpretation einer ribosomalen Beeinträchtigung sowie der Induktion von ER‐Stress unterstützte. Die Bildung von Polyribosomen und begleitende ER‐Schwellungen in behandelten Krebszellen wurden zudem durch TEM‐Messungen bestätigt. Somit scheint eine direkte Wechselwirkung von BOLD‐100 mit ribosomalen Proteinen die ER‐Stressinduktion und die Modulierung von GRP78 in Krebszellen zu begleiten.
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Affiliation(s)
- Benjamin Neuditschko
- Institut für Anorganische ChemieFakultät für ChemieUniversität WienWähringer Str. 421090WienÖsterreich
- Institut für Analytische ChemieFakultät für ChemieUniversität WienWähringer Str. 381090WienÖsterreich
| | - Anton A. Legin
- Institut für Anorganische ChemieFakultät für ChemieUniversität WienWähringer Str. 421090WienÖsterreich
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science”Universität WienWähringer Str. 421090WienÖsterreich
| | - Dina Baier
- Institut für Anorganische ChemieFakultät für ChemieUniversität WienWähringer Str. 421090WienÖsterreich
- Institut für Krebsforschung und Comprehensive Cancer CenterUniversitätsklinik für Innere Medizin IMedizinische Universität WienBorschkegasse 8a1090WienÖsterreich
- Forschungscluster “Translational Cancer Therapy Research”Universität WienWähringer Str. 421090WienÖsterreich
| | - Arno Schintlmeister
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science”Universität WienWähringer Str. 421090WienÖsterreich
- Großgeräteeinrichtung für Umwelt- und Isotopen-MassenspektrometrieZentrum für Mikrobiologie und UmweltsystemwissenschaftUniversität WienAlthanstr. 141090WienÖsterreich
| | - Siegfried Reipert
- Core Facility für Cell Imaging und UltrastrukturforschungAlthanstr. 141090WienÖsterreich
| | - Michael Wagner
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science”Universität WienWähringer Str. 421090WienÖsterreich
- Großgeräteeinrichtung für Umwelt- und Isotopen-MassenspektrometrieZentrum für Mikrobiologie und UmweltsystemwissenschaftUniversität WienAlthanstr. 141090WienÖsterreich
| | - Bernhard K. Keppler
- Institut für Anorganische ChemieFakultät für ChemieUniversität WienWähringer Str. 421090WienÖsterreich
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science”Universität WienWähringer Str. 421090WienÖsterreich
- Forschungscluster “Translational Cancer Therapy Research”Universität WienWähringer Str. 421090WienÖsterreich
| | - Walter Berger
- Institut für Krebsforschung und Comprehensive Cancer CenterUniversitätsklinik für Innere Medizin IMedizinische Universität WienBorschkegasse 8a1090WienÖsterreich
- Forschungscluster “Translational Cancer Therapy Research”Universität WienWähringer Str. 421090WienÖsterreich
| | - Samuel M. Meier‐Menches
- Institut für Analytische ChemieFakultät für ChemieUniversität WienWähringer Str. 381090WienÖsterreich
- Forschungscluster “Translational Cancer Therapy Research”Universität WienWähringer Str. 421090WienÖsterreich
| | - Christopher Gerner
- Institut für Analytische ChemieFakultät für ChemieUniversität WienWähringer Str. 381090WienÖsterreich
- Joint Metabolome FacilityUniversität Wien und Medizinische Universität WienWähringer Str. 381090WienÖsterreich
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14
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Neuditschko B, Legin AA, Baier D, Schintlmeister A, Reipert S, Wagner M, Keppler BK, Berger W, Meier‐Menches SM, Gerner C. Inside Cover: Interaction with Ribosomal Proteins Accompanies Stress Induction of the Anticancer Metallodrug BOLD‐100/KP1339 in the Endoplasmic Reticulum (Angew. Chem. Int. Ed. 10/2021). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/anie.202100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamin Neuditschko
- Institute of Inorganic Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 42 1090 Vienna Austria
- Department of Analytical Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 38 1090 Vienna Austria
| | - Anton A. Legin
- Institute of Inorganic Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 42 1090 Vienna Austria
- Research Network “Chemistry, Microbiology and Environmental Systems Science” University of Vienna Währinger Str. 42 1090 Vienna Austria
| | - Dina Baier
- Institute of Inorganic Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 42 1090 Vienna Austria
- Institute of Cancer Research and Comprehensive Cancer Center Department of Medicine I Medical University of Vienna Borschkegasse 8a 1090 Vienna Austria
- Research Cluster “Translational Cancer Therapy Research” University of Vienna Waehringer Str. 42 1090 Vienna Austria
| | - Arno Schintlmeister
- Research Network “Chemistry, Microbiology and Environmental Systems Science” University of Vienna Währinger Str. 42 1090 Vienna Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry Centre for Microbiology and Environmental Systems Science University of Vienna Althanstr. 14 1090 Vienna Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure Research Althanstr. 14 1090 Vienna Austria
| | - Michael Wagner
- Research Network “Chemistry, Microbiology and Environmental Systems Science” University of Vienna Währinger Str. 42 1090 Vienna Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry Centre for Microbiology and Environmental Systems Science University of Vienna Althanstr. 14 1090 Vienna Austria
| | - Bernhard K. Keppler
- Institute of Inorganic Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 42 1090 Vienna Austria
- Research Network “Chemistry, Microbiology and Environmental Systems Science” University of Vienna Währinger Str. 42 1090 Vienna Austria
- Research Cluster “Translational Cancer Therapy Research” University of Vienna Waehringer Str. 42 1090 Vienna Austria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer Center Department of Medicine I Medical University of Vienna Borschkegasse 8a 1090 Vienna Austria
- Research Cluster “Translational Cancer Therapy Research” University of Vienna Waehringer Str. 42 1090 Vienna Austria
| | - Samuel M. Meier‐Menches
- Department of Analytical Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 38 1090 Vienna Austria
- Research Cluster “Translational Cancer Therapy Research” University of Vienna Waehringer Str. 42 1090 Vienna Austria
| | - Christopher Gerner
- Department of Analytical Chemistry Faculty of Chemistry University of Vienna Waehringer Str. 38 1090 Vienna Austria
- Joint Metabolome Facility University of Vienna and Medical University of Vienna Waehringer Str. 38 1090 Vienna Austria
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15
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Neuditschko B, Legin AA, Baier D, Schintlmeister A, Reipert S, Wagner M, Keppler BK, Berger W, Meier‐Menches SM, Gerner C. Interaction with Ribosomal Proteins Accompanies Stress Induction of the Anticancer Metallodrug BOLD-100/KP1339 in the Endoplasmic Reticulum. Angew Chem Int Ed Engl 2021; 60:5063-5068. [PMID: 33369073 PMCID: PMC7986094 DOI: 10.1002/anie.202015962] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 02/06/2023]
Abstract
The ruthenium-based anticancer agent BOLD-100/KP1339 has shown promising results in several in vitro and in vivo tumour models as well as in early clinical trials. However, its mode of action remains to be fully elucidated. Recent evidence identified stress induction in the endoplasmic reticulum (ER) and concomitant down-modulation of HSPA5 (GRP78) as key drug effects. By exploiting the naturally formed adduct between BOLD-100 and human serum albumin as an immobilization strategy, we were able to perform target-profiling experiments that revealed the ribosomal proteins RPL10, RPL24, and the transcription factor GTF2I as potential interactors of this ruthenium(III) anticancer agent. Integrating these findings with proteomic profiling and transcriptomic experiments supported ribosomal disturbance and concomitant induction of ER stress. The formation of polyribosomes and ER swelling of treated cancer cells revealed by TEM validated this finding. Thus, the direct interaction of BOLD-100 with ribosomal proteins seems to accompany ER stress-induction and modulation of GRP78 in cancer cells.
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Affiliation(s)
- Benjamin Neuditschko
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 421090ViennaAustria
- Department of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 381090ViennaAustria
| | - Anton A. Legin
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 421090ViennaAustria
- Research Network “Chemistry, Microbiology and Environmental Systems Science”University of ViennaWähringer Str. 421090ViennaAustria
| | - Dina Baier
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 421090ViennaAustria
- Institute of Cancer Research and Comprehensive Cancer CenterDepartment of Medicine IMedical University of ViennaBorschkegasse 8a1090ViennaAustria
- Research Cluster “Translational Cancer Therapy Research”University of ViennaWaehringer Str. 421090ViennaAustria
| | - Arno Schintlmeister
- Research Network “Chemistry, Microbiology and Environmental Systems Science”University of ViennaWähringer Str. 421090ViennaAustria
- Large-Instrument Facility for Environmental and Isotope Mass SpectrometryCentre for Microbiology and Environmental Systems ScienceUniversity of ViennaAlthanstr. 141090ViennaAustria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructure ResearchAlthanstr. 141090ViennaAustria
| | - Michael Wagner
- Research Network “Chemistry, Microbiology and Environmental Systems Science”University of ViennaWähringer Str. 421090ViennaAustria
- Large-Instrument Facility for Environmental and Isotope Mass SpectrometryCentre for Microbiology and Environmental Systems ScienceUniversity of ViennaAlthanstr. 141090ViennaAustria
| | - Bernhard K. Keppler
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 421090ViennaAustria
- Research Network “Chemistry, Microbiology and Environmental Systems Science”University of ViennaWähringer Str. 421090ViennaAustria
- Research Cluster “Translational Cancer Therapy Research”University of ViennaWaehringer Str. 421090ViennaAustria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer CenterDepartment of Medicine IMedical University of ViennaBorschkegasse 8a1090ViennaAustria
- Research Cluster “Translational Cancer Therapy Research”University of ViennaWaehringer Str. 421090ViennaAustria
| | - Samuel M. Meier‐Menches
- Department of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 381090ViennaAustria
- Research Cluster “Translational Cancer Therapy Research”University of ViennaWaehringer Str. 421090ViennaAustria
| | - Christopher Gerner
- Department of Analytical ChemistryFaculty of ChemistryUniversity of ViennaWaehringer Str. 381090ViennaAustria
- Joint Metabolome FacilityUniversity of Vienna and Medical University of ViennaWaehringer Str. 381090ViennaAustria
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16
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Neuditschko B, Legin AA, Baier D, Schintlmeister A, Reipert S, Wagner M, Keppler BK, Berger W, Meier‐Menches SM, Gerner C. Innentitelbild: Die Wechselwirkung mit ribosomalen Proteinen begleitet die Stressinduktion des Wirkstoffkandidaten BOLD‐100/KP1339 im endoplasmatischen Retikulum (Angew. Chem. 10/2021). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Benjamin Neuditschko
- Institut für Anorganische Chemie Fakultät für Chemie Universität Wien Währinger Str. 42 1090 Wien Österreich
- Institut für Analytische Chemie Fakultät für Chemie Universität Wien Währinger Str. 38 1090 Wien Österreich
| | - Anton A. Legin
- Institut für Anorganische Chemie Fakultät für Chemie Universität Wien Währinger Str. 42 1090 Wien Österreich
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science” Universität Wien Währinger Str. 42 1090 Wien Österreich
| | - Dina Baier
- Institut für Anorganische Chemie Fakultät für Chemie Universität Wien Währinger Str. 42 1090 Wien Österreich
- Institut für Krebsforschung und Comprehensive Cancer Center Universitätsklinik für Innere Medizin I Medizinische Universität Wien Borschkegasse 8a 1090 Wien Österreich
- Forschungscluster “Translational Cancer Therapy Research” Universität Wien Währinger Str. 42 1090 Wien Österreich
| | - Arno Schintlmeister
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science” Universität Wien Währinger Str. 42 1090 Wien Österreich
- Großgeräteeinrichtung für Umwelt- und Isotopen-Massenspektrometrie Zentrum für Mikrobiologie und Umweltsystemwissenschaft Universität Wien Althanstr. 14 1090 Wien Österreich
| | - Siegfried Reipert
- Core Facility für Cell Imaging und Ultrastrukturforschung Althanstr. 14 1090 Wien Österreich
| | - Michael Wagner
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science” Universität Wien Währinger Str. 42 1090 Wien Österreich
- Großgeräteeinrichtung für Umwelt- und Isotopen-Massenspektrometrie Zentrum für Mikrobiologie und Umweltsystemwissenschaft Universität Wien Althanstr. 14 1090 Wien Österreich
| | - Bernhard K. Keppler
- Institut für Anorganische Chemie Fakultät für Chemie Universität Wien Währinger Str. 42 1090 Wien Österreich
- Forschungsnetzwerk “Chemistry, Microbiology and Environmental Systems Science” Universität Wien Währinger Str. 42 1090 Wien Österreich
- Forschungscluster “Translational Cancer Therapy Research” Universität Wien Währinger Str. 42 1090 Wien Österreich
| | - Walter Berger
- Institut für Krebsforschung und Comprehensive Cancer Center Universitätsklinik für Innere Medizin I Medizinische Universität Wien Borschkegasse 8a 1090 Wien Österreich
- Forschungscluster “Translational Cancer Therapy Research” Universität Wien Währinger Str. 42 1090 Wien Österreich
| | - Samuel M. Meier‐Menches
- Institut für Analytische Chemie Fakultät für Chemie Universität Wien Währinger Str. 38 1090 Wien Österreich
- Forschungscluster “Translational Cancer Therapy Research” Universität Wien Währinger Str. 42 1090 Wien Österreich
| | - Christopher Gerner
- Institut für Analytische Chemie Fakultät für Chemie Universität Wien Währinger Str. 38 1090 Wien Österreich
- Joint Metabolome Facility Universität Wien und Medizinische Universität Wien Währinger Str. 38 1090 Wien Österreich
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17
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Legin AA, Schintlmeister A, Sommerfeld NS, Eckhard M, Theiner S, Reipert S, Strohhofer D, Jakupec MA, Galanski MS, Wagner M, Keppler BK. Nano-scale imaging of dual stable isotope labeled oxaliplatin in human colon cancer cells reveals the nucleolus as a putative node for therapeutic effect. Nanoscale Adv 2021; 3:249-262. [PMID: 36131874 PMCID: PMC9419577 DOI: 10.1039/d0na00685h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2020] [Indexed: 05/04/2023]
Abstract
Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imaging by nanometer-scale secondary ion mass spectrometry (NanoSIMS) with transmission electron microscopy to investigate the subcellular accumulation of oxaliplatin in three human colon cancer cell lines (SW480, HCT116 wt, HCT116 OxR). Oxaliplatin bearing dual stable isotope labeled moieties, i.e. 2H-labeled diaminocyclohexane (DACH) and 13C-labeled oxalate, were applied for comparative analysis of the subcellular distribution patterns of the central metal and the ligands. In all the investigated cell lines, oxaliplatin was found to have a pronounced tendency for cytoplasmic aggregation in single membrane bound organelles, presumably related to various stages of the endocytic pathway. Moreover, nuclear structures, heterochromatin and in particular nucleoli, were affected by platinum-drug exposure. In order to explore the consequences of oxaliplatin resistance, subcellular drug distribution patterns were investigated in a pair of isogenic malignant cell lines with distinct levels of drug sensitivity (HCT116 wt and HCT116 OxR, the latter with acquired resistance to oxaliplatin). The subcellular platinum distribution was found to be similar in both cell lines, with only slightly higher accumulation in the sensitive HCT116 wt cells which is inconsistent with the resistance factor of more than 20-fold. Instead, the isotopic analysis revealed a disproportionally high accumulation of the oxalate ligand in the resistant cell line.
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Affiliation(s)
- Anton A Legin
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
- Research Cluster "Translational Cancer Therapy Research", University of Vienna A-1090 Vienna Austria
- Research Network "Chemistry Meets Microbiology and Environmental Systems Science", University of Vienna A-1090 Vienna Austria
| | - Arno Schintlmeister
- Research Network "Chemistry Meets Microbiology and Environmental Systems Science", University of Vienna A-1090 Vienna Austria
- Division of Microbial Ecology, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna A-1090 Vienna Austria
| | - Nadine S Sommerfeld
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
| | - Margret Eckhard
- Core Facility Cell Imaging and Ultrastructural Research, University of Vienna A-1090 Vienna Austria
| | - Sarah Theiner
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
- Research Cluster "Translational Cancer Therapy Research", University of Vienna A-1090 Vienna Austria
| | - Siegfried Reipert
- Core Facility Cell Imaging and Ultrastructural Research, University of Vienna A-1090 Vienna Austria
| | - Daniel Strohhofer
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
| | - Michael A Jakupec
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
- Research Cluster "Translational Cancer Therapy Research", University of Vienna A-1090 Vienna Austria
- Research Network "Chemistry Meets Microbiology and Environmental Systems Science", University of Vienna A-1090 Vienna Austria
| | - Mathea S Galanski
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
| | - Michael Wagner
- Research Network "Chemistry Meets Microbiology and Environmental Systems Science", University of Vienna A-1090 Vienna Austria
- Division of Microbial Ecology, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna A-1090 Vienna Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna A-1090 Vienna Austria +43 1 4277 852601 +43 1 4277 52610
- Research Cluster "Translational Cancer Therapy Research", University of Vienna A-1090 Vienna Austria
- Research Network "Chemistry Meets Microbiology and Environmental Systems Science", University of Vienna A-1090 Vienna Austria
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18
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Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M. Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities. ISME J 2020; 15:348-353. [PMID: 32879458 PMCID: PMC7852690 DOI: 10.1038/s41396-020-00761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.
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Affiliation(s)
- Maria Mooshammer
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Arno Schintlmeister
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM-Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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19
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Schneider S, Schintlmeister A, Becana M, Wagner M, Woebken D, Wienkoop S. Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis. Plant Cell Environ 2019; 42:1180-1189. [PMID: 30443991 PMCID: PMC6446814 DOI: 10.1111/pce.13481] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 05/03/2023]
Abstract
Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ("fixed") to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, whereas dicarboxylic acids derived from photosynthetically produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility.
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Affiliation(s)
- Sebastian Schneider
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems BiologyUniversity of ViennaViennaAustria
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
- Large‐Instrument Facility for Advanced Isotope ResearchUniversity of ViennaViennaAustria
| | | | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
- Large‐Instrument Facility for Advanced Isotope ResearchUniversity of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Microbiology”University of ViennaViennaAustria
| | - Stefanie Wienkoop
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems BiologyUniversity of ViennaViennaAustria
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20
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Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C. Rapid Transfer of Plant Photosynthates to Soil Bacteria via Ectomycorrhizal Hyphae and Its Interaction With Nitrogen Availability. Front Microbiol 2019; 10:168. [PMID: 30863368 PMCID: PMC6399413 DOI: 10.3389/fmicb.2019.00168] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/22/2019] [Indexed: 01/03/2023] Open
Abstract
Plant roots release recent photosynthates into the rhizosphere, accelerating decomposition of organic matter by saprotrophic soil microbes ("rhizosphere priming effect") which consequently increases nutrient availability for plants. However, about 90% of all higher plant species are mycorrhizal, transferring a significant fraction of their photosynthates directly to their fungal partners. Whether mycorrhizal fungi pass on plant-derived carbon (C) to bacteria in root-distant soil areas, i.e., incite a "hyphosphere priming effect," is not known. Experimental evidence for C transfer from mycorrhizal hyphae to soil bacteria is limited, especially for ectomycorrhizal systems. As ectomycorrhizal fungi possess enzymatic capabilities to degrade organic matter themselves, it remains unclear whether they cooperate with soil bacteria by providing photosynthates, or compete for available nutrients. To investigate a possible C transfer from ectomycorrhizal hyphae to soil bacteria, and its response to changing nutrient availability, we planted young beech trees (Fagus sylvatica) into "split-root" boxes, dividing their root systems into two disconnected soil compartments. Each of these compartments was separated from a litter compartment by a mesh penetrable for fungal hyphae, but not for roots. Plants were exposed to a 13C-CO2-labeled atmosphere, while 15N-labeled ammonium and amino acids were added to one side of the split-root system. We found a rapid transfer of recent photosynthates via ectomycorrhizal hyphae to bacteria in root-distant soil areas. Fungal and bacterial phospholipid fatty acid (PLFA) biomarkers were significantly enriched in hyphae-exclusive compartments 24 h after 13C-CO2-labeling. Isotope imaging with nanometer-scale secondary ion mass spectrometry (NanoSIMS) allowed for the first time in situ visualization of plant-derived C and N taken up by an extraradical fungal hypha, and in microbial cells thriving on hyphal surfaces. When N was added to the litter compartments, bacterial biomass, and the amount of incorporated 13C strongly declined. Interestingly, this effect was also observed in adjacent soil compartments where added N was only available for bacteria through hyphal transport, indicating that ectomycorrhizal fungi were acting on soil bacteria. Together, our results demonstrate that (i) ectomycorrhizal hyphae rapidly transfer plant-derived C to bacterial communities in root-distant areas, and (ii) this transfer promptly responds to changing soil nutrient conditions.
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Affiliation(s)
- Stefan Gorka
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Werner Mayerhofer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Raphael Gabriel
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Julia Wiesenbauer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Victoria Martin
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Qing Zheng
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Bruna Imai
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Judith Prommer
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Marieluise Weidinger
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Peter Schweiger
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Department of Microbiology and Ecosystem Science, Research Network “Chemistry meets Microbiology”, University of Vienna, Vienna, Austria
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21
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Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, Wu A, Jiang S, Durand HK, Zhou X, Premont RT, Diehl AM, O'Connell TM, Alberts SC, Kartzinel TR, Pringle RM, Dunn RR, Wright JP, David LA. Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol 2018; 3:1441-1450. [PMID: 30374168 PMCID: PMC6264799 DOI: 10.1038/s41564-018-0267-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
Abstract
Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.
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Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Fátima C Pereira
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura P Hale
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Anchi Wu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Xiyou Zhou
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Richard T Premont
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mae Diehl
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas M O'Connell
- Department of Otolaryngology - Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | | | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
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22
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Zumstein MT, Schintlmeister A, Nelson TF, Baumgartner R, Woebken D, Wagner M, Kohler HPE, McNeill K, Sander M. Biodegradation of synthetic polymers in soils: Tracking carbon into CO 2 and microbial biomass. Sci Adv 2018; 4:eaas9024. [PMID: 30050987 PMCID: PMC6059733 DOI: 10.1126/sciadv.aas9024] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/18/2018] [Indexed: 05/22/2023]
Abstract
Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on 13C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.
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Affiliation(s)
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090, Austria
| | | | - Rebekka Baumgartner
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network “Chemistry Meets Biology”, University of Vienna, Vienna 1090, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090, Austria
| | - Hans-Peter E. Kohler
- Environmental Biochemistry Group; Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Corresponding author.
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23
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Volland JM, Schintlmeister A, Zambalos H, Reipert S, Mozetič P, Espada-Hinojosa S, Turk V, Wagner M, Bright M. NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host. ISME J 2018; 12:714-727. [PMID: 29426952 PMCID: PMC5854253 DOI: 10.1038/s41396-018-0069-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 11/09/2022]
Abstract
The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.
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Affiliation(s)
- Jean-Marie Volland
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology" and Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Helena Zambalos
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
| | - Siegfried Reipert
- Cell Imaging and Ultrastructure Research (CIUS), University of Vienna, Vienna, Austria
| | - Patricija Mozetič
- National Institute of Biology, Marine Biology Station, Piran, Slovenia
| | | | - Valentina Turk
- National Institute of Biology, Marine Biology Station, Piran, Slovenia
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology" and Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Monika Bright
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
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24
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Ralls MW, Demehri FR, Feng Y, Raskind S, Ruan C, Schintlmeister A, Loy A, Hanson B, Berry D, Burant CF, Teitelbaum DH. Bacterial nutrient foraging in a mouse model of enteral nutrient deprivation: insight into the gut origin of sepsis. Am J Physiol Gastrointest Liver Physiol 2016; 311:G734-G743. [PMID: 27586649 PMCID: PMC5142194 DOI: 10.1152/ajpgi.00088.2016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/22/2016] [Indexed: 01/31/2023]
Abstract
Total parenteral nutrition (TPN) leads to a shift in small intestinal microbiota with a characteristic dominance of Proteobacteria This study examined how metabolomic changes within the small bowel support an altered microbial community in enterally deprived mice. C57BL/6 mice were given TPN or enteral chow. Metabolomic analysis of jejunal contents was performed by liquid chromatography/mass spectrometry (LC/MS). In some experiments, leucine in TPN was partly substituted with [13C]leucine. Additionally, jejunal contents from TPN-dependent and enterally fed mice were gavaged into germ-free mice to reveal whether the TPN phenotype was transferrable. Small bowel contents of TPN mice maintained an amino acid composition similar to that of the TPN solution. Mass spectrometry analysis of small bowel contents of TPN-dependent mice showed increased concentration of 13C compared with fed mice receiving saline enriched with [13C]leucine. [13C]leucine added to the serosal side of Ussing chambers showed rapid permeation across TPN-dependent jejunum, suggesting increased transmucosal passage. Single-cell analysis by fluorescence in situ hybridization (FISH)-NanoSIMS demonstrated uptake of [13C]leucine by TPN-associated bacteria, with preferential uptake by Enterobacteriaceae Gavage of small bowel effluent from TPN mice into germ-free, fed mice resulted in a trend toward the proinflammatory TPN phenotype with loss of epithelial barrier function. TPN dependence leads to increased permeation of TPN-derived nutrients into the small intestinal lumen, where they are predominately utilized by Enterobacteriaceae The altered metabolomic composition of the intestinal lumen during TPN promotes dysbiosis.
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Affiliation(s)
- Matthew W. Ralls
- 1Department of Surgery, Section of Pediatric Surgery, University of Michigan, Ann Arbor, Michigan;
| | - Farokh R. Demehri
- 1Department of Surgery, Section of Pediatric Surgery, University of Michigan, Ann Arbor, Michigan;
| | - Yongjia Feng
- 1Department of Surgery, Section of Pediatric Surgery, University of Michigan, Ann Arbor, Michigan;
| | - Sasha Raskind
- 2Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan;
| | - Chunhai Ruan
- 2Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan;
| | - Arno Schintlmeister
- 3Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria; ,4Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria; and
| | - Alexander Loy
- 3Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria;
| | - Buck Hanson
- 3Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria;
| | - David Berry
- 3Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria;
| | - Charles F. Burant
- 2Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, Michigan; ,5Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Daniel H. Teitelbaum
- 1Department of Surgery, Section of Pediatric Surgery, University of Michigan, Ann Arbor, Michigan;
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25
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Legin AA, Theiner S, Schintlmeister A, Reipert S, Heffeter P, Jakupec MA, Mayr J, Varbanov HP, Kowol CR, Galanski M, Berger W, Wagner M, Keppler BK. Multi-scale imaging of anticancer platinum(iv) compounds in murine tumor and kidney. Chem Sci 2016; 7:3052-3061. [PMID: 29997796 PMCID: PMC6004953 DOI: 10.1039/c5sc04383b] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023] Open
Abstract
Nano-scale secondary ion mass spectrometry (NanoSIMS) enables trace element and isotope analyses with high spatial resolution. This unique capability has recently been exploited in several studies analyzing the subcellular distribution of Au and Pt anticancer compounds. However, these studies were restricted to cell culture systems. To explore the applicability to the in vivo setting, we developed a combined imaging approach consisting of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), NanoSIMS and transmission electron microscopy (TEM) suitable for multi-scale detection of the platinum distribution in tissues. Applying this approach to kidney and tumor samples upon administration of selected platinum(iv) anticancer prodrugs revealed uneven platinum distributions on both the organ and subcellular scales. Spatial platinum accumulation patterns were quantitatively assessed by LA-ICP-MS in histologically heterogeneous organs (e.g., higher platinum accumulation in kidney cortex than in medulla) and used to select regions of interest for subcellular-scale imaging with NanoSIMS. These analyses revealed cytoplasmic sulfur-rich organelles accumulating platinum in both kidney and malignant cells. Those in the tumor were subsequently identified as organelles of lysosomal origin, demonstrating the potential of the combinatorial approach for investigating therapeutically relevant drug concentrations on a submicrometer scale.
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Affiliation(s)
- A A Legin
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - S Theiner
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - A Schintlmeister
- Department of Microbiology and Ecosystem Science , Research Network "Chemistry meets Microbiology", and Large-Instrument Facility for Advanced Isotope Research , University of Vienna , A-1090 Vienna , Austria
| | - S Reipert
- Core Facility of Cell Imaging and Ultrastructure Research , University of Vienna , A-1090 Vienna , Austria
| | - P Heffeter
- Institute of Cancer Research , Comprehensive Cancer Center and Research Platform "Translational Cancer Therapy Research" , Medical University of Vienna , A-1090 Vienna , Austria
| | - M A Jakupec
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - J Mayr
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - H P Varbanov
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - C R Kowol
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - M Galanski
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
| | - W Berger
- Institute of Cancer Research , Comprehensive Cancer Center and Research Platform "Translational Cancer Therapy Research" , Medical University of Vienna , A-1090 Vienna , Austria
| | - M Wagner
- Department of Microbiology and Ecosystem Science , Research Network "Chemistry meets Microbiology", and Large-Instrument Facility for Advanced Isotope Research , University of Vienna , A-1090 Vienna , Austria
| | - B K Keppler
- Institute of Inorganic Chemistry , Research Platform "Translational Cancer Therapy Research," and Research Network "Chemistry meets Microbiology" , University of Vienna , Währinger Straße 42 , A-1090 Vienna , Austria . ; Tel: +43-1-4277-52600
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26
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Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol 2015; 91:fiv106. [PMID: 26324854 PMCID: PMC4629873 DOI: 10.1093/femsec/fiv106] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/04/2015] [Accepted: 08/24/2015] [Indexed: 11/15/2022] Open
Abstract
The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via (15)N2 and (13)C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a (13)C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.
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Affiliation(s)
- Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
| | - Florian Strasser
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Arno Schintlmeister
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090 Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna 1090 Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network 'Chemistry meets Microbiology', University of Vienna, Vienna 1090 Austria
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27
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Legin A, Theiner S, Schintlmeister A, Reipert S, Heffeter P, Jakupec M, Kowol C, Galanski M, Berger W, Wagner M, Keppler B. 702 Multiscale distribution of anticancer platinum(IV) complexes in murine samples revealed by combination of NanoSIMS, LA-ICP-MS and TEM imaging. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30372-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J 2015; 9:485-96. [PMID: 25303712 PMCID: PMC4303640 DOI: 10.1038/ismej.2014.144] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 06/15/2014] [Accepted: 06/29/2014] [Indexed: 11/09/2022]
Abstract
Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.
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Affiliation(s)
- Dagmar Woebken
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Luke C Burow
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Faris Behnam
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Arno Schintlmeister
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Erich D Fleming
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Steven W Singer
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro López Cortés
- Laboratory of Geomicrobiology and Biotechnology, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Alfred M Spormann
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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29
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Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lücker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 2014; 345:1052-4. [PMID: 25170152 DOI: 10.1126/science.1256985] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed.
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Affiliation(s)
- Hanna Koch
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Alexander Galushko
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria. Large Instrument Facility for Advanced Isotope Research, University of Vienna, 1090 Vienna, Austria
| | - Christiane Gruber-Dorninger
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Sebastian Lücker
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Eric Pelletier
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de génomique, Genoscope, 91057 Evry, France. Centre National de la Recherche Scientifique, UMR8030, 91057 Evry, France. Université d'Evry Val d'Essonne, 91057 Evry, France
| | - Denis Le Paslier
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de génomique, Genoscope, 91057 Evry, France. Centre National de la Recherche Scientifique, UMR8030, 91057 Evry, France. Université d'Evry Val d'Essonne, 91057 Evry, France
| | - Eva Spieck
- Biozentrum Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria.
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30
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Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lücker S, Pelletier E, Le Paslier D, Spieck E, Richter A, Nielsen PH, Wagner M, Daims H. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 2014. [PMID: 25170152 DOI: 10.1126/science.125698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed.
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Affiliation(s)
- Hanna Koch
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Alexander Galushko
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria. Large Instrument Facility for Advanced Isotope Research, University of Vienna, 1090 Vienna, Austria
| | - Christiane Gruber-Dorninger
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Sebastian Lücker
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Eric Pelletier
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de génomique, Genoscope, 91057 Evry, France. Centre National de la Recherche Scientifique, UMR8030, 91057 Evry, France. Université d'Evry Val d'Essonne, 91057 Evry, France
| | - Denis Le Paslier
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de génomique, Genoscope, 91057 Evry, France. Centre National de la Recherche Scientifique, UMR8030, 91057 Evry, France. Université d'Evry Val d'Essonne, 91057 Evry, France
| | - Eva Spieck
- Biozentrum Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria.
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Pernice M, Dunn SR, Tonk L, Dove S, Domart-Coulon I, Hoppe P, Schintlmeister A, Wagner M, Meibom A. A nanoscale secondary ion mass spectrometry study of dinoflagellate functional diversity in reef-building corals. Environ Microbiol 2014; 17:3570-80. [PMID: 24902979 DOI: 10.1111/1462-2920.12518] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 05/25/2014] [Indexed: 11/26/2022]
Abstract
Nutritional interactions between corals and symbiotic dinoflagellate algae lie at the heart of the structural foundation of coral reefs. Whilst the genetic diversity of Symbiodinium has attracted particular interest because of its contribution to the sensitivity of corals to environmental changes and bleaching (i.e. disruption of coral-dinoflagellate symbiosis), very little is known about the in hospite metabolic capabilities of different Symbiodinium types. Using a combination of stable isotopic labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), we investigated the ability of the intact symbiosis between the reef-building coral Isopora palifera, and Symbiodinium C or D types, to assimilate dissolved inorganic carbon (via photosynthesis) and nitrogen (as ammonium). Our results indicate that Symbiodinium types from two clades naturally associated with I. palifera possess different metabolic capabilities. The Symbiodinium C type fixed and passed significantly more carbon and nitrogen to its coral host than the D type. This study provides further insights into the metabolic plasticity among different Symbiodinium types in hospite and strengthens the evidence that the more temperature-tolerant Symbiodinium D type may be less metabolically beneficial for its coral host under non-stressful conditions.
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Affiliation(s)
- Mathieu Pernice
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Plant Functional Biology and Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, NSW, Australia
| | - Simon R Dunn
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Linda Tonk
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Sophie Dove
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Isabelle Domart-Coulon
- UMR7245, Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, Paris, France
| | - Peter Hoppe
- Particle Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Arno Schintlmeister
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria.,Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Center for Advanced Surface Analysis, University of Lausanne, Lausanne, Switzerland
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32
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Legin AA, Schintlmeister A, Jakupec MA, Galanski MS, Lichtscheidl I, Wagner M, Keppler BK. NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-based anticancer drugs. Chem Sci 2014; 5:3135-3143. [PMID: 35919909 PMCID: PMC9273000 DOI: 10.1039/c3sc53426j] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/02/2014] [Indexed: 01/04/2023] Open
Affiliation(s)
- Anton A Legin
- Institute of Inorganic Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
- Research Platform "Translational Cancer Therapy Research", University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
| | - Arno Schintlmeister
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna Althanstrasse 14 A-1090 Vienna Austria
| | - Michael A Jakupec
- Institute of Inorganic Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
- Research Platform "Translational Cancer Therapy Research", University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
| | - Mathea S Galanski
- Institute of Inorganic Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
- Research Platform "Translational Cancer Therapy Research", University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
| | - Irene Lichtscheidl
- Core Facility of Cell Imaging and Ultrastructure Research, University of Vienna Althanstrasse 14 A-1090 Vienna Austria
| | - Michael Wagner
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna Althanstrasse 14 A-1090 Vienna Austria
- Department of Microbiology and Ecosystem Research, Division of Microbial Ecology, University of Vienna Althanstrasse 14 A-1090 Vienna Austria
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
- Research Platform "Translational Cancer Therapy Research", University of Vienna Waehringer Str. 42 A-1090 Vienna Austria
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Langer-Hansel K, Schintlmeister A, Fleig J, Hutter H. Oxygen transport in electroceramics investigated by electrochemical18O/16O isotope exchange and ToF-SIMS. SURF INTERFACE ANAL 2012. [DOI: 10.1002/sia.5134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- K. Langer-Hansel
- Vienna University of Technology; Institute of Chemical Technologies and Analytics; Getreidemarkt 9/164, A-; Vienna; Austria
| | - A. Schintlmeister
- Vienna University of Technology; Institute of Chemical Technologies and Analytics; Getreidemarkt 9/164, A-; Vienna; Austria
| | - J. Fleig
- Vienna University of Technology; Institute of Chemical Technologies and Analytics; Getreidemarkt 9/164, A-; Vienna; Austria
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Gerstl M, Frömling T, Schintlmeister A, Hutter H, Fleig J. Measurement of 18O tracer diffusion coefficients in thin yttria stabilized zirconia films. Solid State Ion 2011; 184:23-26. [PMID: 27570326 PMCID: PMC4986288 DOI: 10.1016/j.ssi.2010.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 08/20/2010] [Accepted: 08/22/2010] [Indexed: 06/06/2023]
Abstract
In this paper we present a method to measure oxygen tracer diffusion coefficients in thin ion conducting films without being limited by slow oxygen incorporation kinetics. The method is based on a two step process. In the first step a substantial amount of 18O tracer is locally incorporated for example into an yttria stabilized zirconia (YSZ) layer at low temperatures with the aid of an electric current, thus overcoming slow thermal oxygen exchange while still limiting lateral diffusion to a minimum. In the second step controlled diffusion takes place at elevated temperatures in ultra high vacuum (UHV) to impede loss of tracer due to oxygen exchange at the film surface. In this second step the surface of the thin film may additionally be modified compared to the oxygen incorporation step. This allows to easily investigate effects of interfaces on ion transport. The achieved in-plane concentration profiles are then measured by secondary ion mass spectrometry (SIMS). Comparison with electrical measurements on YSZ thin films proves the applicability of the method.
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Affiliation(s)
- M. Gerstl
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164/EC, 1060 Vienna, Austria
| | - T. Frömling
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164/EC, 1060 Vienna, Austria
| | - A. Schintlmeister
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164/EC, 1060 Vienna, Austria
| | - H. Hutter
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164/EC, 1060 Vienna, Austria
| | - J. Fleig
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9-164/EC, 1060 Vienna, Austria
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Holzweber M, Kriegl M, Schintlmeister A, Paesold D, Danninger H, Hutter H. Oxygen diffusion in grain boundaries: a ToF-SIMS investigation on hot-rolled steel sheets. Anal Bioanal Chem 2011; 400:659-63. [DOI: 10.1007/s00216-011-4769-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Revised: 01/24/2011] [Accepted: 02/03/2011] [Indexed: 11/28/2022]
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Opitz AK, Schintlmeister A, Hutter H, Fleig J. Visualization of oxygen reduction sites at Pt electrodes on YSZ by means of 18O tracer incorporation: the width of the electrochemically active zone. Phys Chem Chem Phys 2010; 12:12734-45. [DOI: 10.1039/c0cp00309c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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