166 research outputs found
Erratum to: Candidates of trichocyst matrix proteins of the dinoflagellate Oxyrrhis marina
No full textSolvent stress response of the denitrifying bacterium "Aromatoleum aromaticum" strain EbN1
No full textThe denitrifying betaproteobacterium “Aromatoleum aromaticum” strain EbN1 degrades several aromatic compounds, including ethylbenzene, toluene, p-cresol, and phenol, under anoxic conditions. The hydrophobicity of these aromatic solvents determines their toxic properties. Here, we investigated the response of strain EbN1 to aromatic substrates at semi-inhibitory (about 50% growth inhibition) concentrations under two different conditions: first, during anaerobic growth with ethylbenzene (0.32 mM) or toluene (0.74 mM); and second, when anaerobic succinate-utilizing cultures were shocked with ethylbenzene (0.5 mM), toluene (1.2 mM), p-cresol (3.0 mM), and phenol (6.5 mM) as single stressors or as a mixture (total solvent concentration, 2.7 mM). Under all tested conditions impaired growth was paralleled by decelerated nitrate-nitrite consumption. Additionally, alkylbenzene-utilizing cultures accumulated poly(3-hydroxybutyrate) (PHB) up to 10% of the cell dry weight. These physiological responses were also reflected on the proteomic level (as determined by two-dimensional difference gel electrophoresis), e.g., up-regulation of PHB granule-associated phasins, cytochrome cd1 nitrite reductase of denitrification, and several proteins involved in oxidative (e.g., SodB) and general (e.g., ClpB) stress responses
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No full textThe marine heterotrophic roseobacter Phaeobacter gallaeciensis DSM 17395 was grown with glucose in defined mineral medium. Relative abundance changes of global protein (2-D DIGE) and metabolite (GC-MS) profiles were determined across five different time points of growth. In total, 215 proteins were identified and 147 metabolites detected (101 structurally identified), among which 60 proteins and 87 metabolites displayed changed abundances upon entry into stationary growth phase. Glucose breakdown to pyruvate apparently proceeds via the Entner-Doudoroff (ED) pathway, since phosphofructokinase of the Embden-Meyerhof-Parnas pathway is missing and the key metabolite of the ED-pathway, 2-keto-3-desoxygluconate, was detected. The absence of pfk in other genome-sequenced roseobacters suggests that the use of the ED pathway is an important physiological property among these heterotrophic marine bacteria. Upon entry into stationary growth phase (due to glucose starvation), sulfur assimilation (including cysteine biosynthesis) and parts of cell envelope synthesis (e.g. the lipid precursor 1-monooleoylglycerol) were down-regulated and cadaverine formation up-regulated. In contrast, central carbon catabolism remained essentially unchanged, pointing to a metabolic "stand-by" modus as an ecophysiological adaptation strategy. Stationary phase response of P. gallaeciensis differs markedly from that of standard organisms such as Escherichia coli, as evident e.g. by the absence of an rpoS gene
Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea
No full textAnnually recurring phytoplankton spring blooms are characteristic of temperate coastal shelf seas. During these blooms, environmental conditions, including nutrient availability, differ considerably from non-bloom conditions, affecting the entire ecosystem including the bacterioplankton. Accordingly, the emerging ecological niches during bloom transition are occupied by different bacterial populations, with Roseobacter RCA cluster and SAR92 clade members exhibiting high metabolic activity during bloom events. In this study, the functional response of the ambient bacterial community toward a Phaeocystis globosa bloom in the southern North Sea was studied using metaproteomic approaches. In contrast to other metaproteomic studies of marine bacterial communities, this is the first study comparing two different cell lysis and protein preparation methods [using trifluoroethanol (TFE) and in-solution digest as well as bead beating and SDS-based solubilization and in-gel digest (BB GeLC)]. In addition, two different mass spectrometric techniques (ESI-iontrap MS and MALDI-TOF MS) were used for peptide analysis. A total of 585 different proteins were identified, 296 of which were only detected using the TFE and 191 by the BB GeLC method, demonstrating the complementarity of these sample preparation methods. Furthermore, 158 proteins of the TFE cell lysis samples were exclusively detected by ESI-iontrap MS while 105 were only detected using MALDI-TOF MS, underpinning the value of using two different ionization and mass analysis methods. Notably, 12% of the detected proteins represent predicted integral membrane proteins, including the difficult to detect rhodopsin, indicating a considerable coverage of membrane proteins by this approach. This comprehensive approach verified previous metaproteomic studies of marine bacterioplankton, e.g., detection of many transport-related proteins (17% of the detected proteins). In addition, new insights into e.g., carbon and nitrogen metabolism were obtained. For instance, the C1 pathway was more prominent outside the bloom and different strategies for glucose metabolism seem to be applied under the studied conditions. Furthermore, a higher number of nitrogen assimilating proteins were present under non-bloom conditions, reflecting the competition for this limited macro nutrient under oligotrophic conditions. Overall, application of different sample preparation techniques as well as MS methods facilitated a more holistic picture of the marine bacterioplankton response to changing environmental conditions.Deutsche Forschungsgemeinschaft (DFG) [TRR51
Between Scylla and Charybdis: The Mediation of Controversial Ideas in the Boekzaal van Europe, 1692-1701
No full textIn his erudite periodical Pieter Rabus reflected on the most recent developments in the Republic of Letters. As the author of the Boekzaal van Europe, he attempted to convey heterodox ideas to his audience, resulting in several controversies. By depicting Rabus’ propagation of dowsing, his defense of De Betoverde Weereld, and his treatment of influential magistrates, this thesis analyses various ways in which Rabus mediated the controversial content of his periodical to his audience. Between 1694 and 1698 his journal was under censorship for explicitly refuting the doctrines of the Reformed Church. Nonetheless, Rabus sought to further advocate his views, he partially ignored the censorship and chose to express his controversial thought in a veiled manner. When his journal was faced with severe threats of cancellation, Rabus applied his agency as an author to avoid censorship; he captured the benevolence of the city magistrates, and the ecclesiastical censorship was lifted
Regulation of anaerobic alkylbenzene utilization in the denitrifying strain EbN1
No full textThe anaerobic degradation pathways of toluene and ethylbenzene and the adaptation to toxicological effects of these alkylbenzenes are studied with the denitrifying strain EbN1 in a combined physiological and proteomic approach. How specific is the substrate-dependend regulation of the two degradation pathways? Which molecular-physiological effects become apparent at growth with sublethal concentrations? What reaction follows an alkylbenzene-shock in absence of operative degradation pathways
Advancing shaken bioreactors for the characterization of anaerobic microorganisms
No full textAnaerobic microorganisms possess vast potential for the sustainable production of chemicals. Particular organic acids, such as succinate, can be utilized as basic components in the industry. However, since cultivations of anaerobic bacteria are challenging, there is a knowledge gap in understanding their metabolisms and cultivation performance. Advanced and complex cultivation modes such as fed-batch or continuous cultivation even increase the requirements for anaerobicity. As a result, the potential of anaerobic microorganisms for industrial bioprocesses often remains hidden. This study established shaken bioreactors with batch, fed-batch, and continuous operation modes for anaerobic cultivations. Constructive changes were made to the systems for this purpose, and a new gas sensor system was implemented to measure the CO2 and H2 transfer rates online. In axenic cultures of the gut bacterium Phocaeicola vulgatus in batch shake flask experiments, the minimum buffer concentration and an optimal initial pH were identified to mitigate the pH inhibition of P. vulgatus. The initial addition of different acids revealed an inhibitory effect of lactate on P. vulgatus, starting at a concentration of 1 g L 1. A comparison of a pH-buffered and a pH-controlled batch fermentation demonstrated a switch in acid production from lactate to succinate under pH control. Aerobic, membrane-based fed-batch shake flasks were rebuilt into anaerobic cultivation systems and successfully applied in anaerobic conditions. However, an inhibition of the fed-batch process due to high lactate production was observed, which must be considered in future process development. The aerobic continuous shaken cultivation system COSBIOS was also modified into an anaerobic cultivation system, and anaerobic continuous cultivations were performed. Nevertheless, various technical aspects, such as leakages due to tube abrasion, require additional optimization. For a comprehensive analysis, thermal conductivity sensors were implemented to monitor hydrogen production by anaerobes online in the cultivation systems mentioned. Since thermal conductivity sensors are not hydrogen-specific, their cross-sensitivity to CO2 concentration, temperature, and humidity was evaluated. The sensor measurement range was validated with two anaerobes: the highly H2-producing Clostridium pasteurianum and the low H2-producing P. vulgatus. The online monitoring of H2 production enabled the determination of hydrogen transfer rates. In combination with online CO2 transfer rates, molar gas balances of the cultivations were closed, and an anaerobic respiration quotient was introduced. The presented work paves the way for more efficient bioprocesses utilizing anaerobic microorganisms by addressing cultivation challenges and providing online monitoring solutions for gas transfer rates
Metabolic reconstruction and regulation in Desulfobacterium autotrophicum
No full text:i: Desulfobacterium autotrophicum :/i: is a marine sulfate-reducing bacterium, which is metabolically quite versatile. Here the it was tried to investigate metabolic regulation using a physiological, proteomic and RNA based methods. The investigations were focussed on cold-adaption, alcohol metabolism and the terminal oxidation of substrates
Proteomic and genetic studies of aromatic compund degradation in "Aromatoleum aromaticum" strain EbN1
No full textAromatic compounds are widely distributed and abundant in nature being main constituents of crude oil and important products of higher plants. The denitrifying Aromatoleum aromaticum strain EbN1 utilizes a wide range of aromatic and nonaromatic compounds under anoxic and oxic conditions. The recently determined genome sequence revealed corresponding degradation pathways and predicted a fine-tuned regulatory network.This work reports on the analysis of substrate specific regulation of anaerobic and aerobic degradation pathways in "A. aromaticum" strain EbN1 grown with 17 different aromatic and aliphatic compounds under oxic and anoxic conditions applying differential proteomics (2D DIGE). The comprehensive approach enabled the discovery of so far unaccounted catabolic capacities and their subsequent elucidation on the physiological, molecular and regulatory level. The adaptation of strain EbN1 to solvent stress was investigated on the physiological and proteomic level since strain EbN1 is able to degrade several toxic alkylbenzenes and alkylphenols. In addition, a genetic system for strain EbN1 is described enabling unmarked deletion mutagenesis
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