Plantar Vein Thrombosis due to Busy Night Duty on Intensive Care Unit

A 32-year-old woman with severe foot pain came to our emergency department after a busy night duty in hospital followed by an extended sleep period. Physical examination revealed a discrete swelling of the medial aspect of the right foot and a painful plantar arch during digital examination. Magnetic resonance imaging (MRI) with intravenous gadolinium showed filling efects in the lateral plantar vein. Doppler sonography displayed noncompressible structures in the plantar veins without flow signals, suggesting a plantar vein thrombosis. Therapy was initiated with low-molecular-weight heparin in combination with customized elastic bandages for the lower leg. Follow-up sonography 6 weeks later showed complete patency of the plantar veins. To our knowledge, we present the first case of isolated plantar vein thrombosis independent of trauma, surgery, or malignant disease, most probably caused by a busy night duty on the intensive care unit (ICU) followed by a prolonged sleeping period

Impact of surface structure and feed gas composition on Bacillus subtilis endospore inactivation during direct plasma treatment

This study investigated the inactivation efficiency of cold atmospheric pressure plasma treatment on Bacillus subtilis endospores dependent on the used feed gas composition and on the surface, the endospores were attached on. Glass petri-dishes, glass beads, and peppercorns were inoculated with the same endospore density and treated with a radio frequency plasma jet. Generated reactive species were detected using optical emission spectroscopy. A quantitative polymerase chain reaction (qPCR) based ratio detection system was established to monitor the DNA damage during the plasma treatment. Argon + 0.135% vol. oxygen + 0.2% vol. nitrogen as feed gas emitted the highest amounts of UV-C photons and considerable amount of reactive oxygen and nitrogen species. Plasma generated with argon + 0.135% vol. oxygen was characterized by the highest emission of reactive oxygen species (ROS), whereas the UV-C emission was negligible. The use of pure argon showed a negligible emission of UV photons and atomic oxygen, however, the emission of vacuum (V)UV photons was assumed. Similar maximum inactivation results were achieved for the three feed gas compositions. The surface structure had a significant impact on the inactivation efficiency of the plasma treatment. The maximum inactivation achieved was between 2.4 and 2.8 log10 on glass petri-dishes and 3.9 to 4.6 log10 on glass beads. The treatment of peppercorns resulted in an inactivation lower than 1.0 log10. qPCR results showed a significant DNA damage for all gas compositions. Pure argon showed the highest results for the DNA damage ratio values, followed by argon + 0.135% vol. oxygen + 0.2% vol. nitrogen. In case of argon + 0.135% vol. oxygen the inactivation seems to be dominated by the action of ROS. These findings indicate the significant role of VUV and UV photons in the inactivation process of B. subtilis endospores

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

Background: In recent years biogas plants in Germany have been supposed to be involved in amplification and dissemination of pathogenic bacteria causing severe infections in humans and animals. In particular, biogas plants are discussed to contribute to the spreading of Escherichia coli infections in humans or chronic botulism in cattle caused by Clostridium botulinum. Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches. Results: All datasets featured a low abundance of reads that were taxonomically assigned to the genus Escherichia or further selected genera comprising pathogenic species. Higher numbers of reads were taxonomically assigned to the genus Clostridium. However, only very few sequences were predicted to originate from pathogenic clostridial species. Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. Likewise, known virulence determinants could hardly be detected. Only a marginal number of reads showed similarity to sequences described in the Microbial Virulence Database MvirDB such as those encoding protein toxins, virulence proteins or antibiotic resistance determinants. Conclusions: Findings of this first study of metagenomic sequence reads of biogas producing microbial communities suggest that the risk of dissemination of pathogenic bacteria by application of digestates from biogas fermentations as fertilizers is low, because obtained results do not indicate the presence of putative pathogenic microorganisms in the samples analyzed

Impact of process temperature and organic loading rate on cellulolytic/hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Background: Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted. Results: In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and/or acetogenesis. Conclusions: An integrated-omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass. © 2020 The Author(s)

Mikrobiologie zweiphasiger Reaktorsysteme für die Biomethanisierung bei hohen Temperaturen (55 - 75°C)

In den letzten Jahren nahm die Zahl an landwirtschaftlichen Biogasanlagen in Deutschland stetig zu. Im Jahr 2011 wurden 7.215 Biogasanlagen mit einer installierten elektrischen Leistung von 2.904 MW betrieben. Thermophile Temperaturen sowie eine räumliche Trennung der Prozessphasen Hydrolyse und Acidogenese von der Methanogenese können gegenüber den häufig verwendeten, mesophilen, einphasigen Rührkesselreaktoren den Biogasprozess verbessern und stabilisieren. Für eine weitere Optimierung solcher Anlagen ist ein detailliertes Wissen über die bakterielle und archaeelle Gemeinschaft, die am Abbau der Biomasse und der nachfolgenden Methanproduktion beteiligt sind, unabdingbar. In dieser Studie wurden deshalb drei identische Leach-bed Biogasreaktorsysteme mit räumlich getrennten Prozessphasen untersucht, die jeweils mit Roggen-Ganzpflanzensilage und Stroh mit einer Verweilzeit von 21 Tagen betrieben wurden. Jedes Reaktorsystem bestand aus einem Leach-bed Reaktor, dessen Temperatur schrittweise von 55 auf 75 °C erhöht wurde, einem Prozessflüssigkeitsspeicher und einem nachgeschalteten Anaerobfilter, der konstant während des gesamten Versuchs bei 55 °C betrieben wurde. Verschiedene kultivierungsunabhängige Methoden wurden genutzt um die mikrobielle Gemeinschaft im Reaktorsystem zu charakterisieren und zu quantifizieren sowie deren Dynamik zu verfolgen. Neben der Analyse von Genbibliotheken, TRFLP Fingerprintanalysen, Metagenomanalysen und qPCR Analysen wurden die Proben auch mittels Fluoreszenz in situ Hybridisierung sowie DAPI- und Propidiumiodid-Färbung untersucht. Die Studie gibt Aufschluss über Struktur und Dynamik der bakteriellen und archaeellen Gemeinschaft sowie über das genetische Potential zum anaeroben Abbau von pflanzlichen Polysacchariden bei hohen Temperaturen in zweiphasigen Leach-bed Biogassystemen. Insgesamt wurde die beste Reaktorleistung bei Temperaturen von 55 bis 60 °C festgestellt, ein Temperaturbereich, der sich vorteilhaft auf die mikrobielle Gemeinschaft im Reaktorsystem auswirkt. Des Weiteren zeigen die Ergebnisse potentielle prozessrelevante Bakterien sowie Glycosidhydrolasen auf, die als Biomarker für eine Überwachung von weiteren thermophilen Biogassystemen genutzt werden können. Die Ergebnisse dieser Studie dienen somit als Grundlage für eine Prozessüberwachung und eine zukünftige Optimierung von thermophilen Biogasprozessen mit Prozessphasentrennung.In recent years, the number of agricultural biogas plants, as a means of generation of renewable energy, has risen constantly in Germany. In 2011, 7,215 agricultural biogas plants were operated with a total installed electric capacity of 2,904 MW. Thermophilic temperatures and a spatial separation of the process phases hydrolysis and acetogenesis from methanogenesis are known strategies for improving and stabilizing biogas production. A deep understanding of the underlying bacterial and archaeal community involved in the breakdown of plant-derived biomass and the subsequent production of methane in phase-separated, thermophilic systems is of major importance for further improvement. Pursuant to this aim, phase-separated leach-bed biogas systems, which were supplied with rye silage and straw lasting for 21 days, were analyzed. Each system consisted of a leach-bed reactor (LBR), whose temperature was increased stepwise from 55 to 75 °C, a leachate storage reactor and a downstream anaerobic filter reactor, whose temperature remained at 55 °C throughout the experiment. Various culture-independent methods were used for the characterization, quantification and monitoring of the microbial community within these biogas systems. The culture-independent methods were based on the genetic information of cells, applying gene library construction, TRFLP fingerprinting, metagenomic and qPCR analyses and on the microscopical quantification of intact, but not cultivated cells. The present study revealed the composition and dynamics of the microbial community and their genetic potential for carbohydrate degradation in two-phase leach-bed biogas systems at thermophilic to hyperthermophilic temperatures. Temperatures of 55 to 60 °C in the LBR had a positive effect on the microbial community responsible for the production of biogas, leading to the best reactor performance. Furthermore, the results indicated potentially process-relevant bacteria and glycoside hydrolases, which may serve as target for the monitoring of thermophilic biogas reactors in future. Hence, the results gained in this study provide a promising basis for the monitoring and the prospective improvement of thermophilic biogas systems with phase-separation

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

Eikmeyer FG, Rademacher A, Hanreich A, et al. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnology for Biofuels. 2013;6(1): 49.Background In recent years biogas plants in Germany have been supposed to be involved in amplification and dissemination of pathogenic bacteria causing severe infections in humans and animals. In particular, biogas plants are discussed to contribute to the spreading of Escherichia coli infections in humans or chronic botulism in cattle caused by Clostridium botulinum. Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches. Results All datasets featured a low abundance of reads that were taxonomically assigned to the genus Escherichia or further selected genera comprising pathogenic species. Higher numbers of reads were taxonomically assigned to the genus Clostridium. However, only very few sequences were predicted to originate from pathogenic clostridial species. Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. Likewise, known virulence determinants could hardly be detected. Only a marginal number of reads showed similarity to sequences described in the Microbial Virulence Database MvirDB such as those encoding protein toxins, virulence proteins or antibiotic resistance determinants. Conclusions Findings of this first study of metagenomic sequence reads of biogas producing microbial communities suggest that the risk of dissemination of pathogenic bacteria by application of digestates from biogas fermentations as fertilizers is low, because obtained results do not indicate the presence of putative pathogenic microorganisms in the samples analyzed

DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison

Lebuhn M, Derenkó J, Rademacher A, et al. DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison. Bioengineering. 2016;3(1): 7

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Maus I, Klocke M, Derenkó J, et al. Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics. Environmental Microbiome. 2020;15(1): 7.Background Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted. Results In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis. Conclusions An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass