Article
Chemistry, Multidisciplinary
Anna Christina R. Ngo, Catleen Conrad, Alvaro Gomez Baraibar, Anke Matura, Karl-Heinz Van Pee, Dirk Tischler
Summary: Dye-decolorizing peroxidases are a family of enzymes with high degradation capacity, making them promising candidates for applications in bioremediation and organic synthesis. Two novel DyP peroxidases from Rhodococcus opacus 1CP were successfully cloned and expressed, with varying trends in activity and tolerance towards H2O2 observed in this study.
APPLIED SCIENCES-BASEL
(2021)
Article
Biochemistry & Molecular Biology
Anna Christina R. Ngo, Jinqxian Qi, Cindy Juric, Isabel Bento, Dirk Tischler
Summary: Azo dyes are important in various industries, but they contain toxic and carcinogenic substances. Enzymes like Azoreductases have been used to reduce the toxicity of these dyes. AzoRo from Rhodococcus opacus 1CP has a narrow active site and is capable of reducing only methyl red. By studying the crystal structure and designing variants of AzoRo, researchers have identified the key residues involved in substrate binding and enzyme specificity. The results show that AzoRo has a different active site configuration compared to other bacterial azoreductases, and it is more active and efficient towards quinones.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Natalya M. Subbotina, Alexey M. Chernykh, Anton Taranov, Anna D. Shebanova, Olga Moiseeva, Marta Ferraroni, Marina P. Kolomytseva
Summary: The research investigated the gentisate 1,2-dioxygenase from Rhodococcus opacus 1CP, revealing its narrow substrate specificity and potential application in oxidizing gentisate. Analysis of the rho-GDO structure and function unveiled a new mechanism of substrate specificity for this family of enzymes.
Article
Biology
Jinjin Diao, Rhiannon Carr, Tae Seok Moon
Summary: In this study, we identified and studied the transcription factors involved in aromatic degradation in Rhodococcus opacus using GFP-based sensors and comprehensive deletion analyses. Our results indicate that the funneling pathways for different aromatic compounds are regulated by transcriptional activators or repressors. Additionally, the substrate hierarchy in R. opacus may be due to the transcriptional cross-regulation of different aromatic funneling pathways.
COMMUNICATIONS BIOLOGY
(2022)
Article
Environmental Sciences
Shu Ma, Shiwei Huang, Yun Tian, Xiangyang Lu
Summary: In this study, a strain of Rhodococcus erythropolis Y10 capable of aerobic denitrification was screened from surface flow constructed wetlands. The strain removed ammonium through heterotrophic ammonium assimilation and exhibited improved aerobic denitrification efficiency when ammonium was added. The findings shed light on the role of ammonium assimilation in microbial ammonium removal.
Article
Environmental Sciences
Weimin Sun, Xiaoxu Sun
Summary: This study found that methane can be produced through anaerobic degradation of toluene over a long-term enrichment experiment. The DNA-SIP technique identified bacteria in the phylum Proteobacteria as the dominant toluene-degrading bacteria under anaerobic conditions.
WATER AIR AND SOIL POLLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Thanh Trung Tran, Nathan J. Bott, Rebecca van Gelderen, Nam Trung Nguyen, Phuong Minh Thi Chu, Ha Hoang Chu
Summary: Nitrogen compounds, especially ammonia, are produced in aquaculture systems. In this study, two strains of Pseudomonas bacteria isolated from shrimp pond water were analyzed to understand their genetic characteristics and metabolic pathways related to ammonia reduction. The analysis showed that these strains belong to Pseudomonas putida and share a common ancestor with 33 genomes. Three genes, carbamate kinase (arcC), glutamine synthetase (Glul), and aminomethyltransferase (amt), were found to be involved in three metabolic pathways, potentially playing important roles in ammonia reduction and bacterial growth via ammonia assimilation.
FERMENTATION-BASEL
(2022)
Article
Microbiology
Marc Tamisier, Matthias Schmidt, Carsten Vogt, Steffen Kuemmel, Hryhoriy Stryhanyuk, Niculina Musat, Hans-Hermann Richnow, Florin Musat
Summary: The research focused on the stable carbon and hydrogen isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 during growth with hydrogen and iron. The growth resulted in methane with depleted C-13 values, while H-2 values were less impacted by growth phase. The corrosion crusts formed were composed of siderite, calcite, and iron sulfide, with attached cells found on crust surfaces and deep inside crust domes.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Mohammad S. Bin Hudari, Carsten Vogt, Hans H. Richnow
Summary: High-temperature aquifer thermal energy storage (HT-ATES) affects the structure and activities of indigenous aquifer microbial communities, with acetate mineralization inhibited at lower and higher temperatures. Microbial communities adapted to 45 degrees Celsius were found to be resilient to temporary heat changes and mainly consisted of organisms adapted to temperatures between mesophiles and thermophiles.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Xin You, Rene Kallies, Ingolf Kuehn, Matthias Schmidt, Hauke Harms, Antonis Chatzinotas, Lukas Y. Wick
Summary: The study found that lytic phages can co-transport with bacteria, promoting bacterial colonization of new habitats. This co-transport is analogous to invasion processes in macroecology. In water-unsaturated systems, hyphal transport of bacteria and associated phages plays a crucial role in regulating microbial population fitness and composition.
Article
Virology
Xin You, Niclas Klose, Rene Kallies, Hauke Harms, Antonis Chatzinotas, Lukas Y. Wick
Summary: Recent studies have shown that phages can be transported with non-host bacteria, allowing them to invade biofilms and control their composition. A novel approach was developed to isolate non-host bacteria that can co-transport phages from soil. Five phage-carrying bacterial species were identified, and Viridibacillus sp. showed a higher phage adsorption efficiency.
Article
Environmental Sciences
Stefan Trapp, Andreas Libonati Brock, Matthias Kastner, Andreas Schaffer, Dieter Hennecke
Summary: This study evaluated the accuracy and precision of the MTB method for estimating biomass and bioNER formed from the degradation of organic chemicals using experimental data. The results showed that the MTB method provides a robust model for determining the potential amounts of biomass and bioNER formed.
ENVIRONMENTAL SCIENCES EUROPE
(2022)
Letter
Toxicology
Stefan Scholz, Werner Brack, Beate I. Escher, Joerg Hackermuller, Matthias Liess, Martin von Bergen, Lukas Y. Wick, Ana C. Zenclussen, Rolf Altenburger
ARCHIVES OF TOXICOLOGY
(2022)
Article
Microbiology
Bi-Jing Xiong, Claire E. Stanley, Christian Dusny, Dietmar Schlosser, Hauke Harms, Lukas Y. Wick
Summary: Using a microfluidic system and pH-sensitive whole-cell bioreporters, researchers studied the dynamic changes of surface pH along growing hyphae of Coprinopsis cinerea. The pH along hyphal surfaces varied significantly, with the pH at hyphal tips being lower compared to more mature hyphal parts. This study provides important insights into the spatial and pH-dependent hyphal processes, such as organic matter degradation or mineral weathering.
Article
Biotechnology & Applied Microbiology
Mariam Karagulyan, Marc-Oliver Goebel, Dorte Diehl, Abd Alaziz Abu Quba, Matthias Kastner, Jorg Bachmann, Lukas Y. Wick, Gabriele E. Schaumann, Anja Miltner
Summary: Increased drought intensity and frequency expose soil bacteria to prolonged water stress, leading to changes in bacterial cell surface properties. The changes in cell surface hydrophobicity depend on strain and stress type, and affect different bacteria in different ways.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biology
Thierry Kuhn, Matteo Buffi, Saskia Bindschedler, Patrick S. Chain, Diego Gonzalez, Claire E. Stanley, Lukas Y. Wick, Pilar Junier, Xiang-Yi Li Richter
Summary: Researchers have developed 3D printed devices that can be used as abiotic controls to study bacterial dispersal on hydrated surfaces. By separating biotic and abiotic elements, these devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.
Article
Engineering, Environmental
Yuying Jing, Anja Miltner, Trine Eggen, Matthias Kaestner, Karolina M. Nowak
Summary: This study conducted a microcosm test to simulate the fate of pesticides in planted filters, and found that the presence of planted filters can enhance the degradation and adsorption of pesticides.
Article
Microbiology
Kristian Jensen Pedersen, Sven-Bastiaan Haange, Katerina Zizalova, Alina Viehof, Thomas Clavel, Martin Lenicek, Beatrice Engelmann, Lukas Y. Wick, Frank G. Schaap, Nico Jehmlich, Ulrike Rolle-Kampczyk, Martin von Bergen
Summary: Bile acids play a crucial role in lipid uptake and gut-microbiome composition. This study reveals the molecular details of the interaction between bile acid modifying bacteria and other strains, highlighting the influence of co-culturing on bacterial functionality.
Article
Ecology
Nelson Khan, Edward Muge, Francis J. Mulaa, Benson Wamalwa, Martin von Bergen, Nico Jehmlich, Lukas Y. Wick
Summary: Fungi play a crucial role in the biodegradation of soil organochlorine pesticides by facilitating bacterial dispersal and nutrient release. Experimental results indicate that the transfer of nutrients from fungi to bacteria can enhance the degradation of organic pollutants, highlighting the importance of fungal-bacterial interactions.
Article
Soil Science
Tiantian Zheng, Anja Miltner, Chao Liang, Karolina M. Nowak, Matthias Kastner
Summary: Microbial biomass residues play an important role in biogeochemical cycling, but the mechanism by which they are sequestered in soil organic matter remains elusive. This study revealed that bacterial biomass is predominantly utilized by fungi and stabilized as fungal necromass, contributing to soil organic carbon sequestration. The study also identified three phases in the metabolism of microbial biomass residues, with the final phase focused on C preservation rather than energy production.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Microbiology
Joyce Alvarez-Barragan, Cristiana Cravo-Laureau, Bijing Xiong, Lukas Y. Y. Wick, Robert Duran
Summary: This study advances our understanding of fungal-bacterial relationships, specifically the selection and dispersion of bacterial communities by fungi, which are essential for the organization and functioning of microbial communities in coastal PAH-contaminated sediments.
Article
Environmental Sciences
Natalia Malina, Xi Wei, Steffem Kummel, Hans H. Richnow, Carsten Vogt
Summary: This study developed and validated a method based on gas chromatography-isotope ratio mass spectrometry for analyzing the hydrogen and carbon isotope ratios of phenolic compounds, aiming to study their sources and degradation pathways in the environment. Results showed that the variation in hydrogen and carbon isotope ratios can indicate different enzymatic reactions, helping distinguish the mechanisms of different microbes in the degradation process.