Review
Biotechnology & Applied Microbiology
Pankaj Bhatt, Amit Verma, Saurabh Gangola, Geeta Bhandari, Shaohua Chen
Summary: The widespread use of organic pollutants has led to contamination of air, soil, and water, posing hazards to living systems. Microbial glycoconjugates play a key role in enhancing the degradation of these toxicants, increasing bioavailability and accelerating microbial metabolism to mitigate environmental pollution.
MICROBIAL CELL FACTORIES
(2021)
Article
Environmental Sciences
Zhaodi Guo, Mohammed Jalalah, Saeed A. Alsareii, Farid A. Harraz, Nandini Thakur, El-Sayed Salama
Summary: This study investigated the effects of adding different proportions of biochar on biogas production, volatile fatty acids (VFAs), microbial communities, and enzymes. The results showed that 0.5% biochar significantly increased biogas and VFAs production, and also promoted the abundance of specific bacteria and archaea and the activities of corresponding enzymes under certain conditions.
Article
Environmental Sciences
Katarzyna Paraszkiewicz, Magdalena Moryl, Grazyna Plaza, Diksha Bhagat, Surekha K. Satpute, Przemyslaw Bernat
Summary: Biosurfactants are universal molecules produced by microorganisms, exhibiting surface properties often accompanied by desired biological activity. Due to their low toxicity and biodegradable nature, biosurfactants are considered environmentally 'friendly' and have potential applications in various industries. Their antibacterial and antifungal activities make them relevant for inhibitory agents against microbial biofilm, with recent advances in research focusing on their role as antibiofilm agents.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH
(2021)
Article
Limnology
Wang Junhao, Mao Yunxiang, Du Guoying, Li Xiaojiao, Tang Xianghai
Summary: Microorganisms play a crucial role in the growth of Pyropia haitanensis. Through metagenomic analysis, it was found that bacteria were the predominant microorganisms in P. haitanensis, with the phylum Proteobacteria being most abundant. The study revealed the importance of microbial metabolism and carbohydrate-active enzymes in the microbial community of P. haitanensis, with key pathways including ABC transport system and plant growth hormone biosynthesis pathway.
JOURNAL OF OCEANOLOGY AND LIMNOLOGY
(2021)
Article
Environmental Sciences
Mengwei Zhang, Zhigao Zhou, Jinfeng Zhang, Yitian Yu, Liwei Sun, Tao Lu, Haifeng Qian
Summary: Difenoconazole can promote microalgae growth at environmental residual concentrations and aquatic microbial communities can self-regulate to cope with difenoconazole-induced stress. The dissemination of antibiotic resistance genes is enhanced in the short-term.
Article
Environmental Sciences
Ramya Sree Boddu, K. Ajay Prabhakar, K. Divakar
Summary: Soil microorganisms are an important source of biocatalysts/enzymes in industrial and agricultural sectors. Traditional microbiological methods have limitations in extracting genetic information from soil microbiome, whereas metagenomics can reveal microbial population and gene information directly.
GEOMICROBIOLOGY JOURNAL
(2022)
Article
Microbiology
Madangchanok Imchen, V. T. Anju, Siddhardha Busi, Mahima S. Mohan, Pattnaik Subhaswaraj, Madhu Dyavaiah, Ranjith Kumavath
Summary: Biofilms formed by microbial cells on surfaces serve as a breeding ground for drug-resistant pathogens and ARG enrichment, but they also play beneficial roles in promoting plant growth and wastewater treatment. Inhibiting biofilm formation through quorum quenching is a feasible approach. Surveillance of biofilm microbiome is crucial for assessing risks and harnessing bioactive potential. Metagenomics is a preferred method for studying biofilm microbiome and discovering new species.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Environmental Sciences
Jing Zhao, Gaofeng Ni, Maria Piculell, Jie Li, Zhetai Hu, Zhiyao Wang, Jianhua Guo, Zhiguo Yuan, Min Zheng, Shihu Hu
Summary: This study investigated the establishment, structure, and microbial community composition of biofilms in three laboratory-scale moving bed biofilm reactors, and found that the depth of living space significantly influenced the biofilm formation and community composition.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Immunology
Li-Juan Lv, Sheng-Hui Li, Ji-Ying Wen, Guang-Yang Wang, Hui Li, Tian-Wen He, Qing-Bo Lv, Man-Chun Xiao, Hong-Li Duan, Min-Chai Chen, Zhou-Ting Yi, Qiu-Long Yan, Ai-Hua Yin
Summary: This study compared the gut microbiome of patients with preeclampsia (PE) and healthy pregnant women. The results showed that the gut microbiota of PE patients had certain enriched species and microbial functions, while the gut microbiome of healthy pregnant women had different enriched species and functions. The diagnostic potential of gut microbial biomarkers for PE was also developed.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Organic
Gregor Tegl, Peter Rahfeld, Katharina Ostmann, John Hanson, Stephen G. Withers
Summary: Functional screening of a metagenomic library derived from a human gut microbiome led to the identification of four active HexNAcase candidates belonging to CAZy family GH20, with the generation of two new thioglycoligases through detailed kinetic analysis. This work demonstrates the rapid development of useful glycoside-forming mutants of HexNAcases, diversifying the pool of biocatalysts for carbohydrate synthesis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Environmental Sciences
Kun Guo, Naicheng Wu, Wei Li, Annette Baattrup-Pedersen, Tenna Riis
Summary: Stream biofilms are complex aggregates of diverse organism groups that are essential for global carbon and nitrogen cycles. The study found that specific phyla dominated the prokaryotic and eukaryotic communities at most sites, with diversity peaking in July and January. Hydrological and physicochemical variables were significant factors in explaining community composition, but a large portion of variation remained unexplained, likely due to unmeasured factors such as light intensity and biological interactions. A multitrophic level perspective is suggested for future biofilm studies to capture the complexity of trophic and non-trophic interactions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Biochemistry & Molecular Biology
Serina L. Robinson, Jorn Piel, Shinichi Sunagawa
Summary: Metagenomics has generated vast amounts of sequencing data revealing the biosynthetic potential of uncultivated microbes. Despite the availability of genome-resolved information on microbial communities from various environments, accurately predicting biocatalytic functions from sequencing data remains challenging, particularly for enzymes involved in secondary metabolism which are crucial for discovering new enzymology.
NATURAL PRODUCT REPORTS
(2021)
Article
Environmental Sciences
Xiuli Chen, Ji Wang, Chaoyi Pan, Lishi Feng, Sili Chen, Shuguang Xie
Summary: Thallium (Tl) is a highly toxic metal that poses a potential threat to organisms when released into the natural environment. This study investigated the response of river sediment microbiome to a Tl spill and found that residual Tl significantly reduced bacterial community diversity. The increase in Bacteroidetes abundance in Tl-impacted sediments suggested their advantage in resisting Tl pressure. Under Tl stress, genes related to carbon fixation and assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. The study also observed an increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) in Tl-impacted sediments, with their abundance significantly correlated with sediment Tl concentration. Procrustes analysis revealed a significant congruence between profiles of MRGs and bacterial communities. The study provided new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.
ENVIRONMENTAL POLLUTION
(2023)
Article
Urology & Nephrology
Ziyan Yan, Yuchen Wang, Wenli Zeng, Renfei Xia, Yanna Liu, Zhouting Wu, Wenfeng Deng, Miao Zhu, Jian Xu, Haijun Deng, Yun Miao
Summary: This study aimed to investigate the structure and diversity of microbial communities on hemodialysis catheter tips during the perioperative period of kidney transplantation. The microbial composition and diversity of the catheter tips were found to be associated with fasting blood glucose levels, and the microorganisms at the catheter tip mostly originated from the catheter outlet skin and peripheral blood.
Article
Engineering, Environmental
Lapo Mughini-Gras, Rozemarijn Q. J. van der Plaats, Paul W. J. J. van der Wielen, Patrick S. Bauerlein, Ana Maria de Roda Husman
Summary: This study highlights the presence of microplastic pollution in a major riverine environment, impacting microbial communities and potential pathogens. High concentrations of microplastics, primarily polyamide and polyvinylchloride, were found. Different microbial compositions were observed on microplastics of varying sizes, with seasonality and methodological effects also playing a role.
Article
Biotechnology & Applied Microbiology
Carl Simon Strittmatter, Anja Poehlein, Axel Himmelbach, Rolf Daniel, Alexander Steinbuchel
Summary: The number of genes encoding beta-oxidation enzymes in Cupriavidus necator H16 is high, but only two operons, A0459-A0464 and A1526-A1531, were expressed during growth with long-chain-length fatty acids (LCFAs). The deletion of these operons had a negative effect on growth with longer chain fatty acids. RNA-Seq analysis revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Uwe Mamat, Manuel Hein, Doerte Grella, Claire S. Taylor, Thomas Scholzen, Ifey Alio, Wolfgang R. Streit, Pol Huedo, Xavier Coves, Oscar Conchillo-Sole, Andromeda-Celeste Gomez, Isidre Gibert, Daniel Yero, Ulrich E. Schaible
Summary: Using a Tn7-based genomic integration system, improved mini-Tn7 delivery plasmids were constructed to label S. maltophilia with sfGFP, mCherry, tdTomato, and mKate2. The transposition of mini-Tn7 transposons had no adverse effects on the fitness of fluorescently labeled S. maltophilia derivatives. The mini-Tn7 elements remained stably integrated in the genome of S. maltophilia over a prolonged period of time in the absence of antibiotic selection pressure.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Muttalip Caliskan, Gereon Poschmann, Mirja Gudzuhn, Daniel Waldera-Lupa, Rebecka Molitor, Christoph Heinrich Strunk, Wolfgang R. Streit, Karl-Erich Jaeger, Kai Stuehler, Filip Kovacic
Summary: Bacteria adapt their membrane phospholipid composition in response to environmental cues and infections. This study investigates the proteomic changes in the biofilm of a phospholipase mutant in P. aeruginosa, revealing alterations in the abundance of biofilm-related systems and unique phosphorylation patterns. The study also suggests that the phospholipase mutant plays a role in regulating iron-uptake pathways and the global adaptive response in P. aeruginosa.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2023)
Article
Microbiology
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kaempfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon- Wo Kwon
Summary: In this study, two strains of bacteria were isolated from wasps in Germany and Korea. Molecular and phenotypic analysis showed that these strains are closely related to known species but also have distinct characteristics. Therefore, it is proposed to name these strains Aristophania vespae.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Juan Guzman, Anja Poehlein, Rolf Daniel, Peter Kaempfer, Andreas Vilcinskas
Summary: Strain G314FT, isolated from Lucilia sericata in Germany, belongs to the genus Vagococcus. It shows high sequence identity with Vagococcus bubulae, Vagococcus martis, and Vagococcus teuberi, indicating that it represents a new species of the genus. The genome of G314FT is the smallest among the closely related species and has differences in amino acid biosynthesis and carbohydrate metabolism.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Chemistry, Physical
Jonas Dittrich, Milana Popara, Jakub Kubiak, Mykola Dimura, Bastian Schepers, Neha Verma, Birte Schmitz, Peter Dollinger, Filip Kovacic, Karl-Erich Jaeger, Claus A. M. Seidel, Thomas-Otavio Peulen, Holger Gohlke
Summary: Maximum entropy methods (MEMs) combine experimental data with prior information to determine posterior distributions. In this study, MEM was used to reconstruct conformational ensembles of the lipase-specific foldase Lif in the apo state using time-resolved Fo''rster resonance energy transfer (FRET) experiments. Distance distributions estimated from molecular dynamics (MD) simulations served as prior information, and FRET experiments were used for optimization. Different force fields (FFs) were tested as priors, resulting in substantially different posterior ensembles. The study also found that MEM can quantify consistencies between experiment and prior or posterior ensembles, and only ensemble-integrated quantities can be reliably obtained.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Delphine Clara Zemp, Nathaly Guerrero-Ramirez, Fabian Brambach, Kevin Darras, Ingo Grass, Anton Potapov, Alexander Roell, Isabelle Arimond, Johannes Ballauff, Hermann Behling, Dirk Berkelmann, Siria Biagioni, Damayanti Buchori, Dylan Craven, Rolf Daniel, Oliver Gailing, Florian Ellsaesser, Riko Fardiansah, Nina Hennings, Bambang Irawan, Watit Khokthong, Valentyna Krashevska, Alena Krause, Johanna Kueckes, Kevin Li, Hendrik Lorenz, Mark Maraun, Miryam Sarah Merk, Carina C. M. Moura, Yeni A. Mulyani, Gustavo B. Paterno, Herni Dwinta Pebrianti, Andrea Polle, Di Ajeng Prameswari, Lena Sachsenmaier, Stefan Scheu, Dominik Schneider, Fitta Setiajiati, Christina Ani Setyaningsih, Leti Sundawati, Teja Tscharntke, Meike Wollni, Dirk Hoelscher, Holger Kreft
Summary: There are still knowledge gaps in how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes in the United Nations Decade on Ecosystem Restoration. This study presents findings from a 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, showing higher indicators of biodiversity and ecosystem functioning in tree islands compared to conventionally managed oil palm. Enriching oil palm-dominated landscapes with tree islands is a promising ecological restoration strategy that does not decrease oil palm yield.
Article
Environmental Sciences
Jimyung Moon, Anja Schubert, Anja Poehlein, Rolf Daniel, Volker Mueller
Summary: To inactivate the Wood-Ljungdahl pathway in Acetobacterium woodii, two subunits of the methylene-tetrahydrofolate reductase were genetically deleted. The mutant was unable to grow on C1 compounds, lactate, ethanol, or butanediol, but could grow on fructose with lower rates and yields compared to the wild-type. Growth on fructose was restored by the addition of an external electron sink, such as glycine betaine + CO2 or caffeate. Transcriptome analyses revealed enzymes potentially involved in mixed acid fermentation (MAF) from fructose in A. woodii.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2023)
Article
Microbiology
Ines Friedrich, Hannes Neubauer, Alisa Kuritsyn, Bernhard Bodenberger, Faina Tskhay, Sara Hartmann, Anja Poehlein, Mechthild Boemeke, Michael Hoppert, Dominik Schneider, Robert Hertel, Rolf Daniel
Summary: By investigating host-associated metaviromes, we found that the classical isolation technique may miss the diversity of non-plaque forming phages. Through direct plaque-based isolation using new hosts, we discovered a higher phage diversity in Brevundimonas and Serratia. This study demonstrates the potential of combining metavirome analysis with traditional isolation techniques to reveal further phage diversity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Green & Sustainable Science & Technology
Najeeb Al-Amin Iddris, Greta Formaglio, Carola Paul, Volker von Gross, Guantao Chen, Andres Angulo-Rubiano, Dirk Berkelmann, Fabian Brambach, Kevin F. A. Darras, Valentyna Krashevska, Anton Potapov, Arne Wenzel, Bambang Irawan, Muhammad Damris, Rolf Daniel, Ingo Grass, Holger Kreft, Stefan Scheu, Teja Tscharntke, Aiyen Tjoa, Edzo Veldkamp, Marife D. Corre
Summary: This full factorial experiment conducted in an Indonesian state-owned industrial oil palm plantation evaluated the effects of reduced management practices on ecosystem functions and biodiversity. The results showed that mechanical weeding exhibited higher multifunctionality and increased plant species diversity compared to herbicide treatment. Furthermore, reduced fertilization and mechanical weeding increased profit and gross margin while achieving similar yields.
NATURE SUSTAINABILITY
(2023)
Article
Microbiology
Dominik Schneider, Aygun Ganbarzade, Sina Post, Daniela Zuehlke, Tjorven Hinzke, Jacqueline Hollensteiner, Anja Poehlein, Katharina Riedel, Rolf Daniel
Summary: The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was found in a hospital wastewater sample in Greifswald, Germany. Its genome consists of one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome contains 5,322 coding sequences, shows high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Raphael Trischler, A. Poehlein, R. Daniel, Volker Mueller
Summary: The human gut harbours a variety of microorganisms which play important roles in digestion, health and well-being. The genus Blautia, commonly found in the gut, has been shown to grow on glycerol and produce acetate and ethanol. This finding not only contributes to our understanding of microbial activity in the gut, but also has potential implications for bioindustrial production of bioethanol from waste glycerol.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Lydia Alberti, Patricia Koenig, Sabine Zeidler, Anja Poehlein, Rolf Daniel, Beate Averhoff, Volker Mueller
Summary: Acinetobacter baumannii, a nosocomial pathogen, exhibits significant metabolic diversity. Growth on L-arabinose was found, and transcriptome analyses identified two gene clusters responsible for the oxidation of pentonates to a-ketoglutarate. These clusters also encode an uptake system and a regulator for specific pentonate oxidation pathways. Despite a cross-talk between these pathways, growth on pentoses was observed in pathogenic Acinetobacter species, while growth on L-arabinose provided benefits for long-term survival and desiccation resistance in A. baumannii ATCC 19606.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tim Boeer, Frank R. Bengelsdorf, Mechthild Boemeke, Rolf Daniel, Anja Poehlein
Summary: This study reports the complete genome sequences of acetogenic strains from the genus Terrisporobacter, along with functional annotation and pathway reconstruction analysis. The study also identifies species-specific nutrient requirements and constructs a model for acetogenesis in Terrisporobacter.
Article
Microbiology
Simone Anza, Dominik Schneider, Rolf Daniel, Michael Heistermann, Somboon Sangmaneedet, Julia Ostner, Oliver Schuelke
Summary: Maternal glucocorticoids (GCs) can have detrimental effects on offspring development, particularly during early gestation. This study found that high maternal GC levels during early gestation were associated with reduced bacterial richness in the offspring's gut microbiota. The effect of maternal GCs on the gut microbiota worsened with offspring age and was 10 times stronger than the effect of exposure during late prenatal or postnatal periods.