Article
Environmental Sciences
Luca Nalbone, Antonio Panebianco, Filippo Giarratana, Marie Russell
Summary: Nile Red is a lipophilic, metachromatic, and solvatochromic dye used to aid in the identification of microplastics in routine analysis of biological samples. However, its use in biota faces challenges, especially in recognizing small fragments and distinguishing them from organic residues.
MARINE POLLUTION BULLETIN
(2021)
Article
Plant Sciences
Jinjie An, Xin Miao, Lulu Wang, Xu Li, Xiaomin Liu, Hongbo Gao
Summary: By staining the chloroplast envelope with fluorescent dyes, such as Rhodamine or Nile red, the integrity of isolated chloroplasts can be easily checked and distinguished between broken and intact chloroplasts. This method is convenient, quick, and can effectively prevent errors caused by broken chloroplasts in experiments.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Chun Wang, Lijuan Jiang, Ruiqing Liu, Meilin He, Xiaoyu Cui, Changhai Wang
Summary: Monitoring microplastics using the Nile red staining protocol has emerged as a new method, but it still has limitations such as susceptibility and complexity. This study explored the effects of various factors on Nile red staining in microplastics analysis and proposed solutions. Based on fluorescence color and intensity, different types of microplastics could be distinguished, and an improved protocol was suggested to streamline the methodology in microplastics analysis.
MARINE POLLUTION BULLETIN
(2021)
Article
Chemistry, Multidisciplinary
Angelica Bianco, Luca Carena, Nina Peitsaro, Fabrizio Sordello, Davide Vione, Monica Passananti
Summary: Microplastics have become a growing concern for health due to their presence in even remote and pristine environments, ranging from Arctic snow to the Marianne Trench. The occurrence and impact of nanoplastics in ecosystems are largely unknown, mainly due to limitations in current analytical techniques. This study presents a method for quantifying plastic particles in the size range of 0.6-15 μm using flow cytometry, showing promising results in detecting various types of plastic particles.
ENVIRONMENTAL CHEMISTRY LETTERS
(2023)
Article
Environmental Sciences
Joana C. Prata, Joao P. da Costa, Antonio Jose Silva Fernandes, Florinda Mendes da Costa, Armando C. Duarte, Teresa Rocha-Santos
Summary: Combining Nile Red staining with micro-Raman spectroscopy can improve efficiency and accuracy in the identification of microplastics.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Marine & Freshwater Biology
Joana C. Prata
Summary: This study evaluated the influence of plastic particle characteristics on fluorescent emissions after Nile Red staining. It found that particle color significantly affected fluorescence, with different colors showing varying levels of fluorescence intensity. This highlights the importance of considering the interference of plastic pigments in the detection and characterization of plastic particles.
JOURNAL OF SEA RESEARCH
(2023)
Article
Environmental Sciences
Nelle Meyers, Ana Catarino, Annelies M. Declercq, Aisling Brenan, Lisa Devriese, Michiel Vandegehuchte, Bavo De Witte, Colin Janssen, Gert Everaert
Summary: Microplastic pollution is a growing concern due to limited knowledge and difficulties in surveying and monitoring. An innovative approach combining high-throughput screening with automation has been developed to train machine learning models for plastic detection and polymer identification, demonstrating high accuracy in detecting and identifying plastic particles in environmental samples. This method represents a cost-effective, time-efficient, and reliable way to characterize microplastics.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Spectroscopy
Qian Feng, Yiming Song, Yixuan Ma, Yan Deng, Pengyue Xu, Kangjia Sheng, Yongmin Zhang, Jianli Li, Shaoping Wu
Summary: To achieve the visual monitoring of H2Sn levels in vivo, a series of fluorescent probes NR-BS were constructed, among which probe NR-BS4 was optimized due to its wide linear range and low interference from biothiols. NR-BS4 also exhibited a broad pH tolerance range and high sensitivity. The intracellular imaging studies indicated that NR-BS4 can be successfully used to monitor the levels of exogenous and endogenous H2Sn in vivo.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Polymer Science
Se-Bin Oh, Doo-Hong Park, Sung-Chul Hong
Summary: In this study, selective fluorescence staining of microplastics in water was successfully achieved through the combination of a dye and a surfactant, avoiding tedious separation, drying, and staining procedures. This method provides a potential approach for rapid detection and monitoring of microplastics.
Article
Polymer Science
Veronica Canovas, Salvador Garcia-Chumillas, Fuensanta Monzo, Lorena Simo-Cabrera, Carmen Fernandez-Ayuso, Carmen Pire, Rosa Maria Martinez-Espinosa
Summary: The study optimized a method using Haloferax mediterranei as a model to visualize and analyze intracellular PHA granules in living cells through double-fluorescence staining using confocal fluorescence microscopy. This method allows for easy monitoring of PHA production capability in new haloarchaea isolates.
Article
Environmental Sciences
Maria Krishna de Guzman, Mirjana Andjelkovic, Vesna Jovanovic, Jaehak Jung, Juyang Kim, Lea Ann Dailey, Andreja Rajkovic, Bruno De Meulenaer, Tanja Cirkovic Velickovic
Summary: The presence of microplastics in Manila clams from the Korean market was studied. Microplastics of various shapes, mainly composed of polystyrene, were detected. There was a weak correlation between the concentration of microplastics and the physical attributes of the clams. The estimated intake of microplastics by the Korean population through consuming Manila clams was substantial.
MARINE POLLUTION BULLETIN
(2022)
Article
Biochemical Research Methods
Michael T. Sturm, Harald Horn, Katrin Schuhen
Summary: In recent years, there has been extensive research on developing a cost-effective and easily applicable method for detecting microplastics using Nile red and its derivatives. Additionally, the influence of different solvents and water pH values on the dyeing process was investigated by analyzing fluorescence spectra. The developed method was also tested on sea salt samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Shuliang Song, Qiang Wei, Ke Wang, Qiong Yang, Yu Wang, Aiguo Ji, Guanjun Chen
Summary: This study used fluorescently labeled PM to investigate its distribution and pharmacokinetics in vivo. The results showed that FITC-PM had high stability and tended to be distributed in the kidney, liver, and at lower concentrations in the heart, spleen, and lungs after tail vein injection. Pharmacokinetic analysis revealed appropriate elimination rate constant, half-life time, and clearance rate for FITC-PM. The studies of pharmacokinetics and tissue distribution provided basic information that can be used to further clarify the pharmacodynamic mechanisms of PM.
Article
Chemistry, Organic
Rabi Sankar Das, Ayan Mukherjee, Samiran Kar, Tapas Bera, Shreya Das, Arunima Sengupta, Samit Guha
Summary: This article describes a novel red fluorescent mechanically interlocked molecule with dual targeting functionality for live cancer cell specific active targeting and imaging of malignant lysosomes.
Article
Chemistry, Physical
Guobin Mao, Silu Ye, Wen Yin, Yang Yang, Xinghu Ji, Jin He, Yingxia Liu, Junbiao Dai, Zhike He, Yingxin Ma
Summary: This study developed a rapid and reliable diagnostic method for detecting the virus causing COVID-19. The method utilized Si-FITC nanoparticles for fluorescent immunoassay, achieving high sensitivity and accuracy.
Review
Microbiology
Hans-Curt Flemming, Eric D. van Hullebusch, Thomas R. Neu, Per H. Nielsen, Thomas Seviour, Paul Stoodley, Jost Wingender, Stefan Wuertz
Summary: In this review, the authors revisit the understanding of the biofilm matrix and discuss the diversity of its components and the novel aspects of their functional interactions. The biofilm matrix plays a crucial role in stabilizing microbial cells and fulfilling various functions. It is dynamic and influenced by physico-chemical and biological interactions as well as environmental conditions.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Environmental Sciences
J. M. S. Oliveira, J. S. Poulsen, E. Foresti, J. L. Nielsen
Summary: A multiple stage anaerobic system was proven effective for reductive decolorization of azo dyes in the presence of sulfate. The system achieved significant bulk color removal and organic matter and sulfate reduction in separate reactors. By utilizing amplicon sequencing and correlation analysis, the microbial communities and pathways involved in azo dye removal were identified, with reductive decolorization being mainly associated with hydrogen-producing pathways and the involvement of an azoreductase from Lactococcus lactis. The findings enhance our understanding of the role of different microbial communities in anaerobic treatment of azo dyes and can aid in the design of improved solutions for textile effluent treatment.
Article
Ecology
Mantas Sereika, Francesca Petriglieri, Thomas Bygh Nymann Jensen, Artur Sannikov, Morten Hoppe, Per Halkjaer Nielsen, Ian P. G. Marshall, Andreas Schramm, Mads Albertsen
Summary: Cable bacteria are centimeter-long filamentous bacteria capable of long-distance electron transfer. They are currently classified into two candidate genera: Candidatus Electronema, found in freshwater, and Candidatus Electrothrix, found in saltwater. To address the lack of complete genomic information, researchers performed Nanopore long-read and Illumina short-read shotgun sequencing, resulting in the recovery of multiple cable bacteria genomes. Phylogenomic analysis classified two circular genomes as novel species: Ca. Electronema halotolerans and Ca. Electrothrix laxa. The discovery of Ca. Electronema halotolerans in brackish-water sediment suggests its evolutionary link between marine and freshwater cable bacteria lineages.
Article
Engineering, Environmental
Morten Kam Dahl Dueholm, Maaike Besteman, Emil Juel Zeuner, Marie Riisgaard-Jensen, Morten Eneberg Nielsen, Sofie Zacho Vestergaard, Soren Heidelbach, Nicolai Sundgaard Bekker, Per Halkjaer Nielsen
Summary: A study investigated the genomic potential for exopolysaccharide biosynthesis in bacterial species typical in activated sludge (AS) systems based on genome mining and gene synteny analyses. Putative gene clusters associated with the biosynthesis of various exopolysaccharides were identified in AS bacteria. This study provides a comprehensive overview of the genome-resolved potential for these exopolysaccharides in AS bacteria and contributes to a better understanding of EPS composition in wastewater treatment systems.
Article
Agricultural Engineering
Agnieszka Garlicka, Katarzyna Umiejewska, Per Halkjaer Nielsen, Adam Muszynski
Summary: The aim of this project was to increase methane production by combining feedstock pretreatment and co-digestion of maize silage with thickened excess sludge. Results showed that pretreatment of sludge alone increased methane production from 0.192 Nml/gVS (sludge + maize silage) to 0.220 Nml/gVS (pretreated sludge + maize silage). However, the energy balance indicated that the additional energy generated was not enough to cover the energy expenditure for the mechanical pretreatment. 16S rRNA gene amplicon sequencing revealed the composition of the microbial community, with Chloroflexi, Bacteroidota, Firmicutes, Proteobacteria, and Actinobacteriota being the most abundant bacteria phyla.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Jan Struckmann Poulsen, Jeppe Lund Nielsen
Summary: Synthetic plastics, such as PET, are widely used but pose a major threat due to their environmental persistence. The bacterium I. sakaiensis has been discovered to solely thrive on degrading PET films and its monomers. By analyzing protein expression, it was revealed that PET and its monomers induce the MHETase and affect two major pathways: the TCA cycle and the beta-oxidation pathway. The increased expression of proteins involved in these pathways suggests their importance in the degradation process.
JOURNAL OF PROTEOMICS
(2023)
Article
Engineering, Environmental
Martin Hjorth Andersen, Lisette Thomsen, Mikkel Stokholm-Bjerregaard, Susan Hove Hansen, Mads Albertsen, Per Halkjaer Nielsen, Soren Eriksen
Summary: The partial nitritation/anammox process is a popular approach for removing nitrogen from sidestreams, but it requires extensive surveillance and monitoring due to its sensitivity to disturbances. In this study, we utilized online sensor data and Nanopore DNA sequencing to monitor the microbial community and detect system disturbances in two full-scale deammonification reactors over a year. DNA surveillance revealed unexpected variations in anammox bacteria, and the composition and dynamics of the surrounding community indicated causes for occasional process disturbances. Monitoring the ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) could potentially optimize reactor operation. The use of frequent DNA sequencing was found to be an important supplement to online sensor data for process surveillance and control.
Article
Agricultural Engineering
Jan Struckmann Poulsen, Alba Trueba-Santiso, Juan M. Lema, Simon Gregersen Echers, Reinhard Wimmer, Jeppe Lund Nielsen
Summary: In this study, the biodegradability of PBAT monomers in thermophilic conditions was investigated using anaerobic digester sludge. 13C-labelled monomers and proteogenomics were used to track labelled carbon and identify the microorganisms involved in the process. Bacteroides, Ichthyobacterium, and Methanosarcina were found to be directly involved in the metabolization of at least one monomer.
BIORESOURCE TECHNOLOGY
(2023)
Article
Plant Sciences
Jan Struckmann Poulsen, Christina Kjaerager Nielsen, Nina Ahrendt Pedersen, Reinhard Wimmer, Teis Esben Sondergaard, Nadieh de Jonge, Jeppe Lund Nielsen
Summary: Proteomics analysis revealed that combining methicillin with three cannabinoid compounds could decrease energy production and increase the production of penicillin-binding protein 2 (PBP2), which is associated with antibiotic resistance in MRSA.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Environmental Sciences
Maria Takman, Ola Svahn, Catherine Paul, Michael Cimbritz, Stefan Blomqvist, Jan Struckmann Poulsen, Jeppe Lund Nielsen, Asa Davidsson
Summary: This study examined a full-scale membrane bioreactor (MBR) with ultrafiltration and granular activated carbon (GAC) for the potential reuse of treated water as drinking water or for irrigation. The MBR removed most of the bacteria, while the GAC removed a significant amount of organic micropollutants. Seasonal variations in inflow and infiltration resulted in concentrated influent during summer and diluted influent in winter. The effluent concentrations of E. coli met irrigation water standards but exceeded drinking water standards in Sweden.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Marie Riisgaard-Jensen, Giulia Dottorini, Marta Nierychlo, Per Halkjaer Nielsen
Summary: The immigration of bacteria in influent wastewater has a strong impact on the microbial community of activated sludge in wastewater treatment plants. The use of primary settlers can selectively increase or reduce the abundance of certain bacteria. The process of primary settling changes the microbial community of influent wastewater and can be a candidate for upstream control to optimize the assembly of microbial communities in activated sludge.
Article
Multidisciplinary Sciences
Troels Pank Arboll, Sophie Lund Rasmussen, Nadieh de Jonge, Anne Haslund Hansen, Cino Pertoldi, Jeppe Lund Nielsen
Summary: The recent development of ancient DNA sequencing techniques has provided valuable insights into previous civilizations, but their full potential has not yet been realized. In this study, researchers extracted ancient DNA from a 2900-year-old clay brick from the palace of King Ashurnasirpal II in Nimrud, Iraq. They identified 34 unique taxonomic groups of plants, making the pioneering discovery that ancient DNA can be effectively protected and successfully extracted from well-preserved clay. Future research in this area has significant scientific prospects and could lead to a deeper understanding of ancient and lost civilizations.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Jan Struckmann Poulsen, Williane Vieira Macedo, Torben Bonde, Jeppe Lund Nielsen
Summary: This study used genomic techniques and engineered systems to investigate the biogas production potential and microbial communities involved in anaerobic digestion of lignocellulosic-rich residues, revealing the key roles of diverse microbial populations in cellulose degradation and methane production.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2023)
Article
Biotechnology & Applied Microbiology
Maarten D. Verhoeven, Per H. Nielsen, Morten K. D. Dueholm
Summary: The researchers introduced an experimental setup, combining 16S rRNA gene amplicon sequencing with plating of dispersed activated sludge bacteria, to rapidly identify the growth conditions that allow for the isolation of key microbial species in activated sludge. They found that agarose plates supplemented with various carbon sources support the growth of many previously uncultivated activated sludge bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Engineering, Environmental
A. Margarida Teixeira, Ivone Vaz-Moreira, David Calderon-Franco, David Weissbrodt, Sabina Purkrtova, Stanislav Gajdos, Giulia Dottorini, Per Halkjaer Nielsen, Leron Khalifa, Eddie Cytryn, Jan Bartacek, Celia M. Manaia
Summary: Urban wastewater treatment plants (UWTPs) are crucial for reducing pollutant load and protecting water bodies, but they also emit antibiotic resistant bacteria and resistance genes, which have impacts on downstream environments. This study tested a set of biomarkers for antibiotic resistance monitoring and found that qPCR can be a cost-effective and technically accessible approach for monitoring wastewater and downstream environments.
