Article
Multidisciplinary Sciences
Ke Zhang, Rongnan Lin, Yujun Chang, Qing Zhou, Zhi Zhang
Summary: 16S-FASAS is a valuable tool for processing and interpreting full-length 16S rRNA gene sequencing results. It includes modules for data quality control, denovo assembly, annotation, and visualization, and has demonstrated excellent performance on mock communities and fecal samples.
Article
Environmental Sciences
Marielle Hollstein, Mattheau Comerford, Michael Uhl, Michael Abel, Scott P. Egan, Lauren B. Stadler
Summary: Constructed Wetlands (CWs) are effective and sustainable for wastewater treatment, with microbial communities playing a significant role in pollutant removal. This study analyzed the microbial communities in a full-scale CW treating wastewater from a plastics manufacturing plant. The results showed temporal shifts in bacterial communities and a correlation between microbial biodiversity and water quality improvements. Despite changes in microbial community structure after a freeze event, the CW demonstrated functional resilience.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Microbiology
Nikhil Bose, Sean D. Moore
Summary: This study challenges the belief that 16S rRNA gene variable region sequences provide little information for intra-genus classification and that single nucleotide variations within them are inconsequential. The researchers found that even small sequence changes in variable regions can negatively affect the performance of 16S rRNA in Escherichia coli. Additionally, they discovered that certain Escherichia and Shigella species can be distinguished using a multi-allelic 16S rRNA variable region single nucleotide polymorphism (SNP). The study emphasizes the importance of considering variable region sequences in taxonomic assignments and highlights the potential for multiple 16S rRNA gene alleles to provide more detailed phylogenetic and taxonomic information.
MICROBIOLOGY SPECTRUM
(2023)
Article
Environmental Sciences
Moonil Kim, Fenghao Cui
Summary: This study used 16S rRNA gene pyrosequencing to identify bacterial communities in wastewater and investigate the evolution of bacterial communities in the Anammox process. Four lab-scale Anammox reactors inoculated with different types of wastewater treatment sludge were operated under identical conditions for over 400 days. The study found that the presence of the Nitrospira genus and symbiotic association with other functional groups can lead to successful nitrogen removal in the Anammox process.
Article
Agricultural Engineering
Philip M. Roveto, Adwaith Gupta, Andrew J. Schuler
Summary: The study showed that surface skewness has significant impacts on biofilm development, with surfaces with negative skewness promoting nitrite oxidation and biomass growth. Analysis of 16s rRNA gene sequencing revealed differences in bacterial populations, and PCoA analysis indicated divergence between populations on skew and flat surfaces.
BIORESOURCE TECHNOLOGY
(2021)
Article
Environmental Sciences
Konstantina Tsigkou, Antonia Terpou, Laura Treu, Panagiotis G. Kougias, Michael Kornaros
Summary: The study focused on utilizing olive mill wastewater for efficient biogas production under thermophilic conditions, testing its performance and analyzing the microbial community. Results showed potential for further exploitation of olive mill wastewater for biogas production.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Chemistry, Multidisciplinary
Wenping Liu, Yue Li, Huanhuan Lu, Youjin Hao, Ke Zhang, Xiaoqun Dang, Xiaodong Fan, Huan Zhang, Zeyang Zhou, Chaodong Zhu, Arong Luo, Dunyuan Huang
Summary: Insect-associated microorganisms are important for insect health and development. This study analyzed the bacterial community in the larval gut, nest soil, and brood provision of Osmia excavata. Sequencing of the microorganisms revealed differences in diversity and composition among the three environments, but similarities were observed in the gut microbiota across different locations. The results suggest that habitat similarity influences the bacterial community diversity in the gut of O. excavata.
APPLIED SCIENCES-BASEL
(2023)
Article
Environmental Sciences
Jonathan Wijaya, Seungdae Oh
Summary: The study developed a machine-learning framework based on microbiome data to successfully predict the operational characteristics of three representative full-scale wastewater systems and identified Ferruginibacter as a keystone taxon in MBR systems. The study demonstrated that the model can detect complex and non-linear relationships between keystone taxa and environmental conditions that conventional methods cannot.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biology
Yuan-Mao Hung, Wei-Ni Lyu, Ming-Lin Tsai, Chiang-Lin Liu, Liang-Chuan Lai, Mong-Hsun Tsai, Eric Y. Chuang
Summary: This study compares the accuracy of several widely-used 16S sequence classifiers and recommends the most suitable 16S training dataset for each classifier.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Multidisciplinary Sciences
Jinuk Jeong, Kyeongeui Yun, Seyoung Mun, Won-Hyong Chung, Song-Yi Choi, Young-do Nam, Mi Young Lim, Chang Pyo Hong, ChanHyeok Park, Yong Ahn, Kyudong Han
Summary: This study compared sFL16S and V3V4 sequencing methods on human gut microbiota samples and found that sFL16S showed better resolution and identification accuracy at the species level. This indicates that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Weihong Zhang, Wenke Yuan, Lu Chen, Chen Ye, Ying Jiang, Yuyi Yang
Summary: The study revealed the unique characteristics of the microbial communities on microplastics, including the enrichment of opportunistic pathogens and bacteria with biodegradation functions on microplastics, as well as the differences in bacterial communities between microplastics and water, sediment, and soil.
Article
Biotechnology & Applied Microbiology
Weihong Zhang, Lu Chen, Haiyang Chen, Wenzhi Liu, Yuyi Yang
Summary: This study investigates the assembly processes and potential ecological mechanisms of bacterial communities on microplastics in the Three Gorges Reservoir area. The results show that the assembly processes are dominated by geographic dispersal limitation, which differs from those in water and sediment. The bacterial communities on microplastics have a narrower niche width and higher similarity to sediment than to water.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
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
Biodiversity Conservation
Hui Gao, Sai Jiang, Yinan Wang, Meng Hu, Yuyan Xue, Bing Cao, Hailong Dou, Ran Li, Xianfeng Yi, Lina Jiang, Bin Zhang, Yujian Li
Summary: There are numerous microorganisms in the gut of insects that have a symbiotic relationship with the host, influencing various aspects such as nutrition, physiology, development, immunity, and stress tolerance. However, the composition of gut microbes in Hyphantria cunea is still unclear. This study used PacBio sequencing technology to analyze the intestinal microbiota of H. cunea larvae feeding on different host plants. The results revealed significant differences in the microbial communities based on host diet, laying a foundation for understanding the interaction between intestinal microorganisms and H. cunea and suggesting new strategies for prevention and control.
BIODIVERSITY DATA JOURNAL
(2023)
Article
Plant Sciences
Chakrit Bunyoo, Peerapat Roongsattham, Sirikorn Khumwan, Juthaporn Phonmakham, Passorn Wonnapinij, Arinthip Thamchaipenet
Summary: This study investigated the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions using 16S rRNA amplicon sequencing. The results showed that Proteobacteria was the dominant phylum in duckweed samples. A total of 24 microbial genera were identified as a core microbiome, with consistent proportions across all duckweed subtypes. The diversity of microbial communities decreased after nutrient-deficient stress, but the relative abundance of certain genera significantly increased. Functional prediction of the metagenome data revealed enrichment of essential pathways involved in DAB colonization and biodegradation under stress condition.
Article
Energy & Fuels
Lia Paula Poloni Batista, Ana Paula Paulinetti, Antonio Djalma Nunes Ferraz Jr, Roberta Albanez, Suzana Maria Ratusznei, Claudia Etchebehere, Giovanna Lovato, Jose Alberto Domingues Rodrigues
Summary: The goal of this study was to compare the efficiency of a single-stage and two-stage system for anaerobic digestion and bioenergy production using a sequencing batch and fed-batch biofilm reactor. The results showed that the single-stage system achieved better performance with high organic matter removal, methane productivity, and yield. Temperature also influenced the microbial community diversity and the abundance of Methanosarcina genus.
CHEMICAL ENGINEERING AND PROCESSING-PROCESS INTENSIFICATION
(2023)
Article
Engineering, Environmental
Nerea Uri-Carreno, Per H. Nielsen, Krist V. Gernaey, Qian Wang, Ulla Gro Nielsen, Marta Nierychlo, Susan H. Hansen, Lisette Thomsen, Xavier Flores-Alsina
Summary: Membrane-Aerated Biofilm Reactors (MABRs) are an effective alternative for wastewater treatment plants (WWTP) with enhanced nitrogen removal capacity and reduced energy consumption. This study demonstrates the impact of oxidation-reduction potential (ORP) on the performance of MABRs, showing that low ORP conditions can hinder nitrification. By increasing ORP and replacing/cleaning membranes, nitrification rates and the abundance of nitrifying organisms were significantly improved. The study also suggests that low ORP conditions promote the reduction of iron and sulfur compounds, leading to deposition in the biofilm and inhibiting nitrifiers growth.
CHEMICAL ENGINEERING JOURNAL
(2023)
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
Biochemical Research Methods
Tue Sparholt Jorgensen, Martin Schou Pedersen, Kai Blin, Franziska Kuntke, Henrik K. Salling, Rasmus L. Marvig, Thomas Y. Michaelsen, Mads Albertsen, Helene Larsen
Summary: SpikeSeq is a Sanger sequencing-based method for detecting Variants of Concern (VOC) and key mutations of the novel coronavirus. It is simple, cost-effective, and can be implemented in any diagnostic lab.
JOURNAL OF VIROLOGICAL METHODS
(2023)
Article
Engineering, Environmental
Agustina Ziliani, Patricia Bovio-Winkler, Angela Cabezas, Claudia Etchebehere, Hector A. Garcia, Carlos M. Lopez-Vazquez, Damir Brdjanovic, Mark C. M. van Loosdrecht, Francisco J. Rubio-Rincon
Summary: Ca. Accumulibacter was found to be the predominant microorganism (67 +/- 5% relative FISH bio-abundance) in a lab-scale sequential batch reactor for enhanced biological phosphorus removal (EBPR) using glucose and acetate as carbon sources (1:1 COD-based ratio). The reactor showed high performance in terms of P/C ratio, phosphorous release and uptake, and overall kinetic and stoichiometric parameters for EBPR systems. The research also discovered that Ca. Accumulibacter can potentially utilize glucose as the sole carbon source for phosphate removal, challenging conventional theories.
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
Engineering, Environmental
Giulia Dottorini, Dorottya Sarolta Wagner, Mikkel Stokholm-Bjerregaard, Sergey Kucheryavskiy, Thomas Yssing Michaelsen, Marta Nierychlo, Miriam Peces, Rohan Williams, Per Henrik Nielsen, Kasper Skytte Andersen, Per Halkjaer Nielsen
Summary: Well-functioning and stable microbial communities are critical for the operation of activated sludge wastewater treatment plants. Bioaugmentation has the potential to recover deteriorated systems or support specific processes, but its application in full-scale plants is problematic. In a transplantation experiment between two similar full-scale plants, the treatment performance and effluent quality remained stable, but the recipient plant's microbial community almost completely restored its pre-transplantation structure after 40 days. The addition of unique species from the donor AS was not successful in increasing the abundance of desired species or reducing unwanted bacteria in the recipient plant.
Article
Microbiology
Ayesha Z. Beg, Faraz Rashid, Absar Talat, Mohd Azam Haseen, Nadeem Raza, Kafil Akhtar, Morten Kam Dahl Dueholm, Asad U. Khan
Summary: The Fap operon of Pseudomonas aeruginosa plays a crucial role in pathoadaptation during pulmonary infection. Its presence increases pathogenesis and biofilm sustainability by modulating bacterial physiology. Targeting amyloids could be a potential clinical application to exploit the pathoadaptive role of Fap in pulmonary infections. The genetic conservation and extracellular exposure of Fap make it a commendable target for interventions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Patricia Bovio-Winkler, Leandro D. Guerrero, Leonardo Erijman, Pia Oyarzua, Maria Eugenia Suarez-Ojeda, Angela Cabezas, Claudia Etchebehere
Summary: This study used a metagenomic approach to investigate the diversity and metabolic potential of Chloroflexi in three environmentally different bioreactors. The genomes of 17 new Chloroflexi species were assembled, two of which are proposed as new Candidatus genus. Common metabolic features were found in these genomes, including anaerobic metabolism, fermentative pathways, and genes coding for hydrolytic enzymes. The analysis also indicated a potential role of Chloroflexi in nitrogen conversion and adhesion.
Article
Engineering, Environmental
Jose A. Contreras, Edgardo I. Valenzuela, Patricia Bovio-Winkler, Claudia Etchebehere, Carmen Gabaldon, Guillermo Quijano
Summary: The anaerobic oxidation of methane coupled to denitrification (N-AOM) is a promising biotechnology for reducing the environmental impact of anaerobic effluents. In this study, a continuous N-AOM reactor was used to evaluate its performance, achieving methane elimination capacity values of 20-39 g m -3h- 1 with NO3- as the electron acceptor, and 48-61 g m -3h- 1 with a mixture of NO3- and NO2-. The pH value was found to be a critical factor influencing the process. Metagenomic analysis revealed potential metabolic mechanisms involved in N-AOM.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biodiversity Conservation
B. M. Dellagnezze, P. Bovio-Winkler, C. Lavergne, D. A. Menoni, F. Mosquillo, L. Cabrol, M. Barret, C. Etchebehere
Summary: The activity of methanogenic archaea is expected to be affected by warmer temperatures, leading to increased greenhouse gas emissions in the Arctic. A study was conducted to investigate microbial adaptation and tolerance to higher temperatures and acetate concentrations. The results showed that acetate amendment significantly changed the archaeal diversity, favoring methanogens from Methanosarcinales. Temperature did not have a significant influence on methanogens' diversity, indicating their adaptability to warmer conditions. The study also revealed faster microbial response to CH4 production rates at warmer temperatures, providing insights for potential biotechnological applications.
Article
Environmental Sciences
Chew Lee Leong, Seow Wah How, Mohamad Fairus Rabuni, Alijah Mohd Aris, Bee Chin Khor, Thomas P. Curtis, Adeline Seak May Chua
Summary: Conventionally, high DO concentrations are required for nitrification in biological nitrogen removal (BNR), making the process energy intensive. However, recent studies have shown that efficient ammonium removal and energy reduction can be achieved by operating nitrification at low DO concentrations. This study evaluated the feasibility of nitrogen removal from low COD/N tropical municipal wastewater using a low-DO oxic anoxic process. The results demonstrated high removal efficiency for ammonium and total nitrogen under low DO conditions, contributing to energy efficiency and sustainability.
Article
Environmental Sciences
Yuen Theng Cheong, Adeline Seak May Chua, Gek Cheng Ngoh
Summary: This study demonstrates the use of biodegradable deep eutectic solvent (DES) combined with assistive heating techniques for biomass pretreatment, resulting in an energy-efficient extraction. Sequential ultrasonic irradiation-microwave heating (UMAE) is found to be the most effective method for lignin extraction, achieving a delignification efficiency of 82.7% within 1 hour. The DES-incorporated UMAE method offers a 40% reduction in energy consumption and a 90% decrease in pretreatment duration compared to conventional methods.
WASTE AND BIOMASS VALORIZATION
(2023)
Article
Neurosciences
Yogesh Singh, Christoph Trautwein, Joan Romani, Madhuri S. S. Salker, Peter H. H. Neckel, Isabel Fraccaroli, Mahkameh Abeditashi, Nils Woerner, Jakob Admard, Achal Dhariwal, Morten K. D. Dueholm, Karl-Herbert Schaefer, Florian Lang, Daniel E. E. Otzen, Hilal A. A. Lashuel, Olaf Riess, Nicolas Casadei
Summary: Braak's hypothesis suggests that the progression of Parkinson's disease from the peripheral to the central nervous system can be monitored by detecting the accumulation of alpha-Synuclein protein. This study used various techniques to investigate the role of the gut microbiome in regulating alpha-Synuclein accumulation and found that dysbiosis of the gut microbiome can contribute to Parkinson's disease pathology.
MOLECULAR NEURODEGENERATION
(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.
