Applied and Environmental Science
Research Article | Applied and Environmental ScienceTaxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial CommunityUrban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge...
Research Article | Applied and Environmental ScienceA Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus DetectionTo facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral...
Observation | Applied and Environmental ScienceA Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine PathogensAminoglycosides are important antimicrobials used worldwide for prophylaxis and/or therapy in multiple production animal species. The emergence of new resistance genes jeopardizes current pathogen detection and treatment methods. The risk of resistance gene transfer to other animal and human pathogens is elevated when resistance genes are carried by mobile genetic elements. This study identified a new variant of a spectinomycin/...
Research Article | Applied and Environmental ScienceInhibition of Cyanobacterial Growth on a Municipal Wastewater Sidestream Is Impacted by TemperatureCyanobacteria are viewed as promising platforms to produce fuels and/or high-value chemicals as part of so-called “biorefineries.” Their integration into wastewater treatment systems is particularly interesting because removal of the nitrogen and phosphorus in many wastewater streams is an expensive but necessary part of wastewater treatment. In this study, we evaluated strategies for cultivating Synechococcus sp. strain PCC...
Research Article | Applied and Environmental ScienceAir-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne PathogensMaintaining product safety and reducing the carbon footprint of production are two sustainability goals of the livestock industry. The objective of this study was to study the impact of Tasco, a product derived from the brown macroalga Ascophyllum nodosum, on the rumen microbiome and its function. The inclusion of Tasco altered both rumen and fecal microbiota levels without affecting rumen fermentation. Tasco reduced fecal...
Research Article | Applied and Environmental ScienceA Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial CompositionsBy incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option...
Research Article | Applied and Environmental ScienceHeat Resistance Mediated by pLM58 Plasmid-Borne ClpL in Listeria monocytogenesListeria monocytogenes is a dangerous food pathogen causing the severe illness listeriosis that has a high mortality rate in immunocompromised individuals. Although destroyed by pasteurization, L. monocytogenes is among the most heat-resistant non-spore-forming bacteria. This poses a risk to food...
Research Article | Applied and Environmental SciencePlasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria triticiDisease control through fungicides remains an important means to protect crops from fungal diseases and to secure the harvest. Plant-pathogenic fungi, especially Zymoseptoria tritici, have developed resistance against most currently used active ingredients, reducing or abolishing their efficacy. While target site modification is the most common resistance mechanism against single modes of action, active efflux of multiple drugs...
Research Article | Applied and Environmental ScienceCollection of Viable Aerosolized Influenza Virus and Other Respiratory Viruses in a Student Health Care Center through Water-Based Condensation GrowthThe significance of virus aerosols in the natural transmission of respiratory diseases has been a contentious issue, primarily because it is difficult to collect or sample virus aerosols using currently available air sampling devices. We tested a new air sampler based on water vapor condensation for efficient sampling of viable airborne respiratory viruses in a student health care center as a model of a real world environment. The new...
Research Article | Applied and Environmental ScienceVirioplankton Assemblage Structure in the Lower River and Ocean Continuum of the AmazonThe Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the...