Applied and Environmental Science
Research Article | Applied and Environmental ScienceAdventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic AcidsThe use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of...
Research Article | Applied and Environmental ScienceMethylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater EnvironmentsMost of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study...
Research Article | Applied and Environmental ScienceDiverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador...Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.
Observation | Applied and Environmental ScienceSalmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli IsolateSGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the...
Observation | Applied and Environmental ScienceA Novel Trimethoprim Resistance Gene, dfrA35, Characterized from Escherichia coli from CalvesThe presence of dfrA35 associated with ISCR2 in Escherichia coli from animals, as well as its presence in other E. coli strains from different sources and countries and in Acinetobacter, highlights the global...
Research Article | Applied and Environmental ScienceEffects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and ResistomesA controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce...
Research Article | Applied and Environmental ScienceMarine RNA Virus Quasispecies Are Distributed throughout the OceansVery little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new...
Research Article | Applied and Environmental ScienceInterspecies Social Spreading: Interaction between Two Sessile Soil Bacteria Leads to Emergence of Surface MotilityThe wealth of studies on microbial communities has revealed the complexity and dynamics of the composition of communities in many ecological settings. Fewer studies probe the functional interactions of the community members. Function of the community as a whole may not be fully revealed by characterizing the individuals. In our two-species model community, we find an emergent trait resulting from the interaction of the soil bacteria...
Research Article | Applied and Environmental ScienceWood-Derived Dietary Fibers Promote Beneficial Human Gut MicrobiotaThe architecture of the gut bacterial ecosystem has a profound effect on the physiology and well-being of the host. Modulation of the gut microbiota and the intestinal microenvironment via administration of prebiotics represents a valuable strategy to promote host health. This work provides insights into the ability of two novel wood-derived preparations, AcGGM and AcAGX, to influence human gut microbiota composition and activity. These...
Opinion/Hypothesis | Applied and Environmental ScienceExtracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater LakesHumic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic...