Applied and Environmental Science
Research Article | Applied and Environmental ScienceAntimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance IndoorsThe ubiquitous use of antimicrobial chemicals may have undesired consequences, particularly on microbes in buildings. This study shows that the taxonomy and function of microbes in indoor dust are strongly associated with antimicrobial chemicals—more so than any other feature of the buildings. Moreover, we identified links between antimicrobial chemical concentrations in dust and culturable bacteria that are cross-resistant to three...
Research Article | Applied and Environmental ScienceProteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling BacteroidetesCellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to...
Editor's Pick Research Article | Applied and Environmental ScienceMetatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic MicrobiomeMixed communities of microbes play important roles in health, the environment, agriculture, and biotechnology. While tapping the combined activities of organisms within microbiomes may allow the utilization of a wider range of substrates in preference to the use of pure cultures for biomanufacturing, harnessing the metabolism of these mixed cultures remains a major challenge. Here, we predicted metabolic functions of bacteria in a...
Research Article | Applied and Environmental ScienceMicrobial Functional Responses to Cholesterol Catabolism in Denitrifying SludgeSteroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial...
Research Article | Applied and Environmental ScienceSoil Viruses Are Underexplored Players in Ecosystem Carbon ProcessingThis work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870–880, 2018,...
Editor's Pick Commentary | Applied and Environmental ScienceSizing Up the Uncultured Microbial MajorityPredicting the total number of microbial cells on Earth and exploring the full diversity of life are fundamental research concepts that have undergone paradigm shifts in the genomic era. In this issue, Lloyd and colleagues (K.
Editor's Pick Research Article | Applied and Environmental SciencePhylogenetically Novel Uncultured Microbial Cells Dominate Earth MicrobiomesIn the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of...
Research Article | Applied and Environmental ScienceCoproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese RindsBacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of...
Editor's Pick Research Article | Applied and Environmental ScienceMetagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban WaterwayUnravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of...
Research Article | Applied and Environmental ScienceViromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA VirusesEnteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from...