Applied and Environmental Science
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.
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...
Research Article | Applied and Environmental ScienceTaxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing RunDespite the routine use of standards and blanks in virtually all chemical or physical assays and most biological studies (a kind of “control”), microbiome analysis has traditionally lacked such standards. Here we show that unexpected problems of unknown origin can occur in such sequencing runs and yield completely incorrect results that would not necessarily be detected without the use of standards. Assuming that the microbiome...
Special Issue Perspective | Applied and Environmental ScienceRevival of Archaeal Methane MicrobiologyThe methane concentration in the Earth’s atmosphere is rising, and, as methane is a potent greenhouse gas, it contributes considerably to climate change. It is produced by methanogenic archaea that thrive in anoxic habitats and can be oxidized by methane-oxidizing bacteria or archaea.
Special Issue Perspective | Applied and Environmental ScienceIt Takes a Village: Microbial Communities Thrive through Interactions and Metabolic HandoffsAn enduring theme in microbial ecology is the interdependence of microbial community members. Interactions between community members include provision of cofactors, establishment of redox gradients, and turnover of key nutrients to drive biogeochemical cycles.
Editor's Pick Research Article | Applied and Environmental ScienceOmics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened CheeseFermented foods, in particular, surface-ripened cheese, represent a model to explain the metabolic interactions which regulate microbial succession in complex environments. This study explains the role of individual species in a heterogeneous microbial environment, i.e., the exterior of surface-ripened cheese. Through whole-metagenome shotgun sequencing, it was possible to investigate the metabolic potential of the resident...
Research Article | Applied and Environmental ScienceVitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic ConditionsMicrobial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high...
Research Article | Applied and Environmental ScienceProteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low TemperaturesLactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. ...