Applied and Environmental Science
Research Article | Applied and Environmental ScienceDeciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive CompoundsThis study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel...
Perspective | Applied and Environmental ScienceIntroducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove EcosystemsMangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial...
Editor's Pick Research Article | Applied and Environmental ScienceLong-Term Temporal Stability of the Resistome in Sewage from CopenhagenThe Copenhagen sewage resistome is surprisingly stable in time. The implication is that, at least for cities that are comparable to Copenhagen in terms of sewer infrastructure, few or even single samples provide a robust picture of the resistome within a city.
Research Article | Applied and Environmental ScienceSize Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life CycleBiological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic...
Research Article | Applied and Environmental ScienceDiagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic ModelsMicrobiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three...
Editor's Pick Research Article | Applied and Environmental ScienceMarine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial DiversitySince bacterial resistance to antibiotics is developing worldwide, new antibiotics are needed. Most antibiotics discovered so far have been found in soil-dwelling bacteria, so we instead targeted marine environments as a novel source of bioactive potential. We used amplicon sequencing of bioactive gene clusters in the microbiome of coastal seawater and sandy sediments and found the bioactive potential to be comparable to, but distinct...
Research Article | Applied and Environmental ScienceMicrobiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast MicrobiomesChicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we...
Research Article | Applied and Environmental ScienceNiche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic PathwaysIn the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine...
Research Article | Applied and Environmental ScienceExpanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating MicroorganismsAccurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the ...
Research Article | Applied and Environmental ScienceThe Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosaMicroorganisms need to adapt rapidly to survive harsh environmental changes. Here, we showed the broad influence of the highly studied bacterial stringent stress response under nonstressful conditions that indicate its general physiological importance and might reflect the readiness of bacteria to respond to and activate acute stress responses. Using RNA-Seq to investigate the transcriptional network of...