Applied and Environmental Science
Research Article | Applied and Environmental ScienceNew Provisional Function of OmpA from Acinetobacter sp. Strain SA01 Based on Environmental ChallengesAcinetobacter OmpA is known as a multifaceted protein with multiple functions, including emulsifying properties. Bioemulsifiers are surface-active compounds that can disperse hydrophobic compounds in water and help increase the bioavailability of hydrophobic hydrocarbons to be used by degrading microorganisms.
Research Article | Applied and Environmental ScienceGradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing DataTo solve the problem of amplicon sequencing cannot discern the microbiota absolute abundance, we proposed a gradient internal standard absolute quantification method. We used Chinese liquor fermentation as a model system to demonstrate the reliability and accuracy of the method.
Editor's Pick Research Article | Applied and Environmental ScienceExometabolite Dynamics over Stationary Phase Reveal Strain-Specific ResponsesNongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.
Research Article | Applied and Environmental ScienceIsolation of SAR11 Marine Bacteria from Cryopreserved SeawaterHigh-throughput dilution culture has proved to be a successful approach to bring some difficult-to-isolate planktonic microorganisms into culture, including the highly abundant SAR11 lineage of marine bacteria. While the long-term preservation of bacterial isolates by freezing them in the presence of cryoprotectants, such as glycerol, has been shown to be an effective method of storing viable cells over long time periods (i.e., years),...
Research Article | Applied and Environmental ScienceGenomes of the “Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic ActinobacteriaMicrobiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge.
Research Article | Applied and Environmental ScienceComprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate OxidationIn this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield.
Research Article | Applied and Environmental ScienceRice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil MetabolitesSoil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/...
Research Article | Applied and Environmental ScienceElucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel RelationshipsE. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and...
Research Article | Applied and Environmental ScienceFermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance DeterminantsFermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-...
Editor's Pick Research Article | Applied and Environmental ScienceGeothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, ItalyThe Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that...