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Applied and Environmental Science

  • Open Access
    Metabolic Exchange and Energetic Coupling between Nutritionally Stressed Bacterial Species: Role of Quorum-Sensing Molecules
    Research Article | Applied and Environmental Science
    Metabolic Exchange and Energetic Coupling between Nutritionally Stressed Bacterial Species: Role of Quorum-Sensing Molecules

    Bacteria have usually been studied in single culture in rich media or under specific starvation conditions. However, in nature they coexist with other microorganisms and build an advanced society.

    David Ranava, Cassandra Backes, Ganesan Karthikeyan, Olivier Ouari, Audrey Soric, Marianne Guiral, María Luz Cárdenas, Marie Thérèse Giudici-Orticoni
  • Open Access
    Availability of the Molecular Switch XylR Controls Phenotypic Heterogeneity and Lag Duration during <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Adaptation from Glucose to Xylose
    Research Article | Applied and Environmental Science
    Availability of the Molecular Switch XylR Controls Phenotypic Heterogeneity and Lag Duration during Escherichia coli Adaptation from Glucose to Xylose

    For decades, it was thought that the lags observed when microorganisms switch from one substrate to another are inherent to the time required to adapt the molecular machinery to the new substrate. Here, the lag duration was found to be the time necessary for a subpopulation of adapted cells to emerge and become the main population.

    Manon Barthe, Josué Tchouanti, Pedro Henrique Gomes, Carine Bideaux, Delphine Lestrade, Carl Graham, Jean-Philippe Steyer, Sylvie Meleard, Jérôme Harmand, Nathalie Gorret, Muriel Cocaign-Bousquet, Brice Enjalbert
  • Open Access
    Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats
    Minireview | Applied and Environmental Science
    Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

    Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen.

    Chequita N. Brooks, Erin K. Field
  • Open Access
    Effects of Agricultural Fungicide Use on <span class="named-content genus-species" id="named-content-1">Aspergillus fumigatus</span> Abundance, Antifungal Susceptibility, and Population Structure
    Research Article | Applied and Environmental Science
    Effects of Agricultural Fungicide Use on Aspergillus fumigatus Abundance, Antifungal Susceptibility, and Population Structure

    Antibiotic resistance is an increasing threat to human health. In the case of Aspergillus fumigatus, which is an environmental fungus that also causes life-threatening infections in humans, antimicrobial resistance is suggested to arise from fungicide use in agriculture, as the chemicals used for plant protection are almost identical to the antifungals used clinically...

    Amelia E. Barber, Jennifer Riedel, Tongta Sae-Ong, Kang Kang, Werner Brabetz, Gianni Panagiotou, Holger B. Deising, Oliver Kurzai
  • Open Access
    Different Routes of Protein Folding Contribute to Improved Protein Production in <span class="named-content genus-species" id="named-content-1">Saccharomyces cerevisiae</span>
    Research Article | Applied and Environmental Science
    Different Routes of Protein Folding Contribute to Improved Protein Production in Saccharomyces cerevisiae

    Protein folding plays an important role in protein maturation and secretion. In recombinant protein production, many studies have focused on the folding pathway to improve productivity. Here, we identified two different routes for improving protein production by yeast. We found that improving folding precision is a better strategy. Dysfunction of this process is also associated with several aberrant protein-associated human diseases....

    Qi Qi, Feiran Li, Rosemary Yu, Martin K. M. Engqvist, Verena Siewers, Johannes Fuchs, Jens Nielsen
  • Open Access
    Cryptic or Silent? The Known Unknowns, Unknown Knowns, and Unknown Unknowns of Secondary Metabolism
    Perspective | Applied and Environmental Science
    Cryptic or Silent? The Known Unknowns, Unknown Knowns, and Unknown Unknowns of Secondary Metabolism

    Microbial natural products, particularly those produced by filamentous Actinobacteria, underpin the majority of clinically used antibiotics. Unfortunately, only a few new antibiotic classes have been discovered since the 1970s, which has exacerbated fears of a postapocalyptic world in which antibiotics have lost their utility. Excitingly, the genome sequencing revolution painted an entirely new picture, one in which an average...

    Paul A. Hoskisson, Ryan F. Seipke
  • Open Access
    Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
    Research Article | Applied and Environmental Science
    Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)

    High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-...

    Morten Simonsen Dueholm, Kasper Skytte Andersen, Simon Jon McIlroy, Jannie Munk Kristensen, Erika Yashiro, Søren Michael Karst, Mads Albertsen, Per Halkjær Nielsen
  • Open Access
    Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota
    Research Article | Applied and Environmental Science
    Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota

    Prebiotic fermentation in the gut often leads to the coproduction of short-chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely considered during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic...

    Xiaoqian Yu, Thomas Gurry, Le Thanh Tu Nguyen, Hunter S. Richardson, Eric J. Alm
  • Open Access
    Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation
    Research Article | Applied and Environmental Science
    Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation

    By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving...

    Thomas Seviour, Lan Li Wong, Yang Lu, Sudarsan Mugunthan, Qiaohui Yang, Uma Shankari, Irina Bessarab, David Liebl, Rohan B. H. Williams, Yingyu Law, Staffan Kjelleberg
  • Open Access
    Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds
    Editor's Pick Research Article | Applied and Environmental Science
    Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds

    Here, we provide evidence that Aspergillus terreus encodes a biosynthetic gene cluster containing a repurposed indoleamine 2,3-dioxygenase (IDO) dedicated to secondary metabolite synthesis. The discovery of this neofunctionalized IDO not only enabled discovery of a new compound with an unusual chemical scaffold but also provided insight into the numerous strategies...

    Lindsay K. Caesar, Matthew T. Robey, Michael Swyers, Md N. Islam, Rosa Ye, Purav P. Vagadia, Gary E. Schiltz, Paul M. Thomas, Chengcang C. Wu, Neil L. Kelleher, Nancy P. Keller, Jin Woo Bok

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