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Applied and Environmental Science

  • Open Access
    Interactive Regulation of Formate Dehydrogenase during CO<sub>2</sub> Fixation in Gas-Fermenting Bacteria
    Research Article | Applied and Environmental Science
    Interactive Regulation of Formate Dehydrogenase during CO2 Fixation in Gas-Fermenting Bacteria

    Microbial CO2 fixation and conversion constitute a potential solution to both utilization of greenhouse gas or industrial waste gases and sustainable production of bulk chemicals and fuels. Autotrophic gas-fermenting bacteria play central roles in this bioprocess. This study provides new insights regarding the metabolic regulatory mechanisms underlying CO2 reduction in...

    Lu Zhang, Yanqiang Liu, Ran Zhao, Can Zhang, Weihong Jiang, Yang Gu
  • Open Access
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth
    Research Article | Applied and Environmental Science
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

    Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole...

    John I. Miller, Stephen Techtmann, Dominique Joyner, Nagissa Mahmoudi, Julian Fortney, James A. Fordyce, Nargiz GaraJayeva, Faig S. Askerov, Claudio Cravid, Maarten Kuijper, Oliver Pelz, Terry C. Hazen
  • Open Access
    Quantifying the Transmission of Foot-and-Mouth Disease Virus in Cattle via a Contaminated Environment
    Research Article | Applied and Environmental Science
    Quantifying the Transmission of Foot-and-Mouth Disease Virus in Cattle via a Contaminated Environment

    Effective control of a disease relies on comprehensive understanding of how transmission occurs, in order to design and apply effective control measures. Foot-and-mouth disease virus (FMDV) is primarily spread by direct contact between infected and naive individuals, although the high levels of virus shed by infected animals mean that virus can also be spread through contact with contaminated environments. Using a series of transmission...

    Claire Colenutt, Emma Brown, Noel Nelson, David J. Paton, Phaedra Eblé, Aldo Dekker, José L. Gonzales, Simon Gubbins
  • Open Access
    Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules
    Research Article | Applied and Environmental Science
    Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

    The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical...

    Dan Naylor, Sarah Fansler, Colin Brislawn, William C. Nelson, Kirsten S. Hofmockel, Janet K. Jansson, Ryan McClure
  • Open Access
    Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family <em>Methanoperedenaceae</em>
    Research Article | Applied and Environmental Science
    Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae

    AOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance for the global carbon cycle and climate change modeling. While the oxidation of methane coupled to sulfate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study, we identify a number of...

    Andy O. Leu, Simon J. McIlroy, Jun Ye, Donovan H. Parks, Victoria J. Orphan, Gene W. Tyson
  • Open Access
    Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type
    Research Article | Applied and Environmental Science
    Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

    Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which...

    Allison M. Sharrar, Alexander Crits-Christoph, Raphaël Méheust, Spencer Diamond, Evan P. Starr, Jillian F. Banfield
  • Open Access
    Self-Protection against the Sphingolipid Biosynthesis Inhibitor Fumonisin B<sub>1</sub> Is Conferred by a <em>FUM</em> Cluster-Encoded Ceramide Synthase
    Research Article | Applied and Environmental Science
    Self-Protection against the Sphingolipid Biosynthesis Inhibitor Fumonisin B1 Is Conferred by a FUM Cluster-Encoded Ceramide Synthase

    The biosynthesis of fungal natural products is highly regulated not only in terms of transcription and translation but also regarding the cellular localization of the biosynthetic pathway. In all eukaryotes, the endoplasmic reticulum (ER) is involved in the production of organelles, which are subject to cellular traffic or secretion. Here, we show that in Fusarium...

    Slavica Janevska, Iuliia Ferling, Katarina Jojić, Julia Rautschek, Sandra Hoefgen, Robert H. Proctor, Falk Hillmann, Vito Valiante
  • Open Access
    “<em>Candidatus</em> Ethanoperedens,” a Thermophilic Genus of <em>Archaea</em> Mediating the Anaerobic Oxidation of Ethane
    Research Article | Applied and Environmental Science
    “Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane

    In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-...

    Cedric Jasper Hahn, Rafael Laso-Pérez, Francesca Vulcano, Konstantinos-Marios Vaziourakis, Runar Stokke, Ida Helene Steen, Andreas Teske, Antje Boetius, Manuel Liebeke, Rudolf Amann, Katrin Knittel, Gunter Wegener
  • Open Access
    Multiplex Genetic Engineering Exploiting Pyrimidine Salvage Pathway-Based Endogenous Counterselectable Markers
    Research Article | Applied and Environmental Science
    Multiplex Genetic Engineering Exploiting Pyrimidine Salvage Pathway-Based Endogenous Counterselectable Markers

    This work reports the discovery of a novel genetic toolbox comprising multiple, endogenous selectable markers for targeted genomic insertions of DNAs of interest (DOIs). Marker genes encode proteins involved in 5-fluorocytosine uptake and pyrimidine salvage activities mediating 5-fluorocytosine deamination as well as 5-fluorouracil phosphoribosylation. The requirement for their genomic replacement by DOIs to confer 5-fluorocytosine or 5...

    Lukas Birštonas, Alex Dallemulle, Manuel S. López-Berges, Ilse D. Jacobsen, Martin Offterdinger, Beate Abt, Maria Straßburger, Ingo Bauer, Oliver Schmidt, Bettina Sarg, Herbert Lindner, Hubertus Haas, Fabio Gsaller
  • Open Access
    Adaptive Evolution of <span class="named-content genus-species" id="named-content-1">Geobacter sulfurreducens</span> in Coculture with <span class="named-content genus-species" id="named-content-2">Pseudomonas aeruginosa</span>
    Research Article | Applied and Environmental Science
    Adaptive Evolution of Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa

    Geobacter and Pseudomonas spp. cohabit many of the same environments, where Geobacter spp. often dominate. Both bacteria are capable of extracellular electron transfer (EET) and play important roles in biogeochemical cycling. Although they recently in 2017 were demonstrated to undergo direct interspecies electron transfer (DIET) with one another, the genetic evolution of this syntrophic interaction has not...

    Lucie Semenec, Ismael A. Vergara, Andrew E. Laloo, Steve Petrovski, Philip L. Bond, Ashley E. Franks

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