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Applied and Environmental Microbiology
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bacteria

  • Open Access
    A CRISPR Interference Platform for Selective Downregulation of Gene Expression in <span class="named-content genus-species" id="named-content-1">Borrelia burgdorferi</span>
    Methods | Spotlight
    A CRISPR Interference Platform for Selective Downregulation of Gene Expression in Borrelia burgdorferi

    Gene function studies are facilitated by the availability of rapid and easy-to-use genetic tools. Homologous recombination-based methods traditionally used to genetically investigate gene function remain cumbersome to perform in B. burgdorferi, as they often are relatively inefficient.

    Constantin N. Takacs, Molly Scott, Yunjie Chang, Zachary A. Kloos, Irnov Irnov, Patricia A. Rosa, Jun Liu, Christine Jacobs-Wagner
  • The Ecology and Evolution of Amoeba-Bacterium Interactions
    Minireview
    The Ecology and Evolution of Amoeba-Bacterium Interactions

    Amoebae are protists that have complicated relationships with bacteria, covering the whole spectrum of symbiosis. Amoeba-bacterium interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-...

    Yijing Shi, David C. Queller, Yuehui Tian, Siyi Zhang, Qingyun Yan, Zhili He, Zhenzhen He, Chenyuan Wu, Cheng Wang, Longfei Shu
  • Open Access
    Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach
    Methods | Spotlight
    Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach

    The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our...

    Juliana Young, Joseph H. Skarlupka, Madison S. Cox, Rafael Tassinari Resende, Amelie Fischer, Kenneth F. Kalscheur, Jennifer C. McClure, John B. Cole, Garret Suen, Derek M. Bickhart
  • Open Access
    LuxR Solos in the Plant Endophyte <em>Kosakonia</em> sp. Strain KO348
    Environmental Microbiology
    LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348

    Cell-cell signaling in bacteria allows a synchronized and coordinated behavior of a microbial community. LuxR solos represent a subfamily of proteins in proteobacteria which most commonly detect and respond to signals produced exogenously by other microbes or eukaryotic hosts. Here, we report that a plant-beneficial bacterial endophyte belonging to the novel genus of Kosakonia possesses two LuxR solos; one is involved in the...

    Susan Mosquito, Xianfa Meng, Giulia Devescovi, Iris Bertani, Alexander M. Geller, Asaf Levy, Michael P. Myers, Cristina Bez, Sonia Covaceuszach, Vittorio Venturi
  • Genomic Landscape of <span class="named-content genus-species" id="named-content-1">Ornithobacterium rhinotracheale</span> in Commercial Turkey Production in the United States
    Environmental Microbiology
    Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States

    The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods....

    Emily A. Smith, Elizabeth A. Miller, Bonnie P. Weber, Jeannette Munoz Aguayo, Cristian Flores Figueroa, Jared Huisinga, Jill Nezworski, Michelle Kromm, Ben Wileman, Timothy J. Johnson
  • Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History
    Microbial Ecology
    Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History

    Plant-associated microbiomes are critical for plant health and other important agroecosystem processes. We assessed the bacterial and fungal microbiomes of wheat grown in soils from across a dryland wheat cropping systems in eastern Washington to identify the core microbiome on wheat roots that is consistent across soils from different locations and land use histories. Moreover, cross-domain co-occurrence network analysis identified...

    Daniel C. Schlatter, Chuntao Yin, Scot Hulbert, Timothy C. Paulitz
  • Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation
    Environmental Microbiology
    Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation

    Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle...

    Gordon F. Custer, Linda T. A. van Diepen, William L. Stump
  • Open Access
    Comparative Genomics of Rumen <em>Butyrivibrio</em> spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities
    Evolutionary and Genomic Microbiology | Spotlight
    Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

    Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically...

    Nikola Palevich, William J. Kelly, Sinead C. Leahy, Stuart Denman, Eric Altermann, Jasna Rakonjac, Graeme T. Attwood
  • Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation
    Environmental Microbiology | Spotlight
    Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation

    The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that...

    Rachel E. Joyce, Heather Lavender, Jennifer Farrar, Jason T. Werth, Carolyn F. Weber, Juliana D’Andrilli, Mickaël Vaitilingom, Brent C. Christner
  • Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose
    Environmental Microbiology
    Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose

    We introduce a method for identifying what substrates are consumed by bacteria in natural communities. Our method offers significant improvement over existing methods for studying this characteristic. Our method uses a fluorescently labeled substrate which clearly labels target bacteria (glucose consumers in our case). Previous methods use isotope-labeled substrates, which are notorious for off-target labeling (due to cross-feeding of...

    Junyi Tao, Courtney McCourt, Halima Sultana, Corwin Nelson, John Driver, Timothy J. Hackmann

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