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environmental microbiology

  • Open Access
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
    Research Article | Clinical Science and Epidemiology
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

    Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread.

    Alexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson
  • Open Access
    Natural Bacterial Assemblages in <span class="named-content genus-species" id="named-content-1">Arabidopsis thaliana</span> Tissues Become More Distinguishable and Diverse during Host Development
    Research Article | Host-Microbe Biology
    Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development

    Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed.

    ...
    Kathleen Beilsmith, Matthew Perisin, Joy Bergelson
  • 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
    Microbial Life Deep Underfoot
    Commentary | Ecological and Evolutionary Science
    Microbial Life Deep Underfoot

    Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored.

    Jay T. Lennon
  • Open Access
    Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities
    Research Article | Ecological and Evolutionary Science
    Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities

    Our findings highlight how soil fungal and bacterial communities respond to time, season, and plant species identity. We found that succession shapes the soil bacterial community, while plant species and the type of plant species that grows in the soil drive the assembly of soil fungal communities. Future research on the effects of plants on soil microbes should take into consideration the relative roles of both time and plant growth on...

    S. Emilia Hannula, Anna M. Kielak, Katja Steinauer, Martine Huberty, Renske Jongen, Jonathan R. De Long, Robin Heinen, T. Martijn Bezemer
  • Open Access
    Precedence for the Role of Indole with Pathogens
    Letter to the Editor | Applied and Environmental Science
    Precedence for the Role of Indole with Pathogens
    Thomas K. Wood, Jintae Lee
  • Open Access
    Research Article
    Viral Diversity of House Mice in New York City
    Simon H. Williams, Xiaoyu Che, Joel A. Garcia, John D. Klena, Bohyun Lee, Dorothy Muller, Werner Ulrich, Robert M. Corrigan, Stuart Nichol, Komal Jain, W. Ian Lipkin
  • Open Access
    Research Article
    The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals
    Liam Shaw, Andre L. R. Ribeiro, Adam P. Levine, Nikolas Pontikos, Francois Balloux, Anthony W. Segal, Adam P. Roberts, Andrew M. Smith
  • Open Access
    Minireview
    The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing
    Kevin McCluskey, Katharine B. Barker, Hazel A. Barton, Kyria Boundy-Mills, Daniel R. Brown, Jonathan A. Coddington, Kevin Cook, Philippe Desmeth, David Geiser, Jessie A. Glaeser, Stephanie Greene, Seogchan Kang, Michael W. Lomas, Ulrich Melcher, Scott E. Miller, David R. Nobles, Kristina J. Owens, Jerome H. Reichman, Manuela da Silva, John Wertz, Cale Whitworth, David Smith
  • Open Access
    Letter to the Editor
    A Cautionary Tale: Tn903 aph, Kanamycin Resistance Redux in the Environment
    Vivian P. W. Miao

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