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Applied and Environmental Science

  • Open Access
    Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
    Research Article | Applied and Environmental Science
    Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities

    The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly...

    Zhou Shi, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, Jizhong Zhou
  • Open Access
    Precision Food Safety: a Paradigm Shift in Detection and Control of Foodborne Pathogens
    Special Issue Perspective | Applied and Environmental Science
    Precision Food Safety: a Paradigm Shift in Detection and Control of Foodborne Pathogens

    The implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology.

    Jasna Kovac
  • Open Access
    Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
    Research Article | Applied and Environmental Science
    Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

    Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a...

    Taniya Roy Chowdhury, Joon-Yong Lee, Eric M. Bottos, Colin J. Brislawn, Richard Allen White, Lisa M. Bramer, Joseph Brown, Jeremy D. Zucker, Young-Mo Kim, Ari Jumpponen, Charles W. Rice, Sarah J. Fansler, Thomas O. Metz, Lee Ann McCue, Stephen J. Callister, Hyun-Seob Song, Janet K. Jansson
  • Open Access
    Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Editor's Pick Research Article | Applied and Environmental Science
    Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli

    A particular problem for the biotechnological production of many of the valuable chemicals that we are now able to manufacture in bacterial cells is that these products often poison the cells producing them. Solutions to improve product yields or alleviate such toxicity using the techniques of modern molecular biology first require a detailed understanding of the mechanisms of product toxicity. Here we have studied the economically...

    Calum A. Pattrick, Joseph P. Webb, Jeffrey Green, Roy R. Chaudhuri, Mark O. Collins, David J. Kelly
  • Open Access
    Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers
    Special Issue Perspective | Applied and Environmental Science
    Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers

    Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth.

    Kim M. Handley
  • Open Access
    Soil Viruses: A New Hope
    Special Issue Perspective | Applied and Environmental Science
    Soil Viruses: A New Hope

    As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil.

    Joanne B. Emerson
  • Open Access
    Culturing the Uncultured: Risk versus Reward
    Special Issue Perspective | Applied and Environmental Science
    Culturing the Uncultured: Risk versus Reward

    Isolation of new microorganisms is challenging, but cultures are invaluable resources for experimental validation of phenotype, ecology, and evolutionary processes. Although the number of new isolates continues to grow, the majority of cultivars still come from a limited number of phylogenetic groups and environments, necessitating investment in new cultivation efforts.

    J. Cameron Thrash
  • Open Access
    Moving towards a Robust Definition for a “Healthy” Indoor Microbiome
    Special Issue Perspective | Applied and Environmental Science
    Moving towards a Robust Definition for a “Healthy” Indoor Microbiome

    Buildings of the future should be designed to support human health, both by promoting the presence of beneficial microbes and by reducing exposure to harmful ones. However, we still do not have a robust definition of what constitutes a “healthy” indoor microbiome.

    Karen C. Dannemiller
  • Open Access
    A “Cultural” Renaissance: Genomics Breathes New Life into an Old Craft
    Special Issue Perspective | Applied and Environmental Science
    A “Cultural” Renaissance: Genomics Breathes New Life into an Old Craft

    Sometimes, to move ahead, you must take a look at where you have been. Culturing microbes is a foundational underpinning of microbiology.

    Paul Carini
  • Open Access
    Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling
    Research Article | Applied and Environmental Science
    Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

    Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields...

    Shuo Jiao, Yiqin Xu, Jie Zhang, Xin Hao, Yahai Lu

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