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Applied and Environmental Science

  • Open Access
    Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<em>Candidatus</em> Nitrospira nitrosa”
    Research Article | Applied and Environmental Science
    Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “Candidatus Nitrospira nitrosa”

    Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of...

    Pamela Y. Camejo, Jorge Santo Domingo, Katherine D. McMahon, Daniel R. Noguera
  • Open Access
    Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions
    Editor's Pick Research Article | Applied and Environmental Science
    Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions

    This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system....

    S. Esquivel-Elizondo, Z. E. Ilhan, E. I. Garcia-Peña, R. Krajmalnik-Brown
  • Open Access
    Non-Toxin-Producing <em>Bacillus cereus</em> Strains Belonging to the <em>B. anthracis</em> Clade Isolated from the International Space Station
    Research Article | Applied and Environmental Science
    Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station

    The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed...

    Kasthuri Venkateswaran, Nitin K. Singh, Aleksandra Checinska Sielaff, Robert K. Pope, Nicholas H. Bergman, Sandra P. van Tongeren, Nisha B. Patel, Paul A. Lawson, Masataka Satomi, Charles H. D. Williamson, Jason W. Sahl, Paul Keim, Duane Pierson, Jay Perry
  • Open Access
    Significant Impacts of Increasing Aridity on the Arid Soil Microbiome
    Research Article | Applied and Environmental Science
    Significant Impacts of Increasing Aridity on the Arid Soil Microbiome

    We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically...

    Julia W. Neilson, Katy Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L. Josephson, Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, Raina M. Maier
  • Open Access
    Genome Sequence of the Thermotolerant Foodborne Pathogen <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms
    Research Article | Applied and Environmental Science
    Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms

    Thermal interventions are commonly used in the food industry as a means of mitigating pathogen contamination in food products. Concern over heat-resistant food contaminants has recently increased, with the identification of a conserved locus shown to confer heat resistance in disparate lineages of Gram-negative bacteria. Complete sequence analysis of a historical isolate of ...

    Scott V. Nguyen, Gregory P. Harhay, James L. Bono, Timothy P. L. Smith, Dayna M. Harhay
  • Open Access
    The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
    Editor's Pick Research Article | Applied and Environmental Science
    The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

    Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for...

    Lisa Zeigler Allen, John P. McCrow, Karolina Ininbergs, Christopher L. Dupont, Jonathan H. Badger, Jeffery M. Hoffman, Martin Ekman, Andrew E. Allen, Birgitta Bergman, J. Craig Venter
  • Open Access
    Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing <span class="named-content genus-species" id="named-content-1">Vibrio coralliilyticus</span> S2052 and <span class="named-content genus-species" id="named-content-2">Photobacterium galatheae</span> S2753
    Editor's Pick Research Article | Applied and Environmental Science
    Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753

    The bacterial family Vibrionaceae (vibrios) is considered a major player in the degradation of chitin, the most abundant polymer in the marine environment; however, the majority of studies on the topic have focused on a small number of Vibrio species. In this study, we analyzed the genomes of two vibrios to assess their genetic potential for the degradation of chitin. We then used transcriptomics and metabolomics to...

    Sonia Giubergia, Christopher Phippen, Kristian Fog Nielsen, Lone Gram
  • Open Access
    Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis
    Research Article | Applied and Environmental Science
    Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis

    Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a...

    Yu-Wei Wu, Brendan Higgins, Chaowei Yu, Amitha P. Reddy, Shannon Ceballos, Lawrence D. Joh, Blake A. Simmons, Steven W. Singer, Jean S. VanderGheynst
  • Open Access
    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
    Research Article | Applied and Environmental Science
    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

    Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an...

    Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp
  • Open Access
    mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
    Editor's Pick Resource Report | Applied and Environmental Science
    mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

    The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.

    Nicholas A. Bokulich, Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, J. Gregory Caporaso

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