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Applied and Environmental Science

  • Open Access
    Identifying Composition Novelty in Microbiome Studies: Improvement for Prediction Accuracy
    Letter to the Editor | Applied and Environmental Science
    Identifying Composition Novelty in Microbiome Studies: Improvement for Prediction Accuracy
    Yu Sun, Yanling Li, Qianqian Yuan, Xi Fu
  • 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
    Synthetic Methane-Consuming Communities from a Natural Lake Sediment
    Research Article | Applied and Environmental Science
    Synthetic Methane-Consuming Communities from a Natural Lake Sediment

    The metabolism of methane is an important part of the global carbon cycle. While deciphering the community function and the potential role of the different functional guilds is very difficult when considering native complex communities, synthetic communities, built of species originating from a study site in question, present a simplified model and allow specific questions to be addressed as to carbon, nitrogen, and other nutrient...

    Zheng Yu, Joseph Groom, Yue Zheng, Ludmila Chistoserdova, Jing Huang
  • Open Access
    Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO<sub>2</sub> Fixation
    Research Article | Applied and Environmental Science
    Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation

    Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, “Candidatus Kentron,” associated with marine ciliates. They lack genes for known autotrophic...

    Brandon K. B. Seah, Chakkiath Paul Antony, Bruno Huettel, Jan Zarzycki, Lennart Schada von Borzyskowski, Tobias J. Erb, Angela Kouris, Manuel Kleiner, Manuel Liebeke, Nicole Dubilier, Harald R. Gruber-Vodicka
  • Open Access
    Bacteria Floc, but Do They Flock? Insights from Population Interaction Models of Quorum Sensing
    Research Article | Applied and Environmental Science
    Bacteria Floc, but Do They Flock? Insights from Population Interaction Models of Quorum Sensing

    Our modeling efforts show how cell density can affect chemotaxis; they help to explain the roots of subgroup formation in bacterial populations. Our work also reinforces the notion that bacterial mechanisms are at times exhibited in higher-order organisms.

    Hana Ueda, Kristina Stephens, Konstantina Trivisa, William E. Bentley
  • Open Access
    Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical <em>Dysideidae</em> Sponges
    Research Article | Applied and Environmental Science
    Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges

    Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their...

    Michelle A. Schorn, Peter A. Jordan, Sheila Podell, Jessica M. Blanton, Vinayak Agarwal, Jason S. Biggs, Eric E. Allen, Bradley S. Moore
  • Open Access
    Iron Corrosion via Direct Metal-Microbe Electron Transfer
    Research Article | Applied and Environmental Science
    Iron Corrosion via Direct Metal-Microbe Electron Transfer

    The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of...

    Hai-Yan Tang, Dawn E. Holmes, Toshiyuki Ueki, Paola A. Palacios, Derek R. Lovley
  • Open Access
    Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments
    Research Article | Applied and Environmental Science
    Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments

    Much of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these...

    Jordan T. Bird, Eric D. Tague, Laura Zinke, Jenna M. Schmidt, Andrew D. Steen, Brandi Reese, Ian P. G. Marshall, Gordon Webster, Andrew Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd
  • Open Access
    Red- and Blue-Light Sensing in the Plant Pathogen <span class="named-content genus-species" id="named-content-1">Alternaria alternata</span> Depends on Phytochrome and the White-Collar Protein LreA
    Research Article | Applied and Environmental Science
    Red- and Blue-Light Sensing in the Plant Pathogen Alternaria alternata Depends on Phytochrome and the White-Collar Protein LreA

    Light controls many processes in filamentous fungi. The study of light regulation in a number of model organisms revealed an unexpected complexity. Although the molecular components for light sensing appear to be widely conserved in fungal genomes, the regulatory circuits and the sensitivity of certain species toward specific wavelengths seem different. In N. crassa,...

    Olumuyiwa Igbalajobi, Zhenzhong Yu, Reinhard Fischer
  • Open Access
    Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <em>Methylomicrobium buryatense</em> 5GB1
    Research Article | Applied and Environmental Science
    Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1

    One-carbon compounds such as methane and methanol are of increasing interest as sustainable substrates for biological production of fuels and industrial chemicals. The bacteria that carry out these conversions have been studied for many decades, but gaps exist in our knowledge of their metabolic pathways. One such gap is the difference between growth on methane and growth on methanol. Understanding such metabolism is important, since...

    Yanfen Fu, Lian He, Jennifer Reeve, David A. C. Beck, Mary E. Lidstrom

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