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Applied and Environmental Science

  • Open Access
    Anaerobic Degradation of Non-Methane Alkanes by “<em>Candidatus</em> Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico
    Research Article | Applied and Environmental Science
    Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico

    Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming “Candidatus Argoarchaeum” and “Candidatus Syntrophoarchaeum” are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. “Ca. Methanoliparia” occurs as single cells associated with oil droplets. These archaea...

    Rafael Laso-Pérez, Cedric Hahn, Daan M. van Vliet, Halina E. Tegetmeyer, Florence Schubotz, Nadine T. Smit, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Antje Boetius, Katrin Knittel, Gunter Wegener
  • Open Access
    Streamlined Genetic Manipulation of Diverse <em>Bacteroides</em> and <em>Parabacteroides</em> Isolates from the Human Gut Microbiota
    Research Article | Applied and Environmental Science
    Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

    We have entered an era when studies of the gut microbiota are transitioning from basic questions of composition and host effects to understanding the microbial molecules that underlie compositional shifts and mediate health and disease processes. The importance of the gut Bacteroidales to human health and disease and their potential as a source of engineered live biotherapeutics make these bacteria of particular interest for in...

    Leonor García-Bayona, Laurie E. Comstock
  • Open Access
    Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
    Observation | Applied and Environmental Science
    Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters

    Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates...

    Margarita Lopez-Fernandez, Elias Broman, Domenico Simone, Stefan Bertilsson, Mark Dopson
  • Open Access
    A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators
    Editor's Pick Research Article | Applied and Environmental Science
    A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators

    Access to whole-genome sequences has exposed the general incidence of the so-called cryptic biosynthetic gene clusters (BGCs), thereby renewing their interest for natural product discovery. As a consequence, genome mining is the often first approach implemented to assess the potential of a microorganism for producing novel bioactive metabolites. By revealing a new level of complexity of natural product biosynthesis, we further...

    Loïc Martinet, Aymeric Naômé, Benoit Deflandre, Marta Maciejewska, Déborah Tellatin, Elodie Tenconi, Nicolas Smargiasso, Edwin de Pauw, Gilles P. van Wezel, Sébastien Rigali
  • Open Access
    A Central Small RNA Regulatory Circuit Controlling Bacterial Denitrification and N<sub>2</sub>O Emissions
    Research Article | Applied and Environmental Science
    A Central Small RNA Regulatory Circuit Controlling Bacterial Denitrification and N2O Emissions

    N2O is an important greenhouse gas and a major cause of ozone depletion. Denitrifying bacteria play vital roles in the production and consumption of N2O in many environments. Complete denitrification consists of the conversion of a soluble N-oxyanion, nitrate (NO3-), to an inert gaseous N-oxide, dinitrogen (N2). Incomplete denitrification can occur if conditions are prohibitive, for...

    Hannah Gaimster, Claire L. Hews, Ryan Griffiths, Manuel J. Soriano-Laguna, Mark Alston, David J. Richardson, Andrew J. Gates, Gary Rowley
  • Open Access
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Author Reply | Applied and Environmental Science
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Xiaoquan Su, Gongchao Jing, Daniel McDonald, Honglei Wang, Zengbin Wang, Antonio Gonzalez, Zheng Sun, Shi Huang, Jose Navas, Rob Knight, Jian Xu
  • 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

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