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Applied and Environmental Science

  • Open Access
    Phylogenetic Distribution of Plastic-Degrading Microorganisms
    Research Article | Applied and Environmental Science
    Phylogenetic Distribution of Plastic-Degrading Microorganisms

    We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved.

    Victor Gambarini, Olga Pantos, Joanne M. Kingsbury, Louise Weaver, Kim M. Handley, Gavin Lear
  • Open Access
    Computational Analysis of Microbial Flow Cytometry Data
    Minireview | Applied and Environmental Science
    Computational Analysis of Microbial Flow Cytometry Data

    Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.

    Peter Rubbens, Ruben Props
  • Open Access
    Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
    Research Article | Applied and Environmental Science
    Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

    This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families...

    Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
  • Open Access
    New Provisional Function of OmpA from <em>Acinetobacter</em> sp. Strain SA01 Based on Environmental Challenges
    Research Article | Applied and Environmental Science
    New Provisional Function of OmpA from Acinetobacter sp. Strain SA01 Based on Environmental Challenges

    Acinetobacter OmpA is known as a multifaceted protein with multiple functions, including emulsifying properties. Bioemulsifiers are surface-active compounds that can disperse hydrophobic compounds in water and help increase the bioavailability of hydrophobic hydrocarbons to be used by degrading microorganisms.

    Shahab Shahryari, Mahbubeh Talaee, Kamahldin Haghbeen, Lorenz Adrian, Hojatollah Vali, Hossein Shahbani Zahiri, Kambiz Akbari Noghabi
  • Open Access
    Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data
    Research Article | Applied and Environmental Science
    Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

    To solve the problem of amplicon sequencing cannot discern the microbiota absolute abundance, we proposed a gradient internal standard absolute quantification method. We used Chinese liquor fermentation as a model system to demonstrate the reliability and accuracy of the method.

    Shilei Wang, Qun Wu, Ying Han, Rubing Du, Xiaoyong Wang, Yao Nie, Xiaowei Du, Yan Xu
  • Open Access
    Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater
    Research Article | Applied and Environmental Science
    Isolation of SAR11 Marine Bacteria from Cryopreserved Seawater

    High-throughput dilution culture has proved to be a successful approach to bring some difficult-to-isolate planktonic microorganisms into culture, including the highly abundant SAR11 lineage of marine bacteria. While the long-term preservation of bacterial isolates by freezing them in the presence of cryoprotectants, such as glycerol, has been shown to be an effective method of storing viable cells over long time periods (i.e., years),...

    Elizabeth A. Monaghan, Kelle C. Freel, Michael S. Rappé
  • Open Access
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
    Editor's Pick Research Article | Applied and Environmental Science
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

    Nongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.

    John L. Chodkowski, Ashley Shade
  • Open Access
    Genomes of the “<em>Candidatus</em> Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria
    Research Article | Applied and Environmental Science
    Genomes of the “Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria

    Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge.

    Mario López-Pérez, Jose M. Haro-Moreno, Jaime Iranzo, Francisco Rodriguez-Valera
  • Open Access
    Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation
    Research Article | Applied and Environmental Science
    Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation

    In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield.

    Mauricio Patón, Héctor H. Hernández, Jorge Rodríguez
  • Open Access
    Rice <em>SST</em> Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites
    Research Article | Applied and Environmental Science
    Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

    Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/...

    Tengxiang Lian, Yingyong Huang, Xianan Xie, Xing Huo, Muhammad Qasim Shahid, Lei Tian, Tao Lan, Jing Jin

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