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Applied and Environmental Science

  • Open Access
    Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments
    Research Article | Applied and Environmental Science
    Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

    SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution...

    Asier Zaragoza-Solas, Francisco Rodriguez-Valera, Mario López-Pérez
  • Open Access
    Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <em>Zetaproteobacteria</em> Iron Mats at Marine Hydrothermal Vents
    Editor's Pick Research Article | Applied and Environmental Science
    Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

    Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron...

    Sean M. McAllister, Shawn W. Polson, David A. Butterfield, Brian T. Glazer, Jason B. Sylvan, Clara S. Chan
  • Open Access
    Visualizing Microbial Community Dynamics via a Controllable Soil Environment
    Methods and Protocols | Applied and Environmental Science
    Visualizing Microbial Community Dynamics via a Controllable Soil Environment

    Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in...

    Arunima Bhattacharjee, Dusan Velickovic, Thomas W. Wietsma, Sheryl L. Bell, Janet K. Jansson, Kirsten S. Hofmockel, Christopher R. Anderton
  • Open Access
    Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation
    Research Article | Applied and Environmental Science
    Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation

    Solid-state fermentation (SSF) plays pivotal roles not only in human food but also farm animal diets. Soybean meal (SBM) and corn account for approximately 70% of the global feed consumption. However, the nutritional value of conventional SBM and corn mixed substrates (MS) is limited by antinutritional factors, causing substantial economic loss in livestock production. Although emerging studies have reported that SSF can improve the...

    Cheng Wang, Changyou Shi, Weifa Su, Mingliang Jin, Bocheng Xu, Lihong Hao, Yu Zhang, Zeqing Lu, Fengqin Wang, Yizhen Wang, Huahua Du
  • Open Access
    Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance
    Research Article | Applied and Environmental Science
    Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance

    AD is a biological process widely used for effective waste treatment throughout the world. Biotic interactions among microbes are critical to the assembly and functioning of the microbial community, but the response of microbial interactions to environmental changes and their influence on AD performance are still poorly understood. Using well-replicated time series data of 16S rRNA gene amplicons and functional gene arrays, we...

    Linwei Wu, Xiaoyu Shan, Si Chen, Qiuting Zhang, Qi Qi, Ziyan Qin, Huaqun Yin, Jizhong Zhou, Qiang He, Yunfeng Yang
  • Open Access
    Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates
    Research Article | Applied and Environmental Science
    Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

    Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria...

    Ankita Kothari, Drishti Soneja, Albert Tang, Hans K. Carlson, Adam M. Deutschbauer, Aindrila Mukhopadhyay
  • Open Access
    Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass Spectrometry
    Editor's Pick Methods and Protocols | Applied and Environmental Science
    Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass Spectrometry

    Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection...

    Emilia M. Sogin, Erik Puskás, Nicole Dubilier, Manuel Liebeke
  • Open Access
    Quantifying Methane and Methanol Metabolism of “<em>Methylotuvimicrobium buryatense</em>” 5GB1C under Substrate Limitation
    Research Article | Applied and Environmental Science
    Quantifying Methane and Methanol Metabolism of “Methylotuvimicrobium buryatense” 5GB1C under Substrate Limitation

    Methanotrophic metabolism has been under investigation for decades using biochemical and genetic approaches. Recently, a further step has been taken toward understanding methanotrophic metabolism in a quantitative manner by means of flux balance analysis (FBA), a mathematical approach that predicts fluxes constrained by mass balance and a few experimental measurements. However, no study has previously been undertaken to experimentally...

    Lian He, Yanfen Fu, Mary E. Lidstrom
  • Open Access
    Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils
    Research Article | Applied and Environmental Science
    Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils

    Understanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results...

    Adrienne B. Narrowe, Mikayla A. Borton, David W. Hoyt, Garrett J. Smith, Rebecca A. Daly, Jordan C. Angle, Elizabeth K. Eder, Allison R. Wong, Richard A. Wolfe, Alexandra Pappas, Gil Bohrer, Christopher S. Miller, Kelly C. Wrighton
  • Open Access
    Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach
    Research Article | Applied and Environmental Science
    Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach

    The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is...

    Chandni Sidhu, Vipul Solanki, Anil Kumar Pinnaka, Krishan Gopal Thakur

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