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Applied and Environmental Microbiology
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  • Volatile Organic Compound-Mediated Antifungal Activity of Pichia spp. and Its Effect on the Metabolic Profiles of Fermentation Communities.
    Volatile Organic Compound-Mediated Antifungal Activity of Pichia spp. and Its Effect on the Metabolic Profiles of Fermentation Communities.
  • Localization of Bacterial Communities within Gut Compartments across Cephalotes Turtle Ants.
    Localization of Bacterial Communities within Gut Compartments across Cephalotes Turtle Ants.
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Spotlight

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    Articles of Significant Interest in This Issue
    Spotlight
    Articles of Significant Interest in This Issue

Biodegradation

  • McbG, a LysR Family Transcriptional Regulator, Activates the <em>mcbBCDEF</em> Gene Cluster Involved in the Upstream Pathway of Carbaryl Degradation in <em>Pseudomonas</em> sp. Strain XWY-1
    Biodegradation
    McbG, a LysR Family Transcriptional Regulator, Activates the mcbBCDEF Gene Cluster Involved in the Upstream Pathway of Carbaryl Degradation in Pseudomonas sp. Strain XWY-1

    Pseudomonas sp. strain XWY-1 is a carbaryl-degrading strain that utilizes carbaryl as the sole carbon and energy source for growth. The functional genes involved in the degradation of carbaryl have already been reported.

    Zhijian Ke, Yidong Zhou, Wankui Jiang, Mingliang Zhang, Hui Wang, Yijun Ren, Jiguo Qiu, Minggen Cheng, Qing Hong

Biotechnology

  • Open Access
    Laboratory Evolution and Reverse Engineering of <em>Clostridium thermocellum</em> for Growth on Glucose and Fructose
    Biotechnology
    Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose

    C. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption.

    Johannes Yayo, Teun Kuil, Daniel G. Olson, Lee R. Lynd, Evert K. Holwerda, Antonius J. A. van Maris

Environmental Microbiology

  • Open Access
    Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities
    Environmental Microbiology | Spotlight
    Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities

    Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents.

    Caroline S. Fortunato, David A. Butterfield, Benjamin Larson, Noah Lawrence-Slavas, Christopher K. Algar, Lisa Zeigler Allen, James F. Holden, Giora Proskurowski, Emily Reddington, Lucy C. Stewart, Begüm D. Topçuoğlu, Joseph J. Vallino, Julie A. Huber
  • Two PAAR Proteins with Different C-Terminal Extended Domains Have Distinct Ecological Functions in <span class="named-content genus-species" id="named-content-1">Myxococcus xanthus</span>
    Environmental Microbiology
    Two PAAR Proteins with Different C-Terminal Extended Domains Have Distinct Ecological Functions in Myxococcus xanthus

    The type VI secretion system (T6SS) is a bacterial cell contact-dependent weapon capable of delivering protein effectors into neighboring cells. The PAAR protein is located at the top of the nanomachine and carries an effector for delivery.

    Ya Liu, Jianing Wang, Zheng Zhang, Feng Wang, Ya Gong, Duo-hong Sheng, Yue-zhong Li
  • Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine
    Environmental Microbiology
    Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine

    This work determined that using a combination of isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including...

    Paul E. Moote, Danisa M. Bescucci, Rodrigo Ortega Polo, Richard R. E. Uwiera, G. Douglas Inglis
  • Identification of a Diguanylate Cyclase That Facilitates Biofilm Formation on Electrodes by <span class="named-content genus-species" id="named-content-1">Shewanella oneidensis</span> MR-1
    Environmental Microbiology
    Identification of a Diguanylate Cyclase That Facilitates Biofilm Formation on Electrodes by Shewanella oneidensis MR-1

    Bioelectrochemical systems (BESs) have attracted wide attention owing to their utility in sustainable biotechnology processes, such as microbial fuel cells and electrofermentation systems. In BESs, electrochemically active bacteria (EAB) form biofilms on electrode surfaces, thereby serving as effective catalysts for the interconversion between chemical and electric energy.

    Akiho Matsumoto, Ryota Koga, Robert A. Kanaly, Atsushi Kouzuma, Kazuya Watanabe
  • Open Access
    Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea
    Environmental Microbiology | Spotlight
    Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea

    DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play.

    Ruining Cai, Jing Zhang, Rui Liu, Chaomin Sun
  • A Type VI Secretion System Facilitates Fitness, Homeostasis, and Competitive Advantages for Environmental Adaptability and Efficient Nicotine Biodegradation
    Environmental Microbiology
    A Type VI Secretion System Facilitates Fitness, Homeostasis, and Competitive Advantages for Environmental Adaptability and Efficient Nicotine Biodegradation

    Mixtures of various pollutants and the coexistence of numerous species of organisms are usually found in adverse environments. Concerning biodegradation of nitrogen-heterocyclic contaminants, the scientific community has commonly focused on screening functional enzymes that transform pollutants into intermediates of attenuated toxicity or for primary metabolism. Here, we identified dual roles of the T6SS effector TseN in...

    Jun Li, Linlin Xie, Shulan Qian, Yuhang Tang, Mingjie Shen, Shanshan Li, Jie Wang, Lie Xiong, Jie Lu, Weihong Zhong

Food Microbiology

  • Dietary Inulin Increases <em>Lactiplantibacillus plantarum</em> Strain Lp900 Persistence in Rats Depending on the Dietary-Calcium Level
    Food Microbiology | Spotlight
    Dietary Inulin Increases Lactiplantibacillus plantarum Strain Lp900 Persistence in Rats Depending on the Dietary-Calcium Level

    Synbiotics combine probiotics with prebiotics to synergistically elicit a health benefit in the consumer. Previous studies have shown that prebiotics can selectively stimulate the growth in the intestine of specific bacterial strains.

    Jori Fuhren, Markus Schwalbe, Christiane Rösch, Reindert Nijland, Michiel Wels, Henk A. Schols, Michiel Kleerebezem
  • Vegetable-Derived Carbapenemase-Producing High-Risk <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> ST15 and <span class="named-content genus-species" id="named-content-2">Acinetobacter baumannii</span> ST2 Clones in Japan: Coexistence of <em>bla</em><sub>NDM-1</sub>, <em>bla</em><sub>OXA-66</sub>, <em>bla</em><sub>OXA-72</sub>, and an AbaR4-Like Resistance Island in the Same Sample
    Food Microbiology
    Vegetable-Derived Carbapenemase-Producing High-Risk Klebsiella pneumoniae ST15 and Acinetobacter baumannii ST2 Clones in Japan: Coexistence of blaNDM-1, blaOXA-66, blaOXA-72, and an AbaR4-Like Resistance Island in the Same Sample

    Carbapenemase-producing Gram-negative bacteria (CPGNB) cause severe health care-associated infections and constitute a major public health threat. Here, we investigated the genetic features of CPGNB isolated from fresh vegetable samples in Japan and found CPGNB, including Klebsiella pneumoniae and ...

    Ahmed M. Soliman, Hirofumi Nariya, Daiki Tanaka, Liansheng Yu, Junzo Hisatsune, Shizuo Kayama, Kohei Kondo, Motoyuki Sugai, Toshi Shimamoto, Tadashi Shimamoto
  • Open Access
    Prevalence of <em>Listeria</em> Species on Food Contact Surfaces in Washington State Apple Packinghouses
    Food Microbiology
    Prevalence of Listeria Species on Food Contact Surfaces in Washington State Apple Packinghouses

    Since 2014, fresh apples have been linked to outbreaks and recalls associated with postharvest cross-contamination with the foodborne pathogen L. monocytogenes. These situations drive both public health burden and economic loss and underscore the need for continued scrutiny of packinghouse management to eliminate potential Listeria spp. niches.

    ...
    Blanca Ruiz-Llacsahuanga, Alexis Hamilton, Robyn Zaches, Ines Hanrahan, Faith Critzer
  • Volatile Organic Compound-Mediated Antifungal Activity of <em>Pichia</em> spp. and Its Effect on the Metabolic Profiles of Fermentation Communities
    Food Microbiology | Spotlight
    Volatile Organic Compound-Mediated Antifungal Activity of Pichia spp. and Its Effect on the Metabolic Profiles of Fermentation Communities

    Fermentation of food occurs within communities of interacting species. The importance of microbial interactions in shaping microbial structure and metabolic performance to optimize the traditional fermentation process has long been emphasized, but the interaction mechanisms remain unclear.

    Hongxia Zhang, Hai Du, Yan Xu
  • Transcriptome Analysis of <span class="named-content genus-species" id="named-content-1">Listeria monocytogenes</span> Exposed to Beef Fat Reveals Antimicrobial and Pathogenicity Attenuation Mechanisms
    Food Microbiology
    Transcriptome Analysis of Listeria monocytogenes Exposed to Beef Fat Reveals Antimicrobial and Pathogenicity Attenuation Mechanisms

    Listeria monocytogenes is a bacterial pathogen known for its ability to survive and thrive under adverse environments and, as such, its control poses a significant challenge, especially with the trend of minimally processed and ready-to-eat foods. This work investigated the effectiveness of fatty acids from various sources as natural antimicrobials against...

    Yuan Yao Chen, Arun Kommadath, Payam Vahmani, Jeyachchandran Visvalingam, Michael E. R. Dugan, Xianqin Yang

Genetics and Molecular Biology

  • The Tail-Specific Protease Is Important for <span class="named-content genus-species" id="named-content-1">Legionella pneumophila</span> To Survive Thermal Stress in Water and inside Amoebae
    Genetics and Molecular Biology
    The Tail-Specific Protease Is Important for Legionella pneumophila To Survive Thermal Stress in Water and inside Amoebae

    Lp is a major cause of nosocomial and community-acquired pneumonia. Lp is found in water systems, including hot water distribution systems. Heat treatment is a method of disinfection often used to limit the presence of Lp in such systems; however, the benefit is usually short term, as Lp is able to quickly recolonize these systems.

    Joseph Saoud, Thangadurai Mani, Sébastien P. Faucher

Microbial Ecology

  • Open Access
    Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations
    Microbial Ecology
    Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations

    Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome.

    Zhikang Wang, Ziyun Chen, George A. Kowalchuk, Ziheng Xu, Xiangxiang Fu, Eiko E. Kuramae
  • “<em>Sifarchaeota</em>,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy
    Microbial Ecology
    “Sifarchaeota,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy

    The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important, since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.

    Ibrahim F. Farag, Rui Zhao, Jennifer F. Biddle
  • Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut
    Microbial Ecology
    Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut

    To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable...

    Wesley Loftie-Eaton, Angela Crabtree, David Perry, Jack Millstein, Justin Baytosh, Thibault Stalder, Barrie D. Robison, Larry J. Forney, Eva M. Top
  • Open Access
    Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals
    Microbial Ecology
    Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals

    We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play.

    Kenneth D. Hoadley, Maria Hamilton, Camille L. Poirier, Chang Jae Choi, Cheuk-Man Yung, Alexandra Z. Worden

Physiology

  • Open Access
    Adaptive Laboratory Evolution Restores Solvent Tolerance in Plasmid-Cured <span class="named-content genus-species" id="named-content-1">Pseudomonas putida</span> S12: a Molecular Analysis
    Physiology | Spotlight
    Adaptive Laboratory Evolution Restores Solvent Tolerance in Plasmid-Cured Pseudomonas putida S12: a Molecular Analysis

    Sustainable production of high-value chemicals can be achieved by bacterial biocatalysis. However, bioproduction of biopolymers and aromatic compounds may exert stress on the microbial production host and limit the resulting yield.

    Hadiastri Kusumawardhani, Benjamin Furtwängler, Matthijs Blommestijn, Adelė Kaltenytė, Jaap van der Poel, Jan Kolk, Rohola Hosseini, Johannes H. de Winde
  • The DUG Pathway Governs Degradation of Intracellular Glutathione in <span class="named-content genus-species" id="named-content-1">Aspergillus nidulans</span>
    Physiology
    The DUG Pathway Governs Degradation of Intracellular Glutathione in Aspergillus nidulans

    Glutathione (GSH) is a widely distributed tripeptide in both eukaryotes and prokaryotes. Owing to its very low redox potential, antioxidative character, and high intracellular concentration, GSH profoundly shapes the redox status of cells.

    Barnabás Csaba Gila, Heungyun Moon, Károly Antal, Márton Hajdu, Réka Kovács, Andrea P. Jónás, Tünde Pusztahelyi, Jae-Hyuk Yu, István Pócsi, Tamás Emri
  • Open Access
    The Genome Copy Number of the Thermophilic Cyanobacterium <span class="named-content genus-species" id="named-content-1">Thermosynechococcus elongatus</span> E542 Is Controlled by Growth Phase and Nutrient Availability
    Physiology
    The Genome Copy Number of the Thermophilic Cyanobacterium Thermosynechococcus elongatus E542 Is Controlled by Growth Phase and Nutrient Availability

    The present study revealed that the genome copy number (ploidy) status in the thermophilic cyanobacterium Thermosynechococcus E542 is regulated by growth phase and various environmental parameters to give us a window into understanding the role of polyploidy. An increased ploidy level is found to be associated with higher metabolic activity and increased vigor by acting as backup genetic information to compensate for damage to...

    Sadaf Riaz, Meng Xiao, Pengyu Chen, Meijin Li, Yixuan Cui, Maurycy Daroch

Plant Microbiology

  • Biosurfactants Produced by Phyllosphere-Colonizing Pseudomonads Impact Diesel Degradation but Not Colonization of Leaves of Gnotobiotic <span class="named-content genus-species" id="named-content-1">Arabidopsis thaliana</span>
    Plant Microbiology
    Biosurfactants Produced by Phyllosphere-Colonizing Pseudomonads Impact Diesel Degradation but Not Colonization of Leaves of Gnotobiotic Arabidopsis thaliana

    Many leaf-colonizing bacteria produce surfactants and are able to degrade aliphatic compounds; however, whether surfactant production provides a competitive advantage during leaf colonization is unclear. Furthermore, it is unclear if leaf colonizers take advantage of the aliphatic compounds that constitute the leaf cuticle and cuticular waxes.

    S. Oso, F. Fuchs, C. Übermuth, L. Zander, S. Daunaraviciute, D. M. Remus, I. Stötzel, M. Wüst, L. Schreiber, M. N. P. Remus-Emsermann
  • A Stringent-Response-Defective <span class="named-content genus-species" id="named-content-1">Bradyrhizobium diazoefficiens</span> Strain Does Not Activate the Type 3 Secretion System, Elicits an Early Plant Defense Response, and Circumvents NH<sub>4</sub>NO<sub>3</sub>-Induced Inhibition of Nodulation
    Plant Microbiology
    A Stringent-Response-Defective Bradyrhizobium diazoefficiens Strain Does Not Activate the Type 3 Secretion System, Elicits an Early Plant Defense Response, and Circumvents NH4NO3-Induced Inhibition of Nodulation

    The symbiotic N2 fixation carried out between prokaryotic rhizobia and legume plants performs a substantial contribution to the N cycle in the biosphere. This symbiotic association is initiated when rhizobia infect and penetrate the root hairs, which is followed by the growth and development of root nodules, within which the infective rhizobia are established and protected.

    Julieta Pérez-Giménez, Esteban T. Iturralde, Gonzalo Torres Tejerizo, Juan Ignacio Quelas, Elizaveta Krol, Cecilia Borassi, Anke Becker, José M. Estevez, Aníbal R. Lodeiro
  • Candicidin Isomer Production Is Essential for Biocontrol of Cucumber <em>Rhizoctonia</em> Rot by <span class="named-content genus-species" id="named-content-1">Streptomyces albidoflavus</span> W68
    Plant Microbiology
    Candicidin Isomer Production Is Essential for Biocontrol of Cucumber Rhizoctonia Rot by Streptomyces albidoflavus W68

    This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the...

    Xueyan Yao, Zhenying Zhang, Jun Huang, Shiping Wei, Xianyun Sun, Yihua Chen, Hongwei Liu, Shaojie Li

Public and Environmental Health Microbiology

  • Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas
    Public and Environmental Health Microbiology
    Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas

    Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the...

    Simona Fioriti, Sonia Nina Coccitto, Nicholas Cedraro, Serena Simoni, Gianluca Morroni, Andrea Brenciani, Gianmarco Mangiaterra, Carla Vignaroli, Luigi Vezzulli, Francesca Biavasco, Eleonora Giovanetti

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Applied and Environmental Microbiology: 87 (9)

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  • Interspecies Inhibition of Porphyromonas gingivalis by Yogurt-Derived Lactobacillus delbrueckii Requires Active Pyruvate Oxidase
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