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Table of Contents

May 2019; Volume 85,Issue 9

Spotlight

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

Biotechnology

  • The PlyB Endolysin of Bacteriophage vB_BanS_Bcp1 Exhibits Broad-Spectrum Bactericidal Activity against <em>Bacillus cereus Sensu Lato</em> Isolates
    Biotechnology | Spotlight
    The PlyB Endolysin of Bacteriophage vB_BanS_Bcp1 Exhibits Broad-Spectrum Bactericidal Activity against Bacillus cereus Sensu Lato Isolates

    Organisms of the Bacillus cereus sensu lato lineage are ubiquitous in the environment and are responsible for toxin-mediated infections ranging from severe food poisoning (B. cereus sensu stricto) to anthrax (Bacillus...

    Raymond Schuch, Adam J. Pelzek, Daniel C. Nelson, Vincent A. Fischetti
  • Toxoflavin Produced by <em>Burkholderia gladioli</em> from <em>Lycoris aurea</em> Is a New Broad-Spectrum Fungicide
    Biotechnology
    Toxoflavin Produced by Burkholderia gladioli from Lycoris aurea Is a New Broad-Spectrum Fungicide

    Human fungal infections are a growing problem associated with increased morbidity and mortality. Moreover, a growing number of antifungal-resistant fungal isolates have been reported over the past decade. Thus, the need for novel antifungal agents is imperative. In this study, we show that an endophytic bacterium, Burkholderia gladioli, isolated from the medicinal...

    Xiaodan Li, Yikui Li, Ren Wang, Qizhi Wang, Ling Lu
  • Embedding <span class="named-content genus-species" id="named-content-1">Bacillus velezensis</span> NH-1 in Microcapsules for Biocontrol of Cucumber <em>Fusarium</em> Wilt
    Biotechnology
    Embedding Bacillus velezensis NH-1 in Microcapsules for Biocontrol of Cucumber Fusarium Wilt

    Bacillus species are often used for the biocontrol of various plant pathogens, but the control efficiency of Bacillus is usually unstable in field experiments. To improve the control efficiency of Bacillus, in this study, microcapsules of Bacillus velezensis strain NH-1 were prepared using different wall materials (sodium alginate, chitosan...

    Wenjian Luo, Lidong Liu, Gaofu Qi, Fan Yang, Xuanjie Shi, Xiuyun Zhao

Environmental Microbiology

  • Stress-Responsive Alternative Sigma Factor SigB Plays a Positive Role in the Antifungal Proficiency of <em>Bacillus subtilis</em>
    Environmental Microbiology | Spotlight
    Stress-Responsive Alternative Sigma Factor SigB Plays a Positive Role in the Antifungal Proficiency of Bacillus subtilis

    Biological control using beneficial bacteria (PGPRs) represents an attractive and environment-friendly alternative to pesticides for controlling plant diseases. Different PGPR Bacillus species produce potent biofungicides and stimulate plant defense responses against phytopathogenic fungi. However, very little is known about how PGPRs recognize phytopathogens and process the antifungal response. Here, we report how...

    M. Bartolini, S. Cogliati, D. Vileta, C. Bauman, W. Ramirez, R. Grau
  • Spatiotemporal Dynamics of Free-Living and Particle-Associated <em>Vibrio</em> Communities in the Northern Chinese Marginal Seas
    Environmental Microbiology
    Spatiotemporal Dynamics of Free-Living and Particle-Associated Vibrio Communities in the Northern Chinese Marginal Seas

    The dynamics of Vibrio communities have been shown in many marine habitats that are close to land, including estuary or harbor areas. Here, we investigated the spatiotemporal dynamics of Vibrio populations in the northern Chinese marginal seas, spanning a wide spatial scale. We showed that the abundances of the Vibrio population in the present study were higher than those in most previously studied areas and...

    Jinchang Liang, Jiwen Liu, Xiaolei Wang, Heyu Lin, Jingli Liu, Shun Zhou, Hao Sun, Xiao-Hua Zhang
  • Open Access
    Zinc Toxicity and Iron-Sulfur Cluster Biogenesis in <em>Escherichia coli</em>
    Environmental Microbiology
    Zinc Toxicity and Iron-Sulfur Cluster Biogenesis in Escherichia coli

    Zinc toxicity has been implicated in causing various human diseases. High concentrations of zinc can also inhibit bacterial cell growth. However, the underlying mechanism has not been fully understood. Here, we report that zinc overload in Escherichia coli cells inhibits iron-sulfur cluster biogenesis by targeting specific iron-sulfur cluster assembly proteins....

    Jianghui Li, Xiaojun Ren, Bingqian Fan, Zhaoyang Huang, Wu Wang, Huaibin Zhou, Zhefeng Lou, Huangen Ding, Jianxin Lyu, Guoqiang Tan
  • Low Temperature and Neutral pH Define “<em>Candidatus</em> Nitrotoga sp.” as a Competitive Nitrite Oxidizer in Coculture with <span class="named-content genus-species" id="named-content-1">Nitrospira defluvii</span>
    Environmental Microbiology
    Low Temperature and Neutral pH Define “Candidatus Nitrotoga sp.” as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii

    “Ca. Nitrotoga” is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira...

    Simone Wegen, Boris Nowka, Eva Spieck
  • Open Access
    Two Novel Bacteriophages Improve Survival in <em>Galleria mellonella</em> Infection and Mouse Acute Pneumonia Models Infected with Extensively Drug-Resistant <em>Pseudomonas aeruginosa</em>
    Environmental Microbiology
    Two Novel Bacteriophages Improve Survival in Galleria mellonella Infection and Mouse Acute Pneumonia Models Infected with Extensively Drug-Resistant Pseudomonas aeruginosa

    In this study, two novel P. aeruginosa phages, Bϕ-R656 and Bϕ-R1836, were evaluated in vitro, in silico, and in vivo for therapeutic efficacy and safety as an alternative antibacterial agent to control XDR-PA strains collected from pneumonia patients. Both phages exhibited potent bacteriolytic activity and greatly improved survival in...

    Jongsoo Jeon, Dongeun Yong
  • Population Structure and Morphotype Analysis of “<em>Candidatus</em> Accumulibacter” Using Fluorescence <em>In Situ</em> Hybridization-Staining-Flow Cytometry
    Environmental Microbiology
    Population Structure and Morphotype Analysis of “Candidatus Accumulibacter” Using Fluorescence In Situ Hybridization-Staining-Flow Cytometry

    As one group of the most important functional phosphorus removal organisms, “Candidatus Accumulibacter,” affiliated with the Rhodocyclus group of the Betaproteobacteria, is a widely recognized and studied PAO in the field of biological wastewater treatment. The morphotypes and population structure of clade-level “Candidatus Accumulibacter” were studied through novel FISH-staining-flow cytometry, which...

    Chao Li, Wei Zeng, Ning Li, Yu Guo, Yongzhen Peng
  • The Indoor-Air Microbiota of Pig Farms Drives the Composition of the Pig Farmers’ Nasal Microbiota in a Season-Dependent and Farm-Specific Manner
    Environmental Microbiology
    The Indoor-Air Microbiota of Pig Farms Drives the Composition of the Pig Farmers’ Nasal Microbiota in a Season-Dependent and Farm-Specific Manner

    The airborne microbiota of pig farms poses a potential health hazard and impacts both livestock and humans working in this environment. Therefore, a more thorough understanding of the microbiota composition and dynamics in this setting is needed. This study was of a prospective design (12 months) and used samples from different sites. This means that the microbiota of air, animals (pigs), and humans was simultaneously investigated. Our...

    Julia G. Kraemer, Susanne Aebi, Anne Oppliger, Markus Hilty

Enzymology and Protein Engineering

  • Conversion of Mevalonate 3-Kinase into 5-Phosphomevalonate 3-Kinase by Single Amino Acid Mutations
    Enzymology and Protein Engineering
    Conversion of Mevalonate 3-Kinase into 5-Phosphomevalonate 3-Kinase by Single Amino Acid Mutations

    Isoprenoid is the largest family of natural compounds, including important bioactive molecules such as vitamins, hormones, and natural medicines. The mevalonate pathway is a target for metabolic engineering because it supplies precursors for isoprenoid biosynthesis. Mevalonate 3-kinase is an enzyme involved in the modified mevalonate pathway specific to limited species of thermophilic archaea. Replacement of a single amino acid residue...

    Kento Motoyama, Fumiaki Sobue, Hiroshi Kawaide, Tohru Yoshimura, Hisashi Hemmi
  • A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase
    Enzymology and Protein Engineering | Spotlight
    A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase

    The enzymatic biodegradation of structural polysaccharides is affected by the degree of delignification of lignocellulose during the white-rot fungal decay process. The lignin matrix decreases accessibility to the substrates for LPMOs. H2O2 has been studied as a cosubstrate for LPMOs, but the formation and utilization of H2O2 in the reactions still represent an intriguing focus of current...

    Fei Li, Fuying Ma, Honglu Zhao, Shu Zhang, Lei Wang, Xiaoyu Zhang, Hongbo Yu

Food Microbiology

  • Targeted and Repetitive Chromosomal Integration Enables High-Level Heterologous Gene Expression in <em>Lactobacillus casei</em>
    Food Microbiology
    Targeted and Repetitive Chromosomal Integration Enables High-Level Heterologous Gene Expression in Lactobacillus casei

    Lactic acid bacteria (LAB), including Lactobacillus casei, have the potential for overexpression of heterologous proteins, such as bioactive molecules and enzymes. However, traditional genetic tools for expression of these proteins show genetic instability or low yields of the desired product. In this study, we provide a procedure for repetitive integration of genes...

    Yongping Xin, Yingli Mu, Jian Kong, Tingting Guo
  • Surface Layer of <em>Lactobacillus helveticus</em> MIMLh5 Promotes Endocytosis by Dendritic Cells
    Food Microbiology
    Surface Layer of Lactobacillus helveticus MIMLh5 Promotes Endocytosis by Dendritic Cells

    Beneficial microbes may positively affect host physiology at various levels, e.g., by participating in immune system maturation and modulation, boosting defenses and dampening reactions, thus affecting the whole homeostasis. As a consequence, the use of probiotics is increasingly regarded as suitable for more extended applications for health maintenance, not only microbiota balancing. This implies a deep knowledge of the mechanisms and...

    Valentina Taverniti, Mauro Marengo, Eva Fuglsang, Helene Marie Skovsted, Stefania Arioli, Giacomo Mantegazza, Giorgio Gargari, Stefania Iametti, Francesco Bonomi, Simone Guglielmetti, Hanne Frøkiær
  • Prebiotic Supplementation of <em>In Vitro</em> Fecal Fermentations Inhibits Proteolysis by Gut Bacteria, and Host Diet Shapes Gut Bacterial Metabolism and Response to Intervention
    Food Microbiology
    Prebiotic Supplementation of In Vitro Fecal Fermentations Inhibits Proteolysis by Gut Bacteria, and Host Diet Shapes Gut Bacterial Metabolism and Response to Intervention

    Dietary protein intake is high in Western populations, which could result in potentially harmful metabolites in the gut from proteolysis. In an in vitro fermentation model, the addition of prebiotics reduced the negative consequences of high protein levels. Supplementation with a prebiotic resulted in a reduction of proteolytic metabolites in the model. A difference was seen in protein fermentation between omnivore and...

    Xuedan Wang, Glenn R. Gibson, Adele Costabile, Manuela Sailer, Stephan Theis, Robert A. Rastall

Genetics and Molecular Biology

  • Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity
    Genetics and Molecular Biology
    Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity

    New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated...

    A. Jochim, T. Shi, D. Belikova, S. Schwarz, A. Peschel, S. Heilbronner

Geomicrobiology

  • Open Access
    Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile <em>Methanocaldococcus jannaschii</em> during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer
    Geomicrobiology
    Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

    Hyperthermophilic methanogens and H2-producing heterotrophs are collocated in high-temperature subseafloor environments, such as petroleum reservoirs, mid-ocean ridge flanks, and hydrothermal vents. Abiotic flux of H2 can be very low in these environments, and there is a gap in our knowledge about the origin of CH4 in these habitats. In the hyperthermophile...

    Begüm D. Topçuoğlu, Cem Meydan, Tran B. Nguyen, Susan Q. Lang, James F. Holden

Methods

  • Degradation of Fungal MicroRNAs Triggered by Short Tandem Target Mimics Is via the Small-RNA-Degrading Nuclease
    Methods
    Degradation of Fungal MicroRNAs Triggered by Short Tandem Target Mimics Is via the Small-RNA-Degrading Nuclease

    The development and application of STTM technology to block miR-like RNAs in M. robertsii and A. flavus may allow for efficient generation of miR-like RNA mutants in various fungi, providing a powerful tool for functional genomics of small RNA molecules in fungi.

    Yulong Wang, Zhangxun Wang, Wenjing Yang, Xiangyun Xie, Haiyan Cheng, Li Qin, Guiliang Tang, Bo Huang

Microbial Ecology

  • Differential Effects of Breed and Nursing on Early-Life Colonic Microbiota and Immune Status as Revealed in a Cross-Fostering Piglet Model
    Microbial Ecology
    Differential Effects of Breed and Nursing on Early-Life Colonic Microbiota and Immune Status as Revealed in a Cross-Fostering Piglet Model

    Early-life gut microbiota and immune status are pivotal for postnatal growth. By using an interspecific cross-fostering piglet model, we find that change in nursing mother transiently reshapes preweaning colon microbiota and immune status, while breed shows persistent effects both pre- and postweaning. Piglets nursed by Meishan sows had lower Streptococcus suis counts...

    Chunlong Mu, Gaorui Bian, Yong Su, Weiyun Zhu
  • Recovery of Fungal Cells from Air Samples: a Tale of Loss and Gain
    Microbial Ecology
    Recovery of Fungal Cells from Air Samples: a Tale of Loss and Gain

    This work shed light on a significant issue regarding the loss of fungal spores when recovered from air samples using liquid medium and centrifugation to concentrate air particles before DNA extraction. We provide proof that the loss affects the overall fungal diversity of aerosols and that some taxa are differentially more affected than others. Furthermore, a laboratory experiment confirmed the environmental results obtained during...

    Hamza Mbareche, Marc Veillette, Wieke Teertstra, Willem Kegel, Guillaume J. Bilodeau, Han A. B. Wösten, Caroline Duchaine
  • Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location, and Interaction with Bacteria
    Microbial Ecology | Spotlight
    Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location, and Interaction with Bacteria

    During recent years, human breast milk has been documented as a potential source of bacteria for the newborn. Recently, we have reported the presence of fungi in breast milk from healthy mothers. It is well known that environmental and perinatal factors can affect milk bacteria; however, the impact on milk fungi is still unknown. The current report describes fungal communities (mycobiota) in breast milk samples across different...

    Alba Boix-Amorós, Fernando Puente-Sánchez, Elloise du Toit, Kaisa M. Linderborg, Yumei Zhang, Baoru Yang, Seppo Salminen, Erika Isolauri, Javier Tamames, Alex Mira, Maria Carmen Collado
  • Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens
    Microbial Ecology | Spotlight
    Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens

    The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in...

    John M. Ngunjiri, Kara J. M. Taylor, Michael C. Abundo, Hyesun Jang, Mohamed Elaish, Mahesh KC, Amir Ghorbani, Saranga Wijeratne, Bonnie P. Weber, Timothy J. Johnson, Chang-Won Lee

Physiology

  • Influence of Energy and Electron Availability on <em>In Vivo</em> Methane and Hydrogen Production by a Variant Molybdenum Nitrogenase
    Physiology
    Influence of Energy and Electron Availability on In Vivo Methane and Hydrogen Production by a Variant Molybdenum Nitrogenase

    A variant form of Mo nitrogenase catalyzes the conversion of CO2 and protons to the biofuels CH4 and H2. A constant supply of electrons and ATP is needed to drive these reduction reactions. The bacterium R. palustris generates ATP from light and has a versatile metabolism that makes it ideal for manipulating electron availability...

    Yanning Zheng, Caroline S. Harwood

Plant Microbiology

  • Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance
    Plant Microbiology
    Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance

    Agrobacterium tumefaciens as the causal agent of peach crown gall disease can be controlled by planting resistant cultivars. This study profiles the endophytic bacteria in susceptible and resistant peach cultivars, advancing our understanding of the relationships between endophytic bacterial communities and peach crown gall disease, with potential implications for...

    Qian Li, Rongjun Guo, Yujia Li, Wyatt H. Hartman, Shifang Li, Zhixiang Zhang, Susannah G. Tringe, Hongqing Wang

Public and Environmental Health Microbiology

  • Regulation of Iron Uptake by Fine-Tuning the Iron Responsiveness of the Iron Sensor Fur
    Public and Environmental Health Microbiology
    Regulation of Iron Uptake by Fine-Tuning the Iron Responsiveness of the Iron Sensor Fur

    Iron is a fundamental metal ion for living organisms as it facilitates various biological processes. The ferric uptake regulator (Fur) protein controls iron homeostasis in various bacterial species. It is believed that Fur’s iron-dependent regulatory action is sufficient for it to function as an iron sensor. However, we now establish that the bacterial pathogen Salmonella enables Fur to properly reflect changes in surrounding...

    Jeongjoon Choi, Sangryeol Ryu

Erratum

  • Free
    Erratum for Wegner et al., “Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon”
    Erratum
    Erratum for Wegner et al., “Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon”
    Carl-Eric Wegner, Michael Gaspar, Patricia Geesink, Martina Herrmann, Manja Marz, Kirsten Küsel

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Applied and Environmental Microbiology: 85 (9)

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volume 85, issue 9
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  • Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy
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  • Following Coffee Production from Cherries to Cup: Microbiological and Metabolomic Analysis of Wet Processing of Coffea arabica
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