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Table of Contents

April 2020; Volume 86,Issue 7

Spotlight

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

Minireview

  • Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products
    Minireview | Spotlight
    Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products

    Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/...

    Isaac Cann, Gabriel V. Pereira, Ahmed M. Abdel-Hamid, Heejin Kim, Daniel Wefers, Boniface B. Kayang, Tamotsu Kanai, Takaaki Sato, Rafael C. Bernardi, Haruyuki Atomi, Roderick I. Mackie

Environmental Microbiology

  • Open Access
    DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization
    Environmental Microbiology
    DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization

    Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different...

    Yali Kong, Yakov Kuzyakov, Yang Ruan, Junwei Zhang, Tingting Wang, Min Wang, Shiwei Guo, Qirong Shen, Ning Ling
  • Open Access
    In-Depth Profiling of Calcite Precipitation by Environmental Bacteria Reveals Fundamental Mechanistic Differences with Relevance to Application
    Environmental Microbiology
    In-Depth Profiling of Calcite Precipitation by Environmental Bacteria Reveals Fundamental Mechanistic Differences with Relevance to Application

    Biomineralization triggered by bacteria is important in the natural environment and has many applications in industry and in civil and geotechnical engineering. The diversity in biomineralization capabilities of environmental bacteria is, however, not well understood. This study surveyed environmental bacteria for their ability to precipitate calcium carbonate minerals and investigated both the mechanisms and the resulting crystals. We...

    Bianca J. Reeksting, Timothy D. Hoffmann, Linzhen Tan, Kevin Paine, Susanne Gebhard
  • Functional <em>Bacillus thuringiensis</em> Cyt1Aa Is Necessary To Synergize <em>Lysinibacillus sphaericus</em> Binary Toxin (Bin) against Bin-Resistant and -Refractory Mosquito Species
    Environmental Microbiology
    Functional Bacillus thuringiensis Cyt1Aa Is Necessary To Synergize Lysinibacillus sphaericus Binary Toxin (Bin) against Bin-Resistant and -Refractory Mosquito Species

    One promising management strategy for mosquito control is the utilization of a mixture of L. sphaericus and B. thuringiensis subsp. israelensis insecticidal toxins. From this set, Bin and Cyt1Aa toxins synergize and display toxicity to resistant...

    Nathaly Alexandre Nascimento, Mary Carmen Torres-Quintero, Samira López Molina, Sabino Pacheco, Tatiany Patrícia Romão, Antonio Pereira-Neves, Mario Soberón, Alejandra Bravo, Maria Helena Neves Lobo Silva-Filha
  • A Pathway for Degradation of Uracil to Acetyl Coenzyme A in <span class="named-content genus-species" id="named-content-1">Bacillus megaterium</span>
    Environmental Microbiology
    A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium

    Pyrimidine has wide occurrence in natural environments, where bacteria use it as a nitrogen and carbon source for growth. Detailed biochemical pathways have been investigated with focus mainly on nitrogen assimilation in the past decades. Here, we report the discovery and characterization of two important enzymes, PydD2 and MSDH, which constitute an extension for the reductive pyrimidine catabolic pathway. These two enzymes, prevalent...

    Di Zhu, Yifeng Wei, Jinyu Yin, Dazhi Liu, Ee Lui Ang, Huimin Zhao, Yan Zhang
  • Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota
    Environmental Microbiology
    Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota

    Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the...

    Giulia Alessandri, Christian Milani, Leonardo Mancabelli, Giulia Longhi, Rosaria Anzalone, Gabriele Andrea Lugli, Sabrina Duranti, Francesca Turroni, Maria Cristina Ossiprandi, Douwe van Sinderen, Marco Ventura
  • Open Access
    Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness
    Environmental Microbiology | Spotlight
    Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness

    Microbiologically influenced corrosion (MIC) is a complex process that generates economic losses to the industry every year. Corrosion must be managed to prevent a loss of containment of produced fluids to the external environment. MIC management includes the identification of assets with higher MIC risk, which could be influenced by nutrient levels in the system. Assessing biofilms under different nutrient conditions is essential for...

    Silvia J. Salgar-Chaparro, Katerina Lepkova, Thunyaluk Pojtanabuntoeng, Adam Darwin, Laura L. Machuca
  • A Quorum Quenching Bacterial Isolate Contains Multiple Substrate-Inducible Genes Conferring Degradation of Diffusible Signal Factor
    Environmental Microbiology | Spotlight
    A Quorum Quenching Bacterial Isolate Contains Multiple Substrate-Inducible Genes Conferring Degradation of Diffusible Signal Factor

    Diffusible signal factor (DSF) represents a family of widely conserved quorum sensing signals involved in the regulation of virulence factor production in many Gram-negative bacterial pathogens. In this study, we developed a novel and efficient method for screening highly active DSF degradation microorganisms. With this method, we identified a bacterial isolate, Pseudomonas sp. strain HS-18, with a superb DSF degradation...

    Huishan Wang, Lisheng Liao, Shaohua Chen, Lian-Hui Zhang
  • <span class="named-content genus-species" id="named-content-1">Akkermansia muciniphila</span> Prevents Fatty Liver Disease, Decreases Serum Triglycerides, and Maintains Gut Homeostasis
    Environmental Microbiology
    Akkermansia muciniphila Prevents Fatty Liver Disease, Decreases Serum Triglycerides, and Maintains Gut Homeostasis

    This study investigated the effect of Akkermansia muciniphila on fatty liver disease. Although some research about the effects of A. muciniphila on host health has been published, study of the relationship between A. muciniphila administration and fatty liver, as well as changes in the gut microbiota, has not been conducted. In this study, we...

    Sejeong Kim, Yewon Lee, Yujin Kim, Yeongeun Seo, Heeyoung Lee, Jimyeong Ha, Jeeyeon Lee, Yukyung Choi, Hyemin Oh, Yohan Yoon

Enzymology and Protein Engineering

  • Engineering of Cyclodextrin Glycosyltransferase Reveals pH-Regulated Mechanism of Enhanced Long-Chain Glycosylated Sophoricoside Specificity
    Enzymology and Protein Engineering
    Engineering of Cyclodextrin Glycosyltransferase Reveals pH-Regulated Mechanism of Enhanced Long-Chain Glycosylated Sophoricoside Specificity

    The low water solubility of sophoricoside seriously limits its applications in the food and pharmaceutical industries. Long-chain glycosylated sophoricosides show greatly improved water solubility. Here, the product specificity of cyclodextrin glycosyltransferase (CGTase) for long-chain glycosylated sophoricosides was significantly affected by pH. Our results reveal the pH-regulated mechanism of the glycosylated product specificity of...

    Ruizhi Han, Jie Ni, Jieyu Zhou, Jinjun Dong, Guochao Xu, Ye Ni
  • Open Access
    Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Enzymology and Protein Engineering
    Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in Escherichia coli

    UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited...

    Dolores Linde, Andrés Olmedo, Alejandro González-Benjumea, María Estévez, Chantal Renau-Mínguez, Juan Carro, Elena Fernández-Fueyo, Ana Gutiérrez, Angel T. Martínez

Evolutionary and Genomic Microbiology

  • Open Access
    Dissemination of Quinolone-Resistant <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> in the Norwegian Broiler and Pig Production Chains and Possible Persistence in the Broiler Production Environment
    Evolutionary and Genomic Microbiology
    Dissemination of Quinolone-Resistant Escherichia coli in the Norwegian Broiler and Pig Production Chains and Possible Persistence in the Broiler Production Environment

    Since antimicrobial usage is low in Norwegian animal husbandry, Norway is an ideal country to study antimicrobial resistance in the absence of selective pressure from antimicrobial usage. In particular, the usage of quinolones is very low, which makes it possible to investigate the spread and development of quinolone resistance in natural environments. Comparison of quinolone-resistant...

    Håkon Kaspersen, Camilla Sekse, Eve Zeyl Fiskebeck, Jannice Schau Slettemeås, Roger Simm, Madelaine Norström, Anne Margrete Urdahl, Karin Lagesen

Food Microbiology

  • Open Access
    Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products
    Food Microbiology | Spotlight
    Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products

    In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of...

    Solvej Siedler, Martin Holm Rau, Susanne Bidstrup, Justin M. Vento, Stina Dissing Aunsbjerg, Elleke F. Bosma, Laura M. McNair, Chase L. Beisel, Ana Rute Neves
  • Viable but Nonculturable <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> O157:H7 and <span class="named-content genus-species" id="named-content-2">Salmonella enterica</span> in Fresh Produce: Rapid Determination by Loop-Mediated Isothermal Amplification Coupled with a Propidium Monoazide Treatment
    Food Microbiology
    Viable but Nonculturable Escherichia coli O157:H7 and Salmonella enterica in Fresh Produce: Rapid Determination by Loop-Mediated Isothermal Amplification Coupled with a Propidium Monoazide Treatment

    VBNC pathogenic bacteria pose a potential risk to the food industry because they do not multiply on routine microbiological media and thus can evade detection in conventional plating assays. Both E. coli O157:H7 and S. enterica have been reported to enter the VBNC state under a range of...

    Lu Han, Kaidi Wang, Lina Ma, Pascal Delaquis, Susan Bach, Jinsong Feng, Xiaonan Lu
  • Role of Cecal Microbiota in the Differential Resistance of Inbred Chicken Lines to Colonization by <em>Campylobacter jejuni</em>
    Food Microbiology
    Role of Cecal Microbiota in the Differential Resistance of Inbred Chicken Lines to Colonization by Campylobacter jejuni

    Campylobacter is a leading cause of foodborne diarrheal disease worldwide. Poultry are a key source of human infections, but there are currently few effective measures against Campylobacter in poultry during production. One option to control Campylobacter may be to alter the composition of microbial communities in the avian intestines by introducing beneficial bacteria, which exclude the harmful ones. We...

    Cosmin Chintoan-Uta, Trong Wisedchanwet, Laura Glendinning, Abi Bremner, Androniki Psifidi, Lonneke Vervelde, Kellie Watson, Mick Watson, Mark P. Stevens

Genetics and Molecular Biology

  • The Cell Wall Integrity Pathway Contributes to the Early Stages of <em>Aspergillus fumigatus</em> Asexual Development
    Genetics and Molecular Biology
    The Cell Wall Integrity Pathway Contributes to the Early Stages of Aspergillus fumigatus Asexual Development

    A remarkable feature of the human pathogen Aspergillus fumigatus is its ability to produce impressive amounts of infectious propagules known as conidia. These particles reach immunocompromised patients and may initiate a life-threatening mycosis. The conidiation process in Aspergillus is governed by a sequence of proteins that coordinate the development of...

    Marina Campos Rocha, João Henrique Tadini Marilhano Fabri, Isabelle Taira Simões, Rafael Silva-Rocha, Daisuke Hagiwara, Anderson Ferreira da Cunha, Gustavo Henrique Goldman, David Cánovas, Iran Malavazi
  • Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in <em>Clostridium beijerinckii</em>
    Genetics and Molecular Biology
    Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii

    Solventogenic clostridia are anaerobic bacteria that can produce butanol, ethanol, and acetone, which can be used as biofuels or building block chemicals. Here, we show that AdhR, a σ54-dependent transcriptional activator, senses the intracellular redox status and controls alcohol synthesis in Clostridium beijerinckii. AdhR provides a new example of a GAF...

    Bin Yang, Xiaoqun Nie, Youli Xiao, Yang Gu, Weihong Jiang, Chen Yang

Geomicrobiology

  • Interactions between Biotite and the Mineral-Weathering Bacterium <em>Pseudomonas azotoformans</em> F77
    Geomicrobiology
    Interactions between Biotite and the Mineral-Weathering Bacterium Pseudomonas azotoformans F77

    Bacteria play important roles in mineral weathering and soil formation, although the molecular mechanisms underlying the interactions between bacteria and silicate minerals are poorly understood. In this study, the interactions between biotite and the highly effective mineral-weathering bacterium P. azotoformans F77 were characterized. Our results showed that the...

    Yuan-Li Wang, Li-Jing Sun, Chun-Mei Xian, Feng-Lian Kou, Ying Zhu, Lin-Yan He, Xia-Fang Sheng

Invertebrate Microbiology

  • Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea)
    Invertebrate Microbiology
    Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea)

    The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a...

    Kara A. Tinker, Elizabeth A. Ottesen

Methods

  • Open Access
    The ZKIR Assay, a Real-Time PCR Method for the Detection of <em>Klebsiella pneumoniae</em> and Closely Related Species in Environmental Samples
    Methods | Spotlight
    The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

    The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp...

    Elodie Barbier, Carla Rodrigues, Geraldine Depret, Virginie Passet, Laurent Gal, Pascal Piveteau, Sylvain Brisse

Microbial Ecology

  • Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat
    Microbial Ecology
    Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

    Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other...

    Laurey Steinke, Gordon W. Slysz, Mary S. Lipton, Christian Klatt, James J. Moran, Margie F. Romine, Jason M. Wood, Gordon Anderson, Donald A. Bryant, David M. Ward

Physiology

  • Promiscuous Enzymes Cause Biosynthesis of Diverse Siderophores in <span class="named-content genus-species" id="named-content-1">Shewanella oneidensis</span>
    Physiology
    Promiscuous Enzymes Cause Biosynthesis of Diverse Siderophores in Shewanella oneidensis

    The simultaneous production of multiple siderophores is considered a general strategy for microorganisms to rapidly adapt to their ever-changing environments. In this study, we show that some Shewanella spp. may downscale their capability for siderophore synthesis to facilitate adaptation. Although S. oneidensis lacks an enzyme specifically synthesizing...

    Sijing Wang, Huihui Liang, Lulu Liu, Xinhang Jiang, Shihua Wu, Haichun Gao
  • GlnR Negatively Regulates Glutamate-Dependent Acid Resistance in <span class="named-content genus-species" id="named-content-1">Lactobacillus brevis</span>
    Physiology
    GlnR Negatively Regulates Glutamate-Dependent Acid Resistance in Lactobacillus brevis

    Free-living lactic acid bacteria often encounter acid stresses because of their organic acid-producing features. Several acid resistance mechanisms, such as the glutamate decarboxylase system, F1Fo-ATPase proton pump, and alkali production, are usually employed to relieve growth inhibition caused by acids. The glutamate decarboxylase system is vital for GAD-containing lactic acid bacteria to protect cells from DNA...

    Luchan Gong, Cong Ren, Yan Xu
  • Sml1 Inhibits the DNA Repair Activity of Rev1 in <span class="named-content genus-species" id="named-content-1">Saccharomyces cerevisiae</span> during Oxidative Stress
    Physiology
    Sml1 Inhibits the DNA Repair Activity of Rev1 in Saccharomyces cerevisiae during Oxidative Stress

    Rev1 was critical for cell growth in S. cerevisiae, and the deletion of REV1 caused a severe growth defect in cells exposed to oxidative stress (2 mM H2O2). Furthermore, we found that Sml1 physically interacted with Rev1 and inhibited Rev1 phosphorylation, thereby inhibiting Rev1 DNA antioxidant activity. These findings indicate that...

    Rui Yao, Pei Zhou, Chengjin Wu, Liming Liu, Jing Wu
  • Freshwater Cyanobacterium <em>Synechococcus elongatus</em> PCC 7942 Adapts to an Environment with Salt Stress via Ion-Induced Enzymatic Balance of Compatible Solutes
    Physiology
    Freshwater Cyanobacterium Synechococcus elongatus PCC 7942 Adapts to an Environment with Salt Stress via Ion-Induced Enzymatic Balance of Compatible Solutes

    Most microbes de novo synthesize compatible solutes for adaptation to salt stress or fluctuating salinity environments. However, to date, one of the core questions involved in these physiological processes, i.e., the regulation of salt-induced compatible solute biosynthesis, is still not well understood. Here, this issue was systematically investigated by employing the model freshwater cyanobacterium...

    Yajing Liang, Mingyi Zhang, Min Wang, Wei Zhang, Cuncun Qiao, Quan Luo, Xuefeng Lu

Public and Environmental Health Microbiology

  • Site-Specific Profiling of the Dental Mycobiome Reveals Strong Taxonomic Shifts during Progression of Early-Childhood Caries
    Public and Environmental Health Microbiology | Spotlight
    Site-Specific Profiling of the Dental Mycobiome Reveals Strong Taxonomic Shifts during Progression of Early-Childhood Caries

    Early-childhood caries is one of the most prevalent diseases in children worldwide and, while preventable, remains a global public health concern. Untreated cavities are painful and expensive and can lead to tooth loss and a lower quality of life. Caries are driven by acid production via microbial fermentation of dietary carbohydrates, resulting in enamel erosion. While caries is a well-studied disease, most research has focused on...

    Lauren M. O’Connell, Ryan Santos, Garrett Springer, Robert A. Burne, Marcelle M. Nascimento, Vincent P. Richards
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Aspergillus fumigatus</span> Mitochondrial Acetyl Coenzyme A Acetyltransferase as an Antifungal Target
    Public and Environmental Health Microbiology
    Aspergillus fumigatus Mitochondrial Acetyl Coenzyme A Acetyltransferase as an Antifungal Target

    A growing number of people worldwide are suffering from invasive aspergillosis caused by the human opportunistic fungal pathogen A. fumigatus. Current therapeutic options rely on a limited repertoire of antifungals. Ergosterol is an essential component of the fungal cell membrane as well as a target of current antifungals. Approximately 20 enzymes are involved in...

    Yuanwei Zhang, Wenfan Wei, Jialu Fan, Cheng Jin, Ling Lu, Wenxia Fang

Erratum

  • Free
    Erratum for Oliveira et al., “K2 Capsule Depolymerase Is Highly Stable, Is Refractory to Resistance, and Protects Larvae and Mice from <span class="named-content genus-species" id="named-content-1">Acinetobacter baumannii</span> Sepsis”
    Erratum
    Erratum for Oliveira et al., “K2 Capsule Depolymerase Is Highly Stable, Is Refractory to Resistance, and Protects Larvae and Mice from Acinetobacter baumannii Sepsis”
    Hugo Oliveira, Ana Mendes, Alexandra G. Fraga, Alice Ferreira, Andreia I. Pimenta, Dalila Mil-Homens, Arsénio M. Fialho, Jorge Pedrosa, Joana Azeredo

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Applied and Environmental Microbiology: 86 (7)

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volume 86, issue 7
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