Spotlight
Minireviews
MinireviewMolecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical ProcessesThe atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement.
MinireviewTo Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the RhizosphereFree-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop production as an alternative to chemical fertilizer, potentially reducing production costs and ameliorating negative environmental impacts of fertilizer N additions.
Biotechnology
Biotechnology | SpotlightIntranasal Immunization with the Commensal Streptococcus mitis Confers Protective Immunity against Pneumococcal Lung InfectionStreptococcus pneumoniae causes various diseases worldwide. Current pneumococcal vaccines protect against a limited number of more than 90 pneumococcal serotypes, accentuating the urgent need to develop novel prophylactic strategies. S. pneumoniae and the commensal...
BiotechnologyBioprospecting of Native Efflux Pumps To Enhance Furfural Tolerance in Ethanologenic Escherichia coliLignocellulosic biomass, especially agricultural residues, represents an important potential feedstock for microbial production of renewable fuels and chemicals. During the deconstruction of hemicellulose by thermochemical processes, side products that inhibit cell growth and production, such as furan aldehydes, are generated, limiting cost-effective lignocellulose conversion. Here, we developed a new approach to increase cellular...
Environmental Microbiology
Environmental Microbiology | SpotlightTaxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut HealthDietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual...
Environmental MicrobiologyProteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane MetabolismNaturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader “Candidatus Dichloromethanomonas elyunquensis” strain RM, suggesting...
Environmental MicrobiologyHomologous Expression and Characterization of Gassericin T and Gassericin S, a Novel Class IIb Bacteriocin Produced by Lactobacillus gasseri LA327Bacteriocins are regarded as potential alternatives for antibiotics in the absence of highly resistant bacteria. In particular, two-peptide (class IIb) bacteriocins exhibit the maximum activity through the synergy of two components, and their antimicrobial spectra are known to be relatively wide. However, there are few reports of synergistic activity of class IIb bacteriocins determined by isolation and purification of individual...
Environmental MicrobiologySucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and MetagenomicsOur ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When genomic or metagenomic data are used, metabolic capacity is inferred from genetic potential. Here, we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase occurs only in a small proportion of haloarchaeal...
Enzymology and Protein Engineering
Enzymology and Protein EngineeringTwo Novel α-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade ArabinanWe identified two novel α-l-arabinofuranosidases, BlArafC and BlArafB, from B. longum subsp. longum JCM 1217, both of which are predicted to be extracellular membrane-bound enzymes. The former specifically acts on α1,2/3-l-arabinofuranosyl linkages, while the latter acts on the α1,5-l-...
Enzymology and Protein EngineeringDiscovery of a Thermostable GH10 Xylanase with Broad Substrate Specificity from the Arctic Mid-Ocean Ridge Vent SystemHot springs at the sea bottom harbor unique biodiversity and are a promising source of enzymes with interesting properties. We describe the functional characterization of a thermophilic and halophilic multidomain xylanase originating from the Arctic Mid-Ocean Ridge vent system, belonging to the well-studied family 10 of glycosyl hydrolases (GH10). This xylanase, AMOR_GH10A, has a surprisingly wide substrate range and is more active...
Evolutionary and Genomic Microbiology
Evolutionary and Genomic MicrobiologyIdentification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilumElastin is an important proteinaceous component of vertebrate connective tissues (e.g., blood vessels, lung, and skin), to which it confers elasticity. Elastases have been identified in a number of pathogenic bacteria. They are thought to be required for tissue penetration and dissemination, acting as “spreading factors.” Flavobacterium psychrophilum is a devastating...
Evolutionary and Genomic MicrobiologyGenomic Diversity, Virulence, and Antimicrobial Resistance of Klebsiella pneumoniae Strains from Cows and HumansWe demonstrate here the genetic diversity of K. pneumoniae isolates from dairy cows and the mixed phylogenetic lineages between bovine and human isolates. The ferric uptake operon kfuABC genes were more prevalent in strains from clinical mastitis cows. Furthermore, we report the emergence of an IncN-type plasmid carrying the blaCTX-M-1 and...
Food Microbiology
Food MicrobiologyIncreased Resistance of Salmonella enterica Serovar Typhimurium and Escherichia coli O157:H7 to 222-Nanometer Krypton-Chlorine Excilamp Treatment by Acid AdaptationThere is a need for novel, mercury-free UV lamp technology to replace germicidal lamps containing harmful mercury, which are routinely utilized for UV pasteurization of apple juice. In addition, consideration of the changes in response to antimicrobial treatments that may occur when pathogens are adapted to the acid in an apple juice matrix is critical to the practical application of this technology. Based on this, an investigation...
Food MicrobiologyFollowing Coffee Production from Cherries to Cup: Microbiological and Metabolomic Analysis of Wet Processing of Coffea arabicaCoffee needs to undergo a long chain of events to transform from coffee cherries to a beverage. The coffee postharvest processing is one of the key phases that convert the freshly harvested cherries into green coffee beans before roasting and brewing. Among multiple existing processing methods, the wet processing has been usually applied for Arabica coffee and produces decent quality of both green coffee beans and the cup of coffee. In...
Food MicrobiologyInactivating Mutations in Irc7p Are Common in Wine Yeasts, Attenuating Carbon-Sulfur β-Lyase Activity and Volatile Sulfur Compound ProductionVolatile sulfur compounds contribute to wine aromas that may be considered pleasant, such as “tropical,” “passionfruit,” and “guava,” as well as aromas that are considered undesirable, such as “rotten eggs,” “onions,” and “sewer.” During fermentation, wine yeasts release some of these compounds from odorless precursor molecules, a process that is most efficient when performed by yeasts that express active forms of the protein Irc7p. We...
Genetics and Molecular Biology
Genetics and Molecular BiologyThe Aspergillus flavus rtfA Gene Regulates Plant and Animal Pathogenesis and Secondary MetabolismIn this study, the epigenetic global regulator rtfA, which encodes a putative RNA-Pol II transcription elongation factor-like protein, was characterized in the mycotoxigenic and opportunistic pathogen A. flavus. Specifically, its involvement in A. flavus pathogenesis in plant and animal...
Genetics and Molecular BiologyMolecular and Functional Analysis of the Type IV Pilus Gene Cluster in Streptococcus sanguinis SK36The proteins and assembly machinery of the type IV pili (Tfp) are conserved throughout bacteria and archaea, and yet the function of this surface structure differs from species to species and even from strain to strain. As seen in Streptococcus sanguinis SK36, the expression of the Tfp gene cluster results in a hairlike surface structure that is much shorter than the...
Genetics and Molecular Biology | SpotlightDevelopment of Aspirin-Inducible Biosensors in Escherichia coli and SimCellsAn aspirin-inducible SalR/Psal regulation system, originally from Acinetobacter baylyi ADP1, has been designed for E. coli strains. SalR is a typical LysR-type transcriptional regulator (LTTR) family protein and activates the Psal promoter in the presence of...
Methods
MethodsRapid and Simple Universal Escherichia coli Genotyping Method Based on Multiple-Locus Variable-Number Tandem-Repeat Analysis Using Single-Tube Multiplex PCR and Standard Gel ElectrophoresisFast typing methods that can easily and accurately distinguish clonal groups and unrelated isolates are of particular interest for microbiologists confronted with outbreaks or performing epidemiological studies. Highly discriminatory universal methods, like PFGE, optical mapping, or WGS, are expensive and/or time-consuming. MLST is useful for phylogeny but is less discriminatory and requires sequencing facilities. PCR methods, which are...
Microbial Ecology
Microbial EcologyLarge-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with DiseaseFlavobacterium psychrophilum is the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), both of which cause substantial losses in farmed fish populations worldwide. To better prevent and control BCWD and RTFS outbreaks, we sought to characterize the genetic diversity of several hundred...
Microbial EcologyThe Mode of Action of Chicory Roots on Skatole Production in Entire Male Pigs Is neither via Reducing the Population of Skatole-Producing Bacteria nor via Increased Butyrate Production in the HindgutCastration is practiced to avoid the development of boar taint, which negatively affects the taste and odor of pork, and undesirable aggressive behavior. Due to animal welfare issues, alternatives to surgical castration are sought, though. Boar taint is a result of high concentrations of skatole and androstenone in back fat. Skatole is produced by microbial fermentation in the large intestine, and therefore, its production can be...
Microbial EcologySuperior Dispersal Ability Can Lead to Persistent Ecological Dominance throughout SuccessionMicrobial communities are ubiquitous and occupy nearly every imaginable habitat and resource, including human-influenced habitats (e.g., fermenting food and hospital surfaces) and habitats with little human influence (e.g., aquatic communities living in carnivorous plant pitchers). We studied yeast communities living in pitchers of the carnivorous purple pitcher plant to understand how and why microbial communities change over time. We...
Microbial EcologyDiversity, Dynamics, and Distribution of Bdellovibrio and Like Organisms in Perialpine LakesThis study highlights the abundance, distribution, and diversity of a poorly known microbial compartment in natural aquatic ecosystems, the Bdellovibrio and like organisms (BALOs). These obligate bacterial predators of other bacteria may have an important functional role. This study shows the relative quantitative importance of the three main families of this group,...
Microbial EcologyResilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant GrowthExploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the...
Microbial EcologyBacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental GradientsSalt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of...
Microbial EcologyBacterial Dispersers along Preferential Flow Paths of a Clay Till Depth ProfileThe ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil...
Physiology
PhysiologyCgHog1-Mediated CgRds2 Phosphorylation Alters Glycerophospholipid Composition To Coordinate Osmotic Stress in Candida glabrataThis study explored the role of CgHog1-mediated CgRds2 phosphorylation in response to osmotic stress in Candida glabrata. CgHog1 interacts with and phosphorylates CgRds2, a zinc cluster transcription factor, under osmotic stress. Phosphorylated CgRds2 plays an important role in increasing glycerophospholipid composition and...
PhysiologyInsights into the Function of the N-Acetyltransferase SatA That Detoxifies Streptothricin in Bacillus subtilis and Bacillus anthracisThis work provides insights into how an abundant antibiotic found in soil is bound to the enzyme that inactivates it. This work identifies residues for the binding of the antibiotic and probes the contributions of substituting side chains for those in the native protein, providing information regarding hydrophobicity, size, and flexibility of the antibiotic binding site.
Plant Microbiology
Plant Microbiology | SpotlightImportance of Poly-3-Hydroxybutyrate Metabolism to the Ability of Herbaspirillum seropedicae To Promote Plant GrowthThe application of bacteria as plant growth promoters is a sustainable alternative to mitigate the use of chemical fertilization in agriculture, reducing negative economic and environmental impacts. Several plant growth-promoting bacteria synthesize and accumulate the intracellular polymer polyhydroxybutyrate (PHB). However, the role of PHB in plant-bacterium interactions is poorly understood. In this study, applying the C4 model grass...
Public and Environmental Health Microbiology
Public and Environmental Health MicrobiologyEffects of Absolute Humidity, Relative Humidity, Temperature, and Wind Speed on Influenza Activity in Toronto, Ontario, CanadaThis study examined the relationship between environmental factors and the occurrence of influenza in general. Since the seasonality of influenza A and B viruses is different in most temperate climates, we also examined each influenza virus separately. This study reports a negative association of both absolute humidity and temperature with influenza A and B viruses and tries to understand the controversial effect of RH on influenza A...
Public and Environmental Health Microbiology | SpotlightHighly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted WatersBacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides. The study also delineates host-specific sequence patterns across...
Public and Environmental Health MicrobiologyHost Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical Enteropathogenic Escherichia coli StrainsAtypical enteropathogenic Escherichia coli (aEPEC) is a diarrheagenic type of E. coli, as it possesses the intimin gene (eae) for attachment and effacement on epithelium. Since aEPEC is ubiquitous even in developed countries, we previously used molecular epidemiological methods to...
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Applied and Environmental Microbiology® (AEM) publishes study results that make significant contributions to applied microbial research, basic microbial ecology research, and genetic and molecular investigations of microbial topics of practical value.
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Dr. Harold L. Drake, Editor in Chief