Spotlight
Minireview
Minireview | SpotlightModulating the Gut Microbiota of Humans by Dietary Intervention with Plant GlycansThe human colon contains a community of microbial species, mostly bacteria, which is often referred to as the gut microbiota. The community is considered essential to human well-being by conferring additional energy-harvesting capacity, niche exclusion of pathogens, and molecular signaling activities that are integrated into human physiological processes.
Biodegradation
BiodegradationThe Operon Encoding Hydrolytic Dehalogenation of 4-Chlorobenzoate Is Transcriptionally Regulated by the TetR-Type Repressor FcbR and Its Ligand 4-Chlorobenzoyl Coenzyme AThe bacterial hydrolytic dehalogenation of 4CBA is a special CoA-activation-type catabolic pathway that plays an important role in the biodegradation of polychlorinated biphenyls and some herbicides. With genetic and biochemical approaches, the present study identified the transcriptional repressor and its cognate effector of a 4CBA hydrolytic dehalogenation operon.
Biotechnology
BiotechnologyA CRISPR/Cas9-Mediated, Homology-Independent Tool Developed for Targeted Genome Integration in Yarrowia lipolyticaThis study describes the development and optimization of a homology-independent targeted genome integration tool mediated by CRISPR/Cas9 in Yarrowia lipolytica. This tool does not require the construction of homologous templates and can be used to rapidly verify genetic elements and to iteratively integrate multiple-gene pathways in...
Biotechnology | SpotlightDiscovery and Functional Analysis of a Salicylic Acid Hydroxylase from Aspergillus nigerNonrenewable petroleum sources are being depleted, and therefore, alternative sources are needed. Plant biomass is one of the most abundant renewable sources on Earth and is efficiently degraded by fungi.
Environmental Microbiology
Environmental Microbiology | SpotlightSignal Synthase-Type versus Catabolic Monooxygenases: Retracing 3-Hydroxylation of 2-Alkylquinolones and Their N-Oxides by Pseudomonas aeruginosa and Other Pulmonary PathogensPseudomonas aeruginosa, Staphylococcus aureus, and Mycobacteroides abscessus are major players in bacterial chronic infections and particularly common colonizers of cystic fibrosis (CF) lung tissue. Whereas...
Environmental MicrobiologyArsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate StressArsenic is widespread in the environment and is one of the most ubiquitous environmental pollutants. Parodoxically, the growth of certain bacteria is enhanced by arsenic when phosphate is limited.
Environmental MicrobiologyHidden Diversity within Common Protozoan Parasites as Revealed by a Novel Genomotyping SchemeGiardia duodenalis assemblage B is a major waterborne pathogen and the most commonly identified genotype causing human giardiasis worldwide. The lack of morphological characters for classification requires the use of molecular techniques for strain differentiation; however, the absence of scalable and affordable next-generation sequencing (NGS)-based typing methods...
Environmental MicrobiologyIn Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture DeviceAntimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits.
Environmental MicrobiologyLighting Effects on the Development and Diversity of Photosynthetic Biofilm Communities in Carlsbad Cavern, New MexicoArtificial lighting in caves visited by tourists (“show caves”) can stimulate photosynthetic algae and cyanobacteria, called “lampenflora,” which are unsightly and damage speleothems and other cave surfaces. The most common mitigation strategy employs bleach, but altering intensities and wavelengths of light might be effective and less harsh.
Environmental MicrobiologyAdditional Role of Nicotinic Acid Hydroxylase for the Transformation of 3-Succinoyl-Pyridine by Pseudomonas sp. Strain JY-Q3-Succinoyl-pyridine (SP) and 6-hydroxy-3-succinoyl-pyridine (HSP) are both valuable chemical precursors to produce insecticides and hypotensive agents. SP and HSP could be renewable through the nicotine microbial degradation pathway, in which 3-succinoylpyridine monooxygenases (Spm) account for transforming SP into HSP in Pseudomonas sp. strain JY-Q.
Enzymology and Protein Engineering
Enzymology and Protein EngineeringStructural and Biochemical Analysis Reveals a Distinct Catalytic Site of Salicylate 5-Monooxygenase NagGH from Rieske DioxygenasesRieske oxygenases are involved in the degradation of various aromatic compounds. These dioxygenases usually carry out hydroxylation of hydrophobic aromatic compounds and supply substrates with hydroxyl groups for extradiol/intradiol dioxygenases to cleave rings, and have been extensively studied. Salicylate 5-hydroxylase NagGH is a novel Rieske monooxygenase with high similarity to Rieske dioxygenases, and also shares reductase and...
Enzymology and Protein EngineeringAlginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate LyaseThe potential markets for seaweed-derived products and seaweed processing technologies are growing, yet commercial enzyme cocktails for complete conversion of seaweed to fermentable sugars are not available. Such an enzyme cocktail would require the catalytic properties of a variety of different enzymes, where fucoidanases, laminarinases, and cellulases together with endo- and exo-acting alginate lyases would be the key enzymes.
...
Evolutionary and Genomic Microbiology
Evolutionary and Genomic MicrobiologyGenomic Insights into Methicillin-Resistant Staphylococcus aureus spa Type t899 Isolates Belonging to Different Sequence TypesThis study showed the genetic diversity and population structure of S. aureus presenting the same spa type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using spa typing only.
Food Microbiology
Food Microbiology | SpotlightNature versus Nurture: Assessing the Impact of Strain Diversity and Pregrowth Conditions on Salmonella enterica, Escherichia coli, and Listeria Species Growth and Survival on Selected Produce ItemsOur findings suggest that inclusion of multiple pregrowth conditions in inoculation studies can best capture the range of growth and survival patterns expected for Salmonella enterica and Escherichia coli present on produce. This is particularly important for fresh and fresh-cut produce, where...
Food MicrobiologyChanges in Bacterial and Chemical Components and Growth Prediction for Lactobacillus sakei during Kimoto-Style Fermentation Starter Preparation in Sake Brewing: a Comprehensive AnalysisIt is important to produce lactic acid in kimoto-style seed mash; however, the bacterial transition is different depending on the sake brewery. The reason why there are diverse bacterial transitions during kimoto-style seed mash preparation for each sake brewery is unclear so far, and it causes difficulty in starting kimoto-style seed mash.
Food MicrobiologyLysR Family Regulator LttR Controls Production of Conjugated Linoleic Acid in Lactobacillus plantarum by Directly Activating the cla OperonOur work has identified a novel transcriptional regulator, LTTR, that regulates the production of CLA by activating the transcription of cla-dh and cla-dc, essential genes participating in CLA synthesis in Lactobacillus plantarum. This study provides insight into the regulatory mechanism of CLA synthesis and broadens our understanding of the...
Food MicrobiologyGeneration of Lactose- and Protease-Positive Probiotic Lacticaseibacillus rhamnosus GG by Conjugation with Lactococcus lactis NCDO 712Probiotic strain Lacticaseibacillus rhamnosus GG (LGG) is widely sold on the market as a probiotic or added as a supplement in dairy foods because of its benefits in human health. However, due to the deficiency of lactose and casein utilization, LGG does not grow well in milk.
Genetics and Molecular Biology
Genetics and Molecular BiologyControl of Competence in Vibrio fischeriThe ability of bacteria to take up DNA (competence) and incorporate foreign DNA into their genomes (transformation) permits them to rapidly evolve and gain new traits and/or acquire antibiotic resistances. It also facilitates laboratory-based investigations into mechanisms of specific phenotypes, such as those involved in host colonization. Vibrio fischeri has long...
Genetics and Molecular BiologyThe Ethanologenic Bacterium Zymomonas mobilis Divides Asymmetrically and Exhibits Heterogeneity in DNA ContentWith increasing environmental concerns about the exhausting use of fossil fuels, development of a sustainable biofuel production platform has been attracting significant public attention. Ethanologenic Z. mobilis species are endowed with an efficient ethanol fermentation capacity that surpasses, in several respects, that of baker’s yeast (...
Genetics and Molecular BiologyA Pseudoalteromonas Clade with Remarkable Biosynthetic PotentialThis study demonstrates that the Pseudoalteromonas strain HM-SA03, isolated from the venomous blue-ringed octopus, Hapalochalaena sp., is a biosynthetically talented organism, capable of producing alterochromides and potentially six other specialized metabolites. We identified a pseudoalterobactin biosynthesis gene cluster and proposed a pathway for the production of the associated siderophore.
Geomicrobiology
GeomicrobiologyMicrobe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyiUnderstanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a...
GeomicrobiologyBacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome AssemblyKarst caves are oligotrophic environments that are dark and humid and have a relatively stable annual temperature. The diversity of bacteria and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems.
Invertebrate Microbiology
Invertebrate MicrobiologyDichotomy between Regulation of Coral Bacterial Communities and Calcification Physiology under Ocean Acidification ConditionsOcean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e., calcification) and disrupting associated bacterial communities.
Invertebrate MicrobiologyEssential Roles of Two FRQ Proteins (Frq1 and Frq2) in Beauveria bassiana’s Virulence, Infection Cycle, and Calcofluor-Specific SignalingOpposite nuclear rhythms of two distinct FRQ proteins (Frq1 and Frq2) coexisting in an asexual fungal insect pathogen have been shown to orchestrate the fungal nonrhythmic conidiation in vitro in a circadian day independent of photoperiod change. This paper reports essential roles of both Frq1 and Frq2, but a greater role for Frq2, in sustaining the fungal virulence and infection cycle since either frq1 or frq2...
Methods
MethodsPortable CRISPR-Cas9N System for Flexible Genome Engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracaseiThis work describes the development of a lactobacillus CRISPR-based editing system for genome manipulations in three Lactobacillus species belonging to the lactic acid bacteria (LAB), which are commonly known for their long history of use in food fermentations and as indigenous members of healthy microbiotas and for their emerging roles in human and animal commercial health-promoting applications. We exploited the established...
MethodsHarnessing CRISPR-Cas9 for Genome Editing in Streptococcus pneumoniae D39VStreptococcus pneumoniae (the pneumococcus) is an important opportunistic human pathogen killing more than 1 million people each year. Having the availability of a system capable of easy genome editing would significantly facilitate drug discovery and efforts to identify new vaccine candidates.
Microbial Ecology
Microbial Ecology | SpotlightFecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child-Shared BacteriaThe initial bacterial colonization of human infants is crucial for lifelong health. Understanding the factors driving this colonization will therefore be of great importance.
Microbial EcologyAdjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and DispersalUnderstanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli.
...
Microbial EcologyThe Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal SampleMetagenome assembly and the recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, the extent to which MAGs can capture the genes of the population they represent remains speculative.
Microbial EcologySalmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in FreshwaterSalmonella is a leading cause of bacterial foodborne illness in the United States, and outbreaks linked to fresh produce are increasing. Understanding Salmonella ecology in freshwater is of importance, especially where irrigation practices or recreational use occur.
Physiology
PhysiologyAcquired Resistance to Severe Ethanol Stress in Saccharomyces cerevisiae Protein Quality ControlAlthough the budding yeast S. cerevisiae, which is used in the production of alcoholic beverages and bioethanol, is highly tolerant of ethanol, high concentrations of ethanol are also stressful to the yeast and cause various adverse effects, including protein denaturation. A pretreatment with mild stress improves the ethanol tolerance of yeast cells; however, it...
PhysiologyAnaerobic Production of Isoprene by Engineered Methanosarcina Species ArchaeaA significant barrier to implementing renewable chemical technologies is high production costs relative to those for petroleum-derived products. Existing technologies using engineered organisms have difficulty competing with petroleum-derived chemicals due to the cost of feedstocks (such as glucose), product extraction, and purification.
PhysiologySwimming Escherichia coli Cells Explore the Environment by Lévy WalkE. coli cells explore the environment in a random walk of alternating runs and tumbles. By tracking the 3D trajectories of E. coli cells in an aqueous environment, we found that their trajectories are superdiffusive, with a power-law shape for the distribution of run lengths, which is...
Physiology | SpotlightFormate-Dependent Heterodisulfide Reduction in a Methanomicrobiales ArchaeonMethanogens from the order Methanomicrobiales are thought to prefer H2 as an electron donor for growth. They are ubiquitous in anaerobic environments, such as in wastewater treatment facilities, anaerobic digesters, and the rumen, where they catalyze the terminal steps in the breakdown of organic matter.
Plant Microbiology
Plant MicrobiologyThe Golgin Protein RUD3 Regulates Fusarium graminearum Growth and VirulenceFusarium head blight (FHB) caused by the fungal pathogen Fusarium graminearum is an economically important disease of wheat and other small grain cereal crops worldwide, and limited effective control strategies are available. A better understanding of the regulation mechanisms of F. graminearum...
Plant MicrobiologyColonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic AbilitiesThe tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress.
Public and Environmental Health Microbiology
Public and Environmental Health MicrobiologyReduced Antibacterial Drug Resistance and blaCTX-M β-Lactamase Gene Carriage in Cattle-Associated Escherichia coli at Low Temperatures, at Sites Dominated by Older Animals, and on Pastureland: Implications for SurveillanceAntibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including tracking impacts of interventions aimed at reducing the prevalence of resistance.
Public and Environmental Health MicrobiologyListeria spp. Isolated from Tonsils of Wild Deer and Boars: Genomic CharacterizationListeria monocytogenes is a foodborne bacterial pathogen responsible for listeriosis. Whole-genome sequencing has been extensively used in public health and food industries to characterize circulating Listeria isolates, but genomic data on isolates occurring in natural environments and wild animals are still scarce.
Public and Environmental Health MicrobiologyLong-Term Survival of Virulent Tularemia Pathogens outside a Host in Conditions That Mimic Natural Aquatic EnvironmentsTularemia, a disease caused by the environmental bacterium Francisella tularensis, is characterized by acute febrile illness. F. tularensis is highly infectious: as few as 10 organisms can cause human disease. Tularemia is not known to be spread from person to person.
Masthead
Current Issue
About AEM
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.
For Authors
Dr. Harold L. Drake, Editor in Chief