Spotlight
Minireview
MinireviewDiamine Biosynthesis: Research Progress and Application ProspectsDiamines are important monomers for polyamide plastics; they include 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, and 1,6-diaminohexane, among others. With increasing attention on environmental problems and green sustainable development, utilizing renewable raw materials for the synthesis of diamines is crucial for the establishment of a sustainable plastics industry. Recently, high-performance microbial factories, such as...
Biotechnology
Biotechnology | SpotlightSynergistic Action of a Lytic Polysaccharide Monooxygenase and a Cellobiohydrolase from Penicillium funiculosum in Cellulose Saccharification under High-Level Substrate LoadingThe enzymatic hydrolysis of cellulosic biomass by cellulases continues to be a significant bottleneck in the development of second-generation biobased industries. While increasing efforts are being made to obtain indigenous cellulases for biomass hydrolysis, the high production cost of this enzyme remains a crucial challenge affecting its wide availability for the efficient utilization of cellulosic materials. This is because it is...
Environmental Microbiology
Environmental MicrobiologyMethane Monooxygenase Gene Transcripts as Quantitative Biomarkers of Methanotrophic Activity in Methylosinus trichosporium OB3bMethanotrophs are naturally occurring microorganisms capable of oxidizing methane and have an impact on global net methane emissions. The genes pmoA and mmoX are used as biomarkers for bacterial methanotrophs. Quantitative relationships between transcript amounts of these genes and methane oxidation rates could facilitate estimation of methanotrophic activity. In this study, a strong correlation was observed between...
Environmental MicrobiologyBiofilm Sampling for Detection of Cryptosporidium Oocysts in a Southeastern Pennsylvania WatershedMonitoring Cryptosporidium occurrence in watersheds that provide drinking water is necessary to determine where limited resources should most effectively be directed to protect consumers from waterborne exposure to pathogenic oocysts. Biofilms are a useful tool to monitor complex watersheds and identify point sources of Cryptosporidium oocyst contamination that need to be managed to protect public health. Compared to...
Environmental MicrobiologyTransformative Approach To Investigate the Microphysical Factors Influencing Airborne Transmission of PathogensA transformative approach to identify the physicochemical processes that impact the biological decay rates of bacteria in aerosol droplets is described. It is shown that the evaporation process and changes in the phase and morphology of the aerosol particle during evaporation impact microorganism viability. The equilibrium droplet size was found to affect airborne bacterial viability. Furthermore, the presence of...
Environmental MicrobiologySeasonal and Geographical Differences in Total and Pathogenic Vibrio parahaemolyticus and Vibrio vulnificus Levels in Seawater and Oysters from the Delaware and Chesapeake Bays Determined Using Several MethodsWhile V. parahaemolyticus and V. vulnificus cause shellfish-associated morbidity and mortality among shellfish consumers, current regulatory assays for vibrios are complex, time-consuming, labor-intensive, and relatively expensive. In this study, the rapid, simple, and inexpensive COPP assay was...
Environmental Microbiology | SpotlightImproved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding RegionsThis model fits predicted pIs to empirical values for a diverse set of viruses. The results suggest that many previously reported discrepancies between theoretical and empirical virus pIs can be explained by coulombic neutralization of PBRs of the inner capsid. Given the diversity of virus capsid structures, this nonarbitrary, heuristic approach to predicting virus pI offers an effective alternative to a simplistic, one-size-fits-all...
Environmental MicrobiologyGenome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion SludgeWastewater treatment generates large amounts of waste-activated sludge (WAS), which consists mainly of recalcitrant microbial cells and particulate organic matter. Though WAS pretreatment is an effective way to release sludge organic matter for subsequent digestion, detailed information on the impact of the sludge pretreatment on the digestion sludge microbiome remains scarce. Our study provides unprecedented genome-centric metagenomic...
Environmental MicrobiologyOuter Membrane c-Type Cytochromes OmcA and MtrC Play Distinct Roles in Enhancing the Attachment of Shewanella oneidensis MR-1 Cells to GoethiteShewanella species are one group of versatile and widespread dissimilatory iron-reducing bacteria, which are capable of respiring insoluble iron minerals via six multiheme c-type cytochromes. Outer membrane c-type cytochromes (c-Cyts) OmcA and MtrC are the terminal reductases in this pathway and have comparable protein structures. In this study, we elucidate the different roles of OmcA and MtrC in the...
Environmental MicrobiologyMetabolic Diversity and Evolutionary History of the Archaeal Phylum “Candidatus Micrarchaeota” Uncovered from a Freshwater Lake MetagenomeThe recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, “Ca. Micrarchaeota,” comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic...
Enzymology and Protein Engineering
Enzymology and Protein EngineeringHigh-Throughput Generation of Product Profiles for Arabinoxylan-Active Enzymes from MetagenomesArabinoxylan is mainly found in the hemicellulosic fractions of rice straw, corn cobs, and rice husk. Converting arabinoxylan into (arabino)xylo-oligosaccharides as added-value products that can be applied in food, feed, and cosmetics presents a sustainable and economic alternative for the biorefinery industries. Efficient and profitable AX degradation requires a set of enzymes with particular characteristics. Therefore, enzyme...
Enzymology and Protein EngineeringMolecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial LaminarinaseHeterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this...
Food Microbiology
Food MicrobiologySpatiotemporal Distribution of the Environmental Microbiota in Food Processing Plants as Impacted by Cleaning and Sanitizing Procedures: the Case of Slaughterhouses and Gaseous OzoneOur in situ survey demonstrates that RNA-based sequencing of 16S rRNA amplicons is a reliable approach to qualitatively probe, at high taxonomic resolution, the changes triggered by new and existing cleaning/sanitizing strategies in the environmental microbiota in human-built environments. This approach could soon represent a fast tool to clearly define which routine sanitizing interventions are more suitable for a specific...
Genetics and Molecular Biology
Genetics and Molecular BiologyA High-Efficacy CRISPR Interference System for Gene Function Discovery in Zymomonas mobilisBiofuels produced by microbial fermentation of plant feedstocks provide renewable and sustainable energy sources that have the potential to mitigate climate change and improve energy security. Engineered strains of the bacterium Z. mobilis can convert sugars extracted from plant feedstocks into next-generation biofuels like isobutanol; however, conversion by these...
Genetics and Molecular BiologyF4- and F18-Positive Enterotoxigenic Escherichia coli Isolates from Diarrhea of Postweaning Pigs: Genomic CharacterizationDiarrhea in the postweaning period due to enterotoxigenic E. coli (ETEC) is an economically relevant disease in pig production worldwide. In Denmark, prevention is mainly achieved by zinc oxide administration (to be discontinued by 2022). In addition, a breeding program has been implemented that aims to reduce the prevalence of this illness. Treatment with...
Geomicrobiology
GeomicrobiologyPossible Involvement of a Tetrathionate Reductase Homolog in Dissimilatory Arsenate Reduction by Anaeromyxobacter sp. Strain PSR-1Dissimilatory As(V)-reducing prokaryotes play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. Generally, such prokaryotes reduce As(V) by means of a respiratory As(V) reductase designated Arr. However, some dissimilatory As(V)-reducing prokaryotes such as Anaeromyxobacter sp. strain PSR-1 lack genes...
Methods
MethodsDead-End Ultrafiltration and DNA-Based Methods for Detection of Cyclospora cayetanensis in Agricultural WaterCyclospora cayetanensis is a protozoan parasite that causes foodborne and waterborne outbreaks of diarrheal illness worldwide. These foodborne outbreaks associated with the consumption of fresh produce and agricultural water could play a role in the contamination process. In this study, a method to detect ...
Microbial Ecology
Microbial EcologyRelationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing WaterIn flowing aquatic systems, cell erosion and deposition are important to the dispersal of cells from one location to another. Very little is known about microbial dispersal and the physical processes that underlie it. This study demonstrates its importance to colonization of downstream surfaces and especially to the recolonization and functioning of disturbed sites. Ecological systems in flowing environments are often, roughly speaking...
Microbial EcologyActive Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope ProbingThe role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that...
Microbial Ecology | SpotlightMulti-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut MicrobiomeDiet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the...
Physiology
Physiology | SpotlightA Structurally Novel Lipoyl Synthase in the Hyperthermophilic Archaeon Thermococcus kodakarensisLipoic acid is an essential cofactor for GCS and 2-oxoacid dehydrogenases, and О±-lipoic acid has been utilized as a medicine and attracted attention as a supplement due to its antioxidant activity. The biosynthesis pathways of lipoic acid have been established in Bacteria and Eucarya but not in Archaea. Although some archaeal species, including Sulfolobus, possess a classical lipoyl synthase (LipA)...
PhysiologyMetabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticumThis study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in Escherichia coli but instead use a reversible membrane-bound proton-pumping enzyme. In such organisms, the charging of tRNA with amino acids may become more reversible. This may contribute to the observed...
PhysiologyFormate-Dependent Acetogenic Utilization of Glucose by the Fecal Acetogen Clostridium bovifaecisThe acetyl-CoA pathway is an ancient pathway of CO2 fixation, which converts 2 mol of CO2 into acetyl-CoA. Autotrophic growth with H2 and CO2 via the acetyl-CoA pathway as the terminal electron accepting process is the most unique feature of acetogenic bacteria. However, the fecal acetogen Clostridium bovifaecis strain BXX displayed poor metabolic capabilities of autotrophic...
PhysiologyCompetence-Stimulating-Peptide-Dependent Localized Cell Death and Extracellular DNA Production in Streptococcus mutans BiofilmsBacterial communities encased by self-produced extracellular polymeric substances (EPSs), known as biofilms, have a wide influence on human health and environmental problems. The importance of biofilm research has increased, as biofilms are the preferred bacterial lifestyle in nature. Furthermore, in recent years it has been noted that the contribution of phenotypic heterogeneity within biofilms requires analysis at the single-cell or...
Public and Environmental Health Microbiology
Public and Environmental Health Microbiology | SpotlightThe Household Resistome: Frequency of ОІ-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and LaunderingThe abundance of antibiotic-resistant bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods, and wastewater treatment plants. In this respect, ОІ-lactams and colistin are of particular interest due to the emergence of multidrug-resistant Gram-negative bacteria. Despite the connection of private households to these environments, only a few studies have focused on the...
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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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