Applied and Environmental Microbiology

Wed, 04/14/2021 - 10:01
Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curacao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta. Flow cytometry analyses of water samples collected from a depth of 10 m identified...
Wed, 04/14/2021 - 10:01
Listeria monocytogenes is a deadly intracellular pathogen mostly associated with consumption of ready-to-eat foods. This study investigated the effectiveness of total beef fat (BF-T) from flaxseed-fed cattle and its fractions enriched with monounsaturated fatty acids (BF-MUFA) and polyunsaturated fatty acids (BF-PUFA), along with commercially available long-chain fatty acids (LC-FA), as natural...
Wed, 04/14/2021 - 10:01
The recently isolated thermophilic cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542 (here Thermosynechococcus E542) is a promising strain for fundamental and applied research. Here, we used several improved ploidy estimation approaches, which include quantitative PCR (qPCR), spectrofluorometry, and flow cytometry, to precisely determine the ploidy level in Thermosynechococcus E542...
Wed, 04/14/2021 - 10:01
The 2014 caramel apple listeriosis outbreak was traced back to cross-contamination between food contact surfaces (FCS) of equipment used for packing and fresh apples. For Washington state, the leading apple producer in the United States with 79% of its total production directed to the fresh market, managing the risk of apple contamination with Listeria monocytogenes within the packing environment...
Wed, 04/14/2021 - 10:01
Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we...
Wed, 04/14/2021 - 10:01
This study was conducted to characterize carbapenemase-producing Klebsiella pneumoniae and Acinetobacter baumannii isolated from fresh vegetables in Japan. Two K. pneumoniae isolates (AO15 and AO22) and one A. baumannii isolate (AO22) were collected from vegetables in the city of Higashihiroshima, Japan, and subjected to antimicrobial susceptibility testing, conjugation experiments, and complete...
Wed, 04/14/2021 - 10:01
By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo...
Sat, 03/27/2021 - 10:01
Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and from their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures, and carcasses of pigs...
Sat, 03/27/2021 - 10:01
This study aimed to assess the cecal microbiome, antimicrobial resistance (AMR), and heavy-metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium, and...
Sat, 03/27/2021 - 10:01
Geobacillus species are important contaminants in the dairy industry, and their presence is often considered an indicator of poor plant hygiene with the potential to cause spoilage. They can form heat-resistant spores that adhere to surfaces of processing equipment and germinate to form biofilms. Therefore, strategies aimed toward preventing or controlling biofilm formation in the dairy industry...
Sat, 03/27/2021 - 10:01
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle. The Regional Dairy Quality Management Alliance (RDQMA) project is a multistate research program involving MAP isolates taken from three intensively studied commercial dairy farms in the northeastern United States, which emphasized...
Fri, 03/12/2021 - 10:01
Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters...
Fri, 03/12/2021 - 10:01
Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial...
Fri, 03/12/2021 - 10:01
Microbial resistance to processing treatments poses a food safety concern, as treatment tolerant pathogens can emerge. Occasional foodborne outbreaks caused by pathogenic Escherichia coli have led to human and economic losses. Therefore, this study screened for the extreme heat resistance (XHR) phenotype as well as one known genetic marker, the locus of heat resistance (LHR), in 4,123 E. coli...
Fri, 03/12/2021 - 10:01
Biological soil amendments of animal origin (BSAAO) increase nutrient levels in soils to support the production of fruits and vegetables. BSAAOs may introduce or extend the survival of bacterial pathogens which can be transferred to fruits and vegetables to cause foodborne illness. Escherichia coli survival over 120 days in soil plots (3 m2) covered with (mulched) or without plastic mulch (not...
Fri, 03/12/2021 - 10:01
Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the...
Sat, 02/27/2021 - 10:02
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by the detection and cleavage of invading foreign DNA. Modified versions of this system can be exploited as a biotechnological tool for precise genome editing at a targeted locus. Here, we developed a replicative plasmid that carries the CRISPR-Cas9 system for RNA-programmable genome editing by...
Sat, 02/27/2021 - 10:02
Salicylic acid plays an important role in the plant immune response, and its degradation is therefore important for plant-pathogenic fungi. However, many nonpathogenic microorganisms can also degrade salicylic acid. In the filamentous fungus Aspergillus niger, two salicylic acid metabolic pathways have been suggested. The first pathway converts salicylic acid to catechol by a salicylate...
Sat, 02/27/2021 - 10:02
The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a coenzyme A (CoA)-activation-type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and inducibly expressed in response to 4CBA....
Sat, 02/27/2021 - 10:02
Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-...
Sat, 02/27/2021 - 10:02
Pseudoalteromonas species produce a diverse range of biologically active compounds, including those biosynthesized by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). Here, we report the biochemical and genomic analysis of Pseudoalteromonas sp. strain HM-SA03, isolated from the blue-ringed octopus, Hapalochlaena sp. Genome mining for secondary metabolite pathways revealed...
Sat, 02/27/2021 - 10:02
Listeria monocytogenes is a major human and animal foodborne pathogen. However, data from environmental reservoirs remain scarce. Here, we used whole-genome sequencing to characterize Listeria species isolates recovered over 1 year from wild animals in their natural habitats in Spain. Three different Listeria spp. (L. monocytogenes [n = 19], Listeria ivanovii subsp. londoniensis [n = 4], and...
Sat, 02/27/2021 - 10:02
Freshwater can support the survival of the enteric pathogen Salmonella, though temporal Salmonella diversity in a large watershed has not been assessed. At 28 locations within the Susquehanna River basin, 10-liter samples were assessed in spring and summer over 2 years. Salmonella prevalence was 49%, and increased river discharge was the main driver of Salmonella presence. The amplicon-based...
Sat, 02/27/2021 - 10:02
High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coli. E. coli survives in extrahost environments (e.g., soil) and could be...
Sat, 02/27/2021 - 10:02
Enzymatic depolymerization of seaweed polysaccharides is gaining interest for the production of functional oligosaccharides and fermentable sugars. Herein, we describe a thermostable alginate lyase that belongs to polysaccharide lyase family 17 (PL17) and was derived from an Arctic Mid-Ocean Ridge (AMOR) metagenomics data set. This enzyme, AMOR_PL17A, is a thermostable exolytic oligoalginate...
Sat, 02/27/2021 - 10:02
Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis) is the causative agent of giardiasis, one of the most common diarrheal infections in humans. Evolutionary relationships among G. duodenalis genotypes (or subtypes) of assemblage B, one of two genetic assemblages causing the majority of human infections, remain unclear due to poor phylogenetic resolution of current typing methods. In...
Sat, 02/27/2021 - 10:02
Inoculation studies are important when assessing microbial survival and growth in food products. These studies typically involve the pregrowth of multiple strains of a target pathogen under a single condition; this emphasizes strain diversity. To gain a better understanding of the impacts of strain diversity ("nature") and pregrowth conditions ("nurture") on subsequent bacterial growth in foods,...
Sat, 02/27/2021 - 10:02
Rieske nonheme iron oxygenases (ROs) catalyze the oxidation of a wide variety of substrates and play important roles in aromatic compound degradation and polycyclic aromatic hydrocarbon degradation. Those Rieske dioxygenases that usually act on hydrophobic substrates have been extensively studied and structurally characterized. Here, we report the crystal structure of a novel Rieske monooxygenase...
Sat, 02/27/2021 - 10:02
Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g., CTX-M β-lactamase-positive Escherichia coli). We collected samples monthly between January 2017 and December 2018 on 53 dairy farms in South West England, along with data for 610 variables concerning antibacterial usage, management practices, and...
Sat, 02/13/2021 - 10:01
Currently, only 5 (SEA to SEE) out of 27 known staphylococcal enterotoxins can be analyzed using commercially available kits. Six genes (seg, sei, sem, sen, seo, and seu), encoding putative and undetectable enterotoxins, are located on the enterotoxin gene cluster (egc), which is part of the Staphylococcus aureus genomic island vSaβ. These enterotoxins have been described as likely being...
Sat, 02/13/2021 - 10:01
Phaeobacter inhibens has been assessed as a probiotic bacterium for application in aquaculture. Studies addressing the efficacy and safety indicate that P. inhibens maintains its antagonistic activity against pathogenic vibrios in aquaculture live cultures (live feed and fish egg/larvae) while having no or a positive effect on the host organisms and a minor impact on the host microbiomes. While P...
Sat, 02/13/2021 - 10:01
Vibrio cholerae, the agent of the deadly human disease cholera, propagates as a curved rod-shaped bacterium in warm waters. It is sensitive to cold but persists in cold waters in the form of viable but nondividing coccoidal-shaped cells. Additionally, V. cholerae is able to form nonproliferating spherical cells in response to cell wall damage. It was recently reported that l-arabinose, a...
Sat, 02/13/2021 - 10:01
Rapid ATP testing and microbiological enumeration are two common methods to monitor the effectiveness of cleaning and sanitation in the food industry. In this study, ATP testing and microbiological enumeration were implemented at a tofu production facility with the goal of improving cleaning practices and overall plant hygiene. Results from ATP monitoring were used to target areas of the...
Sat, 02/13/2021 - 10:01
This study selected and used indicator and surrogate microorganisms for Salmonella to validate the processes for physically heat-treated poultry litter compost in litter processing plants. Initially, laboratory validation studies indicated that reductions of 1.2 to 2.7 log or more of desiccation-adapted Enterococcus faecium NRRL B-2354 were equivalent to >5-log reductions of desiccation-...
Sat, 02/13/2021 - 10:01
Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant, and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate-active gas...
Sat, 02/13/2021 - 10:01
The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which has resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tracts of humans and farmed animals. Genetic exchange of resistance genes between the two ecosystems is now well documented for pathogenic bacteria, but the...
Sat, 01/30/2021 - 10:02
Effective and accurate primer design is an increasingly important skill, as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes, such as 16S rRNA, and characteristic genes, such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance...
Wed, 01/20/2021 - 10:01
Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B6, essential for cellular function in all domains of life. In many organisms, such as Salmonella enterica serovar Typhimurium and Escherichia coli, this cofactor can be synthesized de novo or salvaged from B6 vitamers in the environment. Unexpectedly, S. enterica strains blocked in PLP biosynthesis were able to use exogenous...
Wed, 01/20/2021 - 10:01
N-Acetylmuramoyl-l-alanine amidases are periplasmic hydrolases that cleave the amide bond between N-acetylmuramic acid and alanine in peptidoglycan (PG). Unlike many Gram-negative bacteria that encode redundant periplasmic amidases, Vibrio fischeri appears to encode a single protein that is homologous to AmiB of Vibrio cholerae. We screened a V. fischeri transposon mutant library for strains...
Wed, 01/20/2021 - 10:01
Salmonella spp. are resilient bacterial pathogens in low-moisture foods. There has been a general lack of understanding of critical factors contributing to the enhanced thermal tolerance of Salmonella spp. in dry environments. In this study, we hypothesized that the moisture content (XW) of bacterial cells is a critical intrinsic factor influencing the resistance of Salmonella spp. to thermal...
Wed, 01/20/2021 - 10:01
Significant knowledge gaps exist in our understanding of Campylobacter jejuni contamination of the poultry production continuum. Microbiological surveillance and genotypic characterization were undertaken on C. jejuni isolates longitudinally recovered from three poultry farms (weekly samples), the abattoir at which birds were processed, and at retail over a 542-day period in southwestern Alberta...
Wed, 01/20/2021 - 10:01
Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel...
Wed, 01/20/2021 - 10:01
Rickettsia buchneri is the principal symbiotic bacterium of the medically significant tick Ixodes scapularis. This species has been detected primarily in the ovaries of adult female ticks and is vertically transmitted, but its tissue tropism in other life stages and function with regard to tick physiology is unknown. In order to determine the function of R. buchneri, it may be necessary to...
Wed, 01/20/2021 - 10:01
Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in...
Wed, 01/20/2021 - 10:01
Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere, as they can control phytopathogens and contribute to disease suppression. DAPG can also trigger a systemic resistance response in plants and stimulate root exudation and branching as well as induce plant-beneficial activities in other rhizobacteria. While studies...
Wed, 01/20/2021 - 10:01
Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. The draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from...
Tue, 01/05/2021 - 10:01
The occurrence of viable-but-nonculturable (VBNC) bacteria poses a potential risk to food safety due to failure in conventional colony detection. In this study, induction of VBNC Staphylococcus aureus was conducted by exposure to an atmospheric-pressure air dielectric barrier discharge-nonthermal-plasma (DBD-NTP) treatment with an applied energy of 8.1 kJ. The stress resistance profiles and...
Tue, 01/05/2021 - 10:01
Subcutaneous vaccination of cattle for enterohemorrhagic Escherichia coli O157:H7 reduces the magnitude and duration of fecal shedding, but the often-required, repeated cattle restraint can increase costs, deterring adoption by producers. In contrast, live oral vaccines may be repeatedly administered in feed, without animal restraint. We investigated whether oral immunization with live stx-...
Tue, 01/05/2021 - 10:01
Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have...
Tue, 01/05/2021 - 10:01
The initial steps of Salmonella pathogenesis involve adhesion to and invasion into host epithelial cells. While well-studied for Salmonella enterica serovar Typhimurium, the factors contributing to this process in other, host-adapted serovars remains unexplored. Here, we screened clinical isolates of serovars Gallinarum, Dublin, Choleraesuis, Typhimurium, and Enteritidis for adhesion to and...

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