Counterfactual scenarios reveal historical impact of cropland management on soil organic carbon stocks in the United States.

Natural climate solutions provide opportunities to reduce greenhouse gas emissions and the United States is among a growing number of countries promoting storage of carbon in agricultural soils as part of the climate solution. Historical patterns of soil organic carbon (SOC) stock changes provide context about mitigation potential. Therefore, our objective was to quantify the influence of climate-smart soil practices on SOC stock changes in the top 30 cm of mineral soils for croplands in the United States using the DayCent Ecosystem Model.

Modeling the formulation pH of elderberry syrup with multiple weak acids.

The objective of this work was to develop methods to assess the influence of the ingredients of an acidified elderberry syrup on product pH. A measure of total ingredient buffering (tBeta) was defined as the area under the buffer capacity curve of a food mixture or ingredient for pH 2-12. Citric acid (1% w/v), elderberry juice (75% v/v), and malic acid (0.

Bacteriophages Isolated From Turkeys Infecting Diverse Serovars.

is one of the leading causes of foodborne illnesses worldwide. The rapid emergence of multidrug-resistant strains has increased global concern for salmonellosis. Recent studies have shown that bacteriophages (phages) are novel and the most promising antibacterial agents for biocontrol in foods because phages specifically kill target bacteria without affecting other bacteria, do not alter organoleptic properties or nutritional quality of foods, and are safe and environmentally friendly.

Buffer Models for pH and Acid Changes Occurring in Cucumber Juice Fermented with Lactiplantibacillus pentosus and Leuconostoc mesenteroides.

Abstract: The pH changes that occur during the fermentation of vegetables by lactic acid bacteria depend on the production of weak acids and on the buffering of the fermentation medium. Undefined buffering components of fermentation media make estimates of pH from acid production difficult. The objective of this research was to develop buffer models for a model cucumber fermentation brine system linking pH changes to acid concentrations.

Effects of a brief blanching process on quality, safety, and shelf life of refrigerated cucumber pickles.

Refrigerated pickles are characterized by crisp, crunchy texture, opaque flesh, and fresh flavor. Typically produced without a thermal process, microbial safety relies on preventive controls, brine composition, and sufficient hold time prior to consumption. We hypothesized that brief blanching of whole cucumbers prior to pickling could provide an additional hurdle for pathogenic microbes without negatively impacting finished product quality.

Modeling nitrous oxide mitigation potential of enhanced efficiency nitrogen fertilizers from agricultural systems.

Agriculture soils are responsible for a large proportion of global nitrous oxide (NO) emissions-a potent greenhouse gas and ozone depleting substance. Enhanced-efficiency nitrogen (N) fertilizers (EENFs) can reduce NO emission from N-fertilized soils, but their effect varies considerably due to a combination of factors, including climatic conditions, edaphic characteristics and management practices. In this study, we further developed the DayCent ecosystem model to simulate two EENFs: controlled-release N fertilizers (CRNFs) and nitrification inhibitors (NIs) and evaluated their NO mitigation potentials.

Bacteriophages Infecting Gram-Negative Bacteria in a Commercial Cucumber Fermentation.

Cucumber fermentations are one of the most important vegetable fermentations in the United States. The fermentation is usually driven by lactic acid bacteria (LAB) indigenous to fresh cucumbers. But LAB are greatly outnumbered by many Gram-negative bacteria on fresh cucumbers, which may influence the growth of LAB and the incidence of bloater defect (hollow cavities formed inside fermented cucumbers) leading to serious economic loss to the pickle industry.

Modeling buffer capacity and pH in acid and acidified foods.

Standard ionic equilibria equations may be used for calculating pH of weak acid and base solutions. These calculations are difficult or impossible to solve analytically for foods that include many unknown buffering components, making pH prediction in these systems impractical. We combined buffer capacity (BC) models with a pH prediction algorithm to allow pH prediction in complex food matrices from BC data.

Modeling the buffer capacity of ingredients in salad dressing products.

The pH of most acid food products depends on undefined and complex buffering of ingredients but is critically important for regulatory purposes and food safety. Our objective was to define the buffer capacity (BC) of ingredients in salad dressing products. Ingredients of salad dressings were titrated individually and in combination using concentrations typical of dressing products.

Escherichia coli O157:H7 Stationary-Phase Acid Resistance and Assessment of Survival in a Model Vegetable Fermentation System.

Abstract: Escherichia coli O157:H7 (STEC) acid resistance may aid the pathogen's ability to cross the human gastric barrier, which makes it an organism of concern in acidic foods. Our objective was to determine how STEC acid resistance may correlate with survival during vegetable fermentations. Seven E.

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis.

Experiments that longitudinally collect RNA sequencing (RNA-seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large-scale time-course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification.

Climate and Soil Characteristics Determine Where No-Till Management Can Store Carbon in Soils and Mitigate Greenhouse Gas Emissions.

Adoption of no-till management on croplands has become a controversial approach for storing carbon in soil due to conflicting findings. Yet, no-till is still promoted as a management practice to stabilize the global climate system from additional change due to anthropogenic greenhouse gas emissions, including the 4 per mille initiative promoted through the UN Framework Convention on Climate Change. We evaluated the body of literature surrounding this practice, and found that SOC storage can be higher under no-till management in some soil types and climatic conditions even with redistribution of SOC, and contribute to reducing net greenhouse gas emissions.

Effect of Brine Acidification on Fermentation Microbiota, Chemistry, and Texture Quality of Cucumbers Fermented in Calcium or Sodium Chloride Brines.

Commercial fermentation for bulk preservation of cucumbers relies on natural microbiota and approximately 1 M sodium chloride (NaCl) brines, resulting in large volumes of high-salt wastewater. An alternative process utilizing 0.1 M calcium chloride (CaCl ) as the only salt was developed to eliminate NaCl from fermentation brines for reduced environmental impact.

Effects of Sodium Chloride or Calcium Chloride Concentration on the Growth and Survival of Escherichia coli O157:H7 in Model Vegetable Fermentations.

NaCl and CaCl concentrations affected LAB and STEC strains differently. Growth rates at 6% NaCl were reduced for STEC more than LAB in vegetable broth. Extent of growth was reduced for STEC versus LAB for most vegetable fermentations.

Understanding the drivers of sensitive behavior using Poisson regression from quantitative randomized response technique data.

Understanding sensitive behaviors-those that are socially unacceptable or non-compliant with rules or regulations-is essential for creating effective interventions. Sensitive behaviors are challenging to study, because participants are unlikely to disclose sensitive behaviors for fear of retribution or due to social undesirability. Methods for studying sensitive behavior include randomized response techniques, which provide anonymity to interviewees who answer sensitive questions.

O157:H7 Acid Sensitivity Correlates with Flocculation Phenotype during Nutrient Limitation.

Shiga toxin producing (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3.

Survival and Growth of Probiotic Lactic Acid Bacteria in Refrigerated Pickle Products.

We examined 10 lactic acid bacteria that have been previously characterized for commercial use as probiotic cultures, mostly for dairy products, including 1 Pediococcus and 9 Lactobacilli. Our objectives were to develop a rapid procedure for determining the long-term survivability of these cultures in acidified vegetable products and to identify suitable cultures for probiotic brined vegetable products. We therefore developed assays to measure acid resistance of these cultures to lactic and acetic acids, which are present in pickled vegetable products.

Survival and expression of acid resistance genes in Shiga toxin-producing Escherichia coli acid adapted in pineapple juice and exposed to synthetic gastric fluid.

Aims: The aim of this research was to determine the ability of non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups to survive with exposure to synthetic gastric fluid (SGF) after adaptation to pineapple juice (PJ) at room and refrigerated temperatures compared to E. coli O157:H7 and to examine the relative transcriptional expression of acid resistance (AR) genes, rpoS, gadA and adiA.

Methods And Results: Resistant and sensitive strains belonging to five different STEC serogroups (O26, O103, O104, O111 and O157; n = 10) were used in this study.

Laplace Variational Approximation for Semiparametric Regression in the Presence of Heteroskedastic Errors.

Variational approximations provide fast, deterministic alternatives to Markov Chain Monte Carlo for Bayesian inference on the parameters of complex, hierarchical models. Variational approximations are often limited in practicality in the absence of conjugate posterior distributions. Recent work has focused on the application of variational methods to models with only partial conjugacy, such as in semiparametric regression with heteroskedastic errors.

Complete Genome Sequences of Escherichia coli O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance.

The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with higher resistance to acid may have a lower infectious dose. The complete genome sequences belonging to two strains of Escherichia coli O157:H7 with different levels of acid resistance are presented here.

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods.

Fermented cucumber spoilage (FCS) characterized by rising pH and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. Previous culture-based studies identified the yeasts Pichia manshurica and Issatchenkia occidentalis, 4 Gram-positive bacteria, Lactobacillus buchneri, Lactobacillus parrafaraginis, Clostridium sp., and Propionibacterium and 1 Gram-negative genus, Pectinatus, as relevant in various stages of FCS given their ability to metabolize lactic acid.

Acid Resistance and Molecular Characterization of Escherichia coli O157:H7 and Different Non-O157 Shiga Toxin-Producing E. coli Serogroups.

The objective of this study was to compare the acid resistance (AR) of non-O157 Shiga toxin-producing Escherichia coli (STEC) strains belonging to serogroups O26, O45, O103, O104, O111, O121, and O145 with O157:H7 STEC isolated from various sources in 400 mM acetic acid solutions (AAS) at pH 3.2 and 30 °C for 25 min with or without glutamic acid. Furthermore, the molecular subgrouping of the STEC strains was analyzed with the repetitive sequence-based PCR (rep-PCR) method using a DiversiLab(TM) system.

Microbial ecology of watery kimchi.

The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective media, high-performance liquid chromatography, and high-throughput DNA sequencing of 16S rDNA. Nabak kimchi showed similar trends as dongchimi, with increasing lactic and acetic acids and decreasing pH for each temperature, but differences in microbiota were apparent.

Effects of acetic acid and arginine on pH elevation and growth of Bacillus licheniformis in an acidified cucumber juice medium.

Bacillus licheniformis has been shown to cause pH elevation in tomato products having an initial pH below 4.6 and metabiotic effects that can lead to the growth of pathogenic bacteria. Because of this, the organism poses a potential risk to acidified vegetable products; however, little is known about the growth and metabolism of this organism in these products.

Characterization of the microbial diversity in yacon spontaneous fermentation at 20 °C.

The prebiotic fructooligosaccharide content of yacon makes this root an attractive alternative for the supplementation of a variety of food products. The preservation of yacon by fermentation has been proposed as an alternative to increase the probiotic content of the root concomitantly with its shelf life. Thus the fermented yacon could have significant functional content.