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. We estimated that SOC stocks increased annually in US croplands from 1995 to 2015, with the largest increase in 1996 of 16.6 Mt C (95% confidence interval ranging from 6.1 to 28.2 Mt CO2 eq.) and the lowest increase in 2015 of 10.6 Mt C (95% confidence interval ranging from - 1.8 to 22.2 Mt C). Most climate-smart soil practices contributed to increases in SOC stocks except for winter cover crops, which had a negligible impact due to a relatively small area with cover crop adoption. Our study suggests that there is potential for enhancing C sinks in cropland soils of the United States although some of the potential has been realized due to past adoption of climate-smart soil practices.

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 (N2O) emissions-a potent greenhouse gas and ozone depleting substance. Enhanced-efficiency nitrogen (N) fertilizers (EENFs) can reduce N2O 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 N2O mitigation potentials. We implemented a Bayesian calibration method using the sampling importance resampling (SIR) algorithm to derive a joint posterior distribution of model parameters that was informed by N2O flux measurements from corn production systems a network of experimental sites within the GRACEnet program. The joint posterior distribution can be applied to estimate predictions of N2O reduction factors when EENFs are adopted in place of conventional urea-based N fertilizer. The resulting median reduction factors were - 11.9% for CRNFs (ranging from -51.7% and 0.58%) and - 26.7% for NIs (ranging from -61.8% to 3.1%), which is comparable to the measured reduction factors in the dataset. By incorporating EENFs, the DayCent ecosystem model is able to simulate a broader suite of options to identify best management practices for reducing N2O emissions.

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. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum.

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. However, uncertainties tend to be large, which may make this approach less attractive as a contributor to stabilize the climate system compared to other options. Consequently, no-till may be better viewed as a method for reducing soil erosion, adapting to climate change, and ensuring food security, while any increase in SOC storage is a co-benefit for society in terms of reducing greenhouse gas emissions.

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. A variation on this approach, the quantitative randomized response technique (QRRT), allows researchers to estimate the frequency or quantity of sensitive behaviors. However, to date no studies have used QRRT to identify potential drivers of non-compliant behavior because regression methodology has not been developed for the nonnegative count data produced by QRRT. We develop a Poisson regression methodology for QRRT data, based on maximum likelihood estimation computed via the expectation-maximization (EM) algorithm. The methodology can be implemented with relatively minor modification of existing software for generalized linear models. We derive the Fisher information matrix in this setting and use it to obtain the asymptotic variance-covariance matrix of the regression parameter estimates. Simulation results demonstrate the quality of the asymptotic approximations. The method is illustrated with a case study examining potential drivers of non-compliance with hunting regulations in Sierra Leone. The new methodology allows assessment of the importance of potential drivers of different quantities of non-compliant behavior, using a likelihood-based, information-theoretic approach. Free, open-source software is provided to support QRRT regression.

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. Here, both the mean and log variance functions are modeled as smooth functions of covariates. For this problem, we derive a mean field variational approximation with an embedded Laplace approximation to account for the non-conjugate structure. Empirical results with simulated and real data show that our approximate method has significant computational advantages over traditional Markov Chain Monte Carlo; in this case, a delayed rejection adaptive Metropolis algorithm. The variational approximation is much faster and eliminates the need for tuning parameter selection, achieves good fits for both the mean and log variance functions, and reasonably reflects the posterior uncertainty. We apply the methods to log-intensity data from a small angle X-ray scattering experiment, in which properly accounting for the smooth heteroskedasticity leads to significant improvements in posterior inference for key physical characteristics of an organic molecule.

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. All strains were adapted in PJ (pH 3·8) stored at 4 and 20°C for 24 h, and then the relative transcription levels of genes in all strains were quantified using a real-time quantitative-PCR assay. After adaptation in PJ, the STEC strains were exposed to SGF (pH 1·5 and 2·0) at 37°C for 2 h. Generally, the STEC adapted in PJ at 4°C displayed enhanced survival compared to acid adaptation in PJ at 20°C and nonadapted controls with exposure to SGF (P < 0·05). Moreover, resistant strains exhibited higher survival rates compared to sensitive strains (P < 0·05). Overall, adaptation at 4°C resulted in significantly (P < 0·05) enhanced gene expression levels in PJ, and transcript levels of gadA were higher than those of the rpoS and adiA genes. CONCLUSIONS: The up-regulation of AR genes due to adaptation in PJ at low temperature may increase STEC survival in acidic environments such as the gastrointestinal tract. Some non-O157 STEC strains, including serotypes O103:H2 and O111:H8, showed relatively high AR levels similar to those of STEC O157:H7. SIGNIFICANCE AND IMPACT OF THE STUDY: Induction of AR genes in acidic fruit juice, and potentially in other acidic foods may increase the risk of foodborne illness by non-O157 STEC serogroups.

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. The objective of this research was to characterize the biochemistry and microbiology of spontaneous yacon fermentation with 2% NaCl and define the viability of the proposed process. The biochemical analysis of spontaneous heterolactic fermentation of yacon showed a progressive drop in pH with increased lactic and acetic acids, and the production of mannitol during fermentation. The microbial ecology of yacon fermentation was investigated using culture-dependent and culture-independent methods. Bacterial cell counts revealed a dominance of lactic acid bacteria (LAB) over yeasts, which were also present during the first 2 days of the fermentation. Results showed that the heterofermentative LAB were primarily Leuconostoc species, thus it presents a viable method to achieve long term preservation of this root.

Determination of 5-log reduction times for Escherichia coli O157:H7, Salmonella enterica, or Listeria monocytogenes in acidified foods with pH 3.5 or 3.8 3.

A critical factor in ensuring the safety of acidified foods is the establishment of a thermal process that assures the destruction of acid-resistant vegetative pathogenic and spoilage bacteria. For acidified foods such as dressings and mayonnaises with pH values of 3.5 or higher, the high water phase acidity (acetic acid of 1.5 to 2.5% or higher) can contribute to lethality, but there is a lack of data showing how the use of common ingredients such as acetic acid and preservatives, alone or in combination, can result in a 5-log reduction for strains of Escherichia coli O157:H7, Salmonella enterica, and Listeria monocytogenes in the absence of a postpackaging pasteurization step. In this study, we determined the times needed at 10° C to achieve a 5-log reduction of E. coli O157:H7, S. enterica, and L. monocytogenes in pickling brines with a variety of acetic and benzoic acid combinations at pH 3.5 and 3.8. Evaluation of 15 different acid-pH combinations confirmed that strains of E. coli O157:H7 were significantly more acid resistant than strains of S. enterica and L. monocytogenes. Among the acid conditions tested, holding times of 4 days or less could achieve a 5-log reduction for vegetative pathogens at pH 3.5 with 2.5% acetic acid or at pH 3.8 with 2.5% acetic acid containing 0.1% benzoic acid. These data indicate the efficacy of benzoic acid for reducing the time necessary to achieve a 5-log reduction in target pathogens and may be useful for supporting process filings and the determination of critical controls for the manufacture of acidified foods.

Bacteriophage ecology in a commercial cucumber fermentation.

To reduce high-salt waste from cucumber fermentations, low-salt fermentations are under development. These fermentations may require the use of starter cultures to ensure normal fermentations. Because potential phage infection can cause starter culture failure, it is important to understand phage ecology in the fermentations. This study investigated the phage ecology in a commercial cucumber fermentation. Brine samples taken from a fermentation tank over a 90-day period were plated onto deMan-Rogosa-Sharpe agar plates. A total of 576 lactic acid bacterial isolates were randomly selected to serve as potential hosts for phage isolation. Filtered brine served as a phage source. Fifty-seven independent phage isolates were obtained, indicating that 10% of the bacterial isolates were sensitive to phage attack. Phage hosts include Lactobacillus brevis (67% of all hosts), Lactobacillus plantarum (21%), Weissella paramesenteroides, Weissella cibaria, and Pediococcus ethanolidurans. Nearly 50% of phages were isolated on day 14, and the majority of them attacked L. brevis. Some phages had a broad host range and were capable of infecting multiple hosts in two genera. Other phages were species specific or strain specific. About 30% of phage isolates produced turbid pinpoint plaques or only caused reduced cell growth on the bacterial lawns. Six phages with distinct host ranges were characterized. The data from this study showed that abundant and diverse phages were present in the commercial cucumber fermentation, which could cause significant mortality to the lactic acid bacteria population. Therefore, a phage control strategy may be needed in low-salt cucumber fermentations.

Autocovariance Structures for Radial Averages in Small Angle X-Ray Scattering Experiments.

Small-angle X-ray scattering (SAXS) is a technique for obtaining low-resolution structural information about biological macromolecules, by exposing a dilute solution to a high-intensity X-ray beam and capturing the resulting scattering pattern on a two-dimensional detector. The two-dimensional pattern is reduced to a one-dimensional curve through radial averaging; that is, by averaging across annuli on the detector plane. Subsequent analysis of structure relies on these one-dimensional data. This paper reviews the technique of SAXS and investigates autocorrelation structure in the detector plane and in the radial averages. Across a range of experimental conditions and molecular types, spatial autocorrelation in the detector plane is present and is well-described by a stationary kernel convolution model. The corresponding autocorrelation structure for the radial averages is non-stationary. Implications of the autocorrelation structure for inference about macromolecular structure are discussed.

Properties of antibacterial polypropylene/nanometal composite fibers.

Melt spinning of polypropylene fibers containing silver and zinc nanoparticles was investigated. The nanometals were generally uniformly dispersed in polypropylene, but aggregation of these materials was observed on fiber surface and in fiber cross-sections. The mechanical properties of the resulted composite fibers with low concentration of nanometal were comparable to those for the control PP yarns. Extruded composite fibers that contained 0.72% silver and 0.60% zinc nanoparticles had outstanding antibacterial efficacy as documented by the percentage count reduction growth of Escherichia coli and Staphylococcus aureus. Fibers containing silver particles had improved antistatic properties.

Sequence analysis of Leuconostoc mesenteroides bacteriophage Phi1-A4 isolated from an industrial vegetable fermentation.

Vegetable fermentations rely on the proper succession of a variety of lactic acid bacteria (LAB). Leuconostoc mesenteroides initiates fermentation. As fermentation proceeds, L. mesenteroides dies off and other LAB complete the fermentation. Phages infecting L. mesenteroides may significantly influence the die-off of L. mesenteroides. However, no L. mesenteroides phages have been previously genetically characterized. Knowledge of more phage genome sequences may provide new insights into phage genomics, phage evolution, and phage-host interactions. We have determined the complete genome sequence of L. mesenteroides phage Phi1-A4, isolated from an industrial sauerkraut fermentation. The phage possesses a linear, double-stranded DNA genome consisting of 29,508 bp with a G+C content of 36%. Fifty open reading frames (ORFs) were predicted. Putative functions were assigned to 26 ORFs (52%), including 5 ORFs of structural proteins. The phage genome was modularly organized, containing DNA replication, DNA-packaging, head and tail morphogenesis, cell lysis, and DNA regulation/modification modules. In silico analyses showed that Phi1-A4 is a unique lytic phage with a large-scale genome inversion ( approximately 30% of the genome). The genome inversion encompassed the lysis module, part of the structural protein module, and a cos site. The endolysin gene was flanked by two holin genes. The tail morphogenesis module was interspersed with cell lysis genes and other genes with unknown functions. The predicted amino acid sequences of the phage proteins showed little similarity to other phages, but functional analyses showed that Phi1-A4 clusters with several Lactococcus phages. To our knowledge, Phi1-A4 is the first genetically characterized L. mesenteroides phage.

Lactobacilli and tartrazine as causative agents of red-color spoilage in cucumber pickle products.

The cucumber pickling industry has sporadically experienced spoilage outbreaks in pickled cucumber products characterized by development of red color on the surface of the fruits. Lactobacillus casei and Lactobacillus paracasei were isolated from 2 outbreaks of this spoilage that occurred about 15 y apart during the last 3 decades. Both organisms were shown to produce this spoilage when inoculated into pickled cucumbers while concomitantly degrading the azo dye tartrazine (FD&C yellow nr 5). This food dye is used as a yellow coloring in the brine cover solutions of commercial pickled cucumber products. The red color does not occur in the absence of tartrazine, nor when turmeric is used as a yellow coloring in the pickles. Addition of sodium benzoate to the brine cover solutions of a pickled cucumber product, more specifically hamburger dill pickles, prevented growth of these lactic acid bacteria and the development of the red spoilage.

Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells.

Propidium monoazide (PMA) and ethidium monoazide were used for enumeration of viable Listeria monocytogenes cells in the presence of dead cells. PMA had no antimicrobial effect on L. monocytogenes. Viable cell counts were linearly related to real-time PCR threshold cycle values for PMA-treated cells from planktonic and biofilm sources over a 4-log range.

Comparative genomics of the lactic acid bacteria.

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Resistance of Listeria monocytogenes biofilms to sanitizing agents in a simulated food processing environment.

The objective of this study was to evaluate the resistance of biofilms of Listeria monocytogenes to sanitizing agents under laboratory conditions simulating a food processing environment. Biofilms were initially formed on stainless steel and Teflon coupons using a five-strain mixture of L. monocytogenes. The coupons were then subjected to repeated 24-h daily cycles. Each cycle consisted of three sequential steps: (i) a brief (60 s) exposure of the coupons to a sanitizing agent (a mixture of peroxides) or saline as a control treatment, (ii) storage of the coupons in sterile plastic tubes without any nutrients or water for 15 h, (iii) and incubation of the coupons in diluted growth medium for 8 h. This regimen was repeated daily for up to 3 weeks and was designed to represent stresses encountered by bacteria in a food processing environment. The bacteria on the coupons were reduced in number during the first week of the simulated food processing (SFP) regimen, but then adapted to the stressful conditions and increased in number. Biofilms repeatedly exposed the peroxide sanitizer in the SFP regimen developed resistance to the peroxide sanitizer as well as other sanitizers (quaternary ammonium compounds and chlorine). Interestingly, cells that were removed from the biofilms on peroxide-treated and control coupons were not significantly different in their resistance to sanitizing agents. These data suggest that the resistance of the treated biofilms to sanitizing agents may be due to attributes of extracellular polymeric substances and is not an intrinsic attribute of the cells in the biofilm.

Quantifying the significance of phage attack on starter cultures: a mechanistic model for population dynamics of phage and their hosts isolated from fermenting sauerkraut.

We investigated the possibility of using starter cultures in sauerkraut fermentation and thereby reducing the quantity of salt used in the process. This, in turn, would reduce the amount of waste salt that would enter in our water resources. Phage, naturally present in sauerkraut fermentation, could potentially affect the starter cultures introduced. Thus, a mechanistic mathematical model was developed to quantify the growth kinetics of the phage and starter cultures. The model was validated by independent experiments with two Leuconostoc mesenteroides strains isolated from sauerkraut and their corresponding phage. Model simulations and experimental evidence showed the presence of phage-resistant cell populations in starter cultures which replaced phage-sensitive cells, even when the initial phage density (P(0)) and multiplicity of infection (MOI) were low (P(0) < 1 x 10(3) PFU/ml; MOI < 10(-4)) in the MRS media. Based on the results of model simulation and parameter optimization, it was suggested that the kinetic parameters of phage-host interaction, especially the adsorption rate, vary with the initial phage and host densities and with time. The model was validated in MRS broth. Therefore, the effects of heterogeneity and other environmental factors, such as temperature and pH, should be considered to make the model applicable to commercial fermentations.

Protective effects of organic acids on survival of Escherichia coli O157:H7 in acidic environments.

Outbreaks of disease due to acid-tolerant bacterial pathogens in apple cider and orange juice have raised questions about the safety of acidified foods. Using gluconic acid as a noninhibitory low-pH buffer, we investigated the killing of Escherichia coli O157:H7 strains in the presence or absence of selected organic acids (pH of 3.2), with ionic strength adjusted to 0.60 to 0.68. During a 6-h exposure period in buffered solution (pH 3.2), we found that a population of acid-adapted E. coli O157:H7 strains was reduced by 4 log cycles in the absence of added organic acids. Surprisingly, reduced lethality for E. coli O157:H7 was observed when low concentrations (5 mM) of fully protonated acetic, malic, or l-lactic acid were added. Only a 2- to 3-log reduction in cell counts was observed, instead of the 4-log reduction attributed to pH effects in the buffered solution. Higher concentrations of these acids at the same pH aided in the killing of the E. coli cells, resulting in a 6-log or greater reduction in cell numbers. No protective effect was observed when citric acid was added to the E. coli cells. d-Lactic acid had a greater protective effect than other acids at concentrations of 1 to 20 mM. Less than a 1-log decrease in cell numbers occurred during the 6-h exposure to pH 3.2. To our knowledge, this is the first report of the protective effect of organic acids on the survival of E. coli O15:H7 under low-pH conditions.

Sequence analysis of the Lactobacillus plantarum bacteriophage PhiJL-1.

The complete genomic sequence of a Lactobacillus plantarum virulent phage PhiJL-1 was determined. The phage possesses a linear, double-stranded, DNA genome consisting of 36,677 bp with a G+C content of 39.36%. A total of 52 possible open reading frames (ORFs) were identified. According to N-terminal amino acid sequencing and bioinformatic analyses, proven or putative functions were assigned to 21 ORFs (41%), including 5 structural protein genes. The PhiJL-1 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication, DNA packaging, head and tail morphogenesis, and lysis. This type of modular genomic organization was similar to several other phages infecting lactic acid bacteria. The structural gene maps revealed that the order of the head and tail genes is highly conserved among the genomes of several Siphoviridae phages, allowing the assignment of probable functions to certain uncharacterized ORFs from phage PhiJL-1 and other Siphoviridae phages.