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Sample records for microbial growth model

  1. Mathematical modeling of microbial growth in milk

    Directory of Open Access Journals (Sweden)

    Jhony Tiago Teleken

    2011-12-01

    Full Text Available A mathematical model to predict microbial growth in milk was developed and analyzed. The model consists of a system of two differential equations of first order. The equations are based on physical hypotheses of population growth. The model was applied to five different sets of data of microbial growth in dairy products selected from Combase, which is the most important database in the area with thousands of datasets from around the world, and the results showed a good fit. In addition, the model provides equations for the evaluation of the maximum specific growth rate and the duration of the lag phase which may provide useful information about microbial growth.

  2. Mechanistic model for microbial growth on hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Mallee, F M; Blanch, H W

    1977-12-01

    Based on available information describing the transport and consumption of insoluble alkanes, a mechanistic model is proposed for microbial growth on hydrocarbons. The model describes the atypical growth kinetics observed, and has implications in the design of large scale equipment for single cell protein (SCP) manufacture from hydrocarbons. The model presents a framework for comparison of the previously published experimental kinetic data.

  3. Comparison of Two Mechanistic Microbial Growth Models to Estimate Shelf Life of Perishable Food Package under Dynamic Temperature Conditions

    Directory of Open Access Journals (Sweden)

    Dong Sun Lee

    2014-01-01

    Full Text Available Two mechanistic microbial growth models (Huang’s model and model of Baranyi and Roberts given in differential and integrated equation forms were compared in predicting the microbial growth and shelf life under dynamic temperature storage and distribution conditions. Literatures consistently reporting the microbial growth data under constant and changing temperature conditions were selected to obtain the primary model parameters, set up the secondary models, and apply them to predict the microbial growth and shelf life under fluctuating temperatures. When evaluated by general estimation behavior, bias factor, accuracy factor, and root-mean-square error, Huang’s model was comparable to Baranyi and Roberts’ model in the capability to estimate microbial growth under dynamic temperature conditions. Its simple form of single differential equation incorporating directly the growth rate and lag time may work as an advantage to be used in online shelf life estimation by using the electronic device.

  4. Bifurcations of a periodically forced microbial continuous culture model with restrained growth rate

    Science.gov (United States)

    Ren, Jingli; Yuan, Qigang

    2017-08-01

    A three dimensional microbial continuous culture model with a restrained microbial growth rate is studied in this paper. Two types of dilution rates are considered to investigate the dynamic behaviors of the model. For the unforced system, fold bifurcation and Hopf bifurcation are detected, and numerical simulations reveal that the system undergoes degenerate Hopf bifurcation. When the system is periodically forced, bifurcation diagrams for periodic solutions of period-one and period-two are given by researching the Poincaré map, corresponding to different bifurcation cases in the unforced system. Stable and unstable quasiperiodic solutions are obtained by Neimark-Sacker bifurcation with different parameter values. Periodic solutions of various periods can occur or disappear and even change their stability, when the Poincaré map of the forced system undergoes Neimark-Sacker bifurcation, flip bifurcation, and fold bifurcation. Chaotic attractors generated by a cascade of period doublings and some phase portraits are given at last.

  5. Effect of Nisin's Controlled Release on Microbial Growth as Modeled for Micrococcus luteus.

    Science.gov (United States)

    Balasubramanian, Aishwarya; Lee, Dong Sun; Chikindas, Michael L; Yam, Kit L

    2011-06-01

    The need for safe food products has motivated food scientists and industry to find novel technologies for antimicrobial delivery for improving food safety and quality. Controlled release packaging is a novel technology that uses the package to deliver antimicrobials in a controlled manner and sustain antimicrobial stress on the targeted microorganism over the required shelf life. This work studied the effect of controlled release of nisin to inhibit growth of Micrococcus luteus (a model microorganism) using a computerized syringe pump system to mimic the release of nisin from packaging films which was characterized by an initially fast rate and a slower rate as time progressed. The results show that controlled release of nisin was strikingly more effective than instantly added ("formulated") nisin. While instant addition experiments achieved microbial inhibition only at the beginning, controlled release experiments achieved complete microbial inhibition for a longer time, even when as little as 15% of the amount of nisin was used as compared to instant addition.

  6. New microbial growth factor

    Science.gov (United States)

    Bok, S. H.; Casida, L. E., Jr.

    1977-01-01

    A screening procedure was used to isolate from soil a Penicillium sp., two bacterial isolates, and a Streptomyces sp. that produced a previously unknown microbial growth factor. This factor was an absolute growth requirement for three soil bacteria. The Penicillium sp. and one of the bacteria requiring the factor, an Arthrobacter sp., were selected for more extensive study concerning the production and characteristics of the growth factor. It did not seem to be related to the siderochromes. It was not present in soil extract, rumen fluid, or any other medium component tested. It appears to be a glycoprotein of high molecular weight and has high specific activity. When added to the diets for a meadow-vole mammalian test system, it caused an increased consumption of diet without a concurrent increase in rate of weight gain.

  7. Growth Mechanism of Microbial Colonies

    Science.gov (United States)

    Zhu, Minhui; Martini, K. Michael; Kim, Neil H.; Sherer, Nicholas; Lee, Jia Gloria; Kuhlman, Thomas; Goldenfeld, Nigel

    Experiments on nutrient-limited E. coli colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. Supported by NSF Grant 0822613.

  8. Parameter estimations in predictive microbiology: Statistically sound modelling of the microbial growth rate.

    Science.gov (United States)

    Akkermans, Simen; Logist, Filip; Van Impe, Jan F

    2018-04-01

    When building models to describe the effect of environmental conditions on the microbial growth rate, parameter estimations can be performed either with a one-step method, i.e., directly on the cell density measurements, or in a two-step method, i.e., via the estimated growth rates. The two-step method is often preferred due to its simplicity. The current research demonstrates that the two-step method is, however, only valid if the correct data transformation is applied and a strict experimental protocol is followed for all experiments. Based on a simulation study and a mathematical derivation, it was demonstrated that the logarithm of the growth rate should be used as a variance stabilizing transformation. Moreover, the one-step method leads to a more accurate estimation of the model parameters and a better approximation of the confidence intervals on the estimated parameters. Therefore, the one-step method is preferred and the two-step method should be avoided. Copyright © 2017. Published by Elsevier Ltd.

  9. A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures.

    Science.gov (United States)

    Mazzoleni, Stefano; Landi, Carmine; Cartenì, Fabrizio; de Alteriis, Elisabetta; Giannino, Francesco; Paciello, Lucia; Parascandola, Palma

    2015-07-30

    Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.

  10. Hydrocarbon fermentation: kinetics of microbial cell growth

    Energy Technology Data Exchange (ETDEWEB)

    Goma, G [Institut National des Sciences Appliquees, Toulouse; Ribot, D

    1978-11-01

    Modeling of microbial growth using nonmiscible substrate is studied when kinetics of substrate dissolution is rate limiting. When the substrate concentration is low, the growth rate is described by an analytical relation that can be identified as a Contois relationship. If the substrate concentration is greater than a critical value S/sub crit/, the potentially useful hydrocarbon S* concentration is described by S* = S/sub crit//(1 + S/sub crit//S). A relationship was found between S/sub crit/ and the biomass concentration X. When X increased, S/sub crit/ decreased. The cell growth rate is related to a relation ..mu.. = ..mu../sub m/(A(X/S/sub crit/)(1 + S/sub crit//S) + 1)/sup -1/. This model describes the evolution of the growth rate when exponential or linear growth occurs, which is related to physico-chemical properties and hydrodynamic fermentation conditions. Experimental data to support the model are presented.

  11. Conditioning biomass for microbial growth

    Science.gov (United States)

    Bodie, Elizabeth A; England, George

    2015-03-31

    The present invention relates to methods for improving the yield of microbial processes that use lignocellulose biomass as a nutrient source. The methods comprise conditioning a composition comprising lignocellulose biomass with an enzyme composition that comprises a phenol oxidizing enzyme. The conditioned composition can support a higher rate of growth of microorganisms in a process. In one embodiment, a laccase composition is used to condition lignocellulose biomass derived from non-woody plants, such as corn and sugar cane. The invention also encompasses methods for culturing microorganisms that are sensitive to inhibitory compounds in lignocellulose biomass. The invention further provides methods of making a product by culturing the production microorganisms in conditioned lignocellulose biomass.

  12. Microbial modeling of Alicyclobacillus acidoterrestris CRA 7152 growth in orange juice with nisin added.

    Science.gov (United States)

    Peña, Wilmer Edgard Luera; de Massaguer, Pilar Rodriguez

    2006-08-01

    The adaptation time of Alicyclobacillus acidoterrestris CRA 7152 in orange juice was determined as a response to pH (3 to 5.8), temperature (20 to 54 degrees C), soluble solids concentration ((o)Brix; 11 to 19 (o)Brix), and nisin concentration (0 to 70 IU/ ml) effects. A four-factor central composite rotational design was used. Viable microorganisms were enumerated by plating on K medium (pH 3.7). Two primary models were used to represent growth and adaptation time. A second-order polynomial model was applied to analyze the effects of factors. Results showed that the Baranyi and Roberts model was better than the modified Gompertz model, considering the determination coefficient (R2) for experimental data description. Inhibition of bacteria can be obtained through several studied combinations for at least 47 days of storage. The shortest period of adaptation was observed between 37 to 45 degrees C, with pHs between 4 and 5, yet the longest periods of adaptation could be obtained around 20 degrees C with pHs close to 3.0. Statistical analysis of the quadratic model showed that the adaptation time increased as temperature or pH decreased, and as nisin concentration or soluble solids increased. The model showed that adaptation time has a minimum value for juice without nisin added, with 13.5% soluble solids, pH 5.0, and incubated at 43.8 degrees C. The statistical parameters that validated this model were an R2 of 0.816, a bias factor of 0.96, and an accuracy factor of 1.14. Manipulation of more than one factor, as well as the use of an antimicrobial agent, can be an alternative to preventing the development of A. acidoterrestris in orange juice, thus contributing to increased orange juice shelf life.

  13. Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

    Science.gov (United States)

    Klier, Christine

    2012-03-06

    The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

  14. Microbial growth and substrate utilization kinetics | Okpokwasili ...

    African Journals Online (AJOL)

    Microbial growth on and utilization of environmental contaminants as substrates have been studied by many researchers. Most times, substrate utilization results in removal of chemical contaminant, increase in microbial biomass and subsequent biodegradation of the contaminant. These are all aimed at detoxification of the ...

  15. Microculture model studies on the effect of various gas atmospheres on microbial growth at different temperatures.

    Science.gov (United States)

    Eklund, T; Jarmund, T

    1983-08-01

    A microculture technique, employing 96-well tissue culture plates in plastic bags, was used to test the effect of different gas atmospheres (vacuum, air, nitrogen, and carbon dioxide) on the growth of Escherichia coli, Bacillus macerans, Salmonella typhimurium. Candida albicans, Lactobacillus plantarum, Pseudomonas/Acinetobacter/moraxella-group, Brochothrix thermosphacta and Yersinia enterocolitica at 2, 6, and 20 degrees C. In general, carbon dioxide was the most effective inhibitor. The inhibition increased with decreasing temperature. Only the combination of carbon dioxide and 2 degrees C provided complete inhibition of Broch. thermosphacta and Y. enterocolitica.

  16. Modeling of microbial quality of food

    NARCIS (Netherlands)

    Zwietering, M.

    1993-01-01

    In this thesis it is shown that predictive modeling is a promising tool in food research, to be used to optimize food chains. Various models are developed and validated to be used to describe microbial growth in foods.

    A tool is developed to discriminate between different models and

  17. Modelling microbial interactions and food structure in predictive microbiology

    NARCIS (Netherlands)

    Malakar, P.K.

    2002-01-01

    Keywords: modelling, dynamic models, microbial interactions, diffusion, microgradients, colony growth, predictive microbiology.

    Growth response of microorganisms in foods is a complex process. Innovations in food production and preservation techniques have resulted in adoption of

  18. Genome-scale biological models for industrial microbial systems.

    Science.gov (United States)

    Xu, Nan; Ye, Chao; Liu, Liming

    2018-04-01

    The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

  19. 21 CFR 866.2560 - Microbial growth monitor.

    Science.gov (United States)

    2010-04-01

    ...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth monitor. (a) Identification. A microbial growth monitor is a device intended for medical purposes that...

  20. Impact of warm winters on microbial growth

    Science.gov (United States)

    Birgander, Johanna; Rousk, Johannes; Axel Olsson, Pål

    2014-05-01

    Growth of soil bacteria has an asymmetrical response to higher temperature with a gradual increase with increasing temperatures until an optimum after which a steep decline occurs. In laboratory studies it has been shown that by exposing a soil bacterial community to a temperature above the community's optimum temperature for two months, the bacterial community grows warm-adapted, and the optimum temperature of bacterial growth shifts towards higher temperatures. This result suggests a change in the intrinsic temperature dependence of bacterial growth, as temperature influenced the bacterial growth even though all other factors were kept constant. An intrinsic temperature dependence could be explained by either a change in the bacterial community composition, exchanging less tolerant bacteria towards more tolerant ones, or it could be due to adaptation within the bacteria present. No matter what the shift in temperature tolerance is due to, the shift could have ecosystem scale implications, as winters in northern Europe are getting warmer. To address the question of how microbes and plants are affected by warmer winters, a winter-warming experiment was established in a South Swedish grassland. Results suggest a positive response in microbial growth rate in plots where winter soil temperatures were around 6 °C above ambient. Both bacterial and fungal growth (leucine incorporation, and acetate into ergosterol incorporation, respectively) appeared stimulated, and there are two candidate explanations for these results. Either (i) warming directly influence microbial communities by modulating their temperature adaptation, or (ii) warming indirectly affected the microbial communities via temperature induced changes in bacterial growth conditions. The first explanation is in accordance with what has been shown in laboratory conditions (explained above), where the differences in the intrinsic temperature relationships were examined. To test this explanation the

  1. Effects of Spatial Localization on Microbial Consortia Growth.

    Directory of Open Access Journals (Sweden)

    Michael Venters

    Full Text Available Microbial consortia are commonly observed in natural and synthetic systems, and these consortia frequently result in higher biomass production relative to monocultures. The focus here is on the impact of initial spatial localization and substrate diffusivity on the growth of a model microbial consortium consisting of a producer strain that consumes glucose and produces acetate and a scavenger strain that consumes the acetate. The mathematical model is based on an individual cell model where growth is described by Monod kinetics, and substrate transport is described by a continuum-based, non-equilibrium reaction-diffusion model where convective transport is negligible (e.g., in a biofilm. The first set of results focus on a single producer cell at the center of the domain and surrounded by an initial population of scavenger cells. The impact of the initial population density and substrate diffusivity is examined. A transition is observed from the highest initial density resulting in the greatest cell growth to cell growth being independent of initial density. A high initial density minimizes diffusive transport time and is typically expected to result in the highest growth, but this expected behavior is not predicted in environments with lower diffusivity or larger length scales. When the producer cells are placed on the bottom of the domain with the scavenger cells above in a layered biofilm arrangement, a similar critical transition is observed. For the highest diffusivity values examined, a thin, dense initial scavenger layer is optimal for cell growth. However, for smaller diffusivity values, a thicker, less dense initial scavenger layer provides maximal growth. The overall conclusion is that high density clustering of members of a food chain is optimal under most common transport conditions, but under some slow transport conditions, high density clustering may not be optimal for microbial growth.

  2. Microbial growth on C1 compounds: proceedings

    International Nuclear Information System (INIS)

    Crawford, R.L.; Hanson, R.S.

    1984-01-01

    This book contains individual papers prepared for the 4th International Symposium on Microbial Growth on One Carbon Compounds. Individual reports were abstracted and indexed for EDB. Topics presented were in the areas of the physiology and biochemistry of autotraps, physiology and biochemistry of methylotrophs and methanotrops, physiology and biochemistry of methanogens, genetics of microbes that use C 1 compounds, taxonomy and ecology of microbes tht grow on C 1 compounds, applied aspects of microbes that grow on C 1 compounds, and new directions in C 1 metabolism. (DT)

  3. Accounting for inherent variability of growth in microbial risk assessment.

    Science.gov (United States)

    Marks, H M; Coleman, M E

    2005-04-15

    Risk assessments of pathogens need to account for the growth of small number of cells under varying conditions. In order to determine the possible risks that occur when there are small numbers of cells, stochastic models of growth are needed that would capture the distribution of the number of cells over replicate trials of the same scenario or environmental conditions. This paper provides a simple stochastic growth model, accounting only for inherent cell-growth variability, assuming constant growth kinetic parameters, for an initial, small, numbers of cells assumed to be transforming from a stationary to an exponential phase. Two, basic, microbial sets of assumptions are considered: serial, where it is assume that cells transform through a lag phase before entering the exponential phase of growth; and parallel, where it is assumed that lag and exponential phases develop in parallel. The model is based on, first determining the distribution of the time when growth commences, and then modelling the conditional distribution of the number of cells. For the latter distribution, it is found that a Weibull distribution provides a simple approximation to the conditional distribution of the relative growth, so that the model developed in this paper can be easily implemented in risk assessments using commercial software packages.

  4. A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

    Science.gov (United States)

    Wang, Gangsheng; Post, Wilfred M

    2012-09-01

    We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

  5. Spectrum of microbial growth and antimicrobial usage in an ...

    African Journals Online (AJOL)

    white blood cell count, duration of first antibiotic used, length of ICU stay, length of ... the acute disease process, the presence of comorbidities, invasive devices, ... Against this background, this study aimed to look at the microbial growth.

  6. Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

    Science.gov (United States)

    Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand...

  7. Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach

    NARCIS (Netherlands)

    Koutinas, M.; Kiparissides, A.; Silva-Rocha, R.; Lam, M.C.; Martins Dos Santos, V.A.P.; Lorenzo, de V.; Pistikopoulos, E.N.; Mantalaris, A.

    2011-01-01

    The majority of models describing the kinetic properties of a microorganism for a given substrate are unstructured and empirical. They are formulated in this manner so that the complex mechanism of cell growth is simplified. Herein, a novel approach for modelling microbial growth kinetics is

  8. Effect of temperature on microbial growth rate - thermodynamic analysis, the arrhenius and eyring-polanyi connection

    Science.gov (United States)

    The objective of this work is to develop a new thermodynamic mathematical model for evaluating the effect of temperature on the rate of microbial growth. The new mathematical model is derived by combining the Arrhenius equation and the Eyring-Polanyi transition theory. The new model, suitable for ...

  9. Impact of Microbial Growth on Subsurface Perfluoroalkyl Acid Transport

    Science.gov (United States)

    Weathers, T. S.; Higgins, C. P.; Sharp, J.

    2014-12-01

    The fate and transport of poly and perfluoroalkyl substances (PFASs) in the presence of active microbial communities has not been widely investigated. These emerging contaminants are commonly utilized in aqueous film-forming foams (AFFF) and have often been detected in groundwater. This study explores the transport of a suite of perfluorocarboxylic acids and perfluoroalkylsulfonates, including perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), in microbially active settings. Single point organic carbon normalized sorption coefficients derived by exposing inactive cellular material to PFASs result in more than an order of magnitude increase in sorption compared to soil organic carbon sorption coefficients found in literature. For example, the sorption coefficients for PFOS are 4.05±0.07 L/kg and 2.80±0.08 L/kg for cellular organic carbon and soil organic carbon respectively. This increase in sorption, coupled with enhanced extracellular polymeric substance production observed during growth of a common hydrocarbon degrading soil microbe exposed to source-level concentrations of PFASs (10 mg/L of 11 analytes, 110 mg/L total) may result in PFAS retardation in situ. To address the upscaling of this phenomenon, flow-through columns packed with low-organic carbon sediment and biostimulated with 10 mg/L glucose were exposed to PFAS concentrations from 15 μg/L to 10 mg/L of each 11 analytes. Breakthrough and tailing of each analyte was measured and modeled with Hydrus-1D to explore sorption coefficients over time for microbially active columns.

  10. Susceptibility of green and conventional building materials to microbial growth.

    Science.gov (United States)

    Mensah-Attipoe, J; Reponen, T; Salmela, A; Veijalainen, A-M; Pasanen, P

    2015-06-01

    Green building materials are becoming more popular. However, little is known about their ability to support or limit microbial growth. The growth of fungi was evaluated on five building materials. Two green, two conventional building materials and wood as a positive control were selected. The materials were inoculated with Aspergillus versicolor, Cladosporium cladosporioides and Penicillium brevicompactum, in the absence and presence of house dust. Microbial growth was assessed at four different time points by cultivation and determining fungal biomass using the N-acetylhexosaminidase (NAHA) enzyme assay. No clear differences were seen between green and conventional building materials in their susceptibility to support microbial growth. The presence of dust, an external source of nutrients, promoted growth of all the fungal species similarly on green and conventional materials. The results also showed a correlation coefficient ranging from 0.81 to 0.88 between NAHA activity and culturable counts. The results suggest that the growth of microbes on a material surface depends on the availability of organic matter rather than the classification of the material as green or conventional. NAHA activity and culturability correlated well indicating that the two methods used in the experiments gave similar trends for the growth of fungi on material surfaces. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Accounting for microbial habitats in modeling soil organic matter dynamics

    Science.gov (United States)

    Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

    2017-04-01

    The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

  12. Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

    International Nuclear Information System (INIS)

    Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz

    2002-01-01

    Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. 32 P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

  13. Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

    Energy Technology Data Exchange (ETDEWEB)

    Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

    2002-07-01

    Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. {sup 32} P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

  14. Acoustic and Electrical Property Changes Due to Microbial Growth and Biofilm Formation in Porous Media

    Science.gov (United States)

    A laboratory study was conducted to investigate the effect of microbial growth and biofilm formation on compressional waves, and complex conductivity during stimulated microbial growth. Over the 29 day duration of the experiment, compressional wave amplitudes and arrival times f...

  15. Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene

    DEFF Research Database (Denmark)

    Bælum, Jacob; Prestat, Emmanuel; David, Maude M.

    2012-01-01

    continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate...

  16. Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

    Science.gov (United States)

    Masum, Shakil A.; Thomas, Hywel R.

    2018-06-01

    To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

  17. Conditions for microbial growth in the FILTRA steam absorption tower

    International Nuclear Information System (INIS)

    Nilsson, H.; Roffey, R.

    1983-08-01

    By the appointment of the Southern Sweden Power Supply an experimental study has been carried out in order to evaluate the risk for microbial growth in the planned FILTRA steam absorbtion tower at the nuclear power plant in Barsebaeck. Four modelsystems were supplied with nitrogen atmosphere and a relative humidity of 100, 75, 50 and 25 percent. The fifth system received air and 75 percent relative humidity. Samples were collected and analysed for microbial growth after 1, 2, 4 and 8 months. The amounts of microorganisms and the ATP content was monitored. No measureable growth of any significance could be observed after 8 months in any system. An elementary analyses showed that the level of nitrogen and carbon in the stones was below the limit of detection (<0.3 percent C, <0.2 percent N). (author)

  18. Colonial vs. planktonic type of growth: mathematical modeling of microbial dynamics on surfaces and in liquid, semi-liquid and solid foods.

    Science.gov (United States)

    Skandamis, Panagiotis N; Jeanson, Sophie

    2015-01-01

    Predictive models are mathematical expressions that describe the growth, survival, inactivation, or biochemical processes of foodborne bacteria. During processing of contaminated raw materials and food preparation, bacteria are entrapped into the food residues, potentially transferred to the equipment surfaces (abiotic or inert surfaces) or cross-contaminate other foods (biotic surfaces). Growth of bacterial cells can either occur planktonically in liquid or immobilized as colonies. Colonies are on the surface or confined in the interior (submerged colonies) of structured foods. For low initial levels of bacterial population leading to large colonies, the immobilized growth differs from planktonic growth due to physical constrains and to diffusion limitations within the structured foods. Indeed, cells in colonies experience substrate starvation and/or stresses from the accumulation of toxic metabolites such as lactic acid. Furthermore, the micro-architecture of foods also influences the rate and extent of growth. The micro-architecture is determined by (i) the non-aqueous phase with the distribution and size of oil particles and the pore size of the network when proteins or gelling agent are solidified, and by (ii) the available aqueous phase within which bacteria may swarm or swim. As a consequence, the micro-environment of bacterial cells when they grow in colonies might greatly differs from that when they grow planktonically. The broth-based data used for modeling (lag time and generation time, the growth rate, and population level) are poorly transferable to solid foods. It may lead to an over-estimation or under-estimation of the predicted population compared to the observed population in food. If the growth prediction concerns pathogen bacteria, it is a major importance for the safety of foods to improve the knowledge on immobilized growth. In this review, the different types of models are presented taking into account the stochastic behavior of single cells

  19. Colonial vs planktonic type of growth: mathematical modeling of microbial dynamics on surfaces and in liquid, semi-liquid and solid foods

    Directory of Open Access Journals (Sweden)

    Panagiotis N. Skandamis

    2015-10-01

    Full Text Available Predictive models are mathematical expressions that describe the growth, survival, inactivation or biochemical processes of foodborne bacteria. During processing of contaminated raw materials and food preparation, bacteria are entrapped into the food residues, potentially transferred to the equipment surfaces (abiotic or inert surfaces or cross-contaminate other foods (biotic surfaces. Growth of bacterial cells can either occur planktonically in liquid or immobilized as colonies. Colonies are on the surface or confined in the interior (submerged colonies of structured foods. For low initial levels of bacterial population leading to large colonies, the immobilized growth differs from planktonic growth due to physical constrains and to diffusion limitations within the structured foods. Indeed, cells in colonies experience substrate starvation and/or stresses from the accumulation of toxic metabolites such as lactic acid. Furthermore, the micro-architecture of foods also influences the rate and extent of growth. The micro-architecture is determined by (i the non-aqueous phase with the distribution and size of oil particles and the pore size of the network when proteins or gelling agent are solidified, and by (ii the available aqueous phase within which bacteria may swarm or swim. As a consequence, the micro-environment of bacterial cells when they grow in colonies might greatly differs from that when they grow planktonically. The broth-based data used for modeling (lag time and generation time, the growth rate and population level are poorly transferable to solid foods. It may lead to an over-estimation or under-estimation of the predicted population compared to the observed population in food. If the growth prediction concerns pathogen bacteria, it is a major importance for the safety of foods to improve the knowledge on immobilized growth. In this review, the different types of models are presented taking into account the stochastic behavior of

  20. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

    This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

  1. Simulated Carbon Cycling in a Model Microbial Mat.

    Science.gov (United States)

    Decker, K. L.; Potter, C. S.

    2006-12-01

    We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.

  2. Growth of microbial mixed cultures under anaerobic, alkaline conditions

    International Nuclear Information System (INIS)

    Wenk, M.

    1993-09-01

    Cement and concrete are the most important engineered barrier materials in a repository for low- and intermediate-level waste and thus represent the most significant component of the total disposal inventory. Based on the chemical composition of the concrete used in the repository and the groundwater fluxes in the modelled host rock, it is to be expected that the pH in the near vicinity of the repository could exceed a value of 10.5 for more than a million years. The groundwater in the repository environment also has a limited carbon concentration. Since microorganisms will be present in a repository and can even find suitable living conditions within the waste itself, investigations were carried out in order to establish the extent to which microbial activity is possible under the extreme conditions of the repository near-field. For the investigations, alkalophilic cultures were enriched from samples from alkaline habitats and from Valanginian Marl. Anaerobic bacteria with fermentative, sulfate-reducing and methanogenic metabolism were selected. The growth and activity of the mixed cultures were studied under alkaline conditions and the dependence on pH and carbon concentration determined. All the mixed cultures investigated are alkalophilic. The optimum growth range for the cultures is between pH 9.0 and pH 10.0. The activity limit for the fermentative mixed culture is at pH 12, for the sulfate-reducers at pH 11 and for the methanogens at pH 10.5. Given the limited supply of carbon, the mixed cultures can only grow under slightly alkaline conditions. Only the fermentative cultures are capable of surviving with limited carbon supply at pH 13. (author) 24 figs., 18 tabs., 101 refs

  3. Multiscale Modeling of Microbial Communities

    Science.gov (United States)

    Blanchard, Andrew

    Although bacteria are single-celled organisms, they exist in nature primarily in the form of complex communities, participating in a vast array of social interactions through regulatory gene networks. The social interactions between individual cells drive the emergence of community structures, resulting in an intricate relationship across multiple spatiotemporal scales. Here, I present my work towards developing and applying the tools necessary to model the complex dynamics of bacterial communities. In Chapter 2, I utilize a reaction-diffusion model to determine the population dynamics for a population with two species. One species (CDI+) utilizes contact dependent inhibition to kill the other sensitive species (CDI-). The competition can produce diverse patterns, including extinction, coexistence, and localized aggregation. The emergence, relative abundance, and characteristic features of these patterns are collectively determined by the competitive benefit of CDI and its growth disadvantage for a given rate of population diffusion. The results provide a systematic and statistical view of CDI-based bacterial population competition, expanding the spectrum of our knowledge about CDI systems and possibly facilitating new experimental tests for a deeper understanding of bacterial interactions. In the following chapter, I present a systematic computational survey on the relationship between social interaction types and population structures for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. The impact of deleterious and beneficial interactions on the community are quantified. Deleterious interactions generate an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a

  4. Phosphate solubilization as a microbial strategy for promoting plant growth

    Directory of Open Access Journals (Sweden)

    Mayra Eleonora Beltrán Pineda

    2014-01-01

    Full Text Available Because of the constant application of chemical inputs in Agroecosystem, the cost of crop production and environmental quality of soil and water have been affected. Microorganisms carry out most biogeochemical cycles; therefore, their role is essential for agro ecosystem balance. One such functional group is the phosphate solubilizing microorganisms, which are recognized plant growth promoters. These microbial populations perform an important activity, since in many soils there are large reserves of insoluble phosphorus, as a result of fixing much of the phosphorus fertilizer applied, which cannot be assimilated by the plant. The phosphate solubilizing microorganisms use different solubilization mechanisms such as the production of organic acids, which solubilize theses insoluble phosphates in the rhizosphere region. Soluble phosphates are absorbed by the plant, which enhances their growth and productivity. By using these phosphate reserves in soils, application of chemical fertilizers is decreased, on the one hand, can again be fixed by ions Ca, Al or Fe making them insoluble and, by the other hand, increase the costs of crop production. Microbial populations have been widely studied in different types of ecosystems, both natural and Agroecosystem. Thanks to its effectiveness, in laboratory and field studies, the phosphate solubilizing phenotype is of great interest to microbial ecologists who have begun to establish the molecular basis of the traitr.

  5. Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

    Science.gov (United States)

    Davis, C. A.; Pyrak-Nolte, L. J.; Atekwana, E. A.; Werkema, D. D.; Haugen, M. E.

    2009-12-01

    Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand columns. A control column (non-biostimulated) and a biostimulated column were studied in a 2D acoustic scanning apparatus, and a second set of columns were constructed with Ag-AgCl electrodes for complex conductivity measurements. At the completion of the 29-day experiment, compressional wave amplitudes and arrival times for the control column were observed to be relatively uniform over the scanned 2D region. However, the biostimulated sample exhibited a high degree of spatial variability within the column for both the amplitude and arrival times. Furthermore, portions of the sample exhibited increased attenuation (~ 80%) concurrent with an increase in the arrival times, while other portions exhibited decreased attenuation (~ 45%) and decreased arrival time. The acoustic amplitude and arrival times changed significantly in the biostimulated column between Days 5 and 7 of the experiment and are consistent with a peak in the imaginary conductivity (σ”) values. The σ” response corresponds to different stages of biofilm development. That is, we interpret the peak σ” with the maximum biofilm thickness and decreasing σ” due to cell death or detachment. Environmental scanning electron microscope (ESEM) imaging confirmed microbial cell attachment to sand surfaces in the biostimulated columns, showed apparent differences in the morphology of attached biomass between regions of increased and decreased attenuation, and indicated no mineral precipitation or biomineralization. The heterogeneity in the elastic properties arises from the differences in the morphology and structure of attached biofilms. These results suggest that combining acoustic imaging and complex conductivity techniques

  6. Microbial Communities Model Parameter Calculation for TSPA/SR

    International Nuclear Information System (INIS)

    D. Jolley

    2001-01-01

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M and O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M and O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow ΔG (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M and O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M and O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed

  7. Microbial uptake of radiolabeled substrates: estimates of growth rates from time course measurements

    International Nuclear Information System (INIS)

    Li, W.K.W.

    1984-01-01

    The uptake of [ 3 H]glucose and a mixture of 3 H-labeled amino acids was measured, in time course fashion, in planktonic microbial assemblages of the eastern tropical Pacific Ocean. The average generation times of those portions of the assemblages able to utilize these substrates were estimated from a simple exponential growth model. Other workers have independently used this model in its integrated or differential form. A mathematical verification and an experimental demonstration of the equivalence of the two approaches are presented. A study was made of the size distribution of heterotrophic activity, using time course measurements. It was found that the size distribution and the effect of sample filtration before radiolabeling were dependent on time of incubation. In principle, it was possible to ascribe these time dependences to differences in th specific growth rate and initial standing stock of the microbial assemblages. 33 references

  8. Microbial Communities: Tracing Growth Processes from Antarctic Lakes to Early Earth to Other Planets

    Science.gov (United States)

    Sumner, D. Y.

    2014-12-01

    Life in the Universe is dominated by microbes: they are numerically the most abundant cells in our bodies and in Earth's biosphere, and they are the only life that might be present elsewhere in our solar system. Life beyond our solar system could include macroscopic organisms, but everything we understand about the origin of life suggests it must start with microbes. Thus, understanding microbial ecosystems, in the absence of macroscopic organisms, is critical to understanding early life on Earth and life elsewhere in the Universe - if it exists. But what are the general principles of microbial ecology in the absence of predation? What happens when each cell is a chemical factory that can swap among metabolic processes in response to environmental and emergent cues? Geobiologists and astrobiologists are addressing these questions in diverse ways using both Earth's modern biosphere and its fossil record. Modern microbial communities in shallow, ice-covered lakes, Antarctica (Fig.), provide a model for high productivity microbial ecosystems with no to low predation. In these lakes, photosynthetic communities create macroscopic pinnacles and domes, sometime lithified into stromatolites. They provide an ecological, geochemical and morphological model for Precambrian microbial communities in low sedimentation, low current environments. Insights from these communities include new growth processes for ancient mats, especially some that grew prior to the oxidation of Earth's atmosphere. The diversity of biosignatures created in these communities also provides context for models of life under ice elsewhere in our solar system such as paleolakes on Mars and on icy moons. Results from the Mars Science Laboratory (MSL) team document formerly habitable fluvial and lacustrine environments. Lacustrine environments, in particular, are favorable for preserving biosignatures, and continued investigations by MSL will provide a deeper understanding of the duration of habitable

  9. The effect of concentrating of whitewater to the microbial growth in papermachine; Paperikoneen kiertovesien konsentroitumisen vaikutus mikrobien kasvuun - MPKT 03

    Energy Technology Data Exchange (ETDEWEB)

    Yloestalo, T [Helsinki Univ. of Technology, Otaniemi (Finland)

    1999-12-31

    The closing of the whitewater cycle increases the amount of nutrients available for the micro-organisms living in a papermachine. The microbial flora in papermachines can vary significantly. The type and concentration of nutrients and the operating conditions of the papermachine (for example pH and temperature) affect the type of microbes that may live there. Strong microbial contamination has negative impact to the quality of the products and the operation of the papermachine. In this project microbes isolated from papermachines are cultivated in different concentrations of whitewater and with different pH and temperature values. The cultivations of microbes and modeling of the microbial growth are used for finding out how the closing of the whitewater cycle affects the microbial growth in papermachines. (orig.)

  10. The effect of concentrating of whitewater to the microbial growth in papermachine; Paperikoneen kiertovesien konsentroitumisen vaikutus mikrobien kasvuun - MPKT 03

    Energy Technology Data Exchange (ETDEWEB)

    Yloestalo, T. [Helsinki Univ. of Technology, Otaniemi (Finland)

    1998-12-31

    The closing of the whitewater cycle increases the amount of nutrients available for the micro-organisms living in a papermachine. The microbial flora in papermachines can vary significantly. The type and concentration of nutrients and the operating conditions of the papermachine (for example pH and temperature) affect the type of microbes that may live there. Strong microbial contamination has negative impact to the quality of the products and the operation of the papermachine. In this project microbes isolated from papermachines are cultivated in different concentrations of whitewater and with different pH and temperature values. The cultivations of microbes and modeling of the microbial growth are used for finding out how the closing of the whitewater cycle affects the microbial growth in papermachines. (orig.)

  11. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    WANG,YIFENG; PAPENGUTH,HANS W.

    2000-05-04

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

  12. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Wang, Yifeng; Papenguth, Hans W.

    2000-01-01

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  13. Parameter Estimates in Differential Equation Models for Population Growth

    Science.gov (United States)

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  14. A fermented meat model system for studies of microbial aroma formation

    DEFF Research Database (Denmark)

    Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

    2003-01-01

    A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage....... for multivariate data analysis. Growth of lactic acid bacteria was comparable for model and sausages, whereas survival of S. xylosus was better in the model. Multivariate analysis of volatiles showed that differences between fast and slowly acidified samples were identical for model and sausage. For both sausage...

  15. Stochastic ontogenetic growth model

    Science.gov (United States)

    West, B. J.; West, D.

    2012-02-01

    An ontogenetic growth model (OGM) for a thermodynamically closed system is generalized to satisfy both the first and second law of thermodynamics. The hypothesized stochastic ontogenetic growth model (SOGM) is shown to entail the interspecies allometry relation by explicitly averaging the basal metabolic rate and the total body mass over the steady-state probability density for the total body mass (TBM). This is the first derivation of the interspecies metabolic allometric relation from a dynamical model and the asymptotic steady-state distribution of the TBM is fit to data and shown to be inverse power law.

  16. Predicting the microbial exposure risks in urban floods using GIS, building simulation, and microbial models.

    Science.gov (United States)

    Taylor, Jonathon; Biddulph, Phillip; Davies, Michael; Lai, Ka man

    2013-01-01

    London is expected to experience more frequent periods of intense rainfall and tidal surges, leading to an increase in the risk of flooding. Damp and flooded dwellings can support microbial growth, including mould, bacteria, and protozoa, as well as persistence of flood-borne microorganisms. The amount of time flooded dwellings remain damp will depend on the duration and height of the flood, the contents of the flood water, the drying conditions, and the building construction, leading to particular properties and property types being prone to lingering damp and human pathogen growth or persistence. The impact of flooding on buildings can be simulated using Heat Air and Moisture (HAM) models of varying complexity in order to understand how water can be absorbed and dry out of the building structure. This paper describes the simulation of the drying of building archetypes representative of the English building stock using the EnergyPlus based tool 'UCL-HAMT' in order to determine the drying rates of different abandoned structures flooded to different heights and during different seasons. The results are mapped out using GIS in order to estimate the spatial risk across London in terms of comparative flood vulnerability, as well as for specific flood events. Areas of South and East London were found to be particularly vulnerable to long-term microbial exposure following major flood events. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Elevated temperature alters carbon cycling in a model microbial community

    Science.gov (United States)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  18. Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth.

    Science.gov (United States)

    Du, Wei; Jongbloets, Joeri A; van Boxtel, Coco; Pineda Hernández, Hugo; Lips, David; Oliver, Brett G; Hellingwerf, Klaas J; Branco Dos Santos, Filipe

    2018-01-01

    Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.

  19. Modeling urban fire growth

    International Nuclear Information System (INIS)

    Waterman, T.E.; Takata, A.N.

    1983-01-01

    The IITRI Urban Fire Spread Model as well as others of similar vintage were constrained by computer size and running costs such that many approximations/generalizations were introduced to reduce program complexity and data storage requirements. Simplifications were introduced both in input data and in fire growth and spread calculations. Modern computational capabilities offer the means to introduce greater detail and to examine its practical significance on urban fire predictions. Selected portions of the model are described as presently configured, and potential modifications are discussed. A single tract model is hypothesized which permits the importance of various model details to be assessed, and, other model applications are identified

  20. Understanding the performance of sulfate reducing bacteria based packed bed reactor by growth kinetics study and microbial profiling.

    Science.gov (United States)

    Dev, Subhabrata; Roy, Shantonu; Bhattacharya, Jayanta

    2016-07-15

    A novel marine waste extract (MWE) as alternative nitrogen source was explored for the growth of sulfate reducing bacteria (SRB). Variation of sulfate and nitrogen (MWE) showed that SRB growth follows an uncompetitive inhibition model. The maximum specific growth rates (μmax) of 0.085 and 0.124 h(-1) and inhibition constants (Ki) of 56 and 4.6 g/L were observed under optimized sulfate and MWE concentrations, respectively. The kinetic data shows that MWE improves the microbial growth by 27%. The packed bed bioreactor (PBR) under optimized sulfate and MWE regime showed sulfate removal efficiency of 62-66% and metals removal efficiency of 66-75% on using mine wastewater. The microbial community analysis using DGGE showed dominance of SRB (87-89%). The study indicated the optimum dosing of sulfate and cheap organic nitrogen to promote the growth of SRB over other bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Determination of Nitrate Reductase Assay Depending on the Microbial Growth

    International Nuclear Information System (INIS)

    El-Kabbany, H.M.

    2012-01-01

    A rapid micro-dilution assay for determination of the antimicrobial susceptibility of different bacterial isolates was developed. This assay is based on the ability of the most of viable organisms to reduce nitrates. The MIC or MBC could be determined by nitrate reductase (NR) only after 30 to 90 min of incubation depending on the behaviour of microbial growth. Bacterial viability is detected by a positive nitrite reduction rather than visible turbidity. The nitrate reduction assay was compared with standard micro-assay using 250 isolates of different taxa against 10 antibiotics belonging to different classes. An excellent agreement of 82.5 % was found between the two methods and only 17.5 % of 1794 trials showed difference in the determined MIC by tow-dilution interval above or below the MIC determined by the turbidimetric method under the same test conditions. However, the nitrate reduction assay was more rapid and sensitive in detecting viable bacteria and so, established an accurate estimate of the minimal inhibitory concentration (MIC) or the minimal bacterial concentration (MBC). The nitrate reduction assay offers the additional advantage that it could be used to determine the MBC without having to subculture the broth. 232 cases of resistance were detected by NR and 4 different media were tested for susceptibility test. The bacterial isolates were exposed to ultra violet (UV) light for different period

  2. Microbial Community Structure of Casing Soil During Mushroom Growth

    Institute of Scientific and Technical Information of China (English)

    CAI Wei-Ming; YAO Huai-Ying; FENG Wei-Lin; JIN Qun-Li; LIU Yue-Yan; LI Nan-Yi; ZHENG Zhong

    2009-01-01

    The culturable bacterial population and phospholipid fatty acid (PLFA)profile of casing soil were investigated at different mushroom (Agaricus bisporusI cropping stages.The change in soil bacterial PLFAs was always accompanied by a change in the soil culturable bacterial population in the first flush.Comparatively higher culturable bacterial population and bacterial PLFAs were found in the casing soil at the primordia formation stage of the first flush.There was a significant increase in the ratio of fungal to bacterial PLFAs during mushroom growth.Multivariate analysis of PLFA data demonstrated that the mushroom cropping stage could considerably affect the microbial community structure of the casing soil.The bacterial population increased significantly from casing soil application to the primordia formation stage of the first flush.Casing soil application resulted in an increase in the ratio of gram-negative bacterial PLFAs to gram-positive bacterial PLFAs,suggesting that some gram-negative bacteria might play an important role in mushroom sporophore initiation.

  3. Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

    Science.gov (United States)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

    2014-01-01

    Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

  4. Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach.

    Science.gov (United States)

    Koutinas, Michalis; Kiparissides, Alexandros; Silva-Rocha, Rafael; Lam, Ming-Chi; Martins Dos Santos, Vitor A P; de Lorenzo, Victor; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

    2011-07-01

    The majority of models describing the kinetic properties of a microorganism for a given substrate are unstructured and empirical. They are formulated in this manner so that the complex mechanism of cell growth is simplified. Herein, a novel approach for modelling microbial growth kinetics is proposed, linking biomass growth and substrate consumption rates to the gene regulatory programmes that control these processes. A dynamic model of the TOL (pWW0) plasmid of Pseudomonas putida mt-2 has been developed, describing the molecular interactions that lead to the transcription of the upper and meta operons, known to produce the enzymes for the oxidative catabolism of m-xylene. The genetic circuit model was combined with a growth kinetic model decoupling biomass growth and substrate consumption rates, which are expressed as independent functions of the rate-limiting enzymes produced by the operons. Estimation of model parameters and validation of the model's predictive capability were successfully performed in batch cultures of mt-2 fed with different concentrations of m-xylene, as confirmed by relative mRNA concentration measurements of the promoters encoded in TOL. The growth formation and substrate utilisation patterns could not be accurately described by traditional Monod-type models for a wide range of conditions, demonstrating the critical importance of gene regulation for the development of advanced models closely predicting complex bioprocesses. In contrast, the proposed strategy, which utilises quantitative information pertaining to upstream molecular events that control the production of rate-limiting enzymes, predicts the catabolism of a substrate and biomass formation and could be of central importance for the design of optimal bioprocesses. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Developing Model Benchtop Systems for Microbial Experimental Evolution

    Science.gov (United States)

    Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

    2017-12-01

    Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional

  6. A fermented meat model system for studies of microbial aroma formation

    DEFF Research Database (Denmark)

    Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

    2003-01-01

    A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

  7. Critical control points for the management of microbial growth in HVAC systems

    NARCIS (Netherlands)

    Gommers, S; Franchimon, F.; Bronswijk, van J.E.M.H.; Strøm-Tejsen, P; Olesen, BW; Wargocki, P; Zukowska, D; Toftum, J

    2008-01-01

    Office buildings with HVAC systems consistently report Sick Building Symptoms that are derived from microbial growth. We used the HACCP methodology to find the main critical control points (CCPs) for microbial management of HVAC systems in temperate climates. Desk research revealed relative humidity

  8. Economic Growth Models Transition

    Directory of Open Access Journals (Sweden)

    Coralia Angelescu

    2006-03-01

    Full Text Available The transitional recession in countries of Eastern Europe has been much longer than expected. The legacy and recent policy mistakes have both contributed to the slow progress. As structural reforms and gradual institution building have taken hold, the post-socialist economics have started to recover, with some leading countries building momentum toward faster growth. There is a possibility that in wider context of globalization several of these emerging market economies will be able to catch up with the more advanced industrial economies in a matter of one or two generations. Over the past few years, most candidate countries have made progress in the transition to a competitive market economy, macroeconomic stabilization and structural reform. However their income levels have remained far below those in the Member States. Measured by per capita income in purchasing power standards, there has been a very limited amount of catching up over the past fourteen years. Prior, the distinctions between Solow-Swan model and endogenous growth model. The interdependence between transition and integration are stated in this study. Finally, some measures of macroeconomic policy for sustainable growth are proposed in correlation with real macroeconomic situation of the Romanian economy. Our study would be considered the real convergence for the Romanian economy and the recommendations for the adequate policies to achieve a fast real convergence and sustainable growth.

  9. Economic Growth Models Transition

    Directory of Open Access Journals (Sweden)

    Coralia Angelescu

    2006-01-01

    Full Text Available The transitional recession in countries of Eastern Europe has been much longer than expected. The legacy and recent policy mistakes have both contributed to the slow progress. As structural reforms and gradual institution building have taken hold, the post-socialist economics have started to recover, with some leading countries building momentum toward faster growth. There is a possibility that in wider context of globalization several of these emerging market economies will be able to catch up with the more advanced industrial economies in a matter of one or two generations. Over the past few years, most candidate countries have made progress in the transition to a competitive market economy, macroeconomic stabilization and structural reform. However their income levels have remained far below those in the Member States. Measured by per capita income in purchasing power standards, there has been a very limited amount of catching up over the past fourteen years. Prior, the distinctions between Solow-Swan model and endogenous growth model. The interdependence between transition and integration are stated in this study. Finally, some measures of macroeconomic policy for sustainable growth are proposed in correlation with real macroeconomic situation of the Romanian economy. Our study would be considered the real convergence for the Romanian economy and the recommendations for the adequate policies to achieve a fast real convergence and sustainable growth.

  10. Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection.

    Science.gov (United States)

    Manhart, Michael; Adkar, Bharat V; Shakhnovich, Eugene I

    2018-02-14

    Mutations in a microbial population can increase the frequency of a genotype not only by increasing its exponential growth rate, but also by decreasing its lag time or adjusting the yield (resource efficiency). The contribution of multiple life-history traits to selection is a critical question for evolutionary biology as we seek to predict the evolutionary fates of mutations. Here we use a model of microbial growth to show that there are two distinct components of selection corresponding to the growth and lag phases, while the yield modulates their relative importance. The model predicts rich population dynamics when there are trade-offs between phases: multiple strains can coexist or exhibit bistability due to frequency-dependent selection, and strains can engage in rock-paper-scissors interactions due to non-transitive selection. We characterize the environmental conditions and patterns of traits necessary to realize these phenomena, which we show to be readily accessible to experiments. Our results provide a theoretical framework for analysing high-throughput measurements of microbial growth traits, especially interpreting the pleiotropy and correlations between traits across mutants. This work also highlights the need for more comprehensive measurements of selection in simple microbial systems, where the concept of an ordinary fitness landscape breaks down. © 2018 The Author(s).

  11. Constraint-based modeling in microbial food biotechnology

    Science.gov (United States)

    Rau, Martin H.

    2018-01-01

    Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM. PMID:29588387

  12. A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

    National Research Council Canada - National Science Library

    Campbell, Jason

    2002-01-01

    ... of the modeling approaches affect simulation results. Concepts like microbial growth in the form of a biofilm and spatially varying contaminant concentrations bring the validity of the CSTR assumption into question...

  13. Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

    Science.gov (United States)

    Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

    2013-04-09

    Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

  14. Microbial growth associated with granular activated carbon in a pilot water treatment facility.

    Science.gov (United States)

    Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

    1983-01-01

    The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

  15. Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

    Science.gov (United States)

    Mateos, I; Ranilla, M J; Saro, C; Carro, M D

    2017-11-01

    offered similar results for diets comparison, but both methods presented contrasting results for microbial growth in SOL and LIQ phases. The study showed that fermentation parameters remained fairly stable over the commonly used sampling period (days 8 to 14), but shifts in microbial populations were detected. Moreover, microbial populations differed markedly from those in the inocula, which indicates the difficulty of directly transposing results on microbial populations developed in Rusitec fermenters to in vivo conditions.

  16. Methodology for modeling the microbial contamination of air filters.

    Science.gov (United States)

    Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

    2014-01-01

    In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

  17. Methodology for modeling the microbial contamination of air filters.

    Directory of Open Access Journals (Sweden)

    Yun Haeng Joe

    Full Text Available In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

  18. Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

    Science.gov (United States)

    He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

    2014-12-01

    Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

  19. A Workflow to Model Microbial Loadings in Watersheds

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  20. A Workflow to Model Microbial Loadings in Watersheds (proceedings)

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  1. Modeling microbial processes in porous media

    Science.gov (United States)

    Murphy, Ellyn M.; Ginn, Timothy R.

    The incorporation of microbial processes into reactive transport models has generally proceeded along two separate lines of investigation: (1) transport of bacteria as inert colloids in porous media, and (2) the biodegradation of dissolved contaminants by a stationary phase of bacteria. Research over the last decade has indicated that these processes are closely linked. This linkage may occur when a change in metabolic activity alters the attachment/detachment rates of bacteria to surfaces, either promoting or retarding bacterial transport in a groundwater-contaminant plume. Changes in metabolic activity, in turn, are controlled by the time of exposure of the microbes to electron acceptors/donor and other components affecting activity. Similarly, metabolic activity can affect the reversibility of attachment, depending on the residence time of active microbes. Thus, improvements in quantitative analysis of active subsurface biota necessitate direct linkages between substrate availability, metabolic activity, growth, and attachment/detachment rates. This linkage requires both a detailed understanding of the biological processes and robust quantitative representations of these processes that can be tested experimentally. This paper presents an overview of current approaches used to represent physicochemical and biological processes in porous media, along with new conceptual approaches that link metabolic activity with partitioning of the microorganism between the aqueous and solid phases. Résumé L'introduction des processus microbiologiques dans des modèles de transport réactif a généralement suivi deux voies différentes de recherches: (1) le transport de bactéries sous forme de colloïdes inertes en milieu poreux, et (2) la biodégradation de polluants dissous par une phase stationnaire de bactéries. Les recherches conduites au cours des dix dernières années indiquent que ces processus sont intimement liés. Cette liaison peut intervenir lorsqu

  2. Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production.

    Science.gov (United States)

    Sinsabaugh, Robert L; Moorhead, Daryl L; Xu, Xiaofeng; Litvak, Marcy E

    2017-06-01

    The carbon use efficiency of plants (CUE a ) and microorganisms (CUE h ) determines rates of biomass turnover and soil carbon sequestration. We evaluated the hypothesis that CUE a and CUE h counterbalance at a large scale, stabilizing microbial growth (μ) as a fraction of gross primary production (GPP). Collating data from published studies, we correlated annual CUE a , estimated from satellite imagery, with locally determined soil CUE h for 100 globally distributed sites. Ecosystem CUE e , the ratio of net ecosystem production (NEP) to GPP, was estimated for each site using published models. At the ecosystem scale, CUE a and CUE h were inversely related. At the global scale, the apparent temperature sensitivity of CUE h with respect to mean annual temperature (MAT) was similar for organic and mineral soils (0.029°C -1 ). CUE a and CUE e were inversely related to MAT, with apparent sensitivities of -0.009 and -0.032°C -1 , respectively. These trends constrain the ratio μ : GPP (= (CUE a  × CUE h )/(1 - CUE e )) with respect to MAT by counterbalancing the apparent temperature sensitivities of the component processes. At the ecosystem scale, the counterbalance is effected by modulating soil organic matter stocks. The results suggest that a μ : GPP value of c. 0.13 is a homeostatic steady state for ecosystem carbon fluxes at a large scale. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  3. Effect of dietary olive leaves and rosemary on microbial growth and ...

    African Journals Online (AJOL)

    Effect of dietary olive leaves and rosemary on microbial growth and lipid oxidation of turkey breast during refrigerated storage. ... During this period olive leaves were more effective in inhibiting bacterial growth than rosemary. Keywords: Antioxidant additives, α-tocopherol, turkey meat, herbs, spices, meat quality ...

  4. Microbial biofilm growth on irradiated, spent nuclear fuel cladding

    International Nuclear Information System (INIS)

    Bruhn, D.F.; Frank, S.M.; Roberto, F.F.; Pinhero, P.J.; Johnson, S.G.

    2009-01-01

    A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 x 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments

  5. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

    Directory of Open Access Journals (Sweden)

    Reis Maria AM

    2008-07-01

    Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

  6. The contribution of microbial biotechnology to economic growth and employment creation.

    Science.gov (United States)

    Timmis, Kenneth; de Lorenzo, Victor; Verstraete, Willy; Ramos, Juan Luis; Danchin, Antoine; Brüssow, Harald; Singh, Brajesh K; Timmis, James Kenneth

    2017-09-01

    Our communication discusses the profound impact of bio-based economies - in particular microbial biotechnologies - on SDG 8: Promote sustained, inclusive and sustainable economic growth, full and productive employment and decent work for all. A bio-based economy provides significant potential for improving labour supply, education and investment, and thereby for substantially increasing the demographic dividend. This, in turn, improves the sustainable development of economies. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  7. Stochastic growth logistic model with aftereffect for batch fermentation process

    Science.gov (United States)

    Rosli, Norhayati; Ayoubi, Tawfiqullah; Bahar, Arifah; Rahman, Haliza Abdul; Salleh, Madihah Md

    2014-06-01

    In this paper, the stochastic growth logistic model with aftereffect for the cell growth of C. acetobutylicum P262 and Luedeking-Piret equations for solvent production in batch fermentation system is introduced. The parameters values of the mathematical models are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic models numerically. The effciency of mathematical models is measured by comparing the simulated result and the experimental data of the microbial growth and solvent production in batch system. Low values of Root Mean-Square Error (RMSE) of stochastic models with aftereffect indicate good fits.

  8. Stochastic growth logistic model with aftereffect for batch fermentation process

    International Nuclear Information System (INIS)

    Rosli, Norhayati; Ayoubi, Tawfiqullah; Bahar, Arifah; Rahman, Haliza Abdul; Salleh, Madihah Md

    2014-01-01

    In this paper, the stochastic growth logistic model with aftereffect for the cell growth of C. acetobutylicum P262 and Luedeking-Piret equations for solvent production in batch fermentation system is introduced. The parameters values of the mathematical models are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic models numerically. The effciency of mathematical models is measured by comparing the simulated result and the experimental data of the microbial growth and solvent production in batch system. Low values of Root Mean-Square Error (RMSE) of stochastic models with aftereffect indicate good fits

  9. Stochastic growth logistic model with aftereffect for batch fermentation process

    Energy Technology Data Exchange (ETDEWEB)

    Rosli, Norhayati; Ayoubi, Tawfiqullah [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia); Bahar, Arifah; Rahman, Haliza Abdul [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia); Salleh, Madihah Md [Department of Biotechnology Industry, Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia)

    2014-06-19

    In this paper, the stochastic growth logistic model with aftereffect for the cell growth of C. acetobutylicum P262 and Luedeking-Piret equations for solvent production in batch fermentation system is introduced. The parameters values of the mathematical models are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic models numerically. The effciency of mathematical models is measured by comparing the simulated result and the experimental data of the microbial growth and solvent production in batch system. Low values of Root Mean-Square Error (RMSE) of stochastic models with aftereffect indicate good fits.

  10. Modeling adaptation of carbon use efficiency in microbial communities

    Directory of Open Access Journals (Sweden)

    Steven D Allison

    2014-10-01

    Full Text Available In new microbial-biogeochemical models, microbial carbon use efficiency (CUE is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e. become less sensitive to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.

  11. Metabolic network modeling of microbial interactions in natural and engineered environmental systems

    Directory of Open Access Journals (Sweden)

    Octavio ePerez-Garcia

    2016-05-01

    interactions can be used to analyze complex ‘omics’ data and to infer and optimize metabolic processes. Thereby SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, methanogenic fermentation and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.

  12. Design, Modeling, and Development of Microbial Cell Factories

    KAUST Repository

    Kodzius, Rimantas

    2014-03-26

    Using Metagenomic analysis, computational modeling, single cell and genome editing technologies, we will express desired microbial genes and their networks in suitable hosts for mass production of energy, food, and fine chemicals.

  13. Design, Modeling, and Development of Microbial Cell Factories

    KAUST Repository

    Kodzius, Rimantas; Behzad, H.; Archer, John A.C.; Bajic, Vladimir B.; Gojobori, Takashi

    2014-01-01

    Using Metagenomic analysis, computational modeling, single cell and genome editing technologies, we will express desired microbial genes and their networks in suitable hosts for mass production of energy, food, and fine chemicals.

  14. Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China.

    Science.gov (United States)

    Lv, Yang; Hu, Guangyao; Wang, Chunyang; Yuan, Wenjie; Wei, Shanshan; Gao, Jiaoqi; Wang, Boyuan; Song, Fangchao

    2017-04-03

    The microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation.

  15. Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.

    Science.gov (United States)

    Merchant, Sabeeha S; Helmann, John D

    2012-01-01

    Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes. Copyright © 2012

  16. Measures of Microbial Biomass for Soil Carbon Decomposition Models

    Science.gov (United States)

    Mayes, M. A.; Dabbs, J.; Steinweg, J. M.; Schadt, C. W.; Kluber, L. A.; Wang, G.; Jagadamma, S.

    2014-12-01

    Explicit parameterization of the decomposition of plant inputs and soil organic matter by microbes is becoming more widely accepted in models of various complexity, ranging from detailed process models to global-scale earth system models. While there are multiple ways to measure microbial biomass, chloroform fumigation-extraction (CFE) is commonly used to parameterize models.. However CFE is labor- and time-intensive, requires toxic chemicals, and it provides no specific information about the composition or function of the microbial community. We investigated correlations between measures of: CFE; DNA extraction yield; QPCR base-gene copy numbers for Bacteria, Fungi and Archaea; phospholipid fatty acid analysis; and direct cell counts to determine the potential for use as proxies for microbial biomass. As our ultimate goal is to develop a reliable, more informative, and faster methods to predict microbial biomass for use in models, we also examined basic soil physiochemical characteristics including texture, organic matter content, pH, etc. to identify multi-factor predictive correlations with one or more measures of the microbial community. Our work will have application to both microbial ecology studies and the next generation of process and earth system models.

  17. Growth and element flux at fine taxonomic resolution in natural microbial communities

    Science.gov (United States)

    Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

    2015-04-01

    Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

  18. Modeling Exponential Population Growth

    Science.gov (United States)

    McCormick, Bonnie

    2009-01-01

    The concept of population growth patterns is a key component of understanding evolution by natural selection and population dynamics in ecosystems. The National Science Education Standards (NSES) include standards related to population growth in sections on biological evolution, interdependence of organisms, and science in personal and social…

  19. Microbial food safety - modeling and applications

    Science.gov (United States)

    Microbial food safety is a key issue for the food processing industry, and enhancing food safety is everyone’s responsibility from food producers to consumers. Financial losses to the economy due to foodborne illness are in the billions of dollars, annually. Foodborne illness can be caused by patho...

  20. Modeling growth of specific spoilage organisms in tilapia ...

    African Journals Online (AJOL)

    Tilapia is an important aquatic fish, but severe spoilage of tilapia is most likely related to the global aquaculture. The spoilage is mostly caused by specific spoilage organisms (SSO). Therefore, it is very important to use microbial models to predict the growth of SSO in tilapia. This study firstly verified Pseudomonas and Vibrio ...

  1. Integrating microbial diversity in soil carbon dynamic models parameters

    Science.gov (United States)

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  2. Models of microbiome evolution incorporating host and microbial selection.

    Science.gov (United States)

    Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

    2017-09-25

    Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

  3. The relative importance of exogenous and substrate-derived nitrogen for microbial growth during leaf decomposition

    Science.gov (United States)

    B.M. Cheever; J. R. Webster; E. E. Bilger; S. A. Thomas

    2013-01-01

    Heterotrophic microbes colonizing detritus obtain nitrogen (N) for growth by assimilating N from their substrate or immobilizing exogenous inorganic N. Microbial use of these two pools has different implications for N cycling and organic matter decomposition in the face of the global increase in biologically available N. We used sugar maple leaves labeled with

  4. Accelerated microbial turnover but constant growth efficiency with warming in soil

    Science.gov (United States)

    Shannon B. Hagerty; Kees Jan van Groenigen; Steven D. Allison; Bruce A. Hungate; Egbert Schwartz; George W. Koch; Randall K. Kolka; Paul. Dijkstra

    2014-01-01

    Rising temperatures are expected to reduce global soil carbon (C) stocks, driving a positive feedback to climate change1-3. However, the mechanisms underlying this prediction are not well understood, including how temperature affects microbial enzyme kinetics, growth effiency (MGE), and turnover4,5. Here, in a laboratory...

  5. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Energy Technology Data Exchange (ETDEWEB)

    He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

    2015-11-20

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 PgCyr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  6. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    Science.gov (United States)

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-01-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  7. Effects of lag and maximum growth in contaminant transport and biodegradation modeling

    International Nuclear Information System (INIS)

    Wood, B.D.; Dawson, C.N.

    1992-06-01

    The effects of time lag and maximum microbial growth on biodegradation in contaminant transport are discussed. A mathematical model is formulated that accounts for these effects, and a numerical case study is presented that demonstrates how lag influences biodegradation

  8. Determination of rumen microbial growth in vitro form 32P-labelled phosphate incorporation

    International Nuclear Information System (INIS)

    Nevel, C.J. Van; Demeyer, D.I.

    1977-01-01

    The extracellular phosphate pool in incubations of rumen fluid or washed cell suspensions of mixed rumen bacteria (WCS) was labelled with 32 P. From the constant extracellular phosphate pool specific activity and the amount of radioactivity incorporated during incubation, the amount of P incorporated in the microbial fraction was calculated. From the value for nitrogen: P determined in microbial matter, the amount of N incorporated was calculated as a measure of microbial growth. Incorporation of soluble non-protein-N in incubations devoid of substrate protein was 50 and 80% of the values obtained using isotope method for rumen fluid and WCS respectively. Incorporation of 32 P in P-containing microbial components (mainly nucleic acids) was compared with net synthesis of these components in incubations of WCS. When N incorporation, calculated from results obtained using isotope method in incubations with rumen fluid, was compared with the amount of carbohydrate substrate fermented and the type of fermentation, values between 18.3 and 44.6 g N incorporated kg of organic matter fermented were obtained. The use of isotopes for determination of rumen microbial growth in vitro is critically discussed. (author)

  9. The effect of substrate modification on microbial growth on surfaces

    International Nuclear Information System (INIS)

    Brown, Angela Ann

    1998-01-01

    The principle aim of the program was to produce a novel, non-leaching antimicrobial surface for commercial development and future use in the liquid food packaging industry. Antimicrobial surfaces which exist presently have been produced to combat the growth of prokaryotic organisms and usually function as slow release systems. A system which could inhibit eukaryotic growth without contaminating the surrounding 'environment' with the inhibitor was considered of great commercial importance. The remit of this study was concerned with creating a surface which could control the growth of eukaryotic organisms found in fruit juice with particular interest in the yeast, Saccharomyces cerevisiae. Putative antimicrobial surfaces were created by the chemical modification of the test substrate polymers; nylon and ethylvinyl alcohol (EVOH). Surfaces were chemically modified by the covalent coupling of antimicrobial agents known to be active against the yeast Saccharomyces cerevisiae as ascertained by the screening process determining the minimum inhibitory concentration (MIC) values of agents in the desired test medium. During the study it was found that a number of surfaces did appear to inhibit yeast growth in fruit juice, however on further investigation the apparent inhibitory effect was discovered to be the result of un-bound material free in the test medium. On removing the possibility of any un-bound material present on the test surface, by a series of surface washings, the inhibitory effect on yeast growth was eliminated. Of the agents tested only one appeared to have an inhibitory effect which could be attributed to a true antimicrobial surface effect, Amical 48. As there is little known about this agent in the literature, its affect on yeast growth was examined and in particular a proposal for the mode of action on yeast is discussed, providing a plausible explanation for the inhibitory effect observed when this agent is covalently immobilised onto nylon. (author)

  10. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

    Science.gov (United States)

    Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

    2017-01-01

    Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

  11. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

    Directory of Open Access Journals (Sweden)

    Marko Budinich

    Full Text Available Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA and multi-objective flux variability analysis (MO-FVA. Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity that take place at the ecosystem scale.

  12. Influence of heterotrophic microbial growth on biological oxidation of pyrite

    Energy Technology Data Exchange (ETDEWEB)

    Marchand, E.A.; Silverstein, J. [University of Nevada, Reno, NV (United States). Dept. of Civil Engineering

    2002-12-15

    Experiments were carried out to examine the possibility that enhanced growth of heterotrophic (non-iron-oxidising) bacteria would inhibit pyrite oxidation by Acidithiobacillus ferroxidans by out-competing the more slowly growing autotrophs for oxygen, nutrients or even attachment sites on the mineral surface. Glucose was added to microcosms containing pyrite, acidic mineral solution and cultures of A-ferrooxidans and Acidiphilium acidophilus under various experimental conditions. Results suggest that encouraging the growth of heterotrophic microorganisms under acid mine drainage conditions may be a feasible strategy for decreasing both the rate and the extent of sulfide mineral oxidation. 43 refs., 8 figs., 3 tabs.

  13. Micro-Food Web Structure Shapes Rhizosphere Microbial Communities and Growth in Oak

    Directory of Open Access Journals (Sweden)

    Hazel R. Maboreke

    2018-03-01

    Full Text Available The multitrophic interactions in the rhizosphere impose significant impacts on microbial community structure and function, affecting nutrient mineralisation and consequently plant performance. However, particularly for long-lived plants such as forest trees, the mechanisms by which trophic structure of the micro-food web governs rhizosphere microorganisms are still poorly understood. This study addresses the role of nematodes, as a major component of the soil micro-food web, in influencing the microbial abundance and community structure as well as tree growth. In a greenhouse experiment with Pedunculate Oak seedlings were grown in soil, where the nematode trophic structure was manipulated by altering the proportion of functional groups (i.e., bacterial, fungal, and plant feeders in a full factorial design. The influence on the rhizosphere microbial community, the ectomycorrhizal symbiont Piloderma croceum, and oak growth, was assessed. Soil phospholipid fatty acids were employed to determine changes in the microbial communities. Increased density of singular nematode functional groups showed minor impact by increasing the biomass of single microbial groups (e.g., plant feeders that of Gram-negative bacteria, except fungal feeders, which resulted in a decline of all microorganisms in the soil. In contrast, inoculation of two or three nematode groups promoted microbial biomass and altered the community structure in favour of bacteria, thereby counteracting negative impact of single groups. These findings highlight that the collective action of trophic groups in the soil micro-food web can result in microbial community changes promoting the fitness of the tree, thereby alleviating the negative effects of individual functional groups.

  14. Modeling Population Growth and Extinction

    Science.gov (United States)

    Gordon, Sheldon P.

    2009-01-01

    The exponential growth model and the logistic model typically introduced in the mathematics curriculum presume that a population grows exclusively. In reality, species can also die out and more sophisticated models that take the possibility of extinction into account are needed. In this article, two extensions of the logistic model are considered,…

  15. Stochastic models for tumoral growth

    Science.gov (United States)

    Escudero, Carlos

    2006-02-01

    Strong experimental evidence has indicated that tumor growth belongs to the molecular beam epitaxy universality class. This type of growth is characterized by the constraint of cell proliferation to the tumor border and the surface diffusion of cells at the growing edge. Tumor growth is thus conceived as a competition for space between the tumor and the host, and cell diffusion at the tumor border is an optimal strategy adopted for minimizing the pressure and helping tumor development. Two stochastic partial differential equations are reported in this paper in order to correctly model the physical properties of tumoral growth in (1+1) and (2+1) dimensions. The advantage of these models is that they reproduce the correct geometry of the tumor and are defined in terms of polar variables. An analysis of these models allows us to quantitatively estimate the response of the tumor to an unfavorable perturbation during growth.

  16. Towards Sustainable Growth Business Models

    Energy Technology Data Exchange (ETDEWEB)

    Kamp-Roelands, N.; Balkenende, J.P.; Van Ommen, P.

    2012-03-15

    The Dutch Sustainable Growth Coalition (DSGC) has the following objectives: The DSGC aims to pro-actively drive sustainable growth business models along three lines: (1) Shape. DSGC member companies aim to connect economic profitability with environmental and social progress on the basis of integrated sustainable growth business models; (2) Share. DSGC member companies aim for joint advocacy of sustainable growth business models both internationally and nationally; and (3) Stimulate. DSGC member companies aim to stimulate and influence the policy debate on enabling sustainable growth - with a view to finding solutions to the environmental and social challenges we are facing. This is their first report. The vision, actions and mission of DSGC are documented in the Manifesto in Chapter 2 of this publication. Chapter 3 contains an overview of key features of an integrated sustainable growth business model and the roadmap towards such a model. In Chapter 4, project examples of DSGC members are presented, providing insight into the hands-on reality of implementing the good practices. Chapter 5 offers an overview of how the Netherlands provides an enabling environment for sustainable growth business models. Chapter 6 offers the key conclusions.

  17. Prevention of Acid Mine Drainage Through Complexation of Ferric Iron by Soluble Microbial Growth Products

    Science.gov (United States)

    Pandey, S.; Yacob, T. W.; Silverstein, J.; Rajaram, H.; Minchow, K.; Basta, J.

    2011-12-01

    Acid mine drainage (AMD) is a widespread environmental problem with deleterious impacts on water quality in streams and watersheds. AMD is generated largely by the oxidation of metal sulfides (i.e. pyrite) by ferric iron. This abiotic reaction is catalyzed by conversion of ferrous to ferric iron by iron and sulfur oxidizing microorganisms. Biostimulation is currently being investigated as an attempt to inhibit the oxidation of pyrite and growth of iron oxidizing bacteria through addition of organic carbon. This may stimulate growth of indigenous communities of acidophilic heterotrophic bacteria to compete for oxygen. The goal of this research is to investigate a secondary mechanism associated with carbon addition: complexation of free Fe(III) by soluble microbial growth products (SMPs) produced by microorganisms growing in waste rock. Exploratory research at the laboratory scale examined the effect of soluble microbial products (SMPs) on the kinetics of oxidation of pure pyrite during shaker flask experiments. The results confirmed a decrease in the rate of pyrite oxidation that was dependent upon the concentration of SMPs in solution. We are using these data to verify results from a pyrite oxidation model that accounts for SMPs. This reactor model involves differential-algebraic equations incorporating total component mass balances and mass action laws for equilibrium reactions. Species concentrations determined in each time step are applied to abiotic pyrite oxidation rate expressions from the literature to determine the evolution of total component concentrations. The model was embedded in a parameter estimation algorithm to determine the reactive surface area of pyrite in an abiotic control experiment, yielding an optimized value of 0.0037 m2. The optimized model exhibited similar behavior to the experiment for this case; the root mean squared of residuals for Fe(III) was calculated to be 7.58 x 10-4 M, which is several orders of magnitude less than the actual

  18. Green tea yogurt: major phenolic compounds and microbial growth.

    Science.gov (United States)

    Amirdivani, Shabboo; Baba, Ahmad Salihin Hj

    2015-07-01

    The purpose of this study was to evaluate fermentation of milk in the presence of green tea (Camellia sinensis) with respect to changes in antioxidant activity, phenolic compounds and the growth of lactic acid bacteria. Pasteurized full fat cow's milk and starter culture were incubated at 41 °C in the presence of two different types of green tea extracts. The yogurts formed were refrigerated (4 °C) for further analysis. The total phenolic content was highest (p yogurt (MGT) followed by steam-treated green tea (JGT) and plain yogurts. Four major compounds in MGTY and JGTY were detected. The highest concentration of major phenolic compounds in both samples was related to quercetin-rhamnosylgalactoside and quercetin-3-O-galactosyl-rhamnosyl-glucoside for MGTY and JGTY respectively during first 7 day of storage. Diphenyl picrylhydrazyl and ferric reducing antioxidant power methods showed highest antioxidant capacity in MGTY, JGTY and PY. Streptococcus thermophillus and Lactobacillus spp. were highest in MGTY followed by JGTY and PY. This paper evaluates the implementation of green tea yogurt as a new product with functional properties and valuable component to promote the growth of beneficial yogurt bacteria and prevention of oxidative stress by enhancing the antioxidant activity of yogurt.

  19. Modelling and predicting growth of psycrotolerant pseudomonads in milk and cottage cheese

    DEFF Research Database (Denmark)

    Martinez Rios, Veronica; Østergaard, Nina Bjerre; Rosshaug, Per Sand

    2015-01-01

    Introduction: Predictive food microbiology models have the potential to evaluate the effect of temperature on microbial growth during distribution as well as be used to determine how product characteristics can be modified to reduce growth to an acceptable level. Methods: Growth kinetics of psych...

  20. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    International Nuclear Information System (INIS)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-01-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species, multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  1. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

    Science.gov (United States)

    Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

    2011-03-25

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  2. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

    Science.gov (United States)

    Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

    2011-03-01

    The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

  3. Elevated atmospheric CO2 increases microbial growth rates and enzymes activity in soil

    Science.gov (United States)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Dorodnikov, Maxim; Kuzyakov, Yakov

    2010-05-01

    Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO2 can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long-term effect of elevated CO2 in the atmosphere on microbial biomass and specific growth rates in root-free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate-induced respiration response after glucose and/or yeast extract addition to the soil. We evaluated the effect of elevated CO2 on b-glucosidase, chitinase, phosphatase, and sulfatase to estimate the potential enzyme activity after soil amendment with glucose and nutrients. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO2, depending on site, plant species and N fertilization. The μ-values increased linearly with atmospheric CO2 concentration at all three sites. The effect of elevated CO2 on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivumyeast extract then for those growing on glucose, i.e. the effect of elevated CO2 was smoothed on rich vs. simple substrate. So, the r/K strategies ratio can be better revealed by studying growth on simple (glucose) than on rich substrate mixtures (yeast extract). After adding glucose, enzyme activities under elevated CO2 were 1.2-1.9-fold higher than under ambient CO2. This indicates the increased activity of microorganisms, which leads to accelerated C turnover in soil under elevated CO2. Our results clearly showed that the functional characteristics of the soil microbial community (i.e. specific growth rates and enzymes activity) rather than total microbial biomass

  4. Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

    Science.gov (United States)

    Vega Thurber, Rebecca; Burkepile, Deron E.; Correa, Adrienne M. S.; Thurber, Andrew R.; Shantz, Andrew A.; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

    2012-01-01

    With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs. PMID:22957055

  5. Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

    Directory of Open Access Journals (Sweden)

    Rebecca Vega Thurber

    Full Text Available With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1 increases or 2 decreases in microbial taxa already present in corals, 3 establishment of new taxa to the coral microbiome, and 4 vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

  6. Development of a transport model for the microbial degradation of ...

    African Journals Online (AJOL)

    A mathematical model for first order reaction rate under isothermal condition was developed for predicting the diffusivity and transport rate of anthracene and pyrene during biodegradation using two microbial strains (corynebacteria spp and pseudomonas putida) in a heterogeneous porous medium. The formulation ...

  7. Modeling Logistic Performance in Quantitative Microbial Risk Assessment

    NARCIS (Netherlands)

    Rijgersberg, H.; Tromp, S.O.; Jacxsens, L.; Uyttendaele, M.

    2010-01-01

    In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage

  8. Monitoring microbial growth and activity using spectral induced polarization and low-field nuclear magnetic resonance

    Science.gov (United States)

    Zhang, Chi; Keating, Kristina; Revil, Andre

    2015-04-01

    Microbes and microbial activities in the Earth's subsurface play a significant role in shaping subsurface environments and are involved in environmental applications such as remediation of contaminants in groundwater and oil fields biodegradation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface. It is critical to monitor and determine the fate and transportation of microorganisms in the subsurface during such applications. Recent geophysical studies demonstrate the potential of two innovative techniques, spectral induced polarization (SIP) and low-field nuclear magnetic resonance (NMR), for monitoring microbial growth and activities in porous media. The SIP measures complex dielectric properties of porous media at low frequencies of exciting electric field, and NMR studies the porous structure of geologic media and characterizes fluids subsurface. In this laboratory study, we examined both SIP and NMR responses from bacterial growth suspension as well as suspension mixed with silica sands. We focus on the direct contribution of microbes to the SIP and NMR signals in the absence of biofilm formation or biomineralization. We used Zymomonas mobilis and Shewanella oneidensis (MR-1) for SIP and NMR measurements, respectively. The SIP measurements were collected over the frequency range of 0.1 - 1 kHz on Z. mobilis growth suspension and suspension saturated sands at different cell densities. SIP data show two distinct peaks in imaginary conductivity spectra, and both imaginary and real conductivities increased as microbial density increased. NMR data were collected using both CPMG pulse sequence and D-T2 mapping to determine the T2-distribution and diffusion properties on S. oneidensis suspension, pellets (live and dead), and suspension mixed with silica sands. NMR data show a decrease in the T2-distribution in S. oneidensis suspension saturated sands as microbial density increase. A

  9. Increase the Visibility of Microbial Growth in a Winogradsky Column by Substituting Diatomaceous Earth for Sediment

    Directory of Open Access Journals (Sweden)

    Thomas G. Benoit

    2015-02-01

    Full Text Available The difficulty students have seeing the color associated with microbial growth in a traditional Winogradsky column can be overcome by substituting diatomaceous earth (DE for sediment. Microbial growth in a DE column is visible from the early stages of ecological succession and the colors produced appear more vibrant. A flat-sided tissue culture flask can be used as a column container to provide a large surface area for observation. The enhanced visual experience provided by a DE column increases student engagement and learning. Editor's Note:The ASM advocates that students must successfully demonstrate the ability to explain and practice safe laboratory techniques. For more information, read the laboratory safety section of the ASM Curriculum Recommendations: Introductory Course in Microbiology and the Guidelines for Biosafety in Teaching Laboratories, available at www.asm.org. The Editors of JMBE recommend that adopters of the protocols included in this article follow a minimum of Biosafety Level 1 practices.

  10. Model uncertainty in growth empirics

    NARCIS (Netherlands)

    Prüfer, P.

    2008-01-01

    This thesis applies so-called Bayesian model averaging (BMA) to three different economic questions substantially exposed to model uncertainty. Chapter 2 addresses a major issue of modern development economics: the analysis of the determinants of pro-poor growth (PPG), which seeks to combine high

  11. A Model of Controlled Growth

    Science.gov (United States)

    Bressan, Alberto; Lewicka, Marta

    2018-03-01

    We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric shape of the growing tissue is determined by the instantaneous minimization of an elastic deformation energy, subject to a constraint on the volumetric growth. For an initial domain with C}^{2,α boundary, our main result establishes the local existence and uniqueness of a classical solution, up to a rigid motion.

  12. Life-history trait of the Mediterranean keystone species Patella rustica: growth and microbial bioerosion

    Directory of Open Access Journals (Sweden)

    I. PRUSINA

    2015-05-01

    Full Text Available The age and shell growth patterns in populations of Patella rustica of the Adriatic Sea were determined by analyzing the inner growth lines visible in shell sections. Marginal increment analysis showed annual periodicity with annual growth line being deposited in May. The growth analysis of 120 individual shells showed that 90.8 % of collected individuals were less than 4 years of age and only two individuals (1.6 % were older than 6 years. Population structure was described and the generalized von Bertalanffy growth parameters were calculated: asymptotic length (L∞ was 38.22 mm and the growth constant (K was 0.30 year-1. Growth performance index value of P. rustica (Ø’ was 2.64 and is among the lowest ranges reported for limpet species. Patella rustica shells were degraded to different degrees by microbial bioerosion. Microboring organisms identified were pseudofilamentous and filamentous cyanobacteria Hormathonema paulocellulare, Hyella caespitosa, Mastigocoleus testarum and Leptolyngbya sp. The overall intensity of infestation was relatively low, but increased in severity with shell length. The damage was most often restricted to the oldest parts of the shell, i.e. apex of the shell, posing difficulties in determining the exact position of the first growth line. The present study is first to introduce the use of inner growth lines in Patella rustica shell sections as a reliable method for age determination and it provides the first insight into the growth patterns of this keystone species while taking the interference of microbial shell bioerosion in consideration.

  13. Electrochemical and Chemical Complications Resulting from Yeast Extract Addition to Stimulate Microbial Growth

    Science.gov (United States)

    2016-09-22

    including strains of Saccharomyces cerevisiae grown on molasses-based media, debittered brewers yeasts (strains of Saccharo- myces cerevisiae or...RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) Technical Note: Electrochemical and Chemical Complications Resulting from Yeast Extract...Addition to Stimulate Microbial Growth Jason S. Lee‡,* and Brenda J. Little* ABSTRACT Addition of 1 g/L yeast extract (YE) to sterile, aerobic

  14. Extraction of solubles from plant biomass for use as microbial growth stimulant and methods related thereto

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Ming Woei

    2015-12-08

    A method for producing a microbial growth stimulant (MGS) from a plant biomass is described. In one embodiment, an ammonium hydroxide solution is used to extract a solution of proteins and ammonia from the biomass. Some of the proteins and ammonia are separated from the extracted solution to provide the MGS solution. The removed ammonia can be recycled and the proteins are useful as animal feeds. In one embodiment, the method comprises extracting solubles from pretreated lignocellulosic biomass with a cellulase enzyme-producing growth medium (such T. reesei) in the presence of water and an aqueous extract.

  15. Effect of silver nanoparticles on growth performance, metabolism and microbial profile of broiler chickens

    DEFF Research Database (Denmark)

    Pineda, Lane Manalili; Chwalibog, André; Sawosz, Ewa

    2012-01-01

    and intestinal content were collected to evaluate the effects of AgNano on plasma concentration of immunoglobulins and the intestinal microflora, respectively. The provision of water solutions containing different concentrations of AgNano had no effect on postnatal growth performance and the energy metabolism...... (IgG) in the blood plasma of broilers supplemented with AgNano decreased at day 36 (p = 0.012). The results demonstrated that AgNano affects N utilisation and plasma IgG concentration; however, it does not influence the microbial populations in the digestive tract, the energy metabolism and growth...

  16. Mathematical modeling of growth of Salmonella in raw ground beef under isothermal conditions from 10 to 45 Degree C

    Science.gov (United States)

    The objective of this study was to develop primary and secondary models to describe the growth of Salmonella in raw ground beef. Primary and secondary models can be integrated into a dynamic model that can predict the microbial growth under varying environmental conditions. Growth data of Salmonel...

  17. Effect of Chitosan Coating Containing Active Agents on Microbial Growth, Rancidity and Moisture Loss of Meatball During Storage

    OpenAIRE

    Pranoto, Yudi; Rakshit, Sudip Kumar

    2008-01-01

    Edible coatings based on chitosan were applied on meatball product in order to preserve quality during storages atambient and refrigeration temperatures. To improve its efficacy, chitosan coatings were incorporated with garlic oil0.2%, potassium sorbate 0.1 % and nisin 51,000 IU. The qualities of meatball assessed were total microbial growth, TBA value and percentage of moisture loss. All chitosan coatings suppressed microbial growth in meatball and strong- ly revealed when stored at refriger...

  18. A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

    Science.gov (United States)

    Jin, Q.; Zheng, Z.; Zhu, C.

    2006-12-01

    Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the

  19. Gut Microbial Diversity in Rat Model Induced by Rhubarb

    Science.gov (United States)

    Peng, Ying; Wu, Chunfu; Yang, Jingyu; Li, Xiaobo

    2014-01-01

    Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (Panalysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established. PMID:25048267

  20. A dynamic mathematical model for microbial removal of pyritic sulfur from coal.

    Science.gov (United States)

    Kargi, F; Weissman, J G

    1984-06-01

    A dynamic mathematical model has been developed to describe microbial desulfurization of coal by Thiobacillus ferrooxidans. The model considers adsorption and desorption of cells on coal particles and microbial oxidation of pyritic sulfur on particle surfaces. The influence of certain parameters, such as microbial growth rate constants, adsorption-description constants, pulp density, coal particle size, initial cell and solid phase substrate concentration on the maximum rate of pyritic sulfur removal, have been elucidated. The maximum rate of pyritic sulfur removal was strongly dependent upon the number of attached cells per coal particle. At sufficiently high initial cell concentrations, the surfaces of coal particles are nearly saturated by the cells and the maximum leaching rate is limited either by total external surface area of coal particles or by the concentration of pyritic sulfur in the coal phase. The maximum volumetric rate of pyritic sulfur removal (mg S/h cm(3) mixture) increases with the pulp density of coal and reaches a saturation level at high pulp densities (e.g. 45%). The maximum rate also increases with decreasing particle diameter in a hyperbolic form. Increases in adsorption coefficient or decreases in the desorption coefficient also result in considerable improvements in this rate. The model can be applied to other systems consisting of suspended solid substrate particles in liquid medium with microbial oxidation occurring on the particle surfaces (e.g., bacterial ore leaching). The results obtained from this model are in good agreement with published experimental data on microbial desulfurization of coal and bacterial ore leaching.

  1. Effect of gamma irradiation and storage time on microbial growth and physicochemical characteristics of pumpkin (Cucurbita Moschata Duchesne ex Poiret) puree.

    Science.gov (United States)

    Gliemmo, María F; Latorre, María E; Narvaiz, Patricia; Campos, Carmen A; Gerschenson, Lía N

    2014-01-01

    The effect of gamma irradiation (0-2 kGy) and storage time (0-28 days) on microbial growth and physicochemical characteristics of a packed pumpkin puree was studied. For that purpose, a factorial design was applied. The puree contained potassium sorbate, glucose and vanillin was stored at 25°C . Gamma irradiation diminished and storage time increased microbial growth. A synergistic effect between both variables on microbial growth was observed. Storage time decreased pH and color of purees. Sorbate content decreased with storage time and gamma irradiation. Mathematical models of microbial growth generated by the factorial design allowed estimating that a puree absorbing 1.63 kGy would have a shelf-life of 4 days. In order to improve this time, some changes in the applied hurdles were assayed. These included a thermal treatment before irradiation, a reduction of irradiation dose to 0.75 kGy and a decrease in storage temperature at 20°C . As a result, the shelf-life of purees increased to 28 days.

  2. Mudcake growth: Model and implications

    KAUST Repository

    Liu, Q.; Santamarina, Carlos

    2017-01-01

    cementing, and to prevent partial differential sticking. We developed a robust mud cake growth model for water-based mud based on wide stress-range constitutive equations within a Lagrangian reference system to avoid non-natural moving boundary solutions

  3. Biohydrogen production in the suspended and attached microbial growth systems from waste pastry hydrolysate.

    Science.gov (United States)

    Han, Wei; Hu, Yunyi; Li, Shiyi; Li, Feifei; Tang, Junhong

    2016-10-01

    Waste pastry was hydrolyzed by glucoamylase and protease which were obtained from solid state fermentation of Aspergillus awamori and Aspergillus oryzae to produce waste pastry hydrolysate. Then, the effects of hydraulic retention times (HRTs) (4-12h) on hydrogen production rate (HPR) in the suspended microbial growth system (continuous stirred tank reactor, CSTR) and attached microbial growth system (continuous mixed immobilized sludge reactor, CMISR) from waste pastry hydrolysate were investigated. The maximum HPRs of CSTR (201.8mL/(h·L)) and CMISR (255.3mL/(h·L)) were obtained at HRT of 6h and 4h, respectively. The first-order reaction could be used to describe the enzymatic hydrolysis of waste pastry. The carbon content of the waste pastry remained 22.8% in the undigested waste pastry and consumed 77.2% for carbon dioxide and soluble microbial products. To our knowledge, this is the first study which reports biohydrogen production from waste pastry. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

    Science.gov (United States)

    Patil, Rajendra; Gholap, Haribhau; Warule, Sambhaji; Banpurkar, Arun; Kulkarni, Gauri; Gade, Wasudeo

    2015-01-01

    The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet-visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications.

  5. Modeling Approaches for Describing Microbial Population Heterogeneity

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita

    environmental conditions. Three cases are presented and discussed in this thesis. Common to all is the use of S. cerevisiae as model organism, and the use of cell size and cell cycle position as single-cell descriptors. The first case focuses on the experimental and mathematical description of a yeast...

  6. Microbial changes and growth of Listeria monocytogenes during chilled storage of brined shrimp ( Pandalus borealis )

    DEFF Research Database (Denmark)

    Mejlholm, Ole; Kjeldgaard, J.; Modberg, A.

    2008-01-01

    Thirteen storage trials and ten challenge tests were carried out to examine microbial changes, spoilage and the potential growth of Listeria monocytogenes in brined shrimp (Pandalus borealis). Shrimp in brine as well as brined and drained shrimp in modified atmosphere packaging (MAP) were produced...... and lactic acids were studied. Furthermore, the effect of adding diacetate to brined shrimp was evaluated. A single batch of cooked and peeled shrimp was used to study both industrially and manually processed brined shrimp with respect to the effect of process hygiene on microbial changes and the shelf life...... of products. Concentrations of microorganisms on newly produced brined shrimp from an industrial scale processing line were 1.0-2.3 log (CFU g(-1)) higher than comparable concentrations in manually processed samples. This resulted in a substantially shorter shelf life and a more diverse spoilage microflora...

  7. Biomechanical ordering and buckling due to microbial growth confined at oil-water interfaces

    Science.gov (United States)

    Juarez, Gabriel; Stocker, Roman

    2015-11-01

    Bacteria are unicellular organisms that often exist as densely populated, surface-associated communities. Bacteria are also environmental colloids and spontaneously attach and self-assemble at liquid-liquid interfaces. Here, we present results on the growth dynamics of individual rod-shaped bacteria confined to finite oil-water interfaces of varying curvature. Through experiments using microfluidic chambers and time-lapse microscopy, we study the formation of macroscopic structures observed as adsorbed bacteria grow, divide, and self-assemble in a nematic phase due to biomechanical interactions. The continued growth at the interface leads to a jammed monolayer of cells, which then causes the interface to buckle and undergo large deformations including wrinkling and tubulation. These observations highlight the interplay between physical environment, such as confinement and interface curvature, and active biological processes, such as growth, at the scale of individual agents and shape our understanding of macroscale processes such as microbial degradation of oil in the ocean.

  8. PLANT GROWTH-PROMOTING MICROBIAL INOCULANT FOR Schizolobium parahyba pv. parahyba

    Directory of Open Access Journals (Sweden)

    Priscila Jane Romano de Oliveira Gonçalves

    2015-08-01

    Full Text Available ABSTRACTSchizolobium parahyba pv. amazonicum (Huber ex Ducke Barneby (paricá occurs naturally in the Amazon and is significant commercial importance due to its rapid growth and excellent performance on cropping systems. The aim of this paper was to evaluate a microbial inoculants such as arbuscular mycorrhiza fungi (AMF and Rhizobium sp. that promote plant growth. The inocula was 10 g of root colonized and spores of Glomus clarum and/or 1 mL of cell suspension (107 CFU/mL of Rhizobium sp. and/or 100 g of chemical fertilizer NPK 20-05-20 per planting hole. The experimental design was complete randomized blocks with five replications and eight treatments (n = 800. Plant height, stem diameter and plant survival were measured. The results were tested for normality and homogeneity of variances and analyzed by ANOVA and Tukey test (p < 0.05. Rhizobium sp and AM fungi showed no effect on plant growth. Environmental factors probably influenced the effectiveness of symbiosis of both microorganisms and plant growth. The chemical fertilizer increased S. parahyba growth. During the first 120 days plants suffered with drought and frost, and at 180 days plants inoculated with microorganism plus chemical fertilizer showed higher survival when compared with control. The results showed that the microbial inoculants used showed an important role on plant survival after high stress conditions, but not in plant growth. Also was concluded that the planting time should be between November to December to avoid the presence of young plants during winter time that is dry and cold.

  9. Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth.

    Science.gov (United States)

    Buch, Franziska; Rott, Matthias; Rottloff, Sandy; Paetz, Christian; Hilke, Ines; Raessler, Michael; Mithöfer, Axel

    2013-03-01

    Carnivorous plants of the genus Nepenthes possess modified leaves that form pitfall traps in order to capture prey, mainly arthropods, to make additional nutrients available for the plant. These pitchers contain a digestive fluid due to the presence of hydrolytic enzymes. In this study, the composition of the digestive fluid was further analysed with regard to mineral nutrients and low molecular-weight compounds. A potential contribution of microbes to the composition of pitcher fluid was investigated. Fluids from closed pitchers were harvested and analysed for mineral nutrients using analytical techniques based on ion-chromatography and inductively coupled plasma-optical emission spectroscopy. Secondary metabolites were identified by a combination of LC-MS and NMR. The presence of bacteria in the pitcher fluid was investigated by PCR of 16S-rRNA genes. Growth analyses of bacteria and yeast were performed in vitro with harvested pitcher fluid and in vivo within pitchers with injected microbes. The pitcher fluid from closed pitchers was found to be primarily an approx. 25-mm KCl solution, which is free of bacteria and unsuitable for microbial growth probably due to the lack of essential mineral nutrients such as phosphate and inorganic nitrogen. The fluid also contained antimicrobial naphthoquinones, plumbagin and 7-methyl-juglone, and defensive proteins such as the thaumatin-like protein. Challenging with bacteria or yeast caused bactericide as well as fungistatic properties in the fluid. Our results reveal that Nepenthes pitcher fluids represent a dynamic system that is able to react to the presence of microbes. The secreted liquid of closed and freshly opened Nepenthes pitchers is exclusively plant-derived. It is unsuitable to serve as an environment for microbial growth. Thus, Nepenthes plants can avoid and control, at least to some extent, the microbial colonization of their pitfall traps and, thereby, reduce the need to vie with microbes for the prey

  10. In-Drift Microbial Communities Model Validation Calculations

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-09-24

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  11. In-Drift Microbial Communities Model Validation Calculation

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-10-31

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  12. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley

    2001-12-18

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data.

  13. In-Drift Microbial Communities Model Validation Calculations

    International Nuclear Information System (INIS)

    Jolley, D.M.

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS MandO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS MandO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS MandO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS MandO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data

  14. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    International Nuclear Information System (INIS)

    D.M. Jolley

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M andO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M andO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M andO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M andO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data

  15. Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

    Science.gov (United States)

    Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

    2018-01-01

    Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

  16. Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

    Science.gov (United States)

    Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2016-04-01

    The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

  17. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    Science.gov (United States)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  18. Using growth-based methods to determine direct effects of salinity on soil microbial communities

    Science.gov (United States)

    Rath, Kristin; Rousk, Johannes

    2015-04-01

    Soil salinization is a widespread agricultural problem and increasing salt concentrations in soils have been found to be correlated with decreased microbial activity. A central challenge in microbial ecology is to link environmental factors, such as salinity, to responses in the soil microbial community. That is, it can be difficult to distinguish direct from indirect effects. In order to determine direct salinity effects on the community we employed the ecotoxicological concept of Pollution-Induced Community Tolerance (PICT). This concept is built on the assumption that if salinity had an ecologically relevant effect on the community, it should have selected for more tolerant species and strains, resulting in an overall higher community tolerance to salt in communities from saline soils. Growth-based measures, such as the 3H-leucine incorporation into bacterial protein , provide sensitive tools to estimate community tolerance. They can also provide high temporal resolution in tracking changes in tolerance over time. In our study we used growth-based methods to investigate: i) at what levels of salt exposure and over which time scales salt tolerance can be induced in a non-saline soil, and (ii) if communities from high salinity sites have higher tolerance to salt exposure along natural salinity gradients. In the first part of the study, we exposed a non-saline soil to a range of salinities and monitored the development of community tolerance over time. We found that community tolerance to intermediate salinities up to around 30 mg NaCl per g soil can be induced at relatively short time scales of a few days, providing evidence that microbial communities can adapt rapidly to changes in environmental conditions. In the second part of the study we used soil samples originating from natural salinity gradients encompassing a wide range of salinity levels, with electrical conductivities ranging from 0.1 dS/m to >10 dS/m. We assessed community tolerance to salt by

  19. The Growth Rate and Efficiency of Rumen Microbial Protein Digestion of Red Clover Silage (Trifolium pratense cv. Sabatron)

    International Nuclear Information System (INIS)

    Asih Kurniawati

    2004-01-01

    (Trifolium pratense cv. Sabatron). Red clover silage supplemented with different level of carbohydrates has been examined using the in-vitro gas production technique. Cumulative gas production, hydro.gen sulfite production, and ammonia was followed and used as indicators of microbial growth rate and extent of protein degradation. Microbial nitrogen production, VFA, and efficiency microbial production was used as indicator of nitrogen use efficiency. 15 N was used as a microbial marker to estimate the amount of nitrogen incorporation into microbial protein. Supplementation of Red clover with increasing 5 levels; 0 g; 0.625 g; 0.15 g; 0.225 g and 0.3 g of maize starch led to graded increase in microbial growth and protein degradation. This was reflected in the increasing gas production and the accumulation of hydrogen sulfite. Diurnal change in ammonia production reflected the microbial utilization of ammonia for protein synthesis. Protein microbe (P<0.001) as VFA (P<0.001) increased due to carbohydrate addition as well as utilization of nitrogen (P<0.001). There was also the efficiency of nitrogen utilization which increased significantly. This result suggested that energy supply can increased efficiency of nitrogen use in the rumen and may reduce nitrogen losses into the environment. (author)

  20. A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.-S. [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland); Vojinovic, V. [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland); Patino, R. [Cinvestav-Merida, Departamento de Fisica Aplicada, Km. 6 carretera antigua a Progreso, AP 73 Cordemex, 97310 Merida, Yucatan (Mexico); Maskow, Th. [UFZ Centre for Environmental Research, Department of Environmental Microbiology, Permoserstrasse 15, D-04318 Leipzig (Germany); Stockar, U. von [Laboratory of Chemical and Biochemical Engineering, Swiss Federal Institute of Technology, EPFL, CH-1015 Lausanne (Switzerland)]. E-mail: urs.vonStockar@epfl.ch

    2007-06-25

    Thermodynamic analysis may be applied in order to predict microbial growth yields roughly, based on an empirical correlation of the Gibbs energy of the overall growth reaction or Gibbs energy dissipation. Due to the well-known trade-off between high biomass yield and high Gibbs energy dissipation necessary for fast growth, an optimal range of Gibbs energy dissipation exists and it can be correlated to physical characteristics of the growth substrates. A database previously available in the literature has been extended significantly in order to test such correlations. An analysis of the relationship between biomass yield and Gibbs energy dissipation reveals that one does not need a very precise estimation of the latter to predict the former roughly. Approximating the Gibbs energy dissipation with a constant universal value of -500 kJ C-mol{sup -1} of dry biomass grown predicts many experimental growth yields nearly as well as a carefully designed, complex correlation available from the literature, even though a number of predictions are grossly out of range. A new correlation for Gibbs energy dissipation is proposed which is just as accurate as the complex literature correlation despite its dramatically simpler structure.

  1. A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields

    International Nuclear Information System (INIS)

    Liu, J.-S.; Vojinovic, V.; Patino, R.; Maskow, Th.; Stockar, U. von

    2007-01-01

    Thermodynamic analysis may be applied in order to predict microbial growth yields roughly, based on an empirical correlation of the Gibbs energy of the overall growth reaction or Gibbs energy dissipation. Due to the well-known trade-off between high biomass yield and high Gibbs energy dissipation necessary for fast growth, an optimal range of Gibbs energy dissipation exists and it can be correlated to physical characteristics of the growth substrates. A database previously available in the literature has been extended significantly in order to test such correlations. An analysis of the relationship between biomass yield and Gibbs energy dissipation reveals that one does not need a very precise estimation of the latter to predict the former roughly. Approximating the Gibbs energy dissipation with a constant universal value of -500 kJ C-mol -1 of dry biomass grown predicts many experimental growth yields nearly as well as a carefully designed, complex correlation available from the literature, even though a number of predictions are grossly out of range. A new correlation for Gibbs energy dissipation is proposed which is just as accurate as the complex literature correlation despite its dramatically simpler structure

  2. Earthworms (Amynthas spp. increase common bean growth, microbial biomass, and soil respiration

    Directory of Open Access Journals (Sweden)

    Julierme Zimmer Barbosa

    2017-10-01

    Full Text Available Few studies have evaluated the effect of earthworms on plants and biological soil attributes, especially among legumes. The objective of this study was to evaluate the influence of earthworms (Amynthas spp. on growth in the common bean (Phaseolus vulgaris L. and on soil biological attributes. The experiment was conducted in a greenhouse using a completely randomized design with five treatments and eight repetitions. The treatments consisted of inoculation with five different quantities of earthworms of the genus Amynthas (0, 2, 4, 6, and 8 worms per pot. Each experimental unit consisted of a plastic pot containing 4 kg of soil and two common bean plants. The experiment was harvested 38 days after seedling emergence. Dry matter and plant height, soil respiration, microbial respiration, microbial biomass, and metabolic quotient were determined. Earthworm recovery in our study was high in number and mass, with all values above 91.6% and 89.1%, respectively. In addition, earthworm fresh biomass decreased only in the treatment that included eight earthworms per pot. The presence of earthworms increased the plant growth and improved soil biological properties, suggesting that agricultural practices that favor the presence of these organisms can be used to increase the production of common bean, and the increased soil CO2 emission caused by the earthworms can be partially offset by the addition of common bean crop residues to the soil.

  3. Stability of U(VI) and Tc(VII) Reducing Microbial Communities to EnvironmentalPerturbation: Development and Testing of a Thermodynamic Network Model. Technical Report

    International Nuclear Information System (INIS)

    Jonathan D. Istok

    2008-01-01

    'Bioimmobilization' of redox-sensitive metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In this approach, growth-limiting substrates are added to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated precipitation ('bioimmobilization') of targeted contaminants. This project investigated a fundamentally new approach for modeling this process that couples thermodynamic descriptions for microbial growth with associated geochemical reactions. In this approach, a synthetic microbial community is defined as a collection of defined microbial groups; each with a growth equation derived from bioenergetic principles. The growth equations and standard-state free energy yields are appended to a thermodynamic database for geochemical reactions and the combined equations are solved simultaneously to predict the effect of added substrates on microbial biomass, community composition, and system geochemistry. This approach, with a single set of thermodynamic parameters (one for each growth equation), was used to predict the results of laboratory and field bioimmobilization experiments at two geochemically diverse research sites. Predicted effects of ethanol or acetate addition on uranium and technetium solubility, major ion geochemistry, mineralogy, microbial biomass and community composition were in general agreement with experimental observations although the available experimental data precluded rigorous model testing. Model simulations provide insight into the long-standing difficulty in transferring experimental results from the laboratory to the field and from one field site to the next, especially if the form, concentration, or delivery of growth substrate is varied from one experiment to the next. Although originally developed for use in better understanding bioimmobilization of uranium and technetium via reductive precipitation, the

  4. Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

    Energy Technology Data Exchange (ETDEWEB)

    Patil, Rajendra [Department of Biotechnology, Savitribai Phule Pune University, Pune 411007 (India); Gholap, Haribhau, E-mail: haribhau.gholap@fergusson.edu [Department of Physics, Fergusson College, Pune 411004 (India); Warule, Sambhaji [Department of Physics, Nowrosjee Wadia College, Pune 411001 (India); Banpurkar, Arun; Kulkarni, Gauri [Department of Physics, Savitribai Phule Pune University, Pune 411007 (India); Gade, Wasudeo, E-mail: wngade@unipune.ac.in [Department of Biotechnology, Savitribai Phule Pune University, Pune 411007 (India)

    2015-01-30

    Graphical abstract: The visible light upon incident on ZnO/CdTe initiate the phenomenon of photocatalytical impedance of biofilm. - Highlights: • Synthesis of efficient light photocatalyst ZnO/CdTe nanostructures by hydrothermal method. • ZnO/CdTe nanostructures show a good antibacterial activity by action on cell membrane. • ZnO/CdTe nanostructures show a good antibiofilm activity, and also act on the cells inside the biofilm. - Abstract: The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet–visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications.

  5. Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

    International Nuclear Information System (INIS)

    Patil, Rajendra; Gholap, Haribhau; Warule, Sambhaji; Banpurkar, Arun; Kulkarni, Gauri; Gade, Wasudeo

    2015-01-01

    Graphical abstract: The visible light upon incident on ZnO/CdTe initiate the phenomenon of photocatalytical impedance of biofilm. - Highlights: • Synthesis of efficient light photocatalyst ZnO/CdTe nanostructures by hydrothermal method. • ZnO/CdTe nanostructures show a good antibacterial activity by action on cell membrane. • ZnO/CdTe nanostructures show a good antibiofilm activity, and also act on the cells inside the biofilm. - Abstract: The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet–visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications

  6. Preventing microbial growth on pall-rings when upgrading biogas using absorption with water wash

    Energy Technology Data Exchange (ETDEWEB)

    Haakansson, Anna

    2006-07-15

    For produced biogas to be usable as vehicle fuel it has to be upgraded to a higher energy content. This is accomplished by elevation of the methane concentration through removal of carbon dioxide. Absorption with water wash is the most common upgrading method used in Sweden today. The upgrading technique is based on the fact that carbon dioxide is more soluble in water than methane. Upgrading plants that utilises this method have problems with microbial growth in the system. This growth eventually leads to a stop in operation due to the gradually drop in upgrading capacity. The aim of this thesis were to evaluate the possibility to through some kind of water treatment maintain an acceptable level of growth or altogether prevent it in order to maintain an acceptable process capacity and thereby avoid the need to clean. Through collection of literature the implementation possibilities were evaluated with regard to efficiency, economic sustainability and if there would be a release of any harmful substances. In order to prevent the microbial growth in the columns the treatment should either focus on removing microorganisms or limit the accessible nutrients. For the single pass system it is concluded that the treatment should reduce the biofilm formation and be employed in an intermittent way. Among the evaluated treatments focusing on the reduction of microorganisms the addition of peracetic acid seems to be the most promising one. For the regenerating system the treatment method could focus on either one. As for the single pass system peracetic acid could be added to reduce the amount of microorganism. To reduce the amount of organic matter an advanced oxidation process could be deployed with the advantage that it also could remove the microorganisms.

  7. Effect of growth conditions on microbial activity and iron-sulfide production by Desulfovibrio vulgaris

    International Nuclear Information System (INIS)

    Zhou, Chen; Vannela, Raveender; Hayes, Kim F.; Rittmann, Bruce E.

    2014-01-01

    Highlights: • Extended incubation time to 16 days allowed significant FeS crystallization. • A weakly acidic pH greatly enhanced particle growth of mackinawite. • Microbial metabolism of different donors systematically altered the ambient pH. • Greater sulfide accumulation stimulated mackinawite transformation to greigite. - Abstract: Sulfate-reducing bacteria (SRB) can produce iron sulfide (FeS) solids with mineralogical characteristics that may be beneficial for a variety of biogeochemical applications, such as long-term immobilization of uranium. In this study, the growth and metabolism of Desulfovibrio vulgaris, one of the best-studied SRB species, were comprehensively monitored in batch studies, and the biogenic FeS solids were characterized by X-ray diffraction. Controlling the pH by varying the initial pH, the iron-to-sulfate ratio, or the electron donor – affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH (from initial conditions or a decrease caused by less sulfate reduction, FeS precipitation, or using pyruvate as the electron donor) produced larger-sized mackinawite (Fe 1+x S). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and particularly stimulated mackinawite transformation to greigite (Fe 3 S 4 ) when the free sulfide concentration was 29.3 mM. Furthermore, sufficient free Fe 2+ led to the additional formation of vivianite [Fe 3 (PO 4 ) 2 ·8(H 2 O)]. Thus, microbially relevant conditions (initial pH, choice of electron donor, and excess or deficiency of sulfide) are tools to generate biogenic FeS solids of different characteristics

  8. Viscoelastic model of tungsten 'fuzz' growth

    International Nuclear Information System (INIS)

    Krasheninnikov, S I

    2011-01-01

    A viscoelastic model of fuzz growth is presented. The model describes the main features of tungsten fuzz observed in experiments. It gives estimates of fuzz growth rate and temperature range close to experimental ones.

  9. Can Microbial Ecology and Mycorrhizal Functioning Inform Climate Change Models?

    Energy Technology Data Exchange (ETDEWEB)

    Hofmockel, Kirsten; Hobbie, Erik

    2017-07-31

    Our funded research focused on soil organic matter dynamics and plant-microbe interactions by examining the role of belowground processes and mechanisms across scales, including decomposition of organic molecules, microbial interactions, and plant-microbe interactions associated with a changing climate. Research foci included mycorrhizal mediated priming of soil carbon turnover, organic N use and depolymerization by free-living microbes and mycorrhizal fungi, and the use of isotopes as additional constraints for improved modeling of belowground processes. This work complemented the DOE’s mandate to understand both the consequences of atmospheric and climatic change for key ecosystems and the feedbacks on C cycling.

  10. Models for Microbial Fuel Cells: A critical review

    Science.gov (United States)

    Xia, Chengshuo; Zhang, Daxing; Pedrycz, Witold; Zhu, Yingmin; Guo, Yongxian

    2018-01-01

    Microbial fuel cells (MFCs) have been widely viewed as one of the most promising alternative sources of renewable energy. A recognition of needs of efficient development methods based on multidisciplinary research becomes crucial for the optimization of MFCs. Modeling of MFCs is an effective way for not only gaining a thorough understanding of the effects of operation conditions on the performance of power generation but also becomes of essential interest to the successful implementation of MFCs. The MFC models encompass the underlying reaction process and limiting factors of the MFC. The models come in various forms, such as the mathematical equations or the equivalent circuits. Different modeling focuses and approaches of the MFC have emerged. In this study, we present a state of the art of MFCs modeling; the past modeling methods are reviewed as well. Models and modeling methods are elaborated on based on the classification provided by Mechanism-based models and Application-based models. Mechanisms, advantages, drawbacks, and application fields of different models are illustrated as well. We exhibit a complete and comprehensive exposition of the different models for MFCs and offer further guidance to promote the performance of MFCs.

  11. Mudcake growth: Model and implications

    KAUST Repository

    Liu, Q.

    2017-12-15

    Oil and gas account for 60% of the world\\'s energy consumption. Drilling muds that are used to advance oil and gas wells must be engineered to avoid wellbore integrity problems associated with mud cake formation, to favor cake erosion during cementing, and to prevent partial differential sticking. We developed a robust mud cake growth model for water-based mud based on wide stress-range constitutive equations within a Lagrangian reference system to avoid non-natural moving boundary solutions. The comprehensive mud cake growth model readily accommodates environmental factors (e.g., temperature, pH, and ionic concentration) and defines the yield stress distribution for displacement-erosion analyses. Results show that the mud cake thickness is more sensitive to time than to filtration pressure, therefore, time controls the non-uniform distribution of mudcake thickness during drilling. Long filtration time, high permeability, high salinity, high in-situ temperature and low viscosity exacerbate fluid loss and give rise to thick filter cakes. The analysis of residual cake thickness during cement displacement must take into account the effective stress dependent mudcake formation and the time-dependent mud thixotropy. Thixotropy dominates the mud yield stress at high void ratios, e.g. e > 20. The offsetting force that causes differential pressure sticking increases sub-linearly as a power function of the still-time.

  12. Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

    Science.gov (United States)

    Heinzelmann, Sandra M.; Villanueva, Laura; Sinke-Schoen, Danielle; Sinninghe Damsté, Jaap S.; Schouten, Stefan; van der Meer, Marcel T. J.

    2015-01-01

    Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature. PMID:26005437

  13. Effect of Microbial inoculation in combating the aluminium toxicity effect on growth of Zea mays.

    Science.gov (United States)

    Arora, P; Singh, G; Tiwari, A

    2017-07-31

    The present study is aimed at improving the aluminium tolerance in maize crop employing the potential of microbial inoculants in conferring resistance to these toxicities via production of certain chelating compounds like siderophores, exopolysachharides and organic acids. Acid soils have now-a-days become one of the key factors for limiting growth of many agriculturally important crops. Aluminium  is one of the major elements present in acid soils and is mainly responsible for toxicity in the soil. This aluminium is rapidly soluble in soil water and hence absorbed by plant roots under conditions where soil pH is below 5. This toxicity leads to severe root growth inhibition, thereby limiting the production of maize crops. It was observed that use of microbial inoculums can be helpful in elimination of these toxic compounds and prevent the inhibition of root growth . It was found that the soils contaminated with aluminium toxicity decreased the root length of maize plant significantly by 65% but Bacillus and Burkholderia inoculation increased this root length significantly by 1.4- folds and 2- folds respectively thereby combating the effect of aluminium toxicity. Aluminium concentration was found maximum in roots of plants which were grown under aluminium stress condition. But this aluminium accumulation decreased ̴ 2-folds when Burkholderia was used as seed inoculants under aluminium stress conditions. Also, at 60mM aluminium accumulation, phosphorus solubilisation in roots was found to be increased upto 30% on Burkholderia inoculation. However, Bacillus inoculation didn't show any significant difference in either of the case. Thus, the inoculation of seeds with Burkholderia isolates could prove to be a boon in sequestering aluminium toxicity in Zea mays.

  14. Factors limiting microbial growth and activity at a proposed high-level nuclear repository, Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Kieft, T.L.; Kovacik, W.P. Jr.; Ringelberg, D.B.; White, D.C.; Haldeman, D.L.; Amy, P.S.; Hersman, L.E.

    1997-01-01

    As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 X 10(1) to 2.0 X 10(5) cells g-1 [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 X 10(1) to 3.2 X 10(3) CFU g-1 (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g-1) also indicated low microbial biomasses: diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g-1). Potential microbial activity was quantified as 14CO2 production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone

  15. Species Coexistence in Nitrifying Chemostats: A Model of Microbial Interactions

    Directory of Open Access Journals (Sweden)

    Maxime Dumont

    2016-12-01

    Full Text Available In a previous study, the two nitrifying functions (ammonia oxidizing bacteria (AOB or nitrite-oxidizing bacteria (NOB of a nitrification reactor—operated continuously over 525 days with varying inputs—were assigned using a mathematical modeling approach together with the monitoring of bacterial phylotypes. Based on these theoretical identifications, we develop here a chemostat model that does not explicitly include only the resources’ dynamics (different forms of soluble nitrogen but also explicitly takes into account microbial inter- and intra-species interactions for the four dominant phylotypes detected in the chemostat. A comparison of the models obtained with and without interactions has shown that such interactions permit the coexistence of two competing ammonium-oxidizing bacteria and two competing nitrite-oxidizing bacteria in competition for ammonium and nitrite, respectively. These interactions are analyzed and discussed.

  16. Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality

    Directory of Open Access Journals (Sweden)

    Linlin Dong

    2018-03-01

    Full Text Available The cultivation of Panax plants is hindered by replanting problems, which may be caused by plant-driven changes in the soil microbial community. Inoculation with microbial antagonists may efficiently alleviate replanting issues. Through high-throughput sequencing, this study revealed that bacterial diversity decreased, whereas fungal diversity increased, in the rhizosphere soils of adult ginseng plants at the root growth stage under different ages. Few microbial community, such as Luteolibacter, Cytophagaceae, Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed; the relative abundance of microorganisms, namely, Brevundimonas, Enterobacteriaceae, Pandoraea, Cantharellales, Dendryphion, Fusarium, and Chytridiomycota, increased in the soils of adult ginseng plants compared with those in the soils of 2-year-old seedlings. Bacillus subtilis 50-1, a microbial antagonist against the pathogenic Fusarium oxysporum, was isolated through a dual culture technique. These bacteria acted with a biocontrol efficacy of 67.8%. The ginseng death rate and Fusarium abundance decreased by 63.3% and 46.1%, respectively, after inoculation with B. subtilis 50-1. Data revealed that microecological degradation could result from ginseng-driven changes in rhizospheric microbial communities; these changes are associated with the different ages and developmental stages of ginseng plants. Biocontrol using microbial antagonists alleviated the replanting problem. KEY WORDS: Panax ginseng, Microbial communities, Replanting problem, High-throughput sequencing, Different ages, Bioremediation

  17. Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley; T.F. Ehrhorn; J. Horn

    2002-03-19

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C{sub 160}(H{sub 280}O{sub 80})N{sub 30}P{sub 2}S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated

  18. Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

    International Nuclear Information System (INIS)

    Jolley, D.M.; Ehrhorn, T.F.; Horn, J.

    2002-01-01

    Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C 160 (H 280 O 80 )N 30 P 2 S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated and unsaturated

  19. Chemical diversity of microbial volatiles and their potential for plant growth and productivity

    Directory of Open Access Journals (Sweden)

    CHIDANANDA NAGAMANGALA KANCHISWAMY

    2015-03-01

    Full Text Available Microbial volatile organic compounds (MVOCs are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs and their potential physiological effects on crops and analyze potential and actual limitations for MVOC use as a sustainable strategy for improving productivity and reducing pesticide use.

  20. Optimal design of multistage chemostats in series using different microbial growth kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Qasim, Muhammad [Petroleum Engineering Technology, Abu Dhabi Polytechnic (United Arab Emirates)

    2013-07-01

    In this paper, the optimum design of multistage chemostats (CSTRs) was investigated. The optimal design was based on the minimum overall reactor volume using different volume for each chemostat. The paper investigates three different microbial growth kinetics; Monod kinetics, Contois kinetics and the Logistic equation. The total dimensionless residence time (theta Total) was set as the optimization objective function that was minimized by varying the intermediate dimensionless substrate concentration (alfa i). The effect of inlet substrate concentration (S0) to the first reactor on the optimized total dimensionless residence time was investigated at a constant conversion of 0.90. In addition, the effect of conversion on the optimized total dimensionless residence time was also investigated at constant inlet substrate concentration (S0). For each case, optimization was done using up to five chemostats in series.

  1. Latent Growth and Dynamic Structural Equation Models.

    Science.gov (United States)

    Grimm, Kevin J; Ram, Nilam

    2018-05-07

    Latent growth models make up a class of methods to study within-person change-how it progresses, how it differs across individuals, what are its determinants, and what are its consequences. Latent growth methods have been applied in many domains to examine average and differential responses to interventions and treatments. In this review, we introduce the growth modeling approach to studying change by presenting different models of change and interpretations of their model parameters. We then apply these methods to examining sex differences in the development of binge drinking behavior through adolescence and into adulthood. Advances in growth modeling methods are then discussed and include inherently nonlinear growth models, derivative specification of growth models, and latent change score models to study stochastic change processes. We conclude with relevant design issues of longitudinal studies and considerations for the analysis of longitudinal data.

  2. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.

    Directory of Open Access Journals (Sweden)

    Meike T Wortel

    2018-02-01

    Full Text Available Microbes may maximize the number of daughter cells per time or per amount of nutrients consumed. These two strategies correspond, respectively, to the use of enzyme-efficient or substrate-efficient metabolic pathways. In reality, fast growth is often associated with wasteful, yield-inefficient metabolism, and a general thermodynamic trade-off between growth rate and biomass yield has been proposed to explain this. We studied growth rate/yield trade-offs by using a novel modeling framework, Enzyme-Flux Cost Minimization (EFCM and by assuming that the growth rate depends directly on the enzyme investment per rate of biomass production. In a comprehensive mathematical model of core metabolism in E. coli, we screened all elementary flux modes leading to cell synthesis, characterized them by the growth rates and yields they provide, and studied the shape of the resulting rate/yield Pareto front. By varying the model parameters, we found that the rate/yield trade-off is not universal, but depends on metabolic kinetics and environmental conditions. A prominent trade-off emerges under oxygen-limited growth, where yield-inefficient pathways support a 2-to-3 times higher growth rate than yield-efficient pathways. EFCM can be widely used to predict optimal metabolic states and growth rates under varying nutrient levels, perturbations of enzyme parameters, and single or multiple gene knockouts.

  3. Microbial production of polyhydroxybutyrate with tailor-made properties: an integrated modelling approach and experimental validation.

    Science.gov (United States)

    Penloglou, Giannis; Chatzidoukas, Christos; Kiparissides, Costas

    2012-01-01

    The microbial production of polyhydroxybutyrate (PHB) is a complex process in which the final quantity and quality of the PHB depend on a large number of process operating variables. Consequently, the design and optimal dynamic operation of a microbial process for the efficient production of PHB with tailor-made molecular properties is an extremely interesting problem. The present study investigates how key process operating variables (i.e., nutritional and aeration conditions) affect the biomass production rate and the PHB accumulation in the cells and its associated molecular weight distribution. A combined metabolic/polymerization/macroscopic modelling approach, relating the process performance and product quality with the process variables, was developed and validated using an extensive series of experiments and measurements. The model predicts the dynamic evolution of the biomass growth, the polymer accumulation, the consumption of carbon and nitrogen sources and the average molecular weights of the PHB in a bioreactor, under batch and fed-batch operating conditions. The proposed integrated model was used for the model-based optimization of the production of PHB with tailor-made molecular properties in Azohydromonas lata bacteria. The process optimization led to a high intracellular PHB accumulation (up to 95% g of PHB per g of DCW) and the production of different grades (i.e., different molecular weight distributions) of PHB. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Mathematical modeling of Kluyveromyces marxianus growth in solid-state fermentation using a packed-bed bioreactor.

    Science.gov (United States)

    Mazutti, Marcio A; Zabot, Giovani; Boni, Gabriela; Skovronski, Aline; de Oliveira, Débora; Di Luccio, Marco; Rodrigues, Maria Isabel; Maugeri, Francisco; Treichel, Helen

    2010-04-01

    This work investigated the growth of Kluyveromyces marxianus NRRL Y-7571 in solid-state fermentation in a medium composed of sugarcane bagasse, molasses, corn steep liquor and soybean meal within a packed-bed bioreactor. Seven experimental runs were carried out to evaluate the effects of flow rate and inlet air temperature on the following microbial rates: cell mass production, total reducing sugar and oxygen consumption, carbon dioxide and ethanol production, metabolic heat and water generation. A mathematical model based on an artificial neural network was developed to predict the above-mentioned microbial rates as a function of the fermentation time, initial total reducing sugar concentration, inlet and outlet air temperatures. The results showed that the microbial rates were temperature dependent for the range 27-50 degrees C. The proposed model efficiently predicted the microbial rates, indicating that the neural network approach could be used to simulate the microbial growth in SSF.

  5. Biochar increases plant growth and alters microbial communities via regulating the moisture and temperature of green roof substrates.

    Science.gov (United States)

    Chen, Haoming; Ma, Jinyi; Wei, Jiaxing; Gong, Xin; Yu, Xichen; Guo, Hui; Zhao, Yanwen

    2018-09-01

    Green roofs have increasingly been designed and applied to relieve environmental problems, such as water loss, air pollution as well as heat island effect. Substrate and vegetation are important components of green roofs providing ecosystem services and benefiting the urban development. Biochar made from sewage sludge could be potentially used as the substrate amendment for green roofs, however, the effects of biochar on substrate quality and plant performance in green roofs are still unclear. We evaluated the effects of adding sludge biochar (0, 5, 10, 15 and 20%, v/v) to natural soil planted with three types of plant species (ryegrass, Sedum lineare and cucumber) on soil properties, plant growth and microbial communities in both green roof and ground ecosystems. Our results showed that sludge biochar addition significantly increased substrate moisture, adjusted substrate temperature, altered microbial community structure and increased plant growth. The application rate of 10-15% sludge biochar on the green roof exerted the most significant effects on both microbial and plant biomass by 63.9-89.6% and 54.0-54.2% respectively. Path analysis showed that biochar addition had a strong effect on microbial biomass via changing the soil air-filled porosity, soil moisture and temperature, and promoted plant growth through the positive effects on microbial biomass. These results suggest that the applications of biochar at an appropriate rate can significantly alter plant growth and microbial community structure, and increase the ecological benefits of green roofs via exerting effects on the moisture, temperature and nutrients of roof substrates. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

    DEFF Research Database (Denmark)

    Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard Remko

    2014-01-01

    Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH...

  7. Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

    NARCIS (Netherlands)

    Méndez-Garcia, C.; Mesa, V.; Sprenger, R.R.; Richter, M.; Suarez Diez, M.; Solano, J.; Bargiela, R.; Golyshina, O.V.; Manteca, A.; Ramos, J.L.; Gallego, J.R.; Llorente, I.; Martins Dos Santos, V.A.P.; Jensen, O.N.; Paláez, A.I.; Sánchez, J.; Ferrer, M.

    2014-01-01

    Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH

  8. Modeling logistic performance in quantitative microbial risk assessment.

    Science.gov (United States)

    Rijgersberg, Hajo; Tromp, Seth; Jacxsens, Liesbeth; Uyttendaele, Mieke

    2010-01-01

    In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage times, temperatures, gas conditions, and their distributions) are determined. However, the logistic chain with its queues (storages, shelves) and mechanisms for ordering products is usually not taken into account. As a consequence, storage times-mutually dependent in successive steps in the chain-cannot be described adequately. This may have a great impact on the tails of risk distributions. Because food safety risks are generally very small, it is crucial to model the tails of (underlying) distributions as accurately as possible. Logistic performance can be modeled by describing the underlying planning and scheduling mechanisms in discrete-event modeling. This is common practice in operations research, specifically in supply chain management. In this article, we present the application of discrete-event modeling in the context of a QMRA for Listeria monocytogenes in fresh-cut iceberg lettuce. We show the potential value of discrete-event modeling in QMRA by calculating logistic interventions (modifications in the logistic chain) and determining their significance with respect to food safety.

  9. Lévy-based growth models

    DEFF Research Database (Denmark)

    Jónsdóttir, Kristjana Ýr; Schmiegel, Jürgen; Jensen, Eva Bjørn Vedel

    2008-01-01

    In the present paper, we give a condensed review, for the nonspecialist reader, of a new modelling framework for spatio-temporal processes, based on Lévy theory. We show the potential of the approach in stochastic geometry and spatial statistics by studying Lévy-based growth modelling of planar o...... objects. The growth models considered are spatio-temporal stochastic processes on the circle. As a by product, flexible new models for space–time covariance functions on the circle are provided. An application of the Lévy-based growth models to tumour growth is discussed....

  10. Requirements for modeling airborne microbial contamination in space stations

    Science.gov (United States)

    Van Houdt, Rob; Kokkonen, Eero; Lehtimäki, Matti; Pasanen, Pertti; Leys, Natalie; Kulmala, Ilpo

    2018-03-01

    Exposure to bioaerosols is one of the facets that affect indoor air quality, especially for people living in densely populated or confined habitats, and is associated to a wide range of health effects. Good indoor air quality is thus vital and a prerequisite for fully confined environments such as space habitats. Bioaerosols and microbial contamination in these confined space stations can have significant health impacts, considering the unique prevailing conditions and constraints of such habitats. Therefore, biocontamination in space stations is strictly monitored and controlled to ensure crew and mission safety. However, efficient bioaerosol control measures rely on solid understanding and knowledge on how these bioaerosols are created and dispersed, and which factors affect the survivability of the associated microorganisms. Here we review the current knowledge gained from relevant studies in this wide and multidisciplinary area of bioaerosol dispersion modeling and biological indoor air quality control, specifically taking into account the specific space conditions.

  11. Effect of microbial cell-free meat extract on the growth of spoilage bacteria.

    Science.gov (United States)

    Nychas, G-J E; Dourou, D; Skandamis, P; Koutsoumanis, K; Baranyi, J; Sofos, J

    2009-12-01

    This study examined the effect of microbial cell-free meat extract (CFME) derived from spoiled meat, in which quorum sensing (QS) compounds were present, on the growth kinetics (lag phase, and growth rate) of two spoilage bacteria, Pseudomonas fluorescens and Serratia marcescens. Aliquots of CFME from spoiled meat were transferred to Brain Heart Infusion broth inoculated with 10(3) CFU ml(-1) of 18 h cultures of Ps. fluorescens or Ser. marcescens, both fresh meat isolates; CFME derived from unspoiled fresh meat ('clean' meat) served as a control. Changes in impedance measurements were monitored for 48 h, and the detection time (Tdet) was recorded. It was found that in the absence of CFME containing QS compounds the Tdet was shorter (P meat. The rate of growth of Ps. fluorescens, recorded as the maximum slope rate of conductance changes (MSrCC), after Tdet, was higher (P meat. Similar results in MSrCC of impedance changes were obtained for Ser. marcescens. The study indicated that the growth rate (expressed in MSrCC units) of meat spoilage bacteria in vitro was enhanced in samples supplemented with CFME containing QS compounds compared to control samples (i.e., without CFME or with CFME from 'clean' meat). This behaviour may explain the dominant role of these two bacteria in the spoilage of meat. These results illustrate the potential effect of signalling compounds released during storage of meat on the behaviour of meat spoilage bacteria. Understanding such interactions may assist in the control of fresh meat quality and the extension of its shelf life.

  12. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

    2003-12-01

    of organic matter oxidation as the main source of bicarbonate. Model results indicate that pH and Eh are relatively stable. The dissolution-precipitation trends of hematite, pyrite and calcite also coincide with those indicated by the conceptual model. A thorough sensitivity analysis has been performed for the most relevant microbial parameters as well as for initial and boundary POC and DOC concentrations. The results of such analysis indicate that computed concentrations of bicarbonate, sulphate and DOC are sensitive to most of the microbial parameters, including specific growth rates, half-saturation constants, proportionality coefficients and yield coefficients. Model results, however, are less sensitive to the yield coefficient of DOC to ironreducer bacteria. The sensitivity analysis indicates that changes in fermentation microbial parameters affect the growth of the iron-reducer, thus confirming the interconnection of both microbial processes. Computed concentrations of bicarbonate and sulphate are found to be sensitive to changes in the initial concentration of POC and the boundary concentration of DOC, but they lack sensitivity to the initial concentration of DOC and the boundary concentration of POC. The explanation for such result is related to the fact that POC has a low mobility due to its large molecular weight. DOC, however, can migrate downwards. Although a coupled hydro-bio-geochemical 1-D model can reproduce the observed 'unexpected' increase of concentrations of bicarbonate and sulphate at a depth of 70 m, further modelling work is required in order to obtain a similar conclusion under the more realistic two dimensional conditions of the fracture zone.

  13. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    International Nuclear Information System (INIS)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

    2003-12-01

    of organic matter oxidation as the main source of bicarbonate. Model results indicate that pH and Eh are relatively stable. The dissolution-precipitation trends of hematite, pyrite and calcite also coincide with those indicated by the conceptual model. A thorough sensitivity analysis has been performed for the most relevant microbial parameters as well as for initial and boundary POC and DOC concentrations. The results of such analysis indicate that computed concentrations of bicarbonate, sulphate and DOC are sensitive to most of the microbial parameters, including specific growth rates, half-saturation constants, proportionality coefficients and yield coefficients. Model results, however, are less sensitive to the yield coefficient of DOC to ironreducer bacteria. The sensitivity analysis indicates that changes in fermentation microbial parameters affect the growth of the iron-reducer, thus confirming the interconnection of both microbial processes. Computed concentrations of bicarbonate and sulphate are found to be sensitive to changes in the initial concentration of POC and the boundary concentration of DOC, but they lack sensitivity to the initial concentration of DOC and the boundary concentration of POC. The explanation for such result is related to the fact that POC has a low mobility due to its large molecular weight. DOC, however, can migrate downwards. Although a coupled hydro-bio-geochemical 1-D model can reproduce the observed 'unexpected' increase of concentrations of bicarbonate and sulphate at a depth of 70 m, further modelling work is required in order to obtain a similar conclusion under the more realistic two dimensional conditions of the fracture zone

  14. Coupled modeling of groundwater flow solute transport, chemical reactions and microbial processes in the 'SP' island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorg; Changbing, Yang; Zhang, Guoxiang

    2003-12-01

    adding additional evidence for the possibility of organic matter oxidation as the main source of bicarbonate. Model results indicate that pH and Eh are relatively stable. The dissolution-precipitation trends of hematite, pyrite and calcite also coincide with those indicated by the conceptual model. A thorough sensitivity analysis has been performed for the most relevant microbial parameters as well as for initial and boundary POC and DOC concentrations. The results of such analysis indicate that computed concentrations of bicarbonate, sulfate and DOC are sensitive to most of the microbial parameters, including specific growth rates, half-saturation constants, proportionality coefficients and yield coefficients. Model results, however, are less sensitive to the yield coefficient of DOC to iron-reducer bacteria. The sensitivity analysis indicates that changes in fermentation microbial parameters affect the growth of the iron-reducer, thus confirming the interconnection of both microbial processes. Computed concentrations of bicarbonate and sulfate are found to be sensitive to changes in the initial concentration of POC and the boundary concentration of DOC, but they lack sensitivity to the initial concentration of DOC and the boundary concentration of POC. The explanation for such result is related to the fact that POC has a low mobility due to its large molecular weight. DOC, however, can migrate downwards. Although a coupled hydro-bio-geochemical 1-D model can reproduce the observed ''unexpected'' increase of concentrations of bicarbonate and sulfate at a depth of 70 m, further modeling work is required in order to obtain a similar conclusion under the more realistic two dimensional conditions of the fracture zone.

  15. Stochastic models for tumoral growth

    OpenAIRE

    Escudero, Carlos

    2006-01-01

    Strong experimental evidence has indicated that tumor growth belongs to the molecular beam epitaxy universality class. This type of growth is characterized by the constraint of cell proliferation to the tumor border, and surface diffusion of cells at the growing edge. Tumor growth is thus conceived as a competition for space between the tumor and the host, and cell diffusion at the tumor border is an optimal strategy adopted for minimizing the pressure and helping tumor development. Two stoch...

  16. Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

    Science.gov (United States)

    Mark A. Bradford; Ashley D. Keiser; Christian A. Davies; Calley A. Mersmann; Michael S. Strickland

    2012-01-01

    Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant...

  17. Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

    Science.gov (United States)

    Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

    2009-06-01

    The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

  18. Effects of marine microbial biofilms on the biocide release rate from antifouling paints – A model-based analysis

    DEFF Research Database (Denmark)

    Yebra, Diego Meseguer; Kiil, Søren; Erik Weinell, Claus

    2006-01-01

    The antifouling (AF) paint model of Kiil et al. [S. Kiil, C.E. Weinell, M.S. Pedersen, K. Dam-Johansen, Analysis of self-polishing antifouling paints using rotary experiments and mathematical modelling, Ind. Eng. Chem. Res. 40 (2001) 3906-3920] and the simplified biofilm. growth model of Gujer...... and Warmer [W. Gujer, O. Warmer, Modeling mixed population biofilms, in: W.G. Characklis, K.C. Marshall (Eds.), Biofilms, Wiley-Interscience, New York, 1990] are used to provide a reaction engineering-based insight to the effects of marine microbial slimes on biocide leaching and, to a minor extent...

  19. Effects of six selected antibiotics on plant growth and soil microbial and enzymatic activities

    Energy Technology Data Exchange (ETDEWEB)

    Liu Feng [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Tianhe District, Guangzhou 510640 (China); Ying Guangguo, E-mail: guangguo.ying@gmail.co [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Tianhe District, Guangzhou 510640 (China); Tao Ran; Zhao Jianliang; Yang Jifeng [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Tianhe District, Guangzhou 510640 (China); Zhao Lanfeng [College of Resource and Environmental Science, South China Agricultural University, Guangzhou 510642 (China)

    2009-05-15

    The potential impact of six antibiotics (chlortetracycline, tetracycline and tylosin; sulfamethoxazole, sulfamethazine and trimethoprim) on plant growth and soil quality was studied by using seed germination test on filter paper and plant growth test in soil, soil respiration and phosphatase activity tests. The phytotoxic effects varied between the antibiotics and between plant species (sweet oat, rice and cucumber). Rice was most sensitive to sulfamethoxazole with the EC10 value of 0.1 mg/L. The antibiotics tested inhibited soil phosphatase activity during the 22 days' incubation. Significant effects on soil respiration were found for the two sulfonamides (sulfamethoxazole and sulfamethazine) and trimethoprim, whereas little effects were observed for the two tetracyclines and tylosin. The effective concentrations (EC10 values) for soil respiration in the first 2 days were 7 mg/kg for sulfamethoxazole, 13 mg/kg for sulfamethazine and 20 mg/kg for trimethoprim. Antibiotic residues in manure and soils may affect soil microbial and enzyme activities. - Terrestrial ecotoxicological effects of antibiotics are related to their sorption and degradation behavior in soil.

  20. Effects of six selected antibiotics on plant growth and soil microbial and enzymatic activities

    International Nuclear Information System (INIS)

    Liu Feng; Ying Guangguo; Tao Ran; Zhao Jianliang; Yang Jifeng; Zhao Lanfeng

    2009-01-01

    The potential impact of six antibiotics (chlortetracycline, tetracycline and tylosin; sulfamethoxazole, sulfamethazine and trimethoprim) on plant growth and soil quality was studied by using seed germination test on filter paper and plant growth test in soil, soil respiration and phosphatase activity tests. The phytotoxic effects varied between the antibiotics and between plant species (sweet oat, rice and cucumber). Rice was most sensitive to sulfamethoxazole with the EC10 value of 0.1 mg/L. The antibiotics tested inhibited soil phosphatase activity during the 22 days' incubation. Significant effects on soil respiration were found for the two sulfonamides (sulfamethoxazole and sulfamethazine) and trimethoprim, whereas little effects were observed for the two tetracyclines and tylosin. The effective concentrations (EC10 values) for soil respiration in the first 2 days were 7 mg/kg for sulfamethoxazole, 13 mg/kg for sulfamethazine and 20 mg/kg for trimethoprim. Antibiotic residues in manure and soils may affect soil microbial and enzyme activities. - Terrestrial ecotoxicological effects of antibiotics are related to their sorption and degradation behavior in soil.

  1. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbial growth.

    Science.gov (United States)

    Martínez, M E; Ranilla, M J; Tejido, M L; Ramos, S; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of forage to concentrate (F:C) ratio and type of forage in the diet on ruminal fermentation and microbial protein synthesis. The purpose of the study was to assess how closely fermenters can mimic the dietary differences found in vivo. The 4 experimental diets contained F:C ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Microbial growth was determined in both systems using (15)N as a microbial marker. Rusitec fermenters detected differences between diets similar to those observed in sheep by changing F:C ratio on pH; neutral detergent fiber digestibility; total volatile fatty acid concentrations; molar proportions of acetate, propionate, butyrate, isovalerate, and caproate; and amylase activity. In contrast, Rusitec fermenters did not reproduce the dietary differences found in sheep for NH(3)-N and lactate concentrations, dry matter (DM) digestibility, proportions of isobutyrate and valerate, carboxymethylcellulase and xylanase activities, and microbial growth and its efficiency. Regarding the effect of the type of forage in the diet, Rusitec fermenters detected differences between diets similar to those found in sheep for most determined parameters, with the exception of pH, DM digestibility, butyrate proportion, and carboxymethylcellulase activity. Minimum pH and maximal volatile fatty acid concentrations were reached at 2h and at 6 to 8h postfeeding in sheep and fermenters, respectively, indicating that feed fermentation was slower in fermenters compared with that in sheep. There were differences between systems in the magnitude of most determined parameters. In general, fermenters showed lower lactate concentrations, neutral detergent fiber digestibility, acetate:propionate ratios, and enzymatic activities. On the contrary, fermenters showed greater NH(3)-N concentrations, DM digestibility, and proportions of propionate

  2. Testing mechanistic models of growth in insects.

    Science.gov (United States)

    Maino, James L; Kearney, Michael R

    2015-11-22

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg(-1)) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes. © 2015 The Author(s).

  3. Dietary nisin modulates the gastrointestinal microbial ecology and enhances growth performance of the broiler chickens.

    Directory of Open Access Journals (Sweden)

    Damian Józefiak

    Full Text Available Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT. The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC diet was supplemented with salinomycin (60 mg/kg. The nisin (NI diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively of the bacteriocin. The negative control (NC diet contained no additives. At slaughter (35 days of age, activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase in crop, ileum and caeca were significantly higher (P<0.05 in the NC group, and nisin supplementation decreased the enzyme activities to levels observed for the PC group. A similar inhibitory influence on bacterial activity was reflected in the levels of short-chain fatty acids (SCFA and putrefactive SCFA (PSCFA in digesta from crop and ileum; no effect was observed in caeca. Counts of Bacteroides and Enterobacteriacae in ileum digesta were significantly (P<0.001 decreased by nisin and salinomycin, but no effects were observed on the counts of Clostridium perfringens, Lactobacillus/Enterococcus and total bacteria. Like salinomycin, nisin supplementation improved broiler growth performance in a dose-dependent manner; compared to the NC group, the body weight gain of the NI₉₀₀ and NI₂₇₀₀ groups was improved by 4.7 and 8.7%, respectively. Our findings suggest that dietary nisin exerts a mode of action similar to salinomycin and could be considered as a dietary

  4. Characterization and Modeling Of Microbial Carbon Metabolism In Thawing Permafrost

    Science.gov (United States)

    Graham, D. E.; Phelps, T. J.; Xu, X.; Carroll, S.; Jagadamma, S.; Shakya, M.; Thornton, P. E.; Elias, D. A.

    2012-12-01

    Increased annual temperatures in the Arctic are warming the surface and subsurface, resulting in thawing permafrost. Thawing exposes large pools of buried organic carbon to microbial degradation, increasing greenhouse gas generation and emission. Most global-scale land-surface models lack depth-dependent representations of carbon conversion and GHG transport; therefore they do not adequately describe permafrost thawing or microbial mineralization processes. The current work was performed to determine how permafrost thawing at moderately elevated temperatures and anoxic conditions would affect CO2 and CH4 generation, while parameterizing depth-dependent GHG production processes with respect to temperature and pH in biogeochemical models. These enhancements will improve the accuracy of GHG emission predictions and identify key biochemical and geochemical processes for further refinement. Three core samples were obtained from discontinuous permafrost terrain in Fairbanks, AK with a mean annual temperature of -3.3 °C. Each core was sectioned into surface/near surface (0-0.8 m), active layer (0.8-1.6 m), and permafrost (1.6-2.2 m) horizons, which were homogenized for physico-chemical characterization and microcosm construction. Surface samples had low pH values (6.0), low water content (18% by weight), low organic carbon (0.8%), and high C:N ratio (43). Active layer samples had higher pH values (6.4), higher water content (34%), more organic carbon (1.4%) and a lower C:N ratio (24). Permafrost samples had the highest pH (6.5), highest water content (46%), high organic carbon (2.5%) and the lowest C:N ratio (19). Most organic carbon was quantified as labile or intermediate pool versus stable pool in each sample, and all samples had low amounts of carbonate. Surface layer microcosms, containing 20 g sediment in septum-sealed vials, were incubated under oxic conditions, while similar active and permafrost layer samples were anoxic. These microcosms were incubated at -2

  5. [Microbial biomass and growth kinetics of microorganisms in chernozem soils under different farm land use modes].

    Science.gov (United States)

    Blagodatskiĭ, S A; Bogomolova, I N; Blagodatskaia, E V

    2008-01-01

    The carbon content of microbial biomass and the kinetic characteristics of microbial respiration response to substrate introduction have been estimated for chernozem soils of different farm lands: arable lands used for 10, 46, and 76 years, mowed fallow land, non-mowed fallow land, and woodland. Microbial biomass and the content of microbial carbon in humus (Cmic/Corg) decreased in the following order: soils under forest cenoses-mowed fallow land-10-year arable land-46- and 75-year arable land. The amount of microbial carbon in the long-plowed horizon was 40% of its content in the upper horizon of non-mowed fallow land. Arable soils were characterized by a lower metabolic diversity of microbial community and by the highest portion of microorganisms able to grow directly on glucose introduced into soil. The effects of different scenarios of carbon sequestration in soil on the reserves and activity of microbial biomass are discussed.

  6. Effect of galactooligosaccharides and Bifidobacterium animalis Bb-12 on growth of Lactobacillus amylovorus DSM 16698, microbial community structure, and metabolite production in an in vitro colonic model set up with human or pig microbiota

    NARCIS (Netherlands)

    Martinez, R.C.R.; Cardarelli, H.R.; Borst, W.; Albrecht, S.; Schols, H.; Gutiérrez, O.P.; Maathuis, A.J.H.; Melo Franco, B.D.G. de; Martinis, E.C.P. de; Zoetendal, E.G.; Venema, K.; Saad, S.M.I.; Smidt, H.

    2013-01-01

    A validated in vitro model of the large intestine (TIM-2), set up with human or pig faeces, was used to evaluate the impact of potentially probiotic Lactobacillus amylovorus DSM 16698, administered alone (i), in the presence of prebiotic galactooligosaccharides (GOS) (ii), and co-administered with

  7. Growth and lipid production of Umbelopsis isabellina on a solid substrate - Mechanistic modeling and validation

    NARCIS (Netherlands)

    Meeuwse, P.; Klok, A.J.; Haemers, S.; Tramper, J.; Rinzema, A.

    2012-01-01

    Microbial lipids are an interesting feedstock for biodiesel. Their production from agricultural waste streams by fungi cultivated in solid-state fermentation may be attractive, but the yield of this process is still quite low. In this article, a mechanistic model is presented that describes growth,

  8. Experimental Results and Integrated Modeling of Bacterial Growth on an Insoluble Hydrophobic Substrate (Phenanthrene)

    DEFF Research Database (Denmark)

    Adam, Iris K. U.; Rein, Arno; Miltner, Anja

    2014-01-01

    Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested ...

  9. Trajectories and models of individual growth

    Directory of Open Access Journals (Sweden)

    Arseniy Karkach

    2006-11-01

    Full Text Available It has long been recognized that the patterns of growth play an important role in the evolution of age trajectories of fertility and mortality (Williams, 1957. Life history studies would benefit from a better understanding of strategies and mechanisms of growth, but still no comparative research on individual growth strategies has been conducted. Growth patterns and methods have been shaped by evolution and a great variety of them are observed. Two distinct patterns - determinate and indeterminate growth - are of a special interest for these studies since they present qualitatively different outcomes of evolution. We attempt to draw together studies covering growth in plant and animal species across a wide range of phyla focusing primarily on the noted qualitative features. We also review mathematical descriptions of growth, namely empirical growth curves and growth models, and discuss the directions of future research.

  10. Nonconvex Model of Material Growth: Mathematical Theory

    Science.gov (United States)

    Ganghoffer, J. F.; Plotnikov, P. I.; Sokolowski, J.

    2018-06-01

    The model of volumetric material growth is introduced in the framework of finite elasticity. The new results obtained for the model are presented with complete proofs. The state variables include the deformations, temperature and the growth factor matrix function. The existence of global in time solutions for the quasistatic deformations boundary value problem coupled with the energy balance and the evolution of the growth factor is shown. The mathematical results can be applied to a wide class of growth models in mechanics and biology.

  11. Genome-enabled Modeling of Microbial Biogeochemistry using a Trait-based Approach. Does Increasing Metabolic Complexity Increase Predictive Capabilities?

    Science.gov (United States)

    King, E.; Karaoz, U.; Molins, S.; Bouskill, N.; Anantharaman, K.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.; Brodie, E.

    2015-12-01

    The biogeochemical functioning of ecosystems is shaped in part by genomic information stored in the subsurface microbiome. Cultivation-independent approaches allow us to extract this information through reconstruction of thousands of genomes from a microbial community. Analysis of these genomes, in turn, gives an indication of the organisms present and their functional roles. However, metagenomic analyses can currently deliver thousands of different genomes that range in abundance/importance, requiring the identification and assimilation of key physiologies and metabolisms to be represented as traits for successful simulation of subsurface processes. Here we focus on incorporating -omics information into BioCrunch, a genome-informed trait-based model that represents the diversity of microbial functional processes within a reactive transport framework. This approach models the rate of nutrient uptake and the thermodynamics of coupled electron donors and acceptors for a range of microbial metabolisms including heterotrophs and chemolithotrophs. Metabolism of exogenous substrates fuels catabolic and anabolic processes, with the proportion of energy used for cellular maintenance, respiration, biomass development, and enzyme production based upon dynamic intracellular and environmental conditions. This internal resource partitioning represents a trade-off against biomass formation and results in microbial community emergence across a fitness landscape. Biocrunch was used here in simulations that included organisms and metabolic pathways derived from a dataset of ~1200 non-redundant genomes reflecting a microbial community in a floodplain aquifer. Metagenomic data was directly used to parameterize trait values related to growth and to identify trait linkages associated with respiration, fermentation, and key enzymatic functions such as plant polymer degradation. Simulations spanned a range of metabolic complexities and highlight benefits originating from simulations

  12. Modelling the impact of future socio-economic and climate change scenarios on river microbial water quality.

    Science.gov (United States)

    Islam, M M Majedul; Iqbal, Muhammad Shahid; Leemans, Rik; Hofstra, Nynke

    2018-03-01

    Microbial surface water quality is important, as it is related to health risk when the population is exposed through drinking, recreation or consumption of irrigated vegetables. The microbial surface water quality is expected to change with socio-economic development and climate change. This study explores the combined impacts of future socio-economic and climate change scenarios on microbial water quality using a coupled hydrodynamic and water quality model (MIKE21FM-ECOLab). The model was applied to simulate the baseline (2014-2015) and future (2040s and 2090s) faecal indicator bacteria (FIB: E. coli and enterococci) concentrations in the Betna river in Bangladesh. The scenarios comprise changes in socio-economic variables (e.g. population, urbanization, land use, sanitation and sewage treatment) and climate variables (temperature, precipitation and sea-level rise). Scenarios have been developed building on the most recent Shared Socio-economic Pathways: SSP1 and SSP3 and Representative Concentration Pathways: RCP4.5 and RCP8.5 in a matrix. An uncontrolled future results in a deterioration of the microbial water quality (+75% by the 2090s) due to socio-economic changes, such as higher population growth, and changes in rainfall patterns. However, microbial water quality improves under a sustainable scenario with improved sewage treatment (-98% by the 2090s). Contaminant loads were more influenced by changes in socio-economic factors than by climatic change. To our knowledge, this is the first study that combines climate change and socio-economic development scenarios to simulate the future microbial water quality of a river. This approach can also be used to assess future consequences for health risks. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  13. Pollution externalities in a Schumpeterian growth model

    OpenAIRE

    Koesler, Simon

    2010-01-01

    This paper extends a standard Schumpeterian growth model to include an environmental dimension. Thereby, it explicitly links the pollution intensity of economic activity to technological progress. In a second step, it investigates the effect of pollution on economic growth under the assumption that pollution intensities are related to technological progress. Several conclusions emerge from the model. In equilibrium, the economy follows a balanced growth path. The effect of pollution on the ec...

  14. Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied ...

  15. In situ examination of microbial populations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Martiny, Adam Camillo; Nielsen, Alex Toftgaard; Arvin, Erik

    2002-01-01

    A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates...... of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis...... revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from...

  16. Effect of Portulaca oleracea extracts on growth performance and microbial populations in ceca of broilers.

    Science.gov (United States)

    Zhao, X H; He, X; Yang, X F; Zhong, X H

    2013-05-01

    The aim of this study was to investigate the effects of Portulaca oleracea extracts on growth performance and microbial populations in the ceca of broilers. A total of 120 one-day-old broilers were randomly divided into 3 groups. Portulaca oleracea extracts were added to diets at 0.2 and 0.4% (wt/wt; POL-0.2, POL-0.4), respectively. The control (CON) group was administered with no P. oleracea extract supplementation. Body weight gain and feed conversion ratio were recorded every 2 wk. On d 28 and 42, the cecal contents were collected and assayed for Escherichia coli, Lactobacillus, and Bifidobacterium populations. Additionally, the pH of the ileum and cecum was measured. The results showed that both on d 28 and 42 BW gain of P. oleracea extract supplementation groups was significantly higher, whereas the feed conversion ratio was lower (P < 0.05) compared with CON. On d 28 and 42, significantly (P < 0.05) fewer E. coli were recovered from ceca of broilers provided with the POL-0.2 diet than from broilers provided with the control diet. The quantities of Lactobacillus and Bifidobacterium of POL-0.2 were significantly (P < 0.05) higher than CON. Results showed P. oleracea extracts have no distinct influence on intestinal pH. These data suggest that P. oleracea extract supplementation significantly altered the cecal bacterial community without affecting the intestinal pH.

  17. By passing microbial resistance: xylitol controls microorganisms growth by means of its anti-adherence property.

    Science.gov (United States)

    Ferreira, Aline S; Silva-Paes-Leme, Annelisa F; Raposo, Nádia R B; da Silva, Sílvio S

    2015-01-01

    Xylitol is an important polyalcohol suitable for use in odontological, medical and pharmaceutical products and as an additive in food. The first studies on the efficacy of xylitol in the control and treatment of infections started in the late 1970s and it is still applied for this purpose, with safety and very little contribution to resistance. Xylitol seems to act against microorganisms exerting an anti-adherence effect. Some research studies have demonstrated its action against Gram-positive and Gram-negative bacteria and yeasts. However, a clear explanation of how xylitol is effective has not been completely established yet. Some evidence shows that xylitol acts on gene expression, down-regulating the ones which are involved in the microorganisms' virulence, such as capsule formation. Another possible clarification is that xylitol blocks lectin-like receptors. The most important aspect is that, over time, xylitol bypasses microbial resistance and succeeds in controlling infection, either alone or combined with another compound. In this review, the effect of xylitol in inhibiting the growth of a different microorganism is described, focusing on studies in which such an anti-adherent property was highlighted. This is the first mini-review to describe xylitol as an anti-adherent compound and take into consideration how it exerts such action.

  18. Microbial growth and quorum sensing antagonist activities of herbal plants extracts.

    Science.gov (United States)

    Al-Hussaini, Reema; Mahasneh, Adel M

    2009-09-03

    Antimicrobial and antiquorum sensing (AQS) activities of fourteen ethanolic extracts of different parts of eight plants were screened against four Gram-positive, five Gram-negative bacteria and four fungi. Depending on the plant part extract used and the test microorganism, variable activities were recorded at 3 mg per disc. Among the Grampositive bacteria tested, for example, activities of Laurus nobilis bark extract ranged between a 9.5 mm inhibition zone against Bacillus subtilis up to a 25 mm one against methicillin resistant Staphylococcus aureus. Staphylococcus aureus and Aspergillus fumigatus were the most susceptible among bacteria and fungi tested towards other plant parts. Of interest is the tangible antifungal activity of a Tecoma capensis flower extract, which is reported for the first time. However, minimum inhibitory concentrations (MIC's) for both bacteria and fungi were relatively high (0.5-3.0 mg). As for antiquorum sensing activity against Chromobacterium violaceum, superior activity (>17 mm QS inhibition) was associated with Sonchus oleraceus and Laurus nobilis extracts and weak to good activity (8-17 mm) was recorded for other plants. In conclusion, results indicate the potential of these plant extracts in treating microbial infections through cell growth inhibition or quorum sensing antagonism, which is reported for the first time, thus validating their medicinal use.

  19. Microbial Growth and Quorum Sensing Antagonist Activities of Herbal Plants Extracts

    Directory of Open Access Journals (Sweden)

    Reema Al-Hussaini

    2009-09-01

    Full Text Available Antimicrobial and antiquorum sensing (AQS activities of fourteen ethanolic extracts of different parts of eight plants were screened against four Gram-positive, five Gram-negative bacteria and four fungi. Depending on the plant part extract used and the test microorganism, variable activities were recorded at 3 mg per disc. Among the Grampositive bacteria tested, for example, activities of Laurus nobilis bark extract ranged between a 9.5 mm inhibition zone against Bacillus subtilis up to a 25 mm one against methicillin resistant Staphylococcus aureus. Staphylococcus aureus and Aspergillus fumigatus were the most susceptible among bacteria and fungi tested towards other plant parts. Of interest is the tangible antifungal activity of a Tecoma capensis flower extract, which is reported for the first time. However, minimum inhibitory concentrations (MIC's for both bacteria and fungi were relatively high (0.5-3.0 mg. As for antiquorum sensing activity against Chromobacterium violaceum, superior activity (>17 mm QS inhibition was associated with Sonchus oleraceus and Laurus nobilis extracts and weak to good activity (8-17 mm was recorded for other plants. In conclusion, results indicate the potential of these plant extracts in treating microbial infections through cell growth inhibition or quorum sensing antagonism, which is reported for the first time, thus validating their medicinal use.

  20. Growth of the modeling of Escherichia coli in milk

    International Nuclear Information System (INIS)

    Mbangu, N.; Malakasa, M.; Ekalakala, T.; N'dendje, B.; Abedi, M.; Muzembe, K.; Bandejile, M.

    2010-01-01

    Escherichia coli is a contaminant potential of milk. Collective toxinfections implying the bacterium and milk were announced of share the world. However, no identified work proposed a mathematical expression of the growth of the bacterium in milk. The interest of such a step is however undeniable. Under specified conditions, the mathematical formulation of the growth provides the means of considering the population bacterial when the analyses cannot be carried out. It also makes it possible to test the negatiable instruments of the unfavourable circumstances supposed suchas chain breakage of cold on the development of the microbial charge. This work established mathematical expressions of the growth of Escherichia coli in milk for part of its range of temperature of growth suboptimale i.e. between 25 and 35 Deg C. It was not possible to generalize these expressions for predictions on all the range of temperature suboptimal. This work also made it possible to highlight a deviation of the behavoir of the bacterium compared to the model of Ratkowsky without however that it is not possible to provide a univocal explanantion of it. Varoius assumptions were put forth referring to either a singularity of the behavior of the bacterium or a skew of the value of its minimal temperature of growth

  1. Modelling asymmetric growth in crowded plant communities

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2010-01-01

    A class of models that may be used to quantify the effect of size-asymmetric competition in crowded plant communities by estimating a community specific degree of size-asymmetric growth for each species in the community is suggested. The model consists of two parts: an individual size......-asymmetric growth part, where growth is assumed to be proportional to a power function of the size of the individual, and a term that reduces the relative growth rate as a decreasing function of the individual plant size and the competitive interactions from other plants in the neighbourhood....

  2. Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

    Science.gov (United States)

    Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

    2017-04-01

    Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

  3. Modelling the bioconversion of cellulose into microbial products: rate limitations

    Energy Technology Data Exchange (ETDEWEB)

    Asenjo, J A

    1984-12-01

    The direct bioconversion of cellulose into microbial products carried out as a simultaneous saccharification and fermentation has a strong effect on the rates of cellulose degradation because cellobiose and glucose inhibition of the reaction are circumvented. A general mathematical model of the kinetics of this bioconversion has been developed. Its use in representing aerobic systems and in the analysis of the kinetic limitations has been investigated. Simulations have been carried out to find the rate limiting steps in slow fermentations and in rapid ones as determined by the specific rate of product formation. The requirements for solubilising and depolymerising enzyme activities (cellulase and cellobiase) in these systems has been determined. The activity that have been obtained for fungal cellulases are adequate for the kinetic requirements of the fastest fermentative strains. The results also show that for simultaneous bioconversions where strong cellobiose and glucose inhibition is overcome, no additional cellobiase is necessary to increase the rate of product formation. These results are useful for the selection of cellolytic micro-organisms and in the determination of enzymes to be cloned in recombinant strains. 17 references.

  4. Statistical analysis and modeling of pelletized cultivation of Mucor circinelloides for microbial lipid accumulation.

    Science.gov (United States)

    Xia, Chunjie; Wei, Wei; Hu, Bo

    2014-04-01

    Microbial oil accumulation via oleaginous fungi has some potential benefits because filamentous fungi can form pellets during cell growth and these pellets are easier to harvest from the culture broth than individual cells. This research studied the effect of various culture conditions on the pelletized cell growth of Mucor circinelloides and its lipid accumulation. The results showed that cell pelletization was positively correlated to biomass accumulation; however, pellet size was negatively correlated to the oil content of the fungal biomass, possibly due to the mass transfer barriers generated by the pellet structure. How to control the size of the pellet is the key to the success of the pelletized microbial oil accumulation process.

  5. Growth curve models and statistical diagnostics

    CERN Document Server

    Pan, Jian-Xin

    2002-01-01

    Growth-curve models are generalized multivariate analysis-of-variance models. These models are especially useful for investigating growth problems on short times in economics, biology, medical research, and epidemiology. This book systematically introduces the theory of the GCM with particular emphasis on their multivariate statistical diagnostics, which are based mainly on recent developments made by the authors and their collaborators. The authors provide complete proofs of theorems as well as practical data sets and MATLAB code.

  6. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities

    NARCIS (Netherlands)

    Epelde, L.; Becerril, J.M.; Kowalchuk, G.A.; Deng, Y.; Zhou, J.N.; Garbisu, C.

    2010-01-01

    Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses

  7. Effects of probiotic supplement ( and on feed efficiency, growth performance, and microbial population of weaning rabbits

    Directory of Open Access Journals (Sweden)

    Thanh Lam Phuoc

    2017-02-01

    Full Text Available Objective This study aimed to investigate the effects of single or/and double strains of probiotic supplement on feed efficiency, growth performance, and microbial population in distal gastrointestinal tract (GIT of weaning rabbits. Methods Sixty-four weaning (28 days old New Zealand White rabbits were randomly distributed into four groups with treatments including: basal diet without probiotic supplement (control or supplemented as follows: 1×106 cfu/g B. subtilis (BS group, 1×107 cfu/g L. acidophilus (LA group, or 0.5×106 cfu/g B. subtilis plus 0.5×107 cfu/g L. acidophilus (BL group. During the research, the male and female rabbits were fed separately. Body weight of the rabbits was recorded at 28, 42, and 70 d of age. Results There was an increase (p<0.05 in body weight gain for the LA group at 42 d. Rabbits fed BL responsed with a greater growth (p<0.05 and better feed conversion ratio (p<0.05 than those fed with no probiotic. Digestibility coefficients of dry matter, organic matter, crude protein, neutral detergent fiber, and gross energy were higher (p<0.05 in LA and BL groups than those in the control group. Male rabbits had higher (p<0.05 Bacilli spp. and Coliformis spp. in the ileum than female rabbits. Rabbits supplemented with BS had greater (p<0.05 numbers of bacilli in all intestinal segments than those receiving no probiotic, whereas intestinal Lactobacilli populations were greater (p<0.001 in the LA and BL diets compared to control. Average intestinal coliform populations were lowest (p<0.05 in the rabbits supplemented with LA as compared to those fed the control and BS. Conclusion Supplementation of L. acidophilus alone or in combination with B. subtilis at a half of dose could enhance number of gut beneficial bacteria populations, nutrient digestibility, cecal fermentation, feed efficiency, and growth performance, but rabbits receiving only B. subtilis alone were not different from the controls without probiotic.

  8. Quantitative Microbial Risk Assessment Tutorial Installation of Software for Watershed Modeling in Support of QMRA - Updated 2017

    Science.gov (United States)

    This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling: • QMRA Installation • SDMProjectBuilder (which includes the Microbial ...

  9. A Metastable Equilibrium Model for the Relative Abundances of Microbial Phyla in a Hot Spring

    Science.gov (United States)

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

    Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables have rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as “Bison Pool” in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community. The distance from metastable equilibrium of the communities, assessed using an equation derived from energetic considerations that is also consistent with the information-theoretic entropy change, decreases along the outflow channel. Specific divergences from metastable equilibrium, such as an underprediction of the relative abundances of phototrophic organisms at lower temperatures, can be explained by considering additional sources of energy and/or differences in growth efficiency. Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the

  10. On a Versatile Stochastic Growth Model

    Directory of Open Access Journals (Sweden)

    Samiur Arif

    2012-06-01

    Full Text Available Growth phenomena are ubiquitous and pervasive not only in biology and the medical sciences, but also in economics, marketing and the computer and social sciences. We introduce a three-parameter version of the classic pure-birth process growth model when suitably instantiated, can be used to model growth phenomena in many seemingly unrelated application domains. We point out that the model is computationally attractive since it admits of conceptually simple, closed form solutions for the time-dependent probabilities.

  11. Reductive dehalogenation in microbial and electrolytic model systems

    International Nuclear Information System (INIS)

    Criddle, C.S.

    1990-01-01

    This research addresses the principles or reductive dehalogenation, with a focus on microbial processes. Carbon tetrachloride (CT) was selected as a model compound for intensive investigation. Three different experimental systems were studied: pure cultures of Escherichia coli k-12, pure cultures of a denitrifying Pseudomonad isolated from aquifer solids (Pseudomonas sp. strain KC), and an electrolysis cell. The product distributions were consistent with the hypothesis that CT undergoes a rate-limiting reduction to radical species which rapidly react with constituents of the surrounding milieu. In cultures of E. coli k-12, use of oxygen and nitrate as terminal electron acceptors generally prevented CT transformation. At low oxygen levels (∼ 1%), however, transformation of 14 C-CT to 14 C-CO 2 and attachment to cell material did occur in accord with reports of CT fate in mammalian cell cultures. Under fumarate-respiring conditions, 14 C-CT was recovered as 14 C-C 2 , chloroform (CF), and in a non-volatile fraction. In contrast, fermenting conditions resulted in more CF, more cell-bound 14 C, and almost no 14 C-CO 2 . Rates were faster under fermenting conditions than under fumarate-respiring conditions. Rates also decreased over time suggesting the gradual exhaustion of transformation activity. This loss was modeled with a simple exponential decay term. Pseudomonas sp. strain KC converted 14 C-CT to 14 C-CO 2 under denitrifying conditions, without CF production. Strain KC was the only organism of several denitrifiers that transformed CT. Induction of CT transformation by strain KC depended upon the presence of trace metals. Addition of ferrous iron and cobalt inhibited CT transformation. For strain KC, CT transformation is apparently linked to its mechanism for trace metal acquisition

  12. Recent advances in modelling creep crack growth

    International Nuclear Information System (INIS)

    Riedel, H.

    1988-08-01

    At the time of the previous International Conference on Fracture, the C* integral had long been recognized as a promising load parameter for correlating crack growth rates in creep-ductile materials. The measured crack growth rates as a function of C* and of the temperature could be understood on the basis of micromechanical models. The distinction between C*-controlled and K I -controlled creep crack growth had been clarified and first attempts had been made to describe creep crack growth in the transient regime between elastic behavior and steady-state creep. This paper describes the progress in describing transient crack growth including the effect of primary creep. The effect of crack-tip geometry changes by blunting and by crack growth on the crack-tip fields and on the validity of C* is analyzed by idealizing the growing-crack geometry by a sharp notch and using recent solutions for the notch-tip fields. A few new three-dimensional calculations of C* are cited and important theoretical points are emphasized regarding the three-dimensional fields at crack tips. Finally, creep crack growth is described by continuum-damage models for which similarity solutions can be obtained. Crack growth under small-scale creep conditions turns out to be difficult to understand. Slightly different models yield very different crack growth rates. (orig.) With 4 figs

  13. Effects of degradable protein and non-fibre carbohydrates on microbial growth and fermentation in the rumen simulating fermenter (Rusitec

    Directory of Open Access Journals (Sweden)

    Xiang H. Zhao

    2015-05-01

    Full Text Available A rumen simulation technique (Rusitec apparatus with eight 800 ml fermentation vessels was used to investigate the effects of rumen degradable protein (RDP level and non-fibre carbohydrate (NFC type on ruminal fermentation, microbial growth, and populations of ruminal cellulolytic bacteria. Treatments consisted of two NFC types (starch and pectin supplemented with 0 g/d (low RDP or 1.56 g/d (high RDP sodium caseinate. Apparent disappearance of dry matter and organic matter was greater for pectin than for starch treatment (P<0.01 with low or high RDP. A NFC × RDP interaction was observed for neutral detergent fibre disappearance (P=0.01, which was lower for pectin than for starch only under low RDP conditions. Compared with starch, pectin treatment increased the copy numbers of Ruminococcus albus (P≤0.01 and Ruminococcus flavefaciens (P≤0.09, the molar proportion of acetate (P<0.01, the acetate:propionate ratio (P<0.01, and methane production (P<0.01, but reduced the propionate proportion (P<0.01. Increasing dietary RDP increased the production of total VFA (P=0.01, methane (P<0.01, ammonia N (P<0.01, and microbial N (P<0.01. Significant NFC × RDP interaction and interaction tendency were observed for ammonia N production (P=0.01 and daily N flow of total microorganisms (P=0.07, which did not differ under low RDP conditions, but pectin produced greater microbial N and less ammonia N than starch with increased RDP. Results showed NFC type, RDP level, and their interaction affected ruminal fermentation and microbial growth, and under sufficient ruminal degradable N pectin had greater advantage in microbial N synthesis than starch in vitro.

  14. Microbial growth yield estimates from thermodynamics and its importance for degradation of pesticides and formation of biogenic non-extractable residues

    DEFF Research Database (Denmark)

    Brock, Andreas Libonati; Kästner, M.; Trapp, Stefan

    2017-01-01

    NER. Formation of microbial mass can be estimated from the microbial growth yield, but experimental data is rare. Instead, we suggest using prediction methods for the theoretical yield based on thermodynamics. Recently, we presented the Microbial Turnover to Biomass (MTB) method that needs a minimum...... and using the released CO2 as a measure for microbial activity, we predicted a range for the formation of biogenic NER. For the majority of the pesticides, a considerable fraction of the NER was estimated to be biogenic. This novel approach provides a theoretical foundation applicable to the evaluation...

  15. Calibration and analysis of genome-based models for microbial ecology.

    Science.gov (United States)

    Louca, Stilianos; Doebeli, Michael

    2015-10-16

    Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

  16. Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

    Science.gov (United States)

    Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

  17. Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

    Science.gov (United States)

    Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

  18. A model for improving microbial biofuel production using a synthetic feedback loop

    Energy Technology Data Exchange (ETDEWEB)

    Dunlop, Mary; Keasling, Jay; Mukhopadhyay, Aindrila

    2011-07-14

    Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.

  19. Kinetic Model of Growth of Arthropoda Populations

    Science.gov (United States)

    Ershov, Yu. A.; Kuznetsov, M. A.

    2018-05-01

    Kinetic equations were derived for calculating the growth of crustacean populations ( Crustacea) based on the biological growth model suggested earlier using shrimp ( Caridea) populations as an example. The development cycle of successive stages for populations can be represented in the form of quasi-chemical equations. The kinetic equations that describe the development cycle of crustaceans allow quantitative prediction of the development of populations depending on conditions. In contrast to extrapolation-simulation models, in the developed kinetic model of biological growth the kinetic parameters are the experimental characteristics of population growth. Verification and parametric identification of the developed model on the basis of the experimental data showed agreement with experiment within the error of the measurement technique.

  20. Compatible growth models and stand density diagrams

    International Nuclear Information System (INIS)

    Smith, N.J.; Brand, D.G.

    1988-01-01

    This paper discusses a stand average growth model based on the self-thinning rule developed and used to generate stand density diagrams. Procedures involved in testing are described and results are included

  1. Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model.

    Science.gov (United States)

    Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio

    2010-08-10

    Theory and empirical evidence suggest that plant-soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant-microbe-soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.

  2. Raw-appearing Restructured fish models made with Sodium alginate or Microbial transglutaminase and effect of chilled storage

    Directory of Open Access Journals (Sweden)

    Helena Moreno

    2013-03-01

    Full Text Available Restructuring by adding Sodium Alginate or Microbial Transglutaminase (MTGase using cold gelation technology make it possible to obtain many different raw products from minced and/or chopped fish muscle that are suitable for being used as the basis of new restructured products with different physicochemical properties and even different compositions. Special consideration must be given to their shelf-life and the changes that may take place during chilling, both in visual appearance and physicochemical properties. After chilled storage, the restructured models made with different muscular particle size and composition at low temperature (5 °C, it was observed that microbial growth limited the shelf-life to 7-14 days. Mechanical properties increased (p 0.05 was detected during storage.

  3. Microbial growth in Acrocomia aculeata pulp oil, Jatropha curcas oil, and their respective biodiesels under simulated storage conditions

    Directory of Open Access Journals (Sweden)

    Juciana Clarice Cazarolli

    2016-12-01

    Full Text Available With increasing demands for biodiesel in Brazil, diverse oil feedstocks have been investigated for their potentials for biodiesel production. Due to the high biodegradability of natural oils and their respective biodiesels, microbial growths and consequent deterioration of final product quality are generally observed during storage. This study was aimed at evaluating the susceptibility of Acrocomia aculeata pulp oil and Jatropha curcas oil as well as their respective biodiesels to biodeterioration during a simulated storage period. The experiment was conducted in microcosms containing oil/biodiesel and an aqueous phase over 30 d. The levels of microbial contamination included biodiesel and oil as received, inoculated with fungi, and sterile. Samples were collected every 7 d to measure pH, surface tension, acidity index, and microbial biomass. The initial and final ester contents of the biodiesels were also determined by gas chromatography. The major microbial biomass was detected in A. aculeata pulp and J. curcas biodiesels. Significant reductions in pH values were observed for treatments with A. aculeata pulp biodiesel as a carbon source (p

  4. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

  5. The utilization of microbial inoculants based on irradiated compost in dryland remediation to increase the growth of king grass and maize

    International Nuclear Information System (INIS)

    TRD Larasati; N Mulyana; D Sudradjat

    2016-01-01

    This research was conducted to evaluate the capability of functional microbial inoculants to remediate drylands. The microbial inoculants used consist of hydrocarbon-degrading microbial inoculants and plant-growth-promoting microbial inoculants. Compost-based carrier was sterilized by a gamma irradiation dose of 25 kGy to prepare seed inoculants. The irradiated-compost-based hydrocarbon-degrading microbial inoculants and king grass (Pennisetum purpureum Schumach.) were used to remediate oil-sludge-contaminated soil using in-situ composting for 60 days. The results showed that they could reduce THP (total petroleum hydrocarbons) by up to 82.23%. Plant-growth-promoting microbial inoculants were able to increase the dry weight of king grass from 47.39 to 100.66 g/plant, N uptake from 415.53 to 913.67 mg/plant, and P uptake from 76.52 to 178.33 mg/plant. Cow dung and irradiated-compost-based plant-growth-promoting microbial inoculants were able to increase the dry weight of maize (Zea mays L.) from 5.75 to 6.63 ton/ha (12.54%) and dry weight of grain potential from 5.30 to 7.15 ton/ha (35.03%). The results indicate that irradiated-compost-based microbial inoculants are suitable for remediating a dryland and therefore increase potential resources and improve the quality of the environment. (author)

  6. Value function in economic growth model

    Science.gov (United States)

    Bagno, Alexander; Tarasyev, Alexandr A.; Tarasyev, Alexander M.

    2017-11-01

    Properties of the value function are examined in an infinite horizon optimal control problem with an unlimited integrand index appearing in the quality functional with a discount factor. Optimal control problems of such type describe solutions in models of economic growth. Necessary and sufficient conditions are derived to ensure that the value function satisfies the infinitesimal stability properties. It is proved that value function coincides with the minimax solution of the Hamilton-Jacobi equation. Description of the growth asymptotic behavior for the value function is provided for the logarithmic, power and exponential quality functionals and an example is given to illustrate construction of the value function in economic growth models.

  7. Tax Evasion and Economic Growth in an Endogenous Growth Model

    OpenAIRE

    加藤, 秀弥; KATO, Hideya

    2004-01-01

    This paper presents an endogenous growth model with tax evasion where government expenditures affect production. An individual evades a tax so as to maximize his or her utility, the tax authority controls the detection probability to maximize net tax revenue, and the government chooses the income tax rate to maximize individuals’ utility. The main conclusions are as follows. First, the optical income tax rate with tax evasion is higher than that without tax evasion. Second, the rise in a ...

  8. The worm has turned--microbial virulence modeled in Caenorhabditis elegans.

    Science.gov (United States)

    Sifri, Costi D; Begun, Jakob; Ausubel, Frederick M

    2005-03-01

    The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolutionarily conserved mechanisms of microbial pathogenesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian models have been shown to be similarly required for maximum pathogenicity in nematodes. C. elegans has been used in mutation-based screening systems to identify novel virulence-related microbial genes and immune-related host genes, many of which have been validated in mammalian models of disease. C. elegans-based pathogenesis systems hold the potential to simultaneously explore the molecular genetic determinants of both pathogen virulence and host defense.

  9. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities.

    NARCIS (Netherlands)

    Epelde, L.; Becerril, J.M.; Kowalchuk, G.A.; Deng, Y.; Zhou, J.; Garbisu, C.

    2010-01-01

    been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts

  10. Effect of dry mycelium of Penicillium chrysogenum fertilizer on soil microbial community composition, enzyme activities and snap bean growth.

    Science.gov (United States)

    Wang, Bing; Liu, Huiling; Cai, Chen; Thabit, Mohamed; Wang, Pu; Li, Guomin; Duan, Ziheng

    2016-10-01

    The dry mycelium fertilizer (DMF) was produced from penicillin fermentation fungi mycelium (PFFM) following an acid-heating pretreatment to degrade the residual penicillin. In this study, it was applied into soil as fertilizer to investigate its effects on soil properties, phytotoxicity, microbial community composition, enzyme activities, and growth of snap bean in greenhouse. As the results show, pH, total nitrogen, total phosphorus, total potassium, and organic matter of soil with DMF treatments were generally higher than CON treatment. In addition, the applied DMF did not cause heavy metal and residual drug pollution of the modified soil. The lowest GI values (<0.3) were recorded at DMF8 (36 kg DMF/plat) on the first days after applying the fertilizer, indicating that severe phytotoxicity appeared in the DMF8-modified soil. Results of microbial population and enzyme activities illustrated that DMF was rapidly decomposed and the decomposition process significantly affected microbial growth and enzyme activities. The DMF-modified soil phytotoxicity decreased at the late fertilization time. DMF1 was considered as the optimum amount of DMF dose based on principal component analysis scores. Plant height and plant yield of snap bean were remarkably enhanced with the optimum DMF dose.

  11. Modeling Math Growth Trajectory--An Application of Conventional Growth Curve Model and Growth Mixture Model to ECLS K-5 Data

    Science.gov (United States)

    Lu, Yi

    2016-01-01

    To model students' math growth trajectory, three conventional growth curve models and three growth mixture models are applied to the Early Childhood Longitudinal Study Kindergarten-Fifth grade (ECLS K-5) dataset in this study. The results of conventional growth curve model show gender differences on math IRT scores. When holding socio-economic…

  12. A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

    Science.gov (United States)

    Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

    2017-12-01

    A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

  13. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Mahadevan

    2012-10-01

    With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  14. Effect of Probiotic Bacteria on Microbial Host Defense, Growth, and Immune Function in Human Immunodeficiency Virus Type-1 Infection

    Directory of Open Access Journals (Sweden)

    Stig Bengmark

    2011-12-01

    Full Text Available The hypothesis that probiotic administration protects the gut surface and could delay progression of Human Immunodeficiency Virus type1 (HIV-1 infection to the Acquired Immunodeficiency Syndrome (AIDS was proposed in 1995. Over the last five years, new studies have clarified the significance of HIV-1 infection of the gut associated lymphoid tissue (GALT for subsequent alterations in the microflora and breakdown of the gut mucosal barrier leading to pathogenesis and development of AIDS. Current studies show that loss of gut CD4+ Th17 cells, which differentiate in response to normal microflora, occurs early in HIV-1 disease. Microbial translocation and suppression of the T regulatory (Treg cell response is associated with chronic immune activation and inflammation. Combinations of probiotic bacteria which upregulate Treg activation have shown promise in suppressing pro inflammatory immune response in models of autoimmunity including inflammatory bowel disease and provide a rationale for use of probiotics in HIV-1/AIDS. Disturbance of the microbiota early in HIV-1 infection leads to greater dominance of potential pathogens, reducing levels of bifidobacteria and lactobacillus species and increasing mucosal inflammation. The interaction of chronic or recurrent infections, and immune activation contributes to nutritional deficiencies that have lasting consequences especially in the HIV-1 infected child. While effective anti-retroviral therapy (ART has enhanced survival, wasting is still an independent predictor of survival and a major presenting symptom. Congenital exposure to HIV-1 is a risk factor for growth delay in both infected and non-infected infants. Nutritional intervention after 6 months of age appears to be largely ineffective. A meta analysis of randomized, controlled clinical trials of infant formulae supplemented with Bifidobacterium lactis showed that weight gain was significantly greater in infants who received B. lactis compared to

  15. Spring thaw ionic pulses boost nutrient availability and microbial growth in entombed Antarctic Dry Valley cryoconite holes.

    Science.gov (United States)

    Telling, Jon; Anesio, Alexandre M; Tranter, Martyn; Fountain, Andrew G; Nylen, Thomas; Hawkings, Jon; Singh, Virendra B; Kaur, Preeti; Musilova, Michaela; Wadham, Jemma L

    2014-01-01

    The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During the initial melt there was a mean nine times enrichment in dissolved chloride relative to mean concentrations of the initial frozen holes indicative of an ionic pulse, with similar mean nine times enrichments in nitrite, ammonium, and dissolved organic matter. Nitrate was enriched twelve times and dissolved organic nitrogen six times, suggesting net nitrification, while lower enrichments for dissolved organic phosphorus and phosphate were consistent with net microbial phosphorus uptake. Rates of bacterial production were significantly elevated during the ionic pulse, likely due to the increased nutrient availability. There was no concomitant increase in photosynthesis rates, with a net depletion of dissolved inorganic carbon suggesting inorganic carbon limitation. Potential nitrogen fixation was detected in fully melted holes where it could be an important source of nitrogen to support microbial growth, but not during the ionic pulse where nitrogen availability was higher. This study demonstrates that ionic pulses significantly alter the timing and magnitude of microbial activity within entombed cryoconite holes, and adds credence to hypotheses that ionic enrichments during freeze-thaw can elevate rates of microbial growth and activity in other icy habitats, such as ice veins and subglacial regelation zones.

  16. Effect of different film packaging on microbial growth in minimally processed cactus pear (Opuntia ficus-indica).

    Science.gov (United States)

    Palma, A; Mangia, N P; Fadda, A; Barberis, A; Schirra, M; D'Aquino, S

    2013-01-01

    Microorganisms are natural contaminants of fresh produce and minimally processed products, and contamination arises from a number of sources, including the environment, postharvest handling and processing. Fresh-cut products are particularly susceptible to microbial contaminations because of the changes occurring in the tissues during processing. In package gas composition of modified atmosphere packaging (MAP) in combination with low storage temperatures besides reducing physiological activity of packaged produce, can also delay pathogen growth. Present study investigated on the effect of MAPs, achieved with different plastic films, on microbial growth of minimally processed cactus pear (Opuntio ficus-indica) fruit. Five different plastic materials were used for packaging the manually peeled fruit. That is: a) polypropylene film (Termoplast MY 40 micron thickness, O2 transmission rate 300 cc/m2/24h); b) polyethylene film (Bolphane BHE, 11 micron thickness, O2 transmission rate 19000 cc/m2/24h); c) polypropylene laser-perforated films (Mach Packaging) with 8, 16 or 32 100-micron holes. Total aerobic psychrophilic, mesophilic microorganisms, Enterobacteriaceae, yeast, mould populations and in-package CO2, O2 and C2H4 were determined at each storage time. Different final gas compositions, ranging from 7.8 KPa to 17.1 KPa O2, and 12.7 KPa to 2.6 KPa CO2, were achieved with MY and micro perforated films, respectively. Differences were detected in the mesophilic, Enterobacteriaceae and yeast loads, while no difference was detected in psychrophilic microorganisms. At the end of storage, microbial load in fruits sealed with MY film was significantly lower than in those sealed with BHE and micro perforated films. Furthermore, fruits packed with micro-perforated films showed the highest microbial load. This occurrence may in part be related to in-package gas composition and in part to a continuous contamination of microorganisms through micro-holes.

  17. Spring thaw ionic pulses boost nutrient availability and microbial growth in entombed Antarctic Dry Valley cryoconite holes

    Directory of Open Access Journals (Sweden)

    Jon eTelling

    2014-12-01

    Full Text Available The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw towards fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus with longer isolation age. During the initial melt there was a mean nine times enrichment in dissolved chloride relative to mean concentrations of the initial frozen holes indicative of an ionic pulse, with similar mean nine times enrichments in nitrite, ammonium, and dissolved organic matter. Nitrate was enriched twelve times and dissolved organic nitrogen six times, suggesting net nitrification, while lower enrichments for dissolved organic phosphorus and phosphate were consistent with net microbial phosphorus uptake. Rates of bacterial production were significantly elevated during the ionic pulse, likely due to the increased nutrient availability. There was no concomitant increase in photosynthesis rates, with a net depletion of dissolved inorganic carbon suggesting inorganic carbon limitation. Potential nitrogen fixation was detected in fully melted holes where it could be an important source of nitrogen to support microbial growth, but not during the ionic pulse where nitrogen availability was higher. This study demonstrates that ionic pulses significantly alter the timing and magnitude of microbial activity within entombed cryoconite holes, and adds credence to hypotheses that ionic enrichments during freeze-thaw can elevate rates of microbial growth and activity in other icy habitats, such as ice veins and

  18. Nonlinear Growth Models as Measurement Models: A Second-Order Growth Curve Model for Measuring Potential.

    Science.gov (United States)

    McNeish, Daniel; Dumas, Denis

    2017-01-01

    Recent methodological work has highlighted the promise of nonlinear growth models for addressing substantive questions in the behavioral sciences. In this article, we outline a second-order nonlinear growth model in order to measure a critical notion in development and education: potential. Here, potential is conceptualized as having three components-ability, capacity, and availability-where ability is the amount of skill a student is estimated to have at a given timepoint, capacity is the maximum amount of ability a student is predicted to be able to develop asymptotically, and availability is the difference between capacity and ability at any particular timepoint. We argue that single timepoint measures are typically insufficient for discerning information about potential, and we therefore describe a general framework that incorporates a growth model into the measurement model to capture these three components. Then, we provide an illustrative example using the public-use Early Childhood Longitudinal Study-Kindergarten data set using a Michaelis-Menten growth function (reparameterized from its common application in biochemistry) to demonstrate our proposed model as applied to measuring potential within an educational context. The advantage of this approach compared to currently utilized methods is discussed as are future directions and limitations.

  19. Forest growth modeling in the Southern Region, National Forest System

    International Nuclear Information System (INIS)

    Belcher, D.M.

    1988-01-01

    This paper discusses an attempt to combine individual tree growth models and stand level growth models currently available for the Region into one computer program. Operation of the program is explained and growth models are included

  20. Comparison of model microbial allocation parameters in soils of varying texture

    Science.gov (United States)

    Hagerty, S. B.; Slessarev, E.; Schimel, J.

    2017-12-01

    The soil microbial community decomposes the majority of carbon (C) inputs to the soil. However, not all of this C is respired—rather, a substantial portion of the carbon processed by microbes may remain stored in the soil. The balance between C storage and respiration is controlled by microbial turnover rates and C allocation strategies. These microbial community properties may depend on soil texture, which has the potential to influence both the nature and the fate of microbial necromass and extracellular products. To evaluate the role of texture on microbial turnover and C allocation, we sampled four soils from the University of California's Hastings Reserve that varied in texture (one silt loam, two sandy loam, and on clay soil), but support similar grassland plant communities. We added 14C- glucose to the soil and measured the concentration of the label in the carbon dioxide (CO2), microbial biomass, and extractable C pools over 7 weeks. The labeled biomass turned over the slowest in the clay soil; the concentration of labeled biomass was more than 1.5 times the concentration of the other soils after 8 weeks. The clay soil also had the lowest mineralization rate of the label, and mineralization slowed after two weeks. In contrast, in the sandier soils mineralization rates were higher and did not plateau until 5 weeks into the incubation period. We fit the 14C data to a microbial allocation model and estimated microbial parameters; assimilation efficiency, exudation, and biomass specific respiration and turnover for each soil. We compare these parameters across the soil texture gradient to assess the extent to which models may need to account for variability in microbial C allocation across soils of different texture. Our results suggest that microbial C turns over more slowly in high-clay soils than in sandy soils, and that C lost from microbial biomass is retained at higher rates in high-clay soils. Accounting for these differences in microbial allocation

  1. Localisation in a Growth Model with Interaction

    Science.gov (United States)

    Costa, M.; Menshikov, M.; Shcherbakov, V.; Vachkovskaia, M.

    2018-05-01

    This paper concerns the long term behaviour of a growth model describing a random sequential allocation of particles on a finite cycle graph. The model can be regarded as a reinforced urn model with graph-based interaction. It is motivated by cooperative sequential adsorption, where adsorption rates at a site depend on the configuration of existing particles in the neighbourhood of that site. Our main result is that, with probability one, the growth process will eventually localise either at a single site, or at a pair of neighbouring sites.

  2. Residual Structures in Latent Growth Curve Modeling

    Science.gov (United States)

    Grimm, Kevin J.; Widaman, Keith F.

    2010-01-01

    Several alternatives are available for specifying the residual structure in latent growth curve modeling. Two specifications involve uncorrelated residuals and represent the most commonly used residual structures. The first, building on repeated measures analysis of variance and common specifications in multilevel models, forces residual variances…

  3. A microbial model of economic trading and comparative advantage.

    Science.gov (United States)

    Enyeart, Peter J; Simpson, Zachary B; Ellington, Andrew D

    2015-01-07

    The economic theory of comparative advantage postulates that beneficial trading relationships can be arrived at by two self-interested entities producing the same goods as long as they have opposing relative efficiencies in producing those goods. The theory predicts that upon entering trade, in order to maximize consumption both entities will specialize in producing the good they can produce at higher efficiency, that the weaker entity will specialize more completely than the stronger entity, and that both will be able to consume more goods as a result of trade than either would be able to alone. We extend this theory to the realm of unicellular organisms by developing mathematical models of genetic circuits that allow trading of a common good (specifically, signaling molecules) required for growth in bacteria in order to demonstrate comparative advantage interactions. In Conception 1, the experimenter controls production rates via exogenous inducers, allowing exploration of the parameter space of specialization. In Conception 2, the circuits self-regulate via feedback mechanisms. Our models indicate that these genetic circuits can demonstrate comparative advantage, and that cooperation in such a manner is particularly favored under stringent external conditions and when the cost of production is not overly high. Further work could involve implementing the models in living bacteria and searching for naturally occurring cooperative relationships between bacteria that conform to the principles of comparative advantage. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Effect of food microstructure on growth dynamics of Listeria monocytogenes in fish-based model systems.

    Science.gov (United States)

    Verheyen, Davy; Bolívar, Araceli; Pérez-Rodríguez, Fernando; Baka, Maria; Skåra, Torstein; Van Impe, Jan F

    2018-06-01

    Traditionally, predictive growth models for food pathogens are developed based on experiments in broth media, resulting in models which do not incorporate the influence of food microstructure. The use of model systems with various microstructures is a promising concept to get more insight into the influence of food microstructure on microbial dynamics. By means of minimal variation of compositional and physicochemical factors, these model systems can be used to study the isolated effect of certain microstructural aspects on microbial growth, survival and inactivation. In this study, the isolated effect on microbial growth dynamics of Listeria monocytogenes of two food microstructural aspects and one aspect influenced by food microstructure were investigated, i.e., the nature of the food matrix, the presence of fat droplets, and microorganism growth morphology, respectively. To this extent, fish-based model systems with various microstructures were used, i.e., a liquid, a second more viscous liquid system containing xanthan gum, an emulsion, an aqueous gel, and a gelled emulsion. Growth experiments were conducted at 4 and 10 °C, both using homogeneous and surface inoculation (only for the gelled systems). Results regarding the influence of the growth morphology indicated that the lag phase of planktonic cells in the liquid system was similar to the lag phase of submerged colonies in the xanthan system. The lag phase of submerged colonies in each gelled system was considerably longer than the lag phase of surface colonies on these respective systems. The maximum specific growth rate of planktonic cells in the liquid system was significantly lower than for submerged colonies in the xanthan system at 10 °C, while no significant differences were observed at 4 °C. The maximum cell density was higher for submerged colonies than for surface colonies. The nature of the food matrix only exerted an influence on the maximum specific growth rate, which was

  5. Thermal models pertaining to continental growth

    International Nuclear Information System (INIS)

    Morgan, P.; Ashwal, L.

    1988-01-01

    Thermal models are important to understanding continental growth as the genesis, stabilization, and possible recycling of continental crust are closely related to the tectonic processes of the earth which are driven primarily by heat. The thermal energy budget of the earth was slowly decreasing since core formation, and thus the energy driving the terrestrial tectonic engine was decreasing. This fundamental observation was used to develop a logic tree defining the options for continental growth throughout earth history

  6. Structural modelling of economic growth: Technological changes

    Directory of Open Access Journals (Sweden)

    Sukharev Oleg

    2016-01-01

    Full Text Available Neoclassical and Keynesian theories of economic growth assume the use of Cobb-Douglas modified functions and other aggregate econometric approaches to growth dynamics modelling. In that case explanations of economic growth are based on the logic of the used mathematical ratios often including the ideas about aggregated values change and factors change a priori. The idea of assessment of factor productivity is the fundamental one among modern theories of economic growth. Nevertheless, structural parameters of economic system, institutions and technological changes are practically not considered within known approaches, though the latter is reflected in the changing parameters of production function. At the same time, on the one hand, the ratio of structural elements determines the future value of the total productivity of the factors and, on the other hand, strongly influences the rate of economic growth and its mode of innovative dynamics. To put structural parameters of economic system into growth models with the possibility of assessment of such modes under conditions of interaction of new and old combinations is an essential step in the development of the theory of economic growth/development. It allows forming stimulation policy of economic growth proceeding from the structural ratios and relations recognized for this economic system. It is most convenient in such models to use logistic functions demonstrating the resource change for old and new combination within the economic system. The result of economy development depends on starting conditions, and on institutional parameters of velocity change of resource borrowing in favour of a new combination and creation of its own resource. Model registration of the resource is carried out through the idea of investments into new and old combinations.

  7. In silico modeling for tumor growth visualization.

    Science.gov (United States)

    Jeanquartier, Fleur; Jean-Quartier, Claire; Cemernek, David; Holzinger, Andreas

    2016-08-08

    Cancer is a complex disease. Fundamental cellular based studies as well as modeling provides insight into cancer biology and strategies to treatment of the disease. In silico models complement in vivo models. Research on tumor growth involves a plethora of models each emphasizing isolated aspects of benign and malignant neoplasms. Biologists and clinical scientists are often overwhelmed by the mathematical background knowledge necessary to grasp and to apply a model to their own research. We aim to provide a comprehensive and expandable simulation tool to visualizing tumor growth. This novel Web-based application offers the advantage of a user-friendly graphical interface with several manipulable input variables to correlate different aspects of tumor growth. By refining model parameters we highlight the significance of heterogeneous intercellular interactions on tumor progression. Within this paper we present the implementation of the Cellular Potts Model graphically presented through Cytoscape.js within a Web application. The tool is available under the MIT license at https://github.com/davcem/cpm-cytoscape and http://styx.cgv.tugraz.at:8080/cpm-cytoscape/ . In-silico methods overcome the lack of wet experimental possibilities and as dry method succeed in terms of reduction, refinement and replacement of animal experimentation, also known as the 3R principles. Our visualization approach to simulation allows for more flexible usage and easy extension to facilitate understanding and gain novel insight. We believe that biomedical research in general and research on tumor growth in particular will benefit from the systems biology perspective.

  8. Microbial Inoculantes Effects on Growth Promotion of Mangrove and Citrullus vulgaris San Andrés Isla, Colombia

    Directory of Open Access Journals (Sweden)

    Tania Galindo

    2006-01-01

    Full Text Available In order to test the effect of two microbial inoculants (obtained from red and black mangrove roots on the growth and stability of mangrove and watermelon plants, four treatments were carried out in San Andres Island, Colombia. The treatments consisted in the application of the inoculants in: A. germinans propagules collected in a mangrove area, and then individually planted in gavels with sun-pasteurized soil (in order to decrease the microbial load, A. germinans and R. mangle plants collected in the proximity of nursery trees, A. germinans and R. mangle planted and maintained in nursery, and in Citrullus vulgaris seeds planted in a traditional cultivar without chemical fertilizers. The growth and vegetative development variables were: number of nodes, number of leaves and steam length. The inoculants (phosphate solubilizing microorganisms -PSM- and nitrogen fixing bacteria -NFB- were applied in the mentioned vegetable material, doing measures during three months. The results show a positive effect on growth measured by steam length in plants treated specifically with the inoculants in C. vulgaris and A. germinans seedlings maintained in nursery.

  9. Microbial growth and sensory quality of dried potato slices irradiated by electrons

    International Nuclear Information System (INIS)

    Kim, Hyun-Jin; Song, Hyeon-Jeong; Song, Kyung-Bin

    2011-01-01

    Electron beam irradiation was applied to secure the microbial safety of dried purple sweet potato. After purple sweet potato slices had been dehydrated with 20% (w/w) maltodextrin solution, the samples were irradiated at doses 2, 4, 6, 8, and 10 kGy and then stored at 20 o C for 60 days. Microbiological data indicated that the populations of total aerobic bacteria and of yeast and molds significantly decreased with increase in irradiation dosage. Specifically, microbial load was reduced by about three log cycles at 6 kGy compared to those of the control. Based on the color measurement of the potato slices, electron beam irradiation treatment did not affect the color quality. Sensory evaluation results also showed that electron beam irradiation did not affect overall sensory scores during storage. These results suggest that electron beam irradiation could be useful for improving microbial safety without impairing the quality of the potato slices during storage.

  10. Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

    Science.gov (United States)

    Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

    2016-01-01

    Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

  11. Stability of U(VI) and Tc(VII) Reducing Microbial Communities to Environmental Perturbation: Development and Testing of a Thermodynamic Network Model

    International Nuclear Information System (INIS)

    McKinley, James P.; Istok, Jonathan

    2005-01-01

    Previously published research from in situ field experiments at the NABIR Field Research Center have shown that cooperative metabolism of denitrifiers and Fe(III)/sulfate reducers is essential for creating subsurface conditions favorable for U(VI) and Tc(VII) bioreduction (Istok et al., 2004). The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on the composition and functional stability of subsurface microbial communities. The overall scientific hypothesis is that a thermodynamic analysis of the energy-yielding reactions performed by broadly defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change. An interactive computer program was developed to calculate the overall growth equation and free energy yield for microorganisms that grow by coupling selected combinations of electron acceptor and electron donor half-reactions. Each group performs a specific function (e.g. oxidation of acetate coupled to reduction of nitrate); collectively the groups provide a theoretical description of the entire natural microbial community. The microbial growth data are combined with an existing thermodynamic data base for associated geochemical reactions and used to simulate the coupled microbial-geochemical response of a complex natural system to substrate addition or any other environmental perturbations

  12. Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis

    Science.gov (United States)

    Brangarí, Albert C.; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier; Manzoni, Stefano

    2018-06-01

    A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.

  13. Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.

    Science.gov (United States)

    van Baarlen, Peter; van Belkum, Alex; Thomma, Bart P H J

    2007-02-01

    Relatively simple eukaryotic model organisms such as the genetic model weed plant Arabidopsis thaliana possess an innate immune system that shares important similarities with its mammalian counterpart. In fact, some human pathogens infect Arabidopsis and cause overt disease with human symptomology. In such cases, decisive elements of the plant's immune system are likely to be targeted by the same microbial factors that are necessary for causing disease in humans. These similarities can be exploited to identify elementary microbial pathogenicity factors and their corresponding targets in a green host. This circumvents important cost aspects that often frustrate studies in humans or animal models and, in addition, results in facile ethical clearance.

  14. Modelling the growth of a methanotrophic biofilm

    DEFF Research Database (Denmark)

    Arcangeli, J.-P.; Arvin, E.

    1999-01-01

    This article discusses the growth of methanotrophic biofilms. Several independent biofilm growths scenarios involving different inocula were examined. Biofilm growth, substrate removal and product formation were monitored throughout the experiments. Based on the oxygen consumption it was concluded...... that heterotrophs and nitrifiers co-existed with methanotrophs in the biofilm. Heterotrophic biomass grew on soluble polymers formed by the hydrolysis of dead biomass entrapped in the biofilm. Nitrifier populations developed because of the presence of ammonia in the mineral medium. Based on these experimental...... was performed on this model. It indicated that the most influential parameters were those related to the biofilm (i.e. density; solid-volume fraction; thickness). This suggests that in order to improve the model, further research regarding the biofilm structure and composition is needed....

  15. Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

    Science.gov (United States)

    Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

    2010-12-01

    Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns under sulfate-reducing/fermentative conditions exhibited the greatest Cr(VI) reduction capacity. Two sulfate columns evolved to complete lactate fermentation with acetate and propionate produced in the column effluent after 40 days of experiments. These fermenting columns showed a complete removal of injected Cr(VI), visible precipitation of sulfide minerals, and a significant increase in effluent Fe and Mn concentrations. Reactive transport simulations suggested that direct reduction of Cr(VI) by

  16. Modeling Fish Growth in Low Dissolved Oxygen

    Science.gov (United States)

    Neilan, Rachael Miller

    2013-01-01

    This article describes a computational project designed for undergraduate students as an introduction to mathematical modeling. Students use an ordinary differential equation to describe fish weight and assume the instantaneous growth rate depends on the concentration of dissolved oxygen. Published laboratory experiments suggest that continuous…

  17. Stochastic Growth Models with No Discounting

    Czech Academy of Sciences Publication Activity Database

    Sladký, Karel

    2007-01-01

    Roč. 15, č. 4 (2007), s. 88-98 ISSN 0572-3043 R&D Projects: GA ČR(CZ) GA402/06/0990; GA ČR GA402/05/0115 Institutional research plan: CEZ:AV0Z10750506 Keywords : economic dynamics * stochastic version of the Ramsey growth model * Markov decision processes Subject RIV: AH - Economics

  18. Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

    Science.gov (United States)

    Mahadevan, Radhakrishnan; Henson, Michael A

    2012-01-01

    Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  19. The effect of starch, inulin, and degradable protein on ruminal fermentation and microbial growth in rumen simulation technique

    Directory of Open Access Journals (Sweden)

    Xiang H. Zhao

    2014-03-01

    Full Text Available A rumen simulation technique apparatus with eight 800 mL fermentation vessels was used to investigate the effects of rumen degradable protein (RDP level and non-fibre carbohydrate (NFC type on ruminal fermentation, microbial growth, and populations of ruminal cellulolytic bacteria. Treatments consisted of two NFC types (starch and inulin supplemented with 0 g/d (low RDP or 1.56 g/d (high RDP sodium caseinate. No significant differences existed among dietary treatments in the apparent disappearance of dietary nutrients except for dietary N, which increased with increased dietary RDP (P<0.001. Compared with starch, inulin treatments reduced the molar proportion of acetate (P<0.001, the acetate:propionate ratio (P<0.001, and methane production (P=0.006, but increased the butyrate proportion (P<0.001. Increased dietary RDP led to increases in production of total volatile fatty acid (P=0.014 and methane (P=0.050, various measures of N (P≤0.046, and 16s rDNA copy numbers of Ruminococcus flavefaciens (P≤0.010. Non-fibre carbohydrate source did not affect daily microbial N flow regardless of dietary RDP, but ammonia N production was lower for inulin than for starch treatments under high RDP conditions (P<0.001. Compared with starch treatments, inulin depressed the copy numbers of Fibrobacter succinogenes in solid fraction (P=0.023 and R. flavefaciens in liquid (P=0.017 and solid fractions (P=0.007, but it increased the carboxymethylcellulase activity in solid fraction (P=0.045. Current results suggest that starch and inulin differ in ruminal volatile fatty acid fermentation but have similar effects on ruminal digestion and microbial synthesis in vitro, although inulin suppressed the growth of partial ruminal cellulolytic bacteria.

  20. Modelling the microbial quality and safety of foods

    NARCIS (Netherlands)

    Wijtzes, T.

    1996-01-01

    Quality and safety of foods are often influenced by the presence and growth of microorganisms. Microorganisms in foods can be divided into two groups: pathogenic organisms, causing illness, and microorganisms that are not harmful to health, but that can spoil a product. Presence and growth of

  1. The effect of microbial inocula on the growth of black locust, Siberian elm and silver maple seedlings

    Directory of Open Access Journals (Sweden)

    Hajnal-Jafari Timea

    2014-01-01

    Full Text Available Growth and development of forest plants depend mostly on the soil microbial activity since no mineral or organic fertilizers are applied. Microbial processes can be activated and conditions for plants development improved with the introduction of selected microorganisms in the soil. With the aim of obtaining quality planting material in a shorter period of time, the effects of Azotobacter chroococcum and Streptomyces sp. on the early growth of black locust (Robinia pseudoacacia, Siberian elm (Ulmus pumila and silver-leaf maple (Acer dasycarpum were investigated in this study. Microorganisms were applied individually and in a mixture (1:1. Plant height was measured on the 90th, 120th and 180th day after planting. Plant diameter, as well as the number of actinomycetes and azotobacters was measured at the end of the vegetation period (180 days after planting. Applied microorganisms had a positive effect on the seedling height in all three plant species, with the best effect found in the black locust. Effectiveness of applied microorganisms on seedling diameter was the highest in the silver-leaf maple. The largest number of azotobacters was found in the rhizosphere of black locust. Number of microorganisms from both groups was increased in the inoculated variants. [Projekat Ministarstva nauke Republike Srbije, br. III 43002

  2. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  3. Towards the understanding of microbial metabolism in relation to microbial enhanced oil recovery

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Nielsen, Sidsel Marie; Nielsen, Kristian Fog

    2017-01-01

    In this study, Bacillus licheniformis 421 was used as a model organism to understand the effects of microbial cell growth and metabolite production under anaerobic conditions in relation to microbial enhanced oil recovery. The bacterium was able to grow anaerobically on different carbon compounds...

  4. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.

    Science.gov (United States)

    Kerr, B J; Weber, T E; Ziemer, C J

    2015-05-01

    control diet. In Exp. 2, no effect of dietary marker on pig performance was noted. Overall, the data indicate that the inclusion of Cr2O3, Fe2O3, or TiO2 as digestibility markers have little to no impact on microbial ecology, fecal ammonia or VFA concentrations, nutrient digestibility, or pig growth performance indicating they are suitable for use in digestion studies.

  5. Mathematical foundations of the dendritic growth models.

    Science.gov (United States)

    Villacorta, José A; Castro, Jorge; Negredo, Pilar; Avendaño, Carlos

    2007-11-01

    At present two growth models describe successfully the distribution of size and topological complexity in populations of dendritic trees with considerable accuracy and simplicity, the BE model (Van Pelt et al. in J. Comp. Neurol. 387:325-340, 1997) and the S model (Van Pelt and Verwer in Bull. Math. Biol. 48:197-211, 1986). This paper discusses the mathematical basis of these models and analyzes quantitatively the relationship between the BE model and the S model assumed in the literature by developing a new explicit equation describing the BES model (a dendritic growth model integrating the features of both preceding models; Van Pelt et al. in J. Comp. Neurol. 387:325-340, 1997). In numerous studies it is implicitly presupposed that the S model is conditionally linked to the BE model (Granato and Van Pelt in Brain Res. Dev. Brain Res. 142:223-227, 2003; Uylings and Van Pelt in Network 13:397-414, 2002; Van Pelt, Dityatev and Uylings in J. Comp. Neurol. 387:325-340, 1997; Van Pelt and Schierwagen in Math. Biosci. 188:147-155, 2004; Van Pelt and Uylings in Network. 13:261-281, 2002; Van Pelt, Van Ooyen and Uylings in Modeling Dendritic Geometry and the Development of Nerve Connections, pp 179, 2000). In this paper we prove the non-exactness of this assumption, quantify involved errors and determine the conditions under which the BE and S models can be separately used instead of the BES model, which is more exact but considerably more difficult to apply. This study leads to a novel expression describing the BE model in an analytical closed form, much more efficient than the traditional iterative equation (Van Pelt et al. in J. Comp. Neurol. 387:325-340, 1997) in many neuronal classes. Finally we propose a new algorithm in order to obtain the values of the parameters of the BE model when this growth model is matched to experimental data, and discuss its advantages and improvements over the more commonly used procedures.

  6. Tropical terrestrial model ecosystems for evaluation of soil fauna and leaf litter quality effects on litter consumption, soil microbial biomass and plant growth Efeitos de fauna de solo e qualidade de liteira sobre o consumo, biomassa microbiana e crescimento de plantas em modelo de ecossistemas terrestres tropicais

    Directory of Open Access Journals (Sweden)

    Bernhard Förster

    2009-08-01

    Full Text Available The aim of this work was to evaluate whether terrestrial model ecosystems (TMEs are a useful tool for the study of the effects of litter quality, soil invertebrates and mineral fertilizer on litter decomposition and plant growth under controlled conditions in the tropics. Forty-eight intact soil cores (17.5-cm diameter, 30-cm length were taken out from an abandoned rubber plantation on Ferralsol soil (Latossolo Amarelo in Central Amazonia, Brazil, and kept at 28ºC in the laboratory during four months. Leaf litter of either Hevea pauciflora (rubber tree, Flemingia macrophylla (a shrubby legume or Brachiaria decumbens (a pasture grass was put on top of each TME. Five specimens of either Pontoscolex corethrurus or Eisenia fetida (earthworms, Porcellionides pruinosus or Circoniscus ornatus (woodlice, and Trigoniulus corallinus (millipedes were then added to the TMEs. Leaf litter type significantly affected litter consumption, soil microbial biomass and nitrate concentration in the leachate of all TMEs, but had no measurable effect on the shoot biomass of rice seedlings planted in top soil taken from the TMEs. Feeding rates measured with bait lamina were significantly higher in TMEs with the earthworm P. corethrurus and the woodlouse C. ornatus. TMEs are an appropriate tool to assess trophic interactions in tropical soil ecossistems under controlled laboratory conditions.O objetivo deste trabalho foi avaliar o modelo de ecossistema terrestre (TME como ferramenta para o estudo dos efeitos da qualidade da liteira, de invertebrados do solo e da fertilização mineral na decomposição da liteira e no crescimento das plantas em condições controladas. Foram coletados quarenta e oito cilindros de solo intacto (Latossolo Amarelo de 17,5 cm de diâmetro e 30 cm de comprimento em um seringal abandonado na Amazônia Central brasileira e mantidos a 28ºC em laboratório, por quatro meses. Folhas da liteira de Hevea pauciflora (seringueira, ou de Flemingia

  7. Analysis of the microbial growth in 60Co γ-irradiated foods by calorimetry

    International Nuclear Information System (INIS)

    Furuta, Masakazu; Hayashi, Toshio; Hamasaki, Koji; Wirkner, Sandra; Constantinoiu, Elena; Takahashi, Katsutada

    2002-01-01

    Using a heat conduction calorimeter equipped with 24 sample units the heat evolutions from growing 60 Co γ-irradiated bioburden of black pepper seeds and frozen beef were detected in the form of growth thermograms. 60 Co γ-irradiation affected the growth pattern in which a dose-dependent reduction of the growth rate constant was observed together with the retardation in growth, indicating a combination of bactericidal and bacteriostatic effects. We successfully determined the minimal inactivation doses for the two food samples using the relationship between the irradiation dose and the retardation in growth t α , or the growth rate constant μ obtained from the growth thermograms. These results strongly suggested the possibility of calorimetry as measure of predictive microbiology in food irradiation. (author)

  8. Analysis of the microbial growth in 60Co gamma-irradiated foods by calorimetry

    International Nuclear Information System (INIS)

    Furuta, M.; Hamasaki, K.; Wirkner, S.; Constantinoiu, E.; Takahashi, K.; Hayashi, T.

    2002-01-01

    Using a heat conduction calorimeter equipped with 24 sample units the heat evolutions from growing 60Co gamma-irradiated bioburden of black pepper seeds and frozen beef were detected in the form of growth thermograms. 60Co gamma-irradiation affected the growth pattern in which a dose-dependent reduction of the growth rate constant was observed together with the retardation in growth, indicating a combination of bactericidal and bacteriostatic effects. We successfully determined the minimal inactivation doses for the two food samples using the relationship between the irradiation dose and the retardation in growth talpha, or the growth rate constant mu obtained from the growth thermograms. These results strongly suggested the possibility of calorimetry as a measure of predictive microbiology in food irradiation

  9. Modeling error distributions of growth curve models through Bayesian methods.

    Science.gov (United States)

    Zhang, Zhiyong

    2016-06-01

    Growth curve models are widely used in social and behavioral sciences. However, typical growth curve models often assume that the errors are normally distributed although non-normal data may be even more common than normal data. In order to avoid possible statistical inference problems in blindly assuming normality, a general Bayesian framework is proposed to flexibly model normal and non-normal data through the explicit specification of the error distributions. A simulation study shows when the distribution of the error is correctly specified, one can avoid the loss in the efficiency of standard error estimates. A real example on the analysis of mathematical ability growth data from the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 is used to show the application of the proposed methods. Instructions and code on how to conduct growth curve analysis with both normal and non-normal error distributions using the the MCMC procedure of SAS are provided.

  10. Modelling the growth of Listeria monocytogenes on the surface of smear- or mould-ripened cheese

    Directory of Open Access Journals (Sweden)

    Sol eSchvartzman

    2014-07-01

    Full Text Available Surface-ripened cheeses are matured by means of manual or mechanical technologies posing a risk of cross-contamination, if any cheeses are contaminated with Listeria monocytogenes. In predictive microbiology, primary models are used to describe microbial responses, such as growth rate over time and secondary models explain how those responses change with environmental factors. In this way, primary models were used to assess the growth rate of L. monocytogenes during ripening of the cheeses and the secondary models to test how much the growth rate was affected by either the pH and/or the water activity (aw of the cheeses. The two models combined can be used to predict outcomes. The purpose of these experiments was to test three primary (the modified Gompertz equation, the Baranyi and Roberts model and the Logistic model and three secondary (the Cardinal model, the Ratowski model and the Presser model mathematical models in order to define which combination of models would best predict the growth of L. monocytogenes on the surface of artificially contaminated surface-ripened cheeses. Growth on the surface of the cheese was assessed and modelled. The primary models were firstly fitted to the data and the effects of pH and aw on the growth rate (μmax were incorporated and assessed one by one with the secondary models. The Logistic primary model by itself did not show a better fit of the data among the other primary models tested, but the inclusion of the Cardinal secondary model improved the final fit. The aw was not related to the growth of Listeria. This study suggests that surface-ripened cheese should be separately regulated within EU microbiological food legislation and results expressed as counts per surface area rather than per gram.

  11. Modeling the growth of Listeria monocytogenes on the surface of smear- or mold-ripened cheese.

    Science.gov (United States)

    Schvartzman, M Sol; Gonzalez-Barron, Ursula; Butler, Francis; Jordan, Kieran

    2014-01-01

    Surface-ripened cheeses are matured by means of manual or mechanical technologies posing a risk of cross-contamination, if any cheeses are contaminated with Listeria monocytogenes. In predictive microbiology, primary models are used to describe microbial responses, such as growth rate over time and secondary models explain how those responses change with environmental factors. In this way, primary models were used to assess the growth rate of L. monocytogenes during ripening of the cheeses and the secondary models to test how much the growth rate was affected by either the pH and/or the water activity (aw) of the cheeses. The two models combined can be used to predict outcomes. The purpose of these experiments was to test three primary (the modified Gompertz equation, the Baranyi and Roberts model, and the Logistic model) and three secondary (the Cardinal model, the Ratowski model, and the Presser model) mathematical models in order to define which combination of models would best predict the growth of L. monocytogenes on the surface of artificially contaminated surface-ripened cheeses. Growth on the surface of the cheese was assessed and modeled. The primary models were firstly fitted to the data and the effects of pH and aw on the growth rate (μmax) were incorporated and assessed one by one with the secondary models. The Logistic primary model by itself did not show a better fit of the data among the other primary models tested, but the inclusion of the Cardinal secondary model improved the final fit. The aw was not related to the growth of Listeria. This study suggests that surface-ripened cheese should be separately regulated within EU microbiological food legislation and results expressed as counts per surface area rather than per gram.

  12. Integrated Intelligent Modeling, Design and Control of Crystal Growth Processes

    National Research Council Canada - National Science Library

    Prasad, V

    2000-01-01

    .... This MURI program took an integrated approach towards modeling, design and control of crystal growth processes and in conjunction with growth and characterization experiments developed much better...

  13. A unique model system of microbial carbonate precipitation: Stromatolites of Lagoa Vermelha, Brazil

    Science.gov (United States)

    Warthmann, R. J.; Vasoncelos, C.; van Lith, Y.; Visscher, P. T.; McKenzie, J. A.

    2003-04-01

    this unique model ecosystem controlling microbial carbonate, including dolomite precipitation will provide important insights about ancient biomineralization processes, especially during the Precambrian.

  14. Quantification of nitrous oxide (N2O) emissions and soluble microbial product (SMP) production by a modified AOB-NOB-N2O-SMP model.

    Science.gov (United States)

    Kim, MinJeong; Wu, Guangxue; Yoo, ChangKyoo

    2017-03-01

    A modified AOB-NOB-N 2 O-SMP model able to quantify nitrous oxide (N 2 O) emissions and soluble microbial product (SMP) production during wastewater treatment is proposed. The modified AOB-NOB-N 2 O-SMP model takes into account: (1) two-step nitrification by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), (2) N 2 O production by AOB denitrification under oxygen-limited conditions and (3) SMP production by microbial growth and endogenous respiration. Validity of the modified model is demonstrated by comparing the simulation results with experimental data from lab-scale sequencing batch reactors (SBRs). To reliably implement the modified model, a model calibration that adjusts model parameters to fit the model outputs to the experimental data is conducted. The results of this study showed that the modeling accuracy of the modified AOB-NOB-N 2 O-SMP model increases by 19.7% (NH 4 ), 51.0% (NO 2 ), 57.8% (N 2 O) and 16.7% (SMP) compared to the conventional model which does not consider the two-step nitrification and SMP production by microbial endogenous respiration. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

    Directory of Open Access Journals (Sweden)

    Yang Zamin K

    2010-05-01

    Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

  16. Modelling diameter growth, mortality and recruitment of trees in ...

    African Journals Online (AJOL)

    Modelling diameter growth, mortality and recruitment of trees in miombo woodlands of Tanzania. ... Individual tree diameter growth and mortality models, and area-based recruitment models were developed. ... AJOL African Journals Online.

  17. Differences in microbial communities and performance between suspended and attached growth anaerobic membrane bioreactors treating synthetic municipal wastewater

    KAUST Repository

    Harb, Moustapha

    2015-08-14

    Two lab-scale anaerobic membrane bioreactors (AnMBRs), one up-flow attached-growth (UA) and another continuously stirred (CSTR), were operated under mesophilic conditions (35 °C) while treating synthetic municipal wastewater (800 mg L−1 COD). Each reactor was attached to both polyvinylidene fluoride (PVDF) and polyethersulfone (PES) microfiltration (MF) membranes in an external cross-flow configuration. Both reactors were started up and run under the same operating conditions for multiple steady-state experiments. Chemical oxygen demand (COD) removal rates were similar for both reactors (90–96%), but captured methane was found to be 11–18% higher for the CSTR than the UA reactor. Ion Torrent sequencing targeting 16S rRNA genes showed that several operational taxonomic units (OTUs) most closely related to fermentative bacteria (e.g., Microbacter margulisiae) were dominant in the suspended biomass of the CSTR, accounting for 30% of the microbial community. Conversely, methanogenic archaea (e.g., Methanosaeta) and syntrophic bacteria (e.g., Smithella propionica) were found in significantly higher relative abundances in the UA AnMBR as compared to the CSTR due to their affinity for surface attachment. Of the methanogens that were present in the CSTR sludge, hydrogenotrophic methanogens dominated (e.g., Methanobacterium). Measured EPS (both proteins and carbohydrates), which has been broadly linked to fouling, was determined to be consistently lower in the UA AnMBR membrane samples than in CSTR AnMBR membrane samples. Principal component analysis (PCA) based on HPLC profiles of soluble microbial products (SMPs) further demonstrated these differences between reactor types in replicate runs. The results of this study showed that reactor configuration can significantly impact the development of the microbial communities of AnMBRs that are responsible for both membrane and reactor performance.

  18. Inorganic phosphorus fertilizer ameliorates maize growth by reducing metal uptake, improving soil enzyme activity and microbial community structure.

    Science.gov (United States)

    Wu, Wencheng; Wu, Jiahui; Liu, Xiaowen; Chen, Xianbin; Wu, Yingxin; Yu, Shixiao

    2017-09-01

    Recently, several studies have showed that both organic and inorganic fertilizers are effective in immobilizing heavy metals at low cost, in comparison to other remediation strategies for heavy metal-contaminated farmlands. A pot trial was conducted in this study to examine the effects of inorganic P fertilizer and organic fertilizer, in single application or in combination, on growth of maize, heavy metal availabilities, enzyme activities, and microbial community structure in metal-contaminated soils from an electronic waste recycling region. Results showed that biomass of maize shoot and root from the inorganic P fertilizer treatments were respectively 17.8 and 10.0 folds higher than the un-amended treatments (CK), while the biomass in the organic fertilizer treatments was only comparable to the CK. In addition, there were decreases of 85.0% in Cd, 74.3% in Pb, 66.3% in Cu, and 91.9% in Zn concentrations in the roots of maize grown in inorganic P fertilizer amended soil. Consistently, urease and catalase activities in the inorganic P fertilizer amended soil were 3.3 and 2.0 times higher than the CK, whereas no enhancement was observed in the organic fertilizer amended soil. Moreover, microbial community structure was improved by the application of inorganic P fertilizer, but not by organic fertilizer; the beneficial microbial groups such as Kaistobacter and Koribacter were most frequently detected in the inorganic P fertilizer amended soil. The negligible effect from the organic fertilizer might be ascribed to the decreased pH value in soils. The results suggest that the application of inorganic P fertilizer (or in combination with organic fertilizer) might be a promising strategy for the remediation of heavy metals contaminated soils in electronic waste recycling region. Copyright © 2017. Published by Elsevier Inc.

  19. Combined treatment with mild heat, manothermosonication and pulsed electric fields reduces microbial growth in milk

    OpenAIRE

    Halpin, R. M.; Cregenzan-Alberti, O.; Whyte, P.; Lyng, J. G.; Noci, F.

    2013-01-01

    In recent years, there has been considerable interest in non-thermal milk processing. The objective of the present study was to assess the efficacy of two non-thermal technologies (manothermosonication; MTS, and pulsed electric fields; PEF) in comparison to thermal pasteurisation, by assessing the microbial levels of each of these milk samples post-processing. Homogenised milk was subjected to MTS (frequency; 20 kHz, amplitude; 27.9 μm, pressure; 225 kPa) at two temperatures (37 °C or 55 °C),...

  20. Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis

    Science.gov (United States)

    Chen, Mingjie; Abriola, Linda M.; Amos, Benjamin K.; Suchomel, Eric J.; Pennell, Kurt D.; Löffler, Frank E.; Christ, John A.

    2013-08-01

    Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time

  1. Influence of Inoculation, Nitrogen and Phosphorus Levels on Wheat Growth and Soil Microbial Biomass-N Using 15N Techniques

    International Nuclear Information System (INIS)

    Galal, Y.G.; El-Ghandour, I.A.; Abdel Raouf, A.M.; Osman, M.E.

    2003-01-01

    Pot experiment was carried out with wheat that cultivated in virgin sandy soil and inoculated with Rhizobium (Rh), mycorrhizea (VAM) and mixture of both. The objective of this work was to verify the potential of these inoculum on wheat production, nutrient acquisition and microbial biomass N (MBN) contribution as affected by N and P fertilizers levels. MBN was detected through the fumigation-extraction method. Nitrogen and phosphorus fertilizers were applied at three levels, 0; 25 ppm N and 3.3 ppm P and 50 ppm N and 6.6 ppm P in the form of ( 15 NH 4 ) 2 SO 4 , 5% atom excess and super-phosphate, respectively. The effect of inoculation and chemical fertilizers on dry matter (DM), N and P uptake (shoot and grain) and MBN were traced. The obtained data revealed that the highest DM and N uptake by wheat shoot were recorded with the dual inoculation (Rh + VAM) at the highest level of N and P fertilizers. The highest grain yield was detected with single inoculum of AM fungi while N and P uptake were with dual inoculation at the same rate of fertilizers. Inoculation with Rh either alone or in combination with VAM have a positive and stimulative effect on wheat growth and N and P uptake indicating the possibilities of extending the use of symbiotic microorganisms to be applied with cereals. The fluctuation in the soil microbial biomass N did not gave a chance to recognize, exactly, the impact of inoculation and/or fertilization levels

  2. Effects of forage:concentrate ratio and forage type on apparent digestibility, ruminal fermentation, and microbial growth in goats.

    Science.gov (United States)

    Cantalapiedra-Hijar, G; Yáñez-Ruiz, D R; Martín-García, A I; Molina-Alcaide, E

    2009-02-01

    The effects of forage type and forage:concentrate ratio (F:C) on apparent nutrient digestibility, ruminal fermentation, and microbial growth were investigated in goats. A comparison between liquid (LAB) and solid (SAB)-associated bacteria to estimate microbial N flow (MNF) from urinary purine derivative excretion was also examined. Treatments were a 2 x 2 factorial arrangement of forage type (grass hay vs. alfalfa hay) and high vs. low F:C (70:30 and 30:70, respectively). Four ruminally cannulated goats were fed, at maintenance intake, 4 experimental diets according to a 4 x 4 Latin square design. High-concentrate diets resulted in greater (P 0.05) when diets included alfalfa hay. Total protozoa numbers and holotricha proportion were greater and less (P forage used. The MNF measured in goats fed different diets was influenced by the bacterial pellet (LAB or SAB). In addition, the purine bases:N ratio values found were different from those reported in the literature, which underlines the need for these variables to be analyzed directly in pellets isolated from specific animals and experimental conditions.

  3. Inhibition of Microbial Growth by Fatty Amine Catalysts from Polyurethane Foam Test Tube Plugs

    Science.gov (United States)

    Bach, John A.; Wnuk, Richard J.; Martin, Delano G.

    1975-01-01

    When polyurethane foam test tube plugs are autoclaved, they release volatile fatty amines that inhibit the growth of some microorganisms. The chemical structures of these amines were determined by the use of a gas chromatographmass spectrometer. They are catalysts used to produce the foam. The problem of contaminating growth media with toxic substances released from polymeric materials is discussed. PMID:1096816

  4. Modeling time-series data from microbial communities.

    Science.gov (United States)

    Ridenhour, Benjamin J; Brooker, Sarah L; Williams, Janet E; Van Leuven, James T; Miller, Aaron W; Dearing, M Denise; Remien, Christopher H

    2017-11-01

    As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

  5. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

    Science.gov (United States)

    Metcalf, Jessica L; Wegener Parfrey, Laura; Gonzalez, Antonio; Lauber, Christian L; Knights, Dan; Ackermann, Gail; Humphrey, Gregory C; Gebert, Matthew J; Van Treuren, Will; Berg-Lyons, Donna; Keepers, Kyle; Guo, Yan; Bullard, James; Fierer, Noah; Carter, David O; Knight, Rob

    2013-01-01

    Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI: http://dx.doi.org/10.7554/eLife.01104.001 PMID:24137541

  6. Growth models and analysis of development

    Energy Technology Data Exchange (ETDEWEB)

    Mathur, G

    1979-10-01

    This paper deals with remnants of neoclassical elements in Keynesian and post-Keynesian thought, and attempts to demonstrate that the elimination of these elements from our modes of thinking would not impoverish economic analysis as a means of solving real problems. In the Keynesian analysis the causation from investment to savings is exhibited in terms of income determination. When put in terms of a capital-theory model, the vector of savings is represented in two ways: real savings and counterpart real savings. The former coincides with the investment vector and the latter with the vector of consumption goods foregone for diverting resources towards equipment making. Thus the Keynesian causation in capital theory terms makes the concept of national savings as an independent variable redudant. The Robinsonian causation in a golden age with full employment and its reversal of direction in a steady state with non-employment are then considered. But in each of these, variables like rate of savings and output/capital ratio are found to be dormant variables. They are termed as null variables which, being of no account in both full-employment and unemployment situations, could, without loss, be deleted from the repertory of analytical tools. The Harrod formula of warranted rate of growth, when put in causal form, thus becomes a redundant portion of economics of growth. The real determinants of the growth rate and real wage rate on which the analysis of growth or of development should be based, are also depicted.

  7. The effect of dosages of microbial consortia formulation and synthetic fertilizer on the growth and yield of field-grown chili

    Science.gov (United States)

    Istifadah, N.; Sapta, D.; Krestini, H.; Natalie, B.; Suryatmana, P.; Nurbaity, A.; Hidersah, R.

    2018-03-01

    Chili (Capsicum annuum, L) is one of important horticultural crop in Indonesia. Formulation of microbial consortia containing Bacillus subtilis, Pseudomonas sp., Azotobacter chroococcum and Trichoderma harzianum has been developed. This study evaluated the effects of dosage of the microbial formulation combined with NPK fertilizer on growth and yield of chili plants in the field experiment. The experiment was arranged in completely randomized design of factorial, in which the first factor was dosage of formulation (0, 2.5, 5.0, 7.5, 10 g per plant) and the second factor was NPK fertilizer dosage (0, 25, 50 and 75% of the standard dosage). The treatments were replicated three times. For application, the formulation was mixed with chicken manure 1:10 (w/v). The results showed that application of microbial formulation solely improved the chili growth. There was interaction between dosages of the microbial formulation and NPK fertilizer in improving plant height, nitrogen availability and the chili yield, while there was no interaction between those dosages in improving the root length. Combination between microbial formulation at the dosage of 5.0-7.5 g per plant combined with NPK fertilizer with the dosage 50 or 75% of the standard dosage support relatively better growth and the chili yield.

  8. Mechanistic model coupling gas exchange dynamics and Listeria monocytogenes growth in modified atmosphere packaging of non respiring food.

    Science.gov (United States)

    Chaix, E; Broyart, B; Couvert, O; Guillaume, C; Gontard, N; Guillard, V

    2015-10-01

    A mechanistic model coupling O2 and CO2 mass transfer (namely diffusion and solubilisation in the food itself and permeation through the packaging material) to microbial growth models was developed aiming at predicting the shelf life of modified atmosphere packaging (MAP) systems. It was experimentally validated on a non-respiring food by investigating concomitantly the O2/CO2 partial pressure in packaging headspace and the growth of Listeria monocytogenes (average microbial count) within the food sample. A sensitivity analysis has revealed that the reliability of the prediction by this "super-parametrized" model (no less than 47 parameters were required for running one simulation) was strongly dependent on the accuracy of the microbial input parameters. Once validated, this model was used to decipher the role of O2/CO2 mass transfer on microbial growth and as a MAP design tool: an example of MAP dimensioning was provided in this paper as a proof of concept. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Modeling and control of greenhouse crop growth

    CERN Document Server

    Rodríguez, Francisco; Guzmán, José Luis; Ramírez-Arias, Armando

    2015-01-01

    A discussion of challenges related to the modeling and control of greenhouse crop growth, this book presents state-of-the-art answers to those challenges. The authors model the subsystems involved in successful greenhouse control using different techniques and show how the models obtained can be exploited for simulation or control design; they suggest ideas for the development of physical and/or black-box models for this purpose. Strategies for the control of climate- and irrigation-related variables are brought forward. The uses of PID control and feedforward compensators, both widely used in commercial tools, are summarized. The benefits of advanced control techniques—event-based, robust, and predictive control, for example—are used to improve on the performance of those basic methods. A hierarchical control architecture is developed governed by a high-level multiobjective optimization approach rather than traditional constrained optimization and artificial intelligence techniques.  Reference trajector...

  10. Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves

    Directory of Open Access Journals (Sweden)

    Huiling Mao

    2017-11-01

    Full Text Available Objective This study was conducted to investigate the effects of weaning times on the growth performance, rumen fermentation and microbial communities of yellow cattle calves. Methods Eighteen calves were assigned to a conventional management group that was normally weaned (NW, n = 3 or to early weaned (EW group where calves were weaned when the feed intake of solid feed (starter reached 500 g (EW500, n = 5, 750 g (EW750, n = 5, or 1,000 g (EW1,000, n = 5. Results Compared with NW, the EW treatments increased average daily gain (p0.05, but changes in bacterial composition were found. Conclusion From the present study, it is inferred that EW is beneficial for rumen fermentation, and weaning when the feed intake of the starter reached 750 g showed much better results.

  11. Production of biosurfactant from Bacillus licheniformis for microbial enhanced oil recovery and inhibition the growth of sulfate reducing bacteria

    Directory of Open Access Journals (Sweden)

    H.S. El-Sheshtawy

    2015-06-01

    Full Text Available In this study, the bacterium Bacillus licheniformis has been isolated from oil reservoir; the ability of this bacterium to produce a biosurfactant was detected. Surface properties of the produced biosurfactant were confirmed by determining the emulsification power as well as surface and interfacial tension. The crude biosurfactant has been extracted from supernatant culture growth, and the yield of crude biosurfactant was about 1 g/l. Also, chemical structure of the produced biosurfactant was confirmed using FTIR analysis. Results revealed that, the emulsification power has been increased up to 96% and the surface tension decreased from 72 of distilled water to 36 mN/m after 72 h of incubation. The potential application of this bacterial species in microbial-enhanced oil recovery (MEOR was investigated. The percent of oil recovery was 16.6% upon application in a sand pack column designed to stimulate an oil recovery. It also showed antimicrobial activity against the growth of different strains of SRB (sulfate reducing bacteria. Results revealed that a complete inhibition of SRB growth using 1.0% crude biosurfactant is achieved after 3 h.

  12. Transitions in a probabilistic interface growth model

    International Nuclear Information System (INIS)

    Alves, S G; Moreira, J G

    2011-01-01

    We study a generalization of the Wolf–Villain (WV) interface growth model based on a probabilistic growth rule. In the WV model, particles are randomly deposited onto a substrate and subsequently move to a position nearby where the binding is strongest. We introduce a growth probability which is proportional to a power of the number n i of bindings of the site i: p i ∝n i ν . Through extensive simulations, in (1 + 1) dimensions, we find three behaviors depending on the ν value: (i) if ν is small, a crossover from the Mullins–Herring to the Edwards–Wilkinson (EW) universality class; (ii) for intermediate values of ν, a crossover from the EW to the Kardar–Parisi–Zhang (KPZ) universality class; and, finally, (iii) for large ν values, the system is always in the KPZ class. In (2 + 1) dimensions, we obtain three different behaviors: (i) a crossover from the Villain–Lai–Das Sarma to the EW universality class for small ν values; (ii) the EW class is always present for intermediate ν values; and (iii) a deviation from the EW class is observed for large ν values

  13. Effects of Resveratrol and Essential Oils on Growth Performance, Immunity, Digestibility and Fecal Microbial Shedding in Challenged Piglets

    Directory of Open Access Journals (Sweden)

    S. T. Ahmed

    2013-05-01

    Full Text Available A study was conducted to evaluate the effects of resveratrol and essential oils from medicinal plants on the growth performance, immunity, digestibility, and fecal microbial shedding of weaned piglets. A total of 48 weaned piglets (8 kg initial weight, 28-d-old were randomly allotted to four dietary treatments with 3 replications of 4 piglets each. The dietary treatments were NC (negative control; basal diet, PC (positive control; basal diet+0.002% apramycin, T1 (basal diet+0.2% resveratrol, and T2 (basal diet+0.0125% essential oil blend. All piglets were orally challenged with 5 ml culture fluid containing 2.3×108 cfu/ml of Escherichia coli KCTC 2571 and 5.9×108 cfu/ml Salmonella enterica serover Typhimurium. The PC group (p0.05. Serum IgG level was increased in the T1 group, whereas TNF-α levels was reduced in the supplemented groups compared to control (p<0.05. The PC diet improved the dry matter (DM digestibility, whereas PC and T2 diets improved nitrogen (N digestibility compared to NC and T1 diets (p<0.05. Fecal Salmonella and E. coli counts were reduced in all treatment groups compared to control (p<0.05. Fecal Lactobacillus spp. count was increased in the T2 group compared to others (p<0.05. Dietary treatments had no significant effect on fecal Bacillus spp. count throughout the entire experimental period. Based on these results, resveratrol showed strong potential as antibiotic alternatives for reversing the adverse effects of weaning stress on growth performance, immunity and microbial environment in E. coli and Salmonella-challenged piglets.

  14. Influence of pulsed magnetic field on soybean (Glycine max L.) seed germination, seedling growth and soil microbial population.

    Science.gov (United States)

    Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

    2013-08-01

    The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean.

  15. Effects of 2-hydroxy-4-(methylthio) butanoic acid (HMB) on microbial growth in continuous culture.

    Science.gov (United States)

    Noftsger, S M; St-Pierre, N R; Karnati, S K R; Firkins, J L

    2003-08-01

    2-Hydroxy-4-(methylthio) butanoic acid (HMB) positively affects milk composition and yield, potentially through ruminal actions. Four continuous culture fermenters were used to determine the optimal concentration of HMB for digestibility of organic matter (OM), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose and synthesis of microbial N. A highly degradable mix of hay and grain was used as a basal diet to simulate a typical lactation diet. Three concentrations of HMB (0, 0.055, and 0.110%) and one concentration of dl-Met (0.097%) were infused into the fermenters according to a 4 x 4 Latin square design. Digesta samples were collected during the last 3 d of each of the four 10-d experimental periods. Digestibility of OM, hemicellulose, and NDF was largely insensitive to treatment. Digestibility of ADF showed a quadratic effect to supplementation of HMB, with 0.055% having lower digestibility than 0 or 0.110%. Total production of VFA was not influenced by HMB supplementation, but differences in concentration and production of individual VFA were seen. Isobutyrate increased linearly with increasing HMB supplementation. Propionate concentration decreased linearly with increased HMB supplementation, but propionate production showed a quadratic trend (P = 0.13). A higher concentration of acetate was detected for dl-Met compared with the highest HMB concentration. There were trends (P HMB. Microbial efficiency was not different among treatments. The proportion of bacterial N produced from NH3-N decreased linearly with increasing HMB, and bacteria receiving dl-Met synthesized more N from NH3-N than those receiving HMB. These data suggest that supplementation of HMB may have a sparing effect on branched chain volatile fatty acids because the fatty acids are not needed to provide carbon for synthesis of valine, isoleucine and leucine with ammonia. Comparisons of bacterial community structure in the fermenter effluent samples using PCR amplicons

  16. Modeling of multibranched crosslike crack growth

    International Nuclear Information System (INIS)

    Canessa, E.; Tanatar, B.

    1991-06-01

    Multibranched crosslike crack patterns formed in concentrically loaded square plates are studied in terms of fractal geometry, where the associated fractal dimension d f is calculated for their characterization. We apply simplest deterministic and stochastic approaches at a phenomenological level in an attempt to find generic features as guidelines for future experimental and theoretical work. The deterministic model for fracture propagation we apply, which is a variant of the discretized Laplace approach for randomly ramified fractal cracks proposed by Takayasu, reproduces the basic ingredients of observed complex fracture patters. The stochastic model, although is not strictly a model for crack propagation, is based on diffusion-limited aggregation (DLA) for fractal growth and produces slightly more realistic assessment of the crosslike growth of the cracks in asymmetric multibranches. Nevertheless, this simple ad-hoc DLA-version for modeling the present phenomena as well as the deterministic approach for fracture propagation give fractal dimensionality for the fracture pattern in accord with our estimations made from recent experimental data. It is found that there is a crossover of two fractal dimensions, corresponding to the core (higher d f ) and multibranched crosslike (lower D f ) regions, that contains loops, that are interpreted as representing different symmetry regions within the square plates of finite size. (author). 26 refs, 5 figs

  17. A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

    Science.gov (United States)

    Yu, Zheng; Krause, Sascha M B; Beck, David A C; Chistoserdova, Ludmila

    2016-01-01

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

  18. PLANT-MICROBIAL INTERACTIONS IN THE RHIZOSPHERE – STRATEGIES FOR PLANT GROWTH-PROMOTION

    Directory of Open Access Journals (Sweden)

    Marius Stefan

    2012-03-01

    Full Text Available Plant growth-promoting rhizobacteria (PGPR are a group of bacteria that can actively colonize plant rootsand enhance plant growth using different mechanisms: production of plant growth regulators like indoleacetic acid,gibberellic acid, cytokinins and ethylene(Zahir et al., 2003, providing the host plant with fixed nitrogen, solubilizationof soil phosphorus, enhance Fe uptake, biocontrol, reducing the concentration of heavy metals. PGPR are perfectcandidates to be used as biofertilizers – eco-friendly alternative to common applied chemical fertilizer in today’sagriculture. The most important benefit of PGPR usage is related to the reduction of environmental pollution in conditionof increasing crop yield. This review presents the main mechanisms involved in PGPR promotion of plant growth.

  19. The porous surface model, a novel experimental system for online quantitative observation of microbial processes under unsaturated conditions

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Or, D.; Gulez, Gamze

    2008-01-01

    Water is arguably the most important constituent of microbial microhabitats due to its control of physical and physiological processes critical to microbial activity. In natural environments, bacteria often live on unsaturated surfaces, in thin (micrometric) liquid films. Nevertheless, no experim....... The PSM constitutes a tool uniquely adapted to study the influence of liquid film geometry on microbial processes. It should therefore contribute to uncovering mechanisms of microbial adaptation to unsaturated environments.......Water is arguably the most important constituent of microbial microhabitats due to its control of physical and physiological processes critical to microbial activity. In natural environments, bacteria often live on unsaturated surfaces, in thin (micrometric) liquid films. Nevertheless......, no experimental systems are available that allow real-time observation of bacterial processes in liquid films of controlled thickness. We propose a novel, inexpensive, easily operated experimental platform, termed the porous surface model (PSM) that enables quantitative real-time microscopic observations...

  20. Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere

    Directory of Open Access Journals (Sweden)

    Patrick M Herron

    2013-09-01

    Full Text Available The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constituitive promoter nptII and luxCDABE (coding for light-emitting proteins from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L., black poplar (Populus nigra L. or tomato (Solanum lycopersicum L. was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1-4 and 20-35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots.

  1. Microbial and Organic Fine Particle Transport Dynamics in Streams - a Combined Experimental and Stochastic Modeling Approach

    Science.gov (United States)

    Drummond, Jen; Davies-Colley, Rob; Stott, Rebecca; Sukias, James; Nagels, John; Sharp, Alice; Packman, Aaron

    2014-05-01

    Transport dynamics of microbial cells and organic fine particles are important to stream ecology and biogeochemistry. Cells and particles continuously deposit and resuspend during downstream transport owing to a variety of processes including gravitational settling, interactions with in-stream structures or biofilms at the sediment-water interface, and hyporheic exchange and filtration within underlying sediments. Deposited cells and particles are also resuspended following increases in streamflow. Fine particle retention influences biogeochemical processing of substrates and nutrients (C, N, P), while remobilization of pathogenic microbes during flood events presents a hazard to downstream uses such as water supplies and recreation. We are conducting studies to gain insights into the dynamics of fine particles and microbes in streams, with a campaign of experiments and modeling. The results improve understanding of fine sediment transport, carbon cycling, nutrient spiraling, and microbial hazards in streams. We developed a stochastic model to describe the transport and retention of fine particles and microbes in rivers that accounts for hyporheic exchange and transport through porewaters, reversible filtration within the streambed, and microbial inactivation in the water column and subsurface. This model framework is an advance over previous work in that it incorporates detailed transport and retention processes that are amenable to measurement. Solute, particle, and microbial transport were observed both locally within sediment and at the whole-stream scale. A multi-tracer whole-stream injection experiment compared the transport and retention of a conservative solute, fluorescent fine particles, and the fecal indicator bacterium Escherichia coli. Retention occurred within both the underlying sediment bed and stands of submerged macrophytes. The results demonstrate that the combination of local measurements, whole-stream tracer experiments, and advanced modeling

  2. Model-Based Analysis of the Potential of Macroinvertebrates as Indicators for Microbial Pathogens in Rivers

    Directory of Open Access Journals (Sweden)

    Rubén Jerves-Cobo

    2018-03-01

    Full Text Available The quality of water prior to its use for drinking, farming or recreational purposes must comply with several physicochemical and microbiological standards to safeguard society and the environment. In order to satisfy these standards, expensive analyses and highly trained personnel in laboratories are required. Whereas macroinvertebrates have been used as ecological indicators to review the health of aquatic ecosystems. In this research, the relationship between microbial pathogens and macrobenthic invertebrate taxa was examined in the Machangara River located in the southern Andes of Ecuador, in which 33 sites, according to their land use, were chosen to collect physicochemical, microbiological and biological parameters. Decision tree models (DTMs were used to generate rules that link the presence and abundance of some benthic families to microbial pathogen standards. The aforementioned DTMs provide an indirect, approximate, and quick way of checking the fulfillment of Ecuadorian regulations for water use related to microbial pathogens. The models built and optimized with the WEKA package, were evaluated based on both statistical and ecological criteria to make them as clear and simple as possible. As a result, two different and reliable models were obtained, which could be used as proxy indicators in a preliminary assessment of pollution of microbial pathogens in rivers. The DTMs can be easily applied by staff with minimal training in the identification of the sensitive taxa selected by the models. The presence of selected macroinvertebrate taxa in conjunction with the decision trees can be used as a screening tool to evaluate sites that require additional follow up analyses to confirm whether microbial water quality standards are met.

  3. Influence of mechanical disintegration on the microbial growth of aerobic sludge biomass: A comparative study of ultrasonic and shear gap homogenizers by oxygen uptake measurements.

    Science.gov (United States)

    Divyalakshmi, P; Murugan, D; Sivarajan, M; Saravanan, P; Lajapathi Rai, C

    2015-11-01

    Wastewater treatment plant incorporates physical, chemical and biological processes to treat and remove the contaminants. The main drawback of conventional activated sludge process is the huge production of excess sludge, which is an unavoidable byproduct. The treatment and disposal of excess sludge costs about 60% of the total operating cost. The ideal way to reduce excess sludge production during wastewater treatment is by preventing biomass formation within the aerobic treatment train rather than post treatment of the generated sludge. In the present investigation two different mechanical devices namely, Ultrasonic and Shear Gap homogenizers have been employed to disintegrate the aerobic biomass. This study is intended to restrict the multiplication of microbial biomass and at the same time degrade the organics present in wastewater by increasing the oxidative capacity of microorganisms. The disintegrability on biomass was determined by biochemical methods. Degree of inactivation provides the information on inability of microorganisms to consume oxygen upon disruption. The soluble COD quantifies the extent of release of intra cellular compounds. The participation of disintegrated microorganism in wastewater treatment process was carried out in two identical respirometeric reactors. The results show that Ultrasonic homogenizer is very effective in the disruption of microorganisms leading to a maximum microbial growth reduction of 27%. On the other hand, Shear gap homogenizer does not favor the sludge growth reduction rather it facilitates the growth. This study also shows that for better microbial growth reduction, floc size reduction alone is not sufficient but also microbial disruption is essential. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Biofilm growth on polyvinylchloride surface incubated in suboptimal microbial warm water and effect of sanitizers on biofilm removal post biofilm formation

    Science.gov (United States)

    An in vitro experiment was conducted to understand the nature of biofilm growth on polyvinyl chloride (PVC) surface when exposed to sub optimal quality microbial water (> 4 log10 cfu/ml) obtained from poultry drinking water source mimicking water in waterlines during the first week of poultry broodi...

  5. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

    Science.gov (United States)

    Garza, Daniel R; Dutilh, Bas E

    2015-11-01

    Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

  6. Analysis of stability to cheaters in models of antibiotic degrading microbial communities.

    Science.gov (United States)

    Szilágyi, András; Boza, Gergely; Scheuring, István

    2017-06-21

    Antibiotic resistance carried out by antibiotic degradation has been suggested recently as a new mechanism to maintain coexistence of microbial species competing on a single limiting resource, even in well-mixed homogeneous environments. Species diversity and community stability, however, critically depend on resistance against social cheaters, mutants that do not invest in production, but still enjoy the benefits provided by others. Here we investigate how different mutant cheaters affect the stability of antibiotic producing and degrading microbial communities. We consider two cheater types, production and degradation cheaters. We generalize the mixed inhibition-zone and chemostat models introduced previously [Kelsic, E. D., Zhao, J., Vetsigian, K., Kishony, R., 2015. Counteraction of an tibiotic production and degradation stabilizes microbial communities. Nature521, 516-519.] to study the population dynamics of microbial communities in well-mixed environment, and analyze the invasion of different cheaters in these models. We show that production cheaters, mutants that cease producing antibiotics, always destroy coexistence whenever there is a cost of producing these antibiotics. Degradation cheaters, mutants that loose their function of producing extracellular antibiotic degrading molecules, induce community collapse only if the cost of producing the degradation factors is above a critical level. Our analytical studies, supported by numerical simulations, highlight the sensitivity of antibiotic producing and degrading communities to loss-of-function mutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Kinetic modeling of cell metabolism for microbial production.

    Science.gov (United States)

    Costa, Rafael S; Hartmann, Andras; Vinga, Susana

    2016-02-10

    Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. A model of optimal protein allocation during phototrophic growth

    Czech Academy of Sciences Publication Activity Database

    Faizi, M.; Zavřel, Tomáš; Loureiro, C.; Červený, Jan; Steuer, Ralf

    2018-01-01

    Roč. 166, apr (2018), s. 26-36 ISSN 0303-2647 R&D Projects: GA MŠk(CZ) LO1415; GA ČR(CZ) GA15-17367S; GA MŠk(CZ) LM2015055 Institutional support: RVO:86652079 Keywords : Cellular protein economy * Cyanobacteria * Microbial growth laws * Photosynthesis * Resource allocation * Systems biology Subject RIV: EI - Biotechnology ; Bionics OBOR OECD: Environmental biotechnology Impact factor: 1.652, year: 2016

  9. Dietary microbial phytase exerts mixed effects on the gut health of tilapia: a possible reason for the null effect on growth promotion.

    Science.gov (United States)

    Hu, Jun; Ran, Chao; He, Suxu; Cao, Yanan; Yao, Bin; Ye, Yuantu; Zhang, Xuezhen; Zhou, Zhigang

    2016-06-01

    The present study evaluated the effects of dietary microbial phytase on the growth and gut health of hybrid tilapia (Oreochromis niloticus ♀×Oreochromis aureus ♂), focusing on the effect on intestinal histology, adhesive microbiota and expression of immune-related cytokine genes. Tilapia were fed either control diet or diet supplemented with microbial phytase (1000 U/kg). Each diet was randomly assigned to four groups of fish reared in cages (3×3×2 m). After 12 weeks of feeding, weight gain and feed conversion ratio of tilapia were not significantly improved by dietary microbial phytase supplementation. However, significantly higher level of P content in the scales, tighter and more regular intestinal mucosa folds were observed in the microbial phytase group and the microvilli density was significantly increased. The adhesive gut bacterial communities were strikingly altered by microbial phytase supplementation (0·41phytase, as indicated by the up-regulated intestinal expressions of the cytokine genes (tnf-α and tgf-β) and hsp70. In addition, the gut microvilli height was significantly decreased in the phytase group. These results indicate that dietary microbial phytase may exert mixed effects on hybrid tilapia, and can guide our future selection of phytases as aquafeed additives - that is, eliminating those that can stimulate intestinal inflammation.

  10. MATHEMATICAL MODELING OF THE ELECTRIC CURRENT GENERATION IN A MICROBIAL FUEL CELL INOCULATED WITH MARINE SEDIMENT

    Directory of Open Access Journals (Sweden)

    J. T. Teleken

    Full Text Available Abstract Microbial fuel cells (MFC are electrochemical devices that utilize the ability of some microorganisms to oxidize organic matter and transfer electrons resulting from their metabolism to an insoluble acceptor. The goal of the present study was to model the kinetics of electrical current generation from an MFC inoculated with marine sediment. For this purpose, a differential equation system was used, including the Nernst-Monod relationship and Ohm's Law, to describe the microbial metabolism and the mechanism of extracellular electron transfer (EET, respectively. The experimental data obtained by cyclic voltammetry analysis were properly described by the model. It was concluded that marine microorganisms preferably use a direct mechanism of EET by means of nanowires to establish the electrochemical contact with the anode. The mathematical modeling could help understand MFC operation and, consequently, contribute to improving power generation from this source.

  11. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production.

    Science.gov (United States)

    Cheng, Xiaoliang; Hiras, Jennifer; Deng, Kai; Bowen, Benjamin; Simmons, Blake A; Adams, Paul D; Singer, Steven W; Northen, Trent R

    2013-01-01

    Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.

  12. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production

    Directory of Open Access Journals (Sweden)

    Xiaoliang eCheng

    2013-12-01

    Full Text Available Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC, Medium 84 + rolled oats, and M9TE + MCC at 45 °C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45 °C than at all other temperatures. While T. bispora is reported to grow optimally at 60 °C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45 °C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.

  13. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

    Directory of Open Access Journals (Sweden)

    Hyunmin Koo

    2017-08-01

    Full Text Available In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1, middle (U2, and inner (U3 decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

  14. Transient negative biochar effects on plant growth are strongest after microbial species loss

    NARCIS (Netherlands)

    Hol, (Gera) W.H.G.; Vestergård, M.; Ten Hooven, F.C.; Duyts, H.; Van de Voorde, T.F.J.; Bezemer, T. Martijn

    2017-01-01

    Biochar has been explored as an organic amendment to improve soil quality and benefit plant growth. The overall positive effects of biochar on crop yields are generally attributed to abiotic changes, while the alternative causal pathway via changes in soil biota is unexplored. We compared plant

  15. Fermented soybean meal improves the growth performance, nutrient digestibility, and microbial flora in piglets

    Directory of Open Access Journals (Sweden)

    Lin Yuan

    2017-03-01

    Full Text Available In order to increase nutritive values of soybean meal (SBM, 3 species of microbes were used to ferment SBM. Through a 3 × 3 orthogonal design and parameter measurements of soybean peptide and anti-nutritional factor contents in the fermented soybean meal (FSBM, it was estimated that the best microbial proportion of Bacillus subtilis, Hansenula anomala and Lactobacillus casei was 2:1:2 for SBM fermentation (P  0.05. However, newly-weaned piglets (d 28–38 fed 10% FSBM and different levels of plasma protein obtained higher average daily gain (ADG and feed conversion ratio (FCR, compared with those without FSBM but with 6% plasma protein (P < 0.05. Piglets (d 38–68 fed diets supplemented with FSBM and soybean protein concentrate (SBPC at 3.75% and 7.5% respectively increased nutrient digestibility, fecal enzyme activity and lactic acid bacteria counts, and decreased fecal Escherichia coli counts (P < 0.05, compared with the control. These data indicated that FSBM had positive effects on nutrient digestibility and fecal microflora for piglets.

  16. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  17. Microbial enhanced oil recovery—a modeling study of the potential of spore-forming bacteria

    DEFF Research Database (Denmark)

    Nielsen, Sidsel Marie; Nesterov, Igor; Shapiro, Alexander

    2016-01-01

    resulted in the following conclusions. In order to obtain sufficient local concentrations of surfactant, substantial amounts of substrate should be supplied; however, massive growth of bacteria increases the risk for clogging at the well inlet areas, causing injectivity loss. In such areas, starvation may......Microbial enhanced oil recovery (MEOR) utilizes microbes for enhancing the recovery by several mechanisms, among which the most studied are the following: (1) reduction of oil-water interfacial tension (IFT) by the produced biosurfactant and (2) selective plugging by microbes and metabolic products...

  18. The Earth Microbiome Project and modeling the planets microbial potential (Invited)

    Science.gov (United States)

    Gilbert, J. A.

    2013-12-01

    The understanding of Earth's climate and ecology requires multiscale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP captures the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >17,000 samples from 40 different biomes. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important functional processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires

  19. Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

    Science.gov (United States)

    Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

    2017-12-01

    Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric

  20. Final Report Coupling in silico microbial models with reactive transport models to predict the fate of contaminants in the subsurface.

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R.

    2012-10-31

    This project successfully accomplished its goal of coupling genome-scale metabolic models with hydrological and geochemical models to predict the activity of subsurface microorganisms during uranium bioremediation. Furthermore, it was demonstrated how this modeling approach can be used to develop new strategies to optimize bioremediation. The approach of coupling genome-scale metabolic models with reactive transport modeling is now well enough established that it has been adopted by other DOE investigators studying uranium bioremediation. Furthermore, the basic principles developed during our studies will be applicable to much broader investigations of microbial activities, not only for other types of bioremediation, but microbial metabolism in diversity of environments. This approach has the potential to make an important contribution to predicting the impact of environmental perturbations on the cycling of carbon and other biogeochemical cycles.

  1. Modeling the mutualistic interactions between tubeworms and microbial consortia.

    Directory of Open Access Journals (Sweden)

    Erik E Cordes

    2005-03-01

    Full Text Available The deep-sea vestimentiferan tubeworm Lamellibrachia luymesi forms large aggregations at hydrocarbon seeps in the Gulf of Mexico that may persist for over 250 y. Here, we present the results of a diagenetic model in which tubeworm aggregation persistence is achieved through augmentation of the supply of sulfate to hydrocarbon seep sediments. In the model, L. luymesi releases the sulfate generated by its internal, chemoautotrophic, sulfide-oxidizing symbionts through posterior root-like extensions of its body. The sulfate fuels sulfate reduction, commonly coupled to anaerobic methane oxidation and hydrocarbon degradation by bacterial-archaeal consortia. If sulfate is released by the tubeworms, sulfide generation mainly by hydrocarbon degradation is sufficient to support moderate-sized aggregations of L. luymesi for hundreds of years. The results of this model expand our concept of the potential benefits derived from complex interspecific relationships, in this case involving members of all three domains of life.

  2. Use of genome-scale microbial models for metabolic engineering

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

    2004-01-01

    Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

  3. An age-structured population balance model for microbial dynamics

    Directory of Open Access Journals (Sweden)

    Duarte M.V.E.

    2003-01-01

    Full Text Available This work presents an age-structured population balance model (ASPBM for a bioprocess in a continuous stirred-tank fermentor. It relates the macroscopic properties and dynamic behavior of biomass to the operational parameters and microscopic properties of cells. Population dynamics is governed by two time- and age-dependent density functions for living and dead cells, accounting for the influence of substrate and dissolved oxygen concentrations on cell division, aging and death processes. The ASPBM described biomass and substrate oscillations in aerobic continuous cultures as experimentally observed. It is noteworthy that a small data set consisting of nonsegregated measurements was sufficient to adjust a complex segregated mathematical model.

  4. Do the ban on use of anti-microbial growth promoter impact on technical change and the efficiency of slaughter-pig production

    DEFF Research Database (Denmark)

    Lawson, Lartey; Otto, Lars; Jensen, Peter Vig

    2005-01-01

    infections, and in effect stimu-lated the utilization of feedstuff and reduced the mortality rate. However, fears for increas-ing bacteria resistance with subsequent health hazards for humans and livestock has lead to societal debates about the pros and cons of its use in livestock production. Antibiotic......This study aims at investigating the effects of the ban on the use of anti-microbial growth promoters in the production of “Finishing Pigs” for slaughter. We investigate if the ban on the use of anti-microbial growth promoters has for specialised pig-producers altered the productivity of inputs......, technical change and the efficiency of production. This paper complements an earlier paper that investigated the impact of the ban on weaned-pig produc-tion. Background: The study is motivated by the fact that antimicrobial growth promoters have been known world wide to protect livestock from bacteria...

  5. A Modeling Comparison of Methanogenesis from Noncompetitive vs Competitive Substrates in a Simulated Hypersaline Microbial Mat

    Science.gov (United States)

    Decker, K. L.; Potter, C.; Hoehler, T.

    2005-12-01

    The well-documented assumption about methanogens that co-occur in hypersaline mat communities with sulfate-reducing bacteria (SRB) is that they rely entirely on non-competitive substrates for methanogenesis. The reason for this is that during sulfate reduction, sulfur-reducing bacteria efficiently utilize H2, leaving a concentration too low for methanogenesis. Early results from recent work on a hypersaline microbial mat from salt evaporation ponds of Guerrero Negro, Baja, Mexico cast doubt that methanogenesis only occurs via non-competitive substrates, because it shows an excess of H2 in the mat rather than a paucity. We explore the use of our simulation model of the microbial biogeochemistry of a hypersaline mat (named MBGC) to compare methane production rates in a 1 cm thick mat when the methanogens use competitive substrates versus noncompetitive substrates. In the `non-competitive substrate' version of the model, methanogens rely exclusively on methylated amines that are accumulated as compatible solutes in cyanobacteria and released after lysis. In contrast, the `competitive substrate' models examine methanogen use of substrates (such as H2 + acetate) with different SRB population sizes (from absent to low). The comparison of these models of methane and sulfide biogeochemistry of a hypersaline mat has both ecological and geobiological significance, as one hypothesis of Archean microbial mats is that they existed in a low sulfate environment.

  6. Microbial background flora in small-scale cheese production facilities does not inhibit growth and surface attachment of Listeria monocytogenes.

    Science.gov (United States)

    Schirmer, B C T; Heir, E; Møretrø, T; Skaar, I; Langsrud, S

    2013-10-01

    The background microbiota of 5 Norwegian small-scale cheese production sites was examined and the effect of the isolated strains on the growth and survival of Listeria monocytogenes was investigated. Samples were taken from the air, food contact surfaces (storage surfaces, cheese molds, and brine) and noncontact surfaces (floor, drains, and doors) and all isolates were identified by sequencing and morphology (mold). A total of 1,314 isolates were identified and found to belong to 55 bacterial genera, 1 species of yeast, and 6 species of mold. Lactococcus spp. (all of which were Lactococcus lactis), Staphylococcus spp., Microbacterium spp., and Psychrobacter sp. were isolated from all 5 sites and Rhodococcus spp. and Chryseobacterium spp. from 4 sites. Thirty-two genera were only found in 1 out of 5 facilities each. Great variations were observed in the microbial background flora both between the 5 producers, and also within the various production sites. The greatest diversity of bacteria was found in drains and on rubber seals of doors. The flora on cheese storage shelves and in salt brines was less varied. A total of 62 bacterial isolates and 1 yeast isolate were tested for antilisterial activity in an overlay assay and a spot-on-lawn assay, but none showed significant inhibitory effects. Listeria monocytogenes was also co-cultured on ceramic tiles with bacteria dominating in the cheese production plants: Lactococcus lactis, Pseudomonas putida, Staphylococcus equorum, Rhodococcus spp., or Psychrobacter spp. None of the tested isolates altered the survival of L. monocytogenes on ceramic tiles. The conclusion of the study was that no common background flora exists in cheese production environments. None of the tested isolates inhibited the growth of L. monocytogenes. Hence, this study does not support the hypothesis that the natural background flora in cheese production environments inhibits the growth or survival of L. monocytogenes. Copyright © 2013 American

  7. Flower Power: Sunflowers as a Model for Logistic Growth

    Science.gov (United States)

    Fernandez, Eileen; Geist, Kristi A.

    2011-01-01

    Logistic growth displays an interesting pattern: It starts fast, exhibiting the rapid growth characteristic of exponential models. As time passes, it slows in response to constraints such as limited resources or reallocation of energy. The growth continues to slow until it reaches a limit, called capacity. When the growth describes a population,…

  8. Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

    Science.gov (United States)

    Hunter, K. S.; Van Cappellen, P.

    2000-01-01

    Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

  9. A model for microbial phosphorus cycling in bioturbated marine sediments

    DEFF Research Database (Denmark)

    Dale, Andrew W.; Boyle, R. A.; Lenton, Timothy M.

    2016-01-01

    A diagenetic model is used to simulate the diagenesis and burial of particulate organic carbon (Corg) and phosphorus (P) in marine sediments underlying anoxic versus oxic bottom waters. The latter are physically mixed by animals moving through the surface sediment (bioturbation) and ventilated...... P pump) allows preferential mineralization of the bulk Porg pool relative to Corg during both aerobic and anaerobic respiration and is consistent with the database. Results with this model show that P burial is strongly enhanced in sediments hosting fauna. Animals mix highly labile Porg away from....... The results also help to explain Corg:Porg ratios in the geological record and the persistence of Porg in ancient marine sediments. © 2016 Elsevier Ltd....

  10. A system-level model for the microbial regulatory genome.

    Science.gov (United States)

    Brooks, Aaron N; Reiss, David J; Allard, Antoine; Wu, Wei-Ju; Salvanha, Diego M; Plaisier, Christopher L; Chandrasekaran, Sriram; Pan, Min; Kaur, Amardeep; Baliga, Nitin S

    2014-07-15

    Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

  11. Mathematical modelling and analysis for a three-tiered microbial food web in a chemostat

    Directory of Open Access Journals (Sweden)

    Miled El hajji

    2017-10-01

    Full Text Available In this article, we present a mathematical six-dimensional dynamical system involving a three-tiered microbial food web without maintenance. We give a qualitative analysis of the model, and an analysis of the local stability of equilibrium points. Under general assumptions of monotonicity, we prove the uniqueness and the local stability of the positive equilibrium point corresponding to the persistence of the three bacteria. Possibilities of periodic orbits are not excluded and asymptotic coexistence is satisfied.

  12. Hydrodynamic modelling of recreational water quality using Escherichia coli as an indicator of microbial contamination

    Science.gov (United States)

    Eregno, Fasil Ejigu; Tryland, Ingun; Tjomsland, Torulv; Kempa, Magdalena; Heistad, Arve

    2018-06-01

    Microbial contamination of recreational beaches is often at its worst after heavy rainfall events due to storm floods that carry fecal matter and other pollutants from the watershed. Similarly, overflows of untreated sewage from combined sewerage systems may discharge directly into coastal water or via rivers and streams. In order to understand the effect of rainfall events, wind-directions and tides on the recreational water quality, GEMSS, an integrated 3D hydrodynamic model was applied to assess the spreading of Escherichia coli (E. coli) at the Sandvika beaches, located in the Oslo fjord. The model was also used to theoretically investigate the effect of discharges from septic tanks from boats on the water quality at local beaches. The model make use of microbial decay rate as the main input representing the survival of microbial pathogens in the ocean, which vary widely depending on the type of pathogen and environmental stress. The predicted beach water quality was validated against observed data after a heavy rainfall event using Nash-Sutcliffe coefficient (E) and the overall result indicated that the model performed quite well and the simulation was in - good agreement with the observed E. coli concentrations for all beaches. The result of this study indicated that: 1) the bathing water quality was poor according to the EU bathing water directive up to two days after the heavy rainfall event depending on the location of the beach site. 2) The discharge from a boat at 300-meter distance to the beaches slightly increased the E. coli levels at the beaches. 3) The spreading of microbial pathogens from its source to the different beaches depended on the wind speed and the wind direction.

  13. Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

    Science.gov (United States)

    Andre, B. J.; Rajaram, H.; Silverstein, J.

    2010-12-01

    Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction

  14. Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

    Science.gov (United States)

    Henson, Michael A

    2015-12-01

    Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

  15. Microbial physiology-based model of ethanol metabolism in subsurface sediments

    Science.gov (United States)

    Jin, Qusheng; Roden, Eric E.

    2011-07-01

    A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

  16. Modeling microbial community structure and functional diversity across time and space.

    Science.gov (United States)

    Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

    2012-07-01

    Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Microbial comparative pan-genomics using binomial mixture models

    Directory of Open Access Journals (Sweden)

    Ussery David W

    2009-08-01

    Full Text Available Abstract Background The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. Results We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection probabilities. Estimated pan-genome sizes range from small (around 2600 gene families in Buchnera aphidicola to large (around 43000 gene families in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely occurring genes in the population. Conclusion Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes.

  18. Microbial comparative pan-genomics using binomial mixture models

    DEFF Research Database (Denmark)

    Ussery, David; Snipen, L; Almøy, T

    2009-01-01

    The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter...... approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. RESULTS: We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection...... probabilities. Estimated pan-genome sizes range from small (around 2600 gene families) in Buchnera aphidicola to large (around 43000 gene families) in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely...

  19. The Impact of Consumer Phase Models in Microbial Risk Analysis

    DEFF Research Database (Denmark)

    Nauta, Maarten; Christensen, Bjarke Bak

    2011-01-01

    In quantitative microbiological risk assessment (QMRA), the consumer phase model (CPM) describes the part of the food chain between purchase of the food product at retail and exposure. Construction of a CPM is complicated by the large variation in consumer food handling practices and a limited...... availability of data. Therefore, several subjective (simplifying) assumptions have to be made when a CPM is constructed, but with a single CPM their impact on the QMRA results is unclear. We therefore compared the performance of eight published CPMs for Campylobacter in broiler meat in an example of a QMRA......, where all the CPMs were analyzed using one single input distribution of concentrations at retail, and the same dose-response relationship. It was found that, between CPMs, there may be a considerable difference in the estimated probability of illness per serving. However, the estimated relative risk...

  20. Microbial Products and Biofertilizers in Improving Growth and Productivity of Apple - a Review.

    Science.gov (United States)

    Mosa, Walid F A E; Sas-Paszt, Lidia; Frąc, Mateusz; Trzciński, Paweł

    2016-08-26

    The excessive use of mineral fertilizers causes many negative consequences for the environment as well as potentially dangerous effects of chemical residues in plant tissues on the health of human and animal consumers. Bio-fertilizers are formulations of beneficial microorganisms, which upon application can increase the availability of nutrients by their biological activity and help to improve soil health. Microbes involved in the formulation of bio-fertilizers not only mobilize N and P but mediate the process of producing crops and foods naturally. This method avoids the use of synthetic chemical fertilizers and genetically modified organisms to influence the growth of crops. In addition to their role in enhancing the growth of the plants, biofertilizers can act as biocontrol agents in the rhizosphere at the same time. Biofertilizers are very safe for human, animal and environment. The use of Azotobacter, Azospirillum, Pseudomonas, Acetobacter, Burkholderia, Bacillus, Paenibacillus and some members of the Enterobacteriaceae is gaining worldwide importance and acceptance and appears to be the trend for the future.

  1. Microbial growth on oxalate by a route not involving glyoxylate carboligase

    Science.gov (United States)

    Blackmore, Maureen A.; Quayle, J. R.

    1970-01-01

    1. The metabolism of oxalate by the pink-pigmented organisms, Pseudomonas AM1, Pseudomonas AM2, Protaminobacter ruber and Pseudomonas extorquens has been compared with that of the non-pigmented Pseudomonas oxalaticus. 2. During growth on oxalate, all the organisms contain oxalyl-CoA decarboxylase, formate dehydrogenase and oxalyl-CoA reductase. This is consistent with oxidation of oxalate to carbon dioxide taking place via oxalyl-CoA, formyl-CoA and formate as intermediates, and also reduction of oxalate to glyoxylate taking place via oxalyl-CoA. 3. The pink-pigmented organisms, when grown on oxalate, contain l-serine–glyoxylate aminotransferase and hydroxypyruvate reductase but do not contain glyoxylate carboligase. The converse of this obtains in oxalate-grown Ps. oxalaticus. This indicates that, in contrast with Ps. oxalaticus, synthesis of C3 compounds from oxalate by the pink-pigmented organisms occurs by a variant of the `serine pathway' used by Pseudomonas AM1 during growth on C1 compounds. 4. Evidence in favour of this scheme is provided by the finding that a mutant of Pseudomonas AM1 that lacks hydroxypyruvate reductase is not able to grow on oxalate. PMID:5472155

  2. Antimicrobial activity of transition metal acid MoO3 prevents microbial growth on material surfaces

    International Nuclear Information System (INIS)

    Zollfrank, Cordt; Gutbrod, Kai; Wechsler, Peter; Guggenbichler, Josef Peter

    2012-01-01

    Serious infectious complications of patients in healthcare settings are often transmitted by materials and devices colonised by microorganisms (nosocomial infections). Current strategies to generate material surfaces with an antimicrobial activity suffer from the consumption of the antimicrobial agent and emerging multidrug-resistant pathogens amongst others. Consequently, materials surfaces exhibiting a permanent antimicrobial activity without the risk of generating resistant microorganisms are desirable. This publication reports on the extraordinary efficient antimicrobial properties of transition metal acids such as molybdic acid (H 2 MoO 4 ), which is based on molybdenum trioxide (MoO 3 ). The modification of various materials (e.g. polymers, metals) with MoO 3 particles or sol–gel derived coatings showed that the modified materials surfaces were practically free of microorganisms six hours after contamination with infectious agents. The antimicrobial activity is based on the formation of an acidic surface deteriorating cell growth and proliferation. The application of transition metal acids as antimicrobial surface agents is an innovative approach to prevent the dissemination of microorganisms in healthcare units and public environments. Highlights: ► The presented modifications of materials surfaces with MoO 3 are non-cytotoxic and decrease biofilm growth and bacteria transmission. ► The material is insensitive towards emerging resistances of bacteria. ► Strong potential to reduce spreading of infectious agents on inanimate surfaces.

  3. Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: informing enzyme based decomposition models

    Directory of Open Access Journals (Sweden)

    Daryl L Moorhead

    2013-08-01

    Full Text Available We re-examined data from a recent litter decay study to determine if additional insights could be gained to inform decomposition modeling. Rinkes et al. (2013 conducted 14-day laboratory incubations of sugar maple (Acer saccharum or white oak (Quercus alba leaves, mixed with sand (0.4% organic C content or loam (4.1% organic C. They measured microbial biomass C, carbon dioxide efflux, soil ammonium, nitrate, and phosphate concentrations, and β-glucosidase (BG, β-N-acetyl-glucosaminidase (NAG, and acid phosphatase (AP activities on days 1, 3, and 14. Analyses of relationships among variables yielded different insights than original analyses of individual variables. For example, although respiration rates per g soil were higher for loam than sand, rates per g soil C were actually higher for sand than loam, and rates per g microbial C showed little difference between treatments. Microbial biomass C peaked on day 3 when biomass-specific activities of enzymes were lowest, suggesting uptake of litter C without extracellular hydrolysis. This result refuted a common model assumption that all enzyme production is constitutive and thus proportional to biomass, and/or indicated that part of litter decay is independent of enzyme activity. The length and angle of vectors defined by ratios of enzyme activities (BG/NAG versus BG/AP represent relative microbial investments in C (length, and N and P (angle acquiring enzymes. Shorter lengths on day 3 suggested low C limitation, whereas greater lengths on day 14 suggested an increase in C limitation with decay. The soils and litter in this study generally had stronger P limitation (angles > 45˚. Reductions in vector angles to < 45˚ for sand by day 14 suggested a shift to N limitation. These relational variables inform enzyme-based models, and are usually much less ambiguous when obtained from a single study in which measurements were made on the same samples than when extrapolated from separate studies.

  4. Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms

    DEFF Research Database (Denmark)

    Klausen, M.; Gjermansen, Morten; Kreft, J.-U.

    2006-01-01

    Surface-associated microbial communities in many cases display dynamic developmental patterns. Model biofilms formed by Pseudomonas aeruginosa and Pseudomonas putida in laboratory flow-chamber setups represent examples of such behaviour. Dependent on the experimental conditions the bacteria...

  5. A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

    National Research Council Canada - National Science Library

    Campbell, Jason

    2002-01-01

    The purpose of this study is to compare different approaches to modeling the reductive dechlorination of chlorinated ethenes in the anaerobic region of an upward flow constructed wetland by microbial consortia...

  6. REFERENCE MODELS OF ENDOGENOUS ECONOMIC GROWTH

    OpenAIRE

    GEAMĂNU MARINELA

    2012-01-01

    The new endogenous growth theories are a very important research area for shaping the most effective policies and long term sustainable development strategies. Endogenous growth theory has emerged as a reaction to the imperfections of neoclassical theory, by the fact that the economic growth is the endogenous product of an economical system.

  7. Modeling urban growth in Kigali city Rwanda

    NARCIS (Netherlands)

    Nduwayezu, G.; Sliuzas, R.V.; Kuffer, M.

    2017-01-01

    The uncontrolled urban growth is the key characteristics in most cities in less developed countries. However, having a good understanding of the key drivers of the city's growth dynamism has proven to be a key instrument to manage urban growth. This paper investigates the main determinants of Kigali

  8. Study of growth kinetic and modeling of ethanol production by ...

    African Journals Online (AJOL)

    ... coefficient (0.96299). Based on Leudking-Piret model, it could be concluded that ethanol batch fermentation is a non-growth associated process. Key words: Kinetic parameters, simulation, cell growth, ethanol, Saccharomyces cerevisiae.

  9. Inhibition of microbial growth by spice extracts and their effect of irradiation

    International Nuclear Information System (INIS)

    Ito, Hitoshi; Meixu, G.

    1994-01-01

    The antimicrobial activity of black pepper, rosemary and red pepper has been tested against 12 microorganisms. Alcoholic extracts of these spices were not exhibited strong activity against gram-negative bacteria in laboratory media. The growth of Bacillus subtilis and Clostridium botulinum type A was inhibited by 1% of black pepper, 0.5% rosemary and 0.03% red pepper. A little reduction of antimicrobial activity to B. subtilis was observed on extracts of gamma-irradiated black pepper or rosemary at 10 and 50 kGy. In the case of red pepper, irradiation of 10 or 50 kGy enhanced a little of antimicrobial activity to B. subtilis. Similar effect of irradiation was also observed on the inhibition of aflatoxin production by Aspergillus parasiticus in SL broth. (author)

  10. Optimization of marine waste based-growth media for microbial lipase production using mixture design methodology.

    Science.gov (United States)

    Sellami, Mohamed; Kedachi, Samiha; Frikha, Fakher; Miled, Nabil; Ben Rebah, Faouzi

    2013-01-01

    Lipase production by Staphylococcus xylosus and Rhizopus oryzae was investigated using a culture medium based on a mixture of synthetic medium and supernatants generated from tuna by-products and Ulva rigida biomass. The proportion of the three medium components was optimized using the simplex-centroid mixture design method (SCMD). Results indicated that the experimental data were in good agreement with predicted values, indicating that SCMD was a reliable method for determining the optimum mixture proportion of the growth medium. Maximal lipase activities of 12.5 and 23.5 IU/mL were obtained with a 50:50 (v:v) mixture of synthetic medium and tuna by-product supernatant for Staphylococcus xylosus and Rhizopus oryzae, respectively. The predicted responses from these mixture proportions were also validated experimentally.

  11. A stepwise-cluster microbial biomass inference model in food waste composting

    International Nuclear Information System (INIS)

    Sun Wei; Huang, Guo H.; Zeng Guangming; Qin Xiaosheng; Sun Xueling

    2009-01-01

    A stepwise-cluster microbial biomass inference (SMI) model was developed through introducing stepwise-cluster analysis (SCA) into composting process modeling to tackle the nonlinear relationships among state variables and microbial activities. The essence of SCA is to form a classification tree based on a series of cutting or mergence processes according to given statistical criteria. Eight runs of designed experiments in bench-scale reactors in a laboratory were constructed to demonstrate the feasibility of the proposed method. The results indicated that SMI could help establish a statistical relationship between state variables and composting microbial characteristics, where discrete and nonlinear complexities exist. Significance levels of cutting/merging were provided such that the accuracies of the developed forecasting trees were controllable. Through an attempted definition of input effects on the output in SMI, the effects of the state variables on thermophilic bacteria were ranged in a descending order as: Time (day) > moisture content (%) > ash content (%, dry) > Lower Temperature (deg. C) > pH > NH 4 + -N (mg/Kg, dry) > Total N (%, dry) > Total C (%, dry); the effects on mesophilic bacteria were ordered as: Time > Upper Temperature (deg. C) > Total N > moisture content > NH 4 + -N > Total C > pH. This study made the first attempt in applying SCA to mapping the nonlinear and discrete relationships in composting processes.

  12. Reactive burn models and ignition & growth concept

    Directory of Open Access Journals (Sweden)

    Shaw M.S.

    2011-01-01

    Full Text Available Plastic-bonded explosives are heterogeneous materials. Experimentally, shock initiation is sensitive to small amounts of porosity, due to the formation of hot spots (small localized regions of high temperature. This leads to the Ignition & Growth concept, introduced by LeeTarver in 1980, as the basis for reactive burn models. A homo- genized burn rate needs to account for three meso-scale physical effects: (i the density of active hot spots or burn centers; (ii the growth of the burn fronts triggered by the burn centers; (iii a geometric factor that accounts for the overlap of deflagration wavelets from adjacent burn centers. These effects can be combined and the burn model defined by specifying the reaction progress variable λ = g(s as a function of a dimensionless reaction length s(t = rbc/ℓbc, rather than by specifying an explicit burn rate. The length scale ℓbc(Ps = [Nbc(Ps]−1/3 is the average distance between burn centers, where Nbc is the number density of burn centers activated by the lead shock. The reaction length rbc(t = ∫t0 D(P(t′dt′ is the distance the burn front propagates from a single burn center, where D(P is the deflagration speed as a function of the local pressure and t is the time since the shock arrival. A key implementation issue is how to determine the lead shock strength in conjunction with a shock capturing scheme. We have developed a robust algorithm for this purpose based on the Hugoniot jump condition for the energy. The algorithm utilizes the time dependence of density, pressure and energy within each cell. The method is independent of the numerical dissipation used for shock capturing. It is local and can be used in one or more space dimensions. The burn model has a small number of parameters which can be calibrated to fit velocity gauge data from shock initiation experiments.

  13. Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves

    Science.gov (United States)

    Mao, Huiling; Xia, Yuefeng; Tu, Yan; Wang, Chong; Diao, Qiyu

    2017-01-01

    Objective This study was conducted to investigate the effects of weaning times on the growth performance, rumen fermentation and microbial communities of yellow cattle calves. Methods Eighteen calves were assigned to a conventional management group that was normally weaned (NW, n = 3) or to early weaned (EW) group where calves were weaned when the feed intake of solid feed (starter) reached 500 g (EW500, n = 5), 750 g (EW750, n = 5), or 1,000 g (EW1,000, n = 5). Results Compared with NW, the EW treatments increased average daily gain (pcalves in EW750 had a higher (pintake than those in EW1,000 from wk 9 to the end of the trial. The concentrations of total volatile fatty acids in EW750 were greater than in NW and EW1,000 (p0.05), but changes in bacterial composition were found. Conclusion From the present study, it is inferred that EW is beneficial for rumen fermentation, and weaning when the feed intake of the starter reached 750 g showed much better results. PMID:28423879

  14. Stochastic modeling of thermal fatigue crack growth

    CERN Document Server

    Radu, Vasile

    2015-01-01

    The book describes a systematic stochastic modeling approach for assessing thermal-fatigue crack-growth in mixing tees, based on the power spectral density of temperature fluctuation at the inner pipe surface. It shows the development of a frequency-temperature response function in the framework of single-input, single-output (SISO) methodology from random noise/signal theory under sinusoidal input. The frequency response of stress intensity factor (SIF) is obtained by a polynomial fitting procedure of thermal stress profiles at various instants of time. The method, which takes into account the variability of material properties, and has been implemented in a real-world application, estimates the probabilities of failure by considering a limit state function and Monte Carlo analysis, which are based on the proposed stochastic model. Written in a comprehensive and accessible style, this book presents a new and effective method for assessing thermal fatigue crack, and it is intended as a concise and practice-or...

  15. Neo-logistic model for the growth of bacteria

    OpenAIRE

    Tashiro, Tohru; Yoshimura, Fujiko

    2017-01-01

    We propose a neo-logistic model that can describe bacterial growth data precisely. This model is not derived by modifying the logistic model formally, but by incorporating the synthesis of inducible enzymes into the logistic model indirectly. Therefore, the meaning of the parameters of the neo-logistic model becomes physically clear. The neo-logistic model can approximate bacterial growth better than models previously presented, and predict the order of the saturated number of bacteria in the...

  16. Modelling the transport and decay processes of microbial tracers in a macro-tidal estuary.

    Science.gov (United States)

    Abu-Bakar, Amyrhul; Ahmadian, Reza; Falconer, Roger A

    2017-10-15

    The Loughor Estuary is a macro-tidal coastal basin, located along the Bristol Channel, in the South West of the U.K. The maximum spring tidal range in the estuary is up to 7.5 m, near Burry Port Harbour. This estuarine region can experience severe coastal flooding during high spring tides, including extreme flooding of the intertidal saltmarshes at Llanrhidian, as well as the lower industrial and residential areas at Llanelli and Gowerton. The water quality of this estuarine basin needs to comply with the designated standards for safe recreational bathing and shellfish harvesting industries. The waterbody however, potentially receives overloading of bacterial inputs that enter the estuarine system from both point and diffuse sources. Therefore, a microbial tracer study was carried out to get a better understanding of the faecal bacteria sources and to enable a hydro-environmental model to be refined and calibrated for both advection and dispersion transport. A two-dimensional hydro-environmental model has been refined and extended to predict the highest water level covering the intertidal floodplains of the Loughor Estuary. The validated hydrodynamic model for both water levels and currents, was included with the injected mass of microbial tracer, i.e. MS2 coliphage from upstream of the estuary, and modelled as a non-conservative tracer over several tidal cycles through the system. The calibration and validation of the transport and decay of microbial tracer was undertaken, by comparing the model results and the measured data at two different sampling locations. The refined model developed as a part of this study, was used to acquire a better understanding of the water quality processes and the potential sources of bacterial pollution in the estuary. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Testing linear growth rate formulas of non-scale endogenous growth models

    NARCIS (Netherlands)

    Ziesemer, Thomas

    2017-01-01

    Endogenous growth theory has produced formulas for steady-state growth rates of income per capita which are linear in the growth rate of the population. Depending on the details of the models, slopes and intercepts are positive, zero or negative. Empirical tests have taken over the assumption of

  18. Solar energy system reduces time taken to inhibit microbial growth in soil

    Energy Technology Data Exchange (ETDEWEB)

    Phitthayarachasak, Thanathep; Thepa, Sirichai; Kongkiattikajorn, Jirasak [Energy Technology Division, School of Energy Environment and Materials, King Mongkut' s University of Technology Thonburi, 126 Prachauthid Road, Tungkru, Bangkok 10140 (Thailand)

    2009-11-15

    This research studied how to reduce the time consumption and to increase and improve the efficiency of the solarization process. The asymmetry compound parabolic concentrator (ACPC) was developed to produce boiling water to be utilized while the solarization process was in operation. This could decrease the time consumed in the solarization process from 4 to 6 weeks to 4 h, with a temperature of approximately 41.25 C at the various depth levels, not exceeding 50 cm. The test to inhibit the growth of Ralstonia solanacearum, the causative agent of wilt in crops leaves, indicated that R. solanacearum was reduced from the total bacterial population of 10.9 x 10{sup 8} colony forming unit/g soil (cfu g{sup -1}) at soil surface to 9.0 x 10{sup 7}, 7.5 x 10{sup 4} and 4.1 x 10{sup 3} cfu g{sup -1} within 1, 2 and 4 h, respectively. (author)

  19. A literature review on growth models and strategies: The missing link in entrepreneurial growth

    Directory of Open Access Journals (Sweden)

    Syed Fida Hussain Shah

    2013-08-01

    Full Text Available This study focuses on the importance of growth models, growth strategies, role of knowledge management system in the formulation of effective strategy for the enterprises following growth. Choice of an appropriate growth strategy is at the heart of any successful entrepreneurial venture. Selection of a strategy may be effective for one entrepreneur while it is not for other. Choice of Growth Strategy depends on various different factors, organisational context and environment which may vary from enterprise to enterprise. Resource based view is very important consideration for the entrepreneurs on the path of growth. Evaluation of all kind of resources helps them to grow their enterprises successfully. Selection of an appropriate growth strategy allows the entrepreneurs in overcoming growth challenges and avoiding the growth reversals and setbacks.

  20. Mathematical modelling of temperature effect on growth kinetics of Pseudomonas spp. on sliced mushroom (Agaricus bisporus).

    Science.gov (United States)

    Tarlak, Fatih; Ozdemir, Murat; Melikoglu, Mehmet

    2018-02-02

    The growth data of Pseudomonas spp. on sliced mushrooms (Agaricus bisporus) stored between 4 and 28°C were obtained and fitted to three different primary models, known as the modified Gompertz, logistic and Baranyi models. The goodness of fit of these models was compared by considering the mean squared error (MSE) and the coefficient of determination for nonlinear regression (pseudo-R 2 ). The Baranyi model yielded the lowest MSE and highest pseudo-R 2 values. Therefore, the Baranyi model was selected as the best primary model. Maximum specific growth rate (r max ) and lag phase duration (λ) obtained from the Baranyi model were fitted to secondary models namely, the Ratkowsky and Arrhenius models. High pseudo-R 2 and low MSE values indicated that the Arrhenius model has a high goodness of fit to determine the effect of temperature on r max . Observed number of Pseudomonas spp. on sliced mushrooms from independent experiments was compared with the predicted number of Pseudomonas spp. with the models used by considering the B f and A f values. The B f and A f values were found to be 0.974 and 1.036, respectively. The correlation between the observed and predicted number of Pseudomonas spp. was high. Mushroom spoilage was simulated as a function of temperature with the models used. The models used for Pseudomonas spp. growth can provide a fast and cost-effective alternative to traditional microbiological techniques to determine the effect of storage temperature on product shelf-life. The models can be used to evaluate the growth behaviour of Pseudomonas spp. on sliced mushroom, set limits for the quantitative detection of the microbial spoilage and assess product shelf-life. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Model-based intensification of a fed-batch microbial process for the maximization of polyhydroxybutyrate (PHB) production rate.

    Science.gov (United States)

    Penloglou, Giannis; Vasileiadou, Athina; Chatzidoukas, Christos; Kiparissides, Costas

    2017-08-01

    An integrated metabolic-polymerization-macroscopic model, describing the microbial production of polyhydroxybutyrate (PHB) in Azohydromonas lata bacteria, was developed and validated using a comprehensive series of experimental measurements. The model accounted for biomass growth, biopolymer accumulation, carbon and nitrogen sources utilization, oxygen mass transfer and uptake rates and average molecular weights of the accumulated PHB, produced under batch and fed-batch cultivation conditions. Model predictions were in excellent agreement with experimental measurements. The validated model was subsequently utilized to calculate optimal operating conditions and feeding policies for maximizing PHB productivity for desired PHB molecular properties. More specifically, two optimal fed-batch strategies were calculated and experimentally tested: (1) a nitrogen-limited fed-batch policy and (2) a nitrogen sufficient one. The calculated optimal operating policies resulted in a maximum PHB content (94% g/g) in the cultivated bacteria and a biopolymer productivity of 4.2 g/(l h), respectively. Moreover, it was demonstrated that different PHB grades with weight average molecular weights of up to 1513 kg/mol could be produced via the optimal selection of bioprocess operating conditions.

  2. Layered growth model and epitaxial growth structures for SiCAlN alloys

    International Nuclear Information System (INIS)

    Liu Zhaoqing; Ni Jun; Su Xiaoao; Dai Zhenhong

    2009-01-01

    Epitaxial growth structures for (SiC) 1-x (AlN) x alloys are studied using a layered growth model. First-principle calculations are used to determine the parameters in the layered growth model. The phase diagrams of epitaxial growth are given. There is a rich variety of the new metastable polytype structures at x=1/6 ,1/5 ,1/4 ,1/3 , and 1/2 in the layered growth phase diagrams. We have also calculated the electronic properties of the short periodical SiCAlN alloys predicted by our layered growth model. The results show that various ordered structures of (SiC) 1-x (AlN) x alloys with the band gaps over a wide range are possible to be synthesized by epitaxial growth.

  3. A Predictive Model for Microbial Counts on Beaches where Intertidal Sand is the Primary Source

    Science.gov (United States)

    Feng, Zhixuan; Reniers, Ad; Haus, Brian K.; Solo-Gabriele, Helena M.; Wang, John D.; Fleming, Lora E.

    2015-01-01

    Human health protection at recreational beaches requires accurate and timely information on microbiological conditions to issue advisories. The objective of this study was to develop a new numerical mass balance model for enterococci levels on nonpoint source beaches. The significant advantage of this model is its easy implementation, and it provides a detailed description of the cross-shore distribution of enterococci that is useful for beach management purposes. The performance of the balance model was evaluated by comparing predicted exceedances of a beach advisory threshold value to field data, and to a traditional regression model. Both the balance model and regression equation predicted approximately 70% the advisories correctly at the knee depth and over 90% at the waist depth. The balance model has the advantage over the regression equation in its ability to simulate spatiotemporal variations of microbial levels, and it is recommended for making more informed management decisions. PMID:25840869

  4. Development and validation of a mathematical model for growth of pathogens in cut melons.

    Science.gov (United States)

    Li, Di; Friedrich, Loretta M; Danyluk, Michelle D; Harris, Linda J; Schaffner, Donald W

    2013-06-01

    Many outbreaks of foodborne illness associated with the consumption of fresh-cut melons have been reported. The objective of our research was to develop a mathematical model that predicts the growth rate of Salmonella on fresh-cut cantaloupe over a range of storage temperatures and to validate that model by using Salmonella and Escherichia coli O157:H7 on cantaloupe, honeydew, and watermelon, using both new data and data from the published studies. The growth of Salmonella on honeydew and watermelon and E. coli O157:H7 on cantaloupe, honeydew, and watermelon was monitored at temperatures of 4 to 25°C. The Ratkowsky (or square-root model) was used to describe Salmonella growth on cantaloupe as a function of storage temperature. Our results show that the levels of Salmonella on fresh-cut cantaloupe with an initial load of 3 log CFU/g can reach over 7 log CFU/g at 25°C within 24 h. No growth was observed at 4°C. A linear correlation was observed between the square root of Salmonella growth rate and temperature, such that √growth rate = 0.026 × (T - 5.613), R(2) = 0.9779. The model was generally suitable for predicting the growth of both Salmonella and E. coli O157:H7 on cantaloupe, honeydew, and watermelon, for both new data and data from the published literature. When compared with existing models for growth of Salmonella, the new model predicts a theoretic minimum growth temperature similar to the ComBase Predictive Models and Pathogen Modeling Program models but lower than other food-specific models. The ComBase Prediction Models results are very similar to the model developed in this study. Our research confirms that Salmonella can grow quickly and reach high concentrations when cut cantaloupe is stored at ambient temperatures, without visual signs of spoilage. Our model provides a fast and cost-effective method to estimate the effects of storage temperature on fresh-cut melon safety and could also be used in subsequent quantitative microbial risk

  5. Role of microbial inoculation and industrial by-product phosphogypsum in growth and nutrient uptake of maize (Zea mays L.) grown in calcareous soil.

    Science.gov (United States)

    Al-Enazy, Abdul-Aziz R; Al-Oud, Saud S; Al-Barakah, Fahad N; Usman, Adel Ra

    2017-08-01

    Alkaline soils with high calcium carbonate and low organic matter are deficient in plant nutrient availability. Use of organic and bio-fertilizers has been suggested to improve their properties. Therefore, a greenhouse experiment was conducted to evaluate the integrative role of phosphogypsum (PG; added at 0.0, 10, 30, and 50 g PG kg -1 ), cow manure (CM; added at 50 g kg -1 ) and mixed microbial inoculation (Incl.; Azotobacter chroococcum, and phosphate-solubilizing bacteria Bacillus megaterium var. phosphaticum and Pseudomonas fluorescens) on growth and nutrients (N, P, K, Fe, Mn, Zn and Cu) uptake of maize (Zea mays L.) in calcareous soil. Treatment effects on soil chemical and biological properties and the Cd and Pb availability to maize plants were also investigated. Applying PG decreased soil pH. The soil available P increased when soil was inoculated and/or treated with CM, especially with PG. The total microbial count and dehydrogenase activity were enhanced with PG+CM+Incl. Inoculated soils treated with PG showed significant increases in NPK uptake and maize plant growth. However, the most investigated treatments showed significant decreases in shoot micronutrients. Cd and Pb were not detected in maize shoots. Applying PG with microbial inoculation improved macronutrient uptake and plant growth. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  6. Forest Growth and Yield Models Viewed From a Different Perspective

    Science.gov (United States)

    Jeffery C. Goelz

    2002-01-01

    Typically, when different forms of growth and yield models are considered, they are grouped into convenient discrete classes. As a heuristic device, I chose to use a contrasting perspective, that all growth and yield models are diameter distribution models that merely differ in regard to which diameter distribution is employed and how the distribution is projected to...

  7. A Stochastic Multi-Media Model of Microbial Transport in Watersheds

    Science.gov (United States)

    Yeghiazarian, L.; Safwat, A.; Whiteaker, T.; Teklitz, A.; Nietch, C.; Maidment, D. R.; Best, E. P.

    2012-12-01

    Fecal contamination is the leading cause of surface-water impairment in the US, and fecal pathogens are capable of triggering massive outbreaks of gastrointestinal disease. The difficulty in prediction of water contamination has its roots in the stochastic variability of fecal pathogens in the environment, and in the complexity of microbial dynamics and interactions on the soil surface and in water. To address these challenges, we have developed a stochastic model whereby the transport of microorganisms in watersheds is considered in two broad categories: microorganisms that are attached to mineral or organic substrates in suspended sediment; and unattached microorganisms suspended in overland flow. The interactions of microorganisms with soil particles on the soil surface and in the overland flow lead to transitions of microorganisms between solid and aqueous media. The strength of attachment of microorganisms to soil particles is determined by the chemical characteristics of soils which are highly correlated with the particle size. The particle size class distribution in the suspended sediment is predicted by the Water Erosion Prediction Project (WEPP). The model is integrated with ArcGIS, resulting in a general transport-modeling framework applicable to a variety of biological and chemical surface water contaminants. Simulations are carried out for a case study of contaminant transport in the East Fork Little Miami River Watershed in Ohio. Model results include the spatial probability distribution of microbes in the watershed and can be used for assessment of (1) mechanisms dominating microbial transport, and (2) time and location of highest likelihood of microbial occurrence, thus yielding information on best water sampling strategies.

  8. Spiral Growth in Plants: Models and Simulations

    Science.gov (United States)

    Allen, Bradford D.

    2004-01-01

    The analysis and simulation of spiral growth in plants integrates algebra and trigonometry in a botanical setting. When the ideas presented here are used in a mathematics classroom/computer lab, students can better understand how basic assumptions about plant growth lead to the golden ratio and how the use of circular functions leads to accurate…

  9. Modeling the formation of soluble microbial products (SMP in drinking water biofiltration

    Directory of Open Access Journals (Sweden)

    Yu Xin

    2008-09-01

    Full Text Available Both a theoretical and an empirical model were developed for predicting the formation of soluble microbial products (SMP during drinking water biofiltration. Four pilot-scale biofilters with ceramsite as the medium were fed with different acetate loadings for the determination of SMP formation. Using numerically simulated and measured parameters, the theoretical model was developed according to the substrate and biomass balance. The results of this model matched the measured data better for higher SMP formation but did not fit well when SMP formation was lower. In order to better simulate the reality and overcome the difficulties of measuring the kinetic parameters, a simpler empirical model was also developed. In this model, SMP formation was expressed as a function of fed organic loadings and the depth of the medium, and a much better fit was obtained.

  10. Modeling how soluble microbial products (SMP) support heterotrophic bacteria in autotroph-based biofilms

    DEFF Research Database (Denmark)

    Merkey, Brian; Rittmann, Bruce E.; Chopp, David L.

    2009-01-01

    . In this paper, we develop and use a mathematical model to describe a model biofilm system that includes autotrophic and heterotrophic bacteria and the key products produced by the bacteria. The model combines the methods of earlier multi-species models with a multi-component biofilm model in order to explore...... the interaction between species via exchange of soluble microbial products (SMP). We show that multiple parameter sets are able to describe the findings of experimental studies, and that heterotrophs growing on autotrophically produced SMP may pursue either r- or K-strategies to sustain themselves when SMP...... is their only substrate. We also show that heterotrophs can colonize some distance from the autotrophs and still be sustained by autotrophically produced SMP. This work defines the feasible range of parameters for utilization of SMP by heterotrophs and the nature of the interactions between autotrophs...

  11. Development and validation of a stochastic model for potential growth of Listeria monocytogenes in naturally contaminated lightly preserved seafood

    DEFF Research Database (Denmark)

    Mejlholm, Ole; Bøknæs, Niels; Dalgaard, Paw

    2015-01-01

    added acetic and/or lactic acids. The stochastic model was developed from an existing deterministic model including the effect of 12 environmental parameters and microbial interaction (O. Mejlholm and P. Dalgaard, Food Microbiology, submitted for publication). Observed maximum population density (MPD...... of the least and most preserved sample of CSGH and CSS were used as input for the existing deterministic model. For both modelling approaches, it was shown that lag time and the effect of microbial interaction needs to be included to accurately predict MPD values of L. monocytogenes. Addition of organic acids...... to CSGH and CSS was confirmed as a suitable mitigation strategy against the risk of growth by L. monocytogenes as both types of products were in compliance with the EU regulation on ready-to-eat foods....

  12. A new model for the spectral induced polarization signature of bacterial growth in porous media

    Science.gov (United States)

    Zhang, C.; Revil, A.; Atekwana, E. A.; Jardani, A.; Smith, S.

    2012-12-01

    Recent biogeophysics studies demonstrated the sensitivity of complex conductivity to bacterial growth and microbial mediated mineral transformations in porous media. Frequency-domain induced polarization is a minimally invasive manner to measure the complex conductivity of a material over a broad range of frequencies. The real component of complex conductivity is associated with electromigration of the charge carriers, and the imaginary component represents reversible energy storage of charge carriers at polarization length scales. Quantitative relationship between frequency-domain induced polarization responses and bacterial growth and decay in porous media is analyzed in this study using a new developed model. We focus on the direct contribution of bacteria themselves to the complex conductivity in porous media in the absence of biomineralization. At low frequencies, the induced polarization of bacteria (α-polarization) is related to the properties of the electrical double layer surrounding the membrane surface of bacteria. Surface conductivity and α-polarization are due to the Stern layer of the counterions occurring in a brush of polymers coating the surface of the bacteria, and can be related to the cation exchange capacity of the bacteria. From the modeling results, at low frequencies (model with reactive transport modeling in which the evolution of bacterial populations are usually described by Monod kinetics, we show that the changes in imaginary conductivity with time can be used to determine bacterial growth kinetics parameters such as the growth and endogenous decay coefficient.

  13. Microbial ecology of extreme environments: Antarctic dry valley yeasts and growth in substrate limited habitats

    Science.gov (United States)

    Vishniac, H. S.

    1981-01-01

    The multiple stresses temperature, moisture, and for chemoheterotrophs, sources of carbon and energy of the Dry Valley Antarctica soils allow at best depauperate communities, low in species diversity and population density. The nature of community structure, the operation of biogeochemical cycles, the evolution and mechanisms of adaptation to this habitat are of interest in informing speculations upon life on other planets as well as in modeling the limits of gene life. Yeasts of the Cryptococcus vishniacil complex (Basidiobiastomycetes) are investigated, as the only known indigenes of the most hostile, lichen free, parts of the Dry Valleys. Methods were developed for isolating these yeasts (methods which do not exclude the recovery of other microbiota). The definition of the complex was refined and the importance of nitrogen sources was established as well as substrate competition in fitness to the Dry Valley habitats.

  14. Growth Kinetics and Modeling of Direct Oxynitride Growth with NO-O2 Gas Mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Everist, Sarah; Nelson, Jerry; Sharangpani, Rahul; Smith, Paul Martin; Tay, Sing-Pin; Thakur, Randhir

    1999-05-03

    We have modeled growth kinetics of oxynitrides grown in NO-O2 gas mixtures from first principles using modified Deal-Grove equations. Retardation of oxygen diffusion through the nitrided dielectric was assumed to be the dominant growth-limiting step. The model was validated against experimentally obtained curves with good agreement. Excellent uniformity, which exceeded expected walues, was observed.

  15. Detecting Growth Shape Misspecifications in Latent Growth Models: An Evaluation of Fit Indexes

    Science.gov (United States)

    Leite, Walter L.; Stapleton, Laura M.

    2011-01-01

    In this study, the authors compared the likelihood ratio test and fit indexes for detection of misspecifications of growth shape in latent growth models through a simulation study and a graphical analysis. They found that the likelihood ratio test, MFI, and root mean square error of approximation performed best for detecting model misspecification…

  16. Modeling Urban Spatial Growth in Mountainous Regions of Western China

    Directory of Open Access Journals (Sweden)

    Guoping Huang

    2017-08-01

    Full Text Available The scale and speed of urbanization in the mountainous regions of western China have received little attention from researchers. These cities are facing rapid population growth and severe environmental degradation. This study analyzed historical urban growth trends in this mountainous region to better understand the interaction between the spatial growth pattern and the mountainous topography. Three major factors—slope, accessibility, and land use type—were studied in light of their relationships with urban spatial growth. With the analysis of historical data as the basis, a conceptual urban spatial growth model was devised. In this model, slope, accessibility, and land use type together create resistance to urban growth, while accessibility controls the sequence of urban development. The model was tested and evaluated using historical data. It serves as a potential tool for planners to envision and assess future urban growth scenarios and their potential environmental impacts to make informed decisions.

  17. A Model of the Effect of the Microbial Biomass on the Isotherm of the Fermenting Solids in Solid-State Fermentation

    Directory of Open Access Journals (Sweden)

    Barbara Celuppi Marques

    2006-01-01

    Full Text Available We compare isotherms for soybeans and soybeans fermented with Rhizopus oryzae, showing that in solid-state fermentation the biomass affects the isotherm of the fermenting solids. Equations are developed to calculate, for a given overall water content of the fermenting solids, the water contents of the biomass and residual substrate, as well as the water activity. A case study, undertaken using a mathematical model of a well-mixed bioreactor, shows that if water additions are made on the basis of the assumption that fermenting solids have the same isotherm as the substrate itself, poor growth can result since the added water does not maintain the water activity at levels favorable for growth. We conclude that the effect of the microbial biomass on the isotherm of the fermenting solids must be taken into account in mathematical models of solid-state fermentation bioreactors.

  18. The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth.

    Science.gov (United States)

    Baćmaga, Małgorzata; Wyszkowska, Jadwiga; Kucharski, Jan

    2016-10-01

    Fungicides are considered to be effective crop protection chemicals in modern agriculture. However, they can also exert toxic effects on non-target organisms, including soil-dwelling microbes. Therefore, the environmental fate of fungicides has to be closely monitored. The aim of this study was to evaluate the influence of the Falcon 460 EC fungicide on microbial diversity, enzyme activity and resistance, and plant growth. Samples of sandy loam with pH KCl 7.0 were collected for laboratory analyses on experimental days 30, 60 and 90. Falcon 460 EC was applied to soil in the following doses: control (soil without the fungicide), dose recommended by the manufacturer, 30-fold higher than the recommended dose, 150-fold higher than the recommended dose and 300-fold higher than the recommended dose. The observed differences in the values of the colony development index and the eco-physiological index indicate that the mixture of spiroxamine, tebuconazole and triadimenol modified the biological diversity of the analyzed groups of soil microorganisms. Bacteria of the genus Bacillus and fungi of the genera Penicillium and Rhizopus were isolated from fungicide-contaminated soil. The tested fungicide inhibited the activity of dehydrogenases, catalase, urease, acid phosphatase and alkaline phosphatase. The greatest changes were induced by the highest fungicide dose 300-fold higher than the recommended dose. Dehydrogenases were most resistant to soil contamination. The Phytotoxkit test revealed that the analyzed fungicide inhibits seed germination capacity and root elongation. The results of this study indicate that excessive doses of the Falcon 460 EC fungicide 30-fold higher than the recommended dose to 300-fold higher than the recommended dose) can induce changes in the biological activity of soil. The analyzed microbiological and biochemical parameters are reliable indicators of the fungicide's toxic effects on soil quality.

  19. Characterization of agarose as immobilization matrix model for a microbial biosensor

    Directory of Open Access Journals (Sweden)

    Pernetti Mimma

    2003-01-01

    Full Text Available Microbial biosensors are promising tools for the detection of specific substances in different fields, such as environmental, biomedical, food or agricultural. They allow rapid measurements, no need for complex sample preparation or specialized personnel and easy handling. In order to enhance the managing, miniaturization and stability of the biosensor and to prevent cell leaching, bacteria immobilization is desirable. A systematic characterization procedure to choose a suitable immobilization method and matrix, was proposed in this study. Physical properties, storage stability mass transport phenomena and biocompatibility were evaluated, employing agarose as the model matrix. Preliminary essays with bioluminescent bacteria detecting Tributyltin were also carried out.

  20. Differential model of macroeconomic growth with endogenic cyclicity

    Directory of Open Access Journals (Sweden)

    Mikhail I. Geraskin

    2017-09-01

    Full Text Available Objective to elaborate a mathematical model of economic growth taking into account the cyclical nature of macroeconomic dynamics with the model parameters based on the Russian economy statistics. Methods economic and mathematical modeling system analysis regression factor analysis econometric time series analysis. Results the article states that under unstable economic growth in Russia forecasting of strategic prospects of the Russian economy is one of the topical directions of scientific studies. Furthermore construction of predictive models should be based on multiple factors taking into account such basic concepts as the neoKeynesian HarrodDomar model Ramsey ndash Cass ndash Koopmans model S. V. Dubovskiyrsquos concept as well as the neoclassical growth model by R. Solow. They served as the basis for developing a multifactor differential economic growth model which is a modification of the neoclassical growth model by R. Solow taking into account the laborsaving and capitalsaving forms of scientifictechnical progress and the Keynesian concept of investment. The model parameters are determined based on the dynamics of actual GDP employment fixed assets and investments in fixed assets for 19652016 in Russia on the basis of official statistics. The generalized model showed the presence of longwave fluctuations that are not detected during the individual periods modeling. The cyclical nature of macroeconomic dynamics with a period of 54 years was found which corresponds to the parameters of long waves by N. D. Kondratiev. Basing on the model the macroeconomic growth forecast was generated which shows that after 2020 the increase of scientifictechnical progress will be negative. Scientific novelty a model is proposed of the scientifictechnical progress indicator showing the growth rate of the capital productivity ratio to the saving rate a differential model of macroeconomic growth is obtained which endogenously takes cyclicity into account

  1. Modeling urban growth in Kigali city Rwanda

    African Journals Online (AJOL)

    kagoyire

    industrialization, land consumption and infrastructural development, have impacted ..... urban growth (reference image) and urban development predicted to the ..... neighboring characteristics (regular water and electricity provision) were not ...

  2. [Influence of Mirabilis jalapa Linn. Growth on the Microbial Community and Petroleum Hydrocarbon Degradation in Petroleum Contaminated Saline-alkali Soil].

    Science.gov (United States)

    Jiao, Hai-hua; Cui, Bing-jian; Wu, Shang-hua; Bai, Zhi-hui; Huang, Zhan-bin

    2015-09-01

    In order to explore the effect of Mirabilis jalapa Linn. growth on the structure characteristics of the microbial community and the degradation of petroleum hydrocarbon (TPH) in the petroleum-contaminated saline-alkali soil, Microbial biomass and species in the rhizosphere soils of Mirabilis jalapa Linn. in the contaminated saline soil were studied with the technology of phospholipid fatty acids (PLFAs) analysis. The results showed that comparing to CK soils without Mirabilis jalapa Linn., the ratio of PLFAs species varied were 71. 4%, 69. 2% and 33. 3% in the spring, summer and autumn season, respectively. In addition, there was distinct difference of the biomasses of the microbial community between the CK and rhizosphere soils and among the difference seasons of growth of Mirabilis jalapa Linn.. Compare to CK soil, the degradation rates of total petroleum hydrocarbon (TPH) was increased by 47. 6%, 28. 3%, and 18. 9% in spring, summer, and autumn rhizosphere soils, respectively. Correlation analysis was used to determine the correlation between TPH degradation and the soil microbial community. 77. 8% of the total soil microbial PLFAs species showed positive correlation to the TPH degradation (the correlation coefficient r > 0), among which, 55. 6% of PLFAs species showed high positive correlation(the correlation coefficient was r≥0. 8). In addition, the relative content of SAT and MONO had high correlation with TPH degradation in the CK sample soils, the corelation coefficient were 0. 92 and 0. 60 respectively; However, the percent of positive correlation was 42. 1% in the rhizosphere soils with 21. 1% of them had high positive correlation. The relative content of TBSAT, MONO and CYCLO had moderate or low correlation in rhizosphere soils, and the correlation coefficient were 0. 56, 0. 50, and 0. 07 respectively. Our study showed that the growth of mirabilis Mirabilis jalapa Linn. had a higher influence on the species and biomass of microbial community in the

  3. Growth of cortical neuronal network in vitro: Modeling and analysis

    International Nuclear Information System (INIS)

    Lai, P.-Y.; Jia, L. C.; Chan, C. K.

    2006-01-01

    We present a detailed analysis and theoretical growth models to account for recent experimental data on the growth of cortical neuronal networks in vitro [Phys. Rev. Lett. 93, 088101 (2004)]. The experimentally observed synchronized firing frequency of a well-connected neuronal network is shown to be proportional to the mean network connectivity. The growth of the network is consistent with the model of an early enhanced growth of connection, but followed by a retarded growth once the synchronized cluster is formed. Microscopic models with dominant excluded volume interactions are consistent with the observed exponential decay of the mean connection probability as a function of the mean network connectivity. The biological implications of the growth model are also discussed

  4. Modeling the effects of ozone on soybean growth and yield.

    Science.gov (United States)

    Kobayashi, K; Miller, J E; Flagler, R B; Heck, W W

    1990-01-01

    A simple mechanistic model was developed based on an existing growth model in order to address the mechanisms of the effects of ozone on growth and yield of soybean [Glycine max. (L.) Merr. 'Davis'] and interacting effects of other environmental stresses. The model simulates daily growth of soybean plants using environmental data including shortwave radiation, temperature, precipitation, irrigation and ozone concentration. Leaf growth, dry matter accumulation, water budget, nitrogen input and seed growth linked to senescence and abscission of leaves are described in the model. The effects of ozone are modeled as reduced photosynthate production and accelerated senescence. The model was applied to the open-top chamber experiments in which soybean plants were exposed to ozone under two levels of soil moisture regimes. After calibrating the model to the growth data and seed yield, goodness-of-fit of the model was tested. The model fitted well for top dry weight in the vegetative growth phase and also at maturity. The effect of ozone on seen yield was also described satisfactorily by the model. The simulation showed apparent interaction between the effect of ozone and soil moisture stress on the seed yield. The model revealed that further work is needed concerning the effect of ozone on the senescence process and the consequences of alteration of canopy microclimate by the open-top chambers.

  5. Tax Evasion in a Model of Endogenous Growth

    OpenAIRE

    Been-Lon Chen

    2003-01-01

    This paper integrates tax evasion into a standard AK growth model with public capital. In the model, the government optimizes the tax rate, while individuals optimize tax evasion. It studies tax rate, tax evasion and economic growth, and compares them with otherwise identical economies except those without tax evasion. It inquires into the effects of three government policies on tax rate, tax evasion, and economic growth. It finds that an increase in both unit cost of tax evasion and punishme...

  6. Testing R&D-Based Endogenous Growth Models

    DEFF Research Database (Denmark)

    Kruse-Andersen, Peter Kjær

    2017-01-01

    R&D-based growth models are tested using US data for the period 1953-2014. A general growth model is developed which nests the model varieties of interest. The model implies a cointegrating relationship between multifactor productivity, research intensity, and employment. This relationship...... is estimated using cointegrated VAR models. The results provide evidence against the widely used fully endogenous variety and in favor of the semi-endogenous variety. Forecasts based on the empirical estimates suggest that the slowdown in US productivity growth will continue. Particularly, the annual long...

  7. Differences in microbial communities and performance between suspended and attached growth anaerobic membrane bioreactors treating synthetic municipal wastewater

    KAUST Repository

    Harb, Moustapha; Xiong, Yanghui; Guest, Jeremy; Amy, Gary L.; Hong, Pei-Ying

    2015-01-01

    operational taxonomic units (OTUs) most closely related to fermentative bacteria (e.g., Microbacter margulisiae) were dominant in the suspended biomass of the CSTR, accounting for 30% of the microbial community. Conversely, methanogenic archaea (e

  8. Kinetic models of cell growth, substrate utilization and bio ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... Aspergillus fumigatus. A simple model was proposed using the Logistic Equation for the growth, ... costs and also involved in less sophisticated fermentation ... apply and they are accurately proved that the model can express ...

  9. Nonlinear Growth Models in M"plus" and SAS

    Science.gov (United States)

    Grimm, Kevin J.; Ram, Nilam

    2009-01-01

    Nonlinear growth curves or growth curves that follow a specified nonlinear function in time enable researchers to model complex developmental patterns with parameters that are easily interpretable. In this article we describe how a variety of sigmoid curves can be fit using the M"plus" structural modeling program and the nonlinear…

  10. Growth rate in the dynamical dark energy models

    International Nuclear Information System (INIS)

    Avsajanishvili, Olga; Arkhipova, Natalia A.; Samushia, Lado; Kahniashvili, Tina

    2014-01-01

    Dark energy models with a slowly rolling cosmological scalar field provide a popular alternative to the standard, time-independent cosmological constant model. We study the simultaneous evolution of background expansion and growth in the scalar field model with the Ratra-Peebles self-interaction potential. We use recent measurements of the linear growth rate and the baryon acoustic oscillation peak positions to constrain the model parameter α that describes the steepness of the scalar field potential. (orig.)

  11. Growth rate in the dynamical dark energy models.

    Science.gov (United States)

    Avsajanishvili, Olga; Arkhipova, Natalia A; Samushia, Lado; Kahniashvili, Tina

    Dark energy models with a slowly rolling cosmological scalar field provide a popular alternative to the standard, time-independent cosmological constant model. We study the simultaneous evolution of background expansion and growth in the scalar field model with the Ratra-Peebles self-interaction potential. We use recent measurements of the linear growth rate and the baryon acoustic oscillation peak positions to constrain the model parameter [Formula: see text] that describes the steepness of the scalar field potential.

  12. Leptin administration affects growth and skeletal development in a rat intrauterine growth restriction model: preliminary study.

    Science.gov (United States)

    Bar-El Dadon, Shimrit; Shahar, Ron; Katalan, Vered; Monsonego-Ornan, Efrat; Reifen, Ram

    2011-09-01

    Skeletal abnormalities are one of the hallmarks of growth delay during gestation. The aim of this study was to determine changes induced by leptin in skeletal growth and development in a rat model of intrauterine growth retardation (IUGR) and to elucidate the possible underlying mechanisms. Intrauterine growth retardation was induced prepartum and the effects of leptin to mothers prenatally or to offspring postnatally were studied. Radii were harvested and tested mechanically and structurally. Tibias were evaluated for growth-plate morphometry. On day 40 postpartum, total bone length and mineral density and tibial growth-plate width and numbers of cells within its zones of offspring treated with leptin were significantly greater than in the control group. Postnatal leptin administration in an IUGR model improves the structural properties and elongation rate of bone. These findings could pave the way to preventing some phenotypic presentations of IUGR. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. A grey box model of glucose fermentation and syntrophic oxidation in microbial fuel cells.

    Science.gov (United States)

    de Los Ángeles Fernandez, Maria; de Los Ángeles Sanromán, Maria; Marks, Stanislaw; Makinia, Jacek; Gonzalez Del Campo, Araceli; Rodrigo, Manuel; Fernandez, Francisco Jesus

    2016-01-01

    In this work, the fermentative and oxidative processes taking place in a microbial fuel cell (MFC) fed with glucose were studied and modeled. The model accounting for the bioelectrochemical processes was based on ordinary, Monod-type differential equations. The model parameters were estimated using experimental results obtained from three H-type MFCs operated at open or closed circuits and fed with glucose or ethanol. The experimental results demonstrate that similar fermentation processes were carried out under open and closed circuit operation, with the most important fermentation products being ethanol (with a yield of 1.81molmol(-1) glucose) and lactic acid (with a yield of 1.36molmol(-1) glucose). A peak in the electricity generation was obtained when glucose and fermentation products coexisted in the liquid bulk. However, almost 90% of the electricity produced came from the oxidation of ethanol. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Bayesian analysis of non-linear differential equation models with application to a gut microbial ecosystem.

    Science.gov (United States)

    Lawson, Daniel J; Holtrop, Grietje; Flint, Harry

    2011-07-01

    Process models specified by non-linear dynamic differential equations contain many parameters, which often must be inferred from a limited amount of data. We discuss a hierarchical Bayesian approach combining data from multiple related experiments in a meaningful way, which permits more powerful inference than treating each experiment as independent. The approach is illustrated with a simulation study and example data from experiments replicating the aspects of the human gut microbial ecosystem. A predictive model is obtained that contains prediction uncertainty caused by uncertainty in the parameters, and we extend the model to capture situations of interest that cannot easily be studied experimentally. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A quantitative microbial risk assessment model for Listeria monocytogenes in RTE sandwiches

    DEFF Research Database (Denmark)

    Tirloni, E.; Stella, S.; de Knegt, Leonardo

    2018-01-01

    within each serving. Then, two dose-response models were alternatively applied: the first used a fixed r value for each of the three population groups, while the second considered a variable r value (lognormal distribution), taking into account the variability in strain virulence and different host...... subpopulations susceptibility. The stochastic model predicted zero cases for total population for both the substrates by using the fixed r approach, while 3 cases were expected when a higher variability (in virulence and susceptibility) was considered in the model; the number of cases increased to 45......A Quantitative Microbial Risk Assessment (QMRA) was performed to estimate the expected number of listeriosis cases due to the consumption, on the last day of shelf life, of 20 000 servings of multi-ingredient sandwiches produced by a medium scale food producer in Italy, by different population...

  16. Porphyromonas gingivalis and Treponema denticola Mixed Microbial Infection in a Rat Model of Periodontal Disease

    Directory of Open Access Journals (Sweden)

    Raj K. Verma

    2010-01-01

    Full Text Available Porphyromonas gingivalis and Treponema denticola are periodontal pathogens that express virulence factors associated with the pathogenesis of periodontitis. In this paper we tested the hypothesis that P. gingivalis and T. denticola are synergistic in terms of virulence; using a model of mixed microbial infection in rats. Groups of rats were orally infected with either P. gingivalis or T. denticola or mixed microbial infections for 7 and 12 weeks. P. gingivalis genomic DNA was detected more frequently by PCR than T. denticola. Both bacteria induced significantly high IgG, IgG2b, IgG1, IgG2a antibody levels indicating a stimulation of Th1 and Th2 immune response. Radiographic and morphometric measurements demonstrated that rats infected with the mixed infection exhibited significantly more alveolar bone loss than shaminfected control rats. Histology revealed apical migration of junctional epithelium, rete ridge elongation, and crestal alveolar bone resorption; resembling periodontal disease lesion. These results showed that P. gingivalis and T. denticola exhibit no synergistic virulence in a rat model of periodontal disease.

  17. Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis.

    Science.gov (United States)

    Zhao, Hongyu; Yao, Zhenyu; Chen, Xiangbin; Wang, Xinquan; Chen, Guo-Qiang

    2017-11-01

    Phasins are unusual amphiphilic proteins that bind to microbial polyhydroxyalkanoate (PHA) granules in nature and show great potential for various applications in biotechnology and medicine. Despite their remarkable diversity, only the crystal structure of PhaP A h from Aeromonas hydrophila has been solved to date. Based on the structure of PhaP A h , homology models of PhaP A z from Azotobacter sp. FA-8 and PhaP TD from Halomonas bluephagenesis TD were successfully established, allowing rational mutagenesis to be conducted to enhance the stability and surfactant properties of these proteins. PhaP A z mutants, including PhaP A z Q38L and PhaP A z Q78L, as well as PhaP TD mutants, including PhaP TD Q38M and PhaP TD Q72M, showed better emulsification properties and improved thermostability (6-10°C higher melting temperatures) compared with their wild-type homologues under the same conditions. Importantly, the established PhaP homology-modelling approach, based on the high-resolution structure of PhaP A h , can be generalized to facilitate the study of other PhaP members. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Graphene growth process modeling: a physical-statistical approach

    Science.gov (United States)

    Wu, Jian; Huang, Qiang

    2014-09-01

    As a zero-band semiconductor, graphene is an attractive material for a wide variety of applications such as optoelectronics. Among various techniques developed for graphene synthesis, chemical vapor deposition on copper foils shows high potential for producing few-layer and large-area graphene. Since fabrication of high-quality graphene sheets requires the understanding of growth mechanisms, and methods of characterization and control of grain size of graphene flakes, analytical modeling of graphene growth process is therefore essential for controlled fabrication. The graphene growth process starts with randomly nucleated islands that gradually develop into complex shapes, grow in size, and eventually connect together to cover the copper foil. To model this complex process, we develop a physical-statistical approach under the assumption of self-similarity during graphene growth. The growth kinetics is uncovered by separating island shapes from area growth rate. We propose to characterize the area growth velocity using a confined exponential model, which not only has clear physical explanation, but also fits the real data well. For the shape modeling, we develop a parametric shape model which can be well explained by the angular-dependent growth rate. This work can provide useful information for the control and optimization of graphene growth process on Cu foil.

  19. Effects of copper particles on a model septic system's function and microbial community.

    Science.gov (United States)

    Taylor, Alicia A; Walker, Sharon L

    2016-03-15

    There is concern surrounding the addition of nanoparticles into consumer products due to toxicity potential and the increased risk of human and environmental exposures to these particles. Copper nanoparticles are found in many common consumer goods; therefore, the disposal and subsequent interactions between potentially toxic Cu-based nanoparticles and microbial communities may have detrimental impacts on wastewater treatment processes. This study investigates the effects of three copper particles (micron- and nano-scale Cu particles, and a nano-scale Cu(OH)2-based fungicide) on the function and operation of a model septic tank. Septic system analyses included water quality evaluations and microbial community characterizations to detect changes in and relationships between the septic tank function and microbial community phenotype/genotype. As would be expected for optimal wastewater treatment, biological oxygen demand (BOD5) was reduced by at least 63% during nano-scale Cu exposure, indicating normal function. pH was reduced to below the optimum anaerobic fermentation range during the micro Cu exposure, suggesting incomplete degradation of organic waste may have occurred. The copper fungicide, Cu(OH)2, caused a 57% increase in total organic carbon (TOC), which is well above the typical range for septic systems and also corresponded to increased BOD5 during the majority of the Cu(OH)2 exposure. The changes in TOC and BOD5 demonstrate that the system was improperly treating waste. Overall, results imply individual exposures to the three Cu particles caused distinct disruptions in septic tank function. However, it was observed that the system was able to recover to typical operating conditions after three weeks post-exposure. These results imply that during periods of Cu introduction, there are likely pulses of improper removal of total organic carbon and significant changes in pH not in the optimal range for the system. Copyright © 2016 Elsevier Ltd. All rights

  20. Mechanical model for filament buckling and growth by phase ordering.

    Science.gov (United States)

    Rey, Alejandro D; Abukhdeir, Nasser M

    2008-02-05

    A mechanical model of open filament shape and growth driven by phase ordering is formulated. For a given phase-ordering driving force, the model output is the filament shape evolution and the filament end-point kinematics. The linearized model for the slope of the filament is the Cahn-Hilliard model of spinodal decomposition, where the buckling corresponds to concentration fluctuations. Two modes are predicted: (i) sequential growth and buckling and (ii) simultaneous buckling and growth. The relation among the maximum buckling rate, filament tension, and matrix viscosity is given. These results contribute to ongoing work in smectic A filament buckling.

  1. Modeling and optimization of algae growth

    NARCIS (Netherlands)

    Thornton, Anthony Richard; Weinhart, Thomas; Bokhove, Onno; Zhang, Bowen; van der Sar, Dick M.; Kumar, Kundan; Pisarenco, Maxim; Rudnaya, Maria; Savcenco, Valeriu; Rademacher, Jens; Zijlstra, Julia; Szabelska, Alicja; Zyprych, Joanna; van der Schans, Martin; Timperio, Vincent; Veerman, Frits

    2010-01-01

    The wastewater from greenhouses has a high amount of mineral contamination and an environmentally-friendly method of removal is to use algae to clean this runoff water. The algae consume the minerals as part of their growth process. In addition to cleaning the water, the created algal bio-mass has a

  2. Stability characterization and modeling of robust distributed benthic microbial fuel cell (DBMFC) system.

    Science.gov (United States)

    Karra, Udayarka; Huang, Guoxian; Umaz, Ridvan; Tenaglier, Christopher; Wang, Lei; Li, Baikun

    2013-09-01

    A novel and robust distributed benthic microbial fuel cell (DBMFC) was developed to address the energy supply issues for oceanographic sensor network applications, especially under scouring and bioturbation by aquatic life. Multi-anode/cathode configuration was employed in the DBMFC system for enhanced robustness and stability in the harsh ocean environment. The results showed that the DBMFC system achieved peak power and current densities of 190mW/m(2) and 125mA/m(2) respectively. Stability characterization tests indicated the DBMFC with multiple anodes achieved higher power generation over the systems with single anode. A computational model that integrated physical, electrochemical and biological factors of MFCs was developed to validate the overall performance of the DBMFC system. The model simulation well corresponded with the experimental results, and confirmed the hypothesis that using a multi anode/cathode MFC configuration results in reliable and robust power generation. Published by Elsevier Ltd.

  3. Electricity generation and modeling of microbial fuel cell from continuous beer brewery wastewater.

    Science.gov (United States)

    Wen, Qing; Wu, Ying; Cao, Dianxue; Zhao, Lixin; Sun, Qian

    2009-09-01

    Electricity production and modeling of microbial fuel cell (MFC) from continuous beer brewery wastewater was studied in this paper. A single air-cathode MFC was constructed, carbon fiber was used as anode and diluted brewery wastewater (COD=626.58 mg/L) as substrate. The MFC displayed an open-circuit voltage of 0.578 V and a maximum power density of 9.52 W/m(3) (264 mW/m(2)). Using the model based on polarization curve, various voltage losses were quantified. At current density of 1.79 A/m(2), reaction kinetic loss and mass transport loss both achieved to 0.248 V; while ohmic loss was 0.046 V. Results demonstrated that it was feasible and stable for producing bioelectricity from brewery wastewater; while the most important factors which influenced the performance of the MFC are reaction kinetic loss and mass transport loss.

  4. Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

    Science.gov (United States)

    Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

    2015-03-01

    A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

  5. Optimal Patent Life in a Variety-Expansion Growth Model

    OpenAIRE

    Lin, Hwan C.

    2013-01-01

    This paper presents more channels through which the optimal patent life is determined in a R&D-based endogenous growth model that permits growth of new varieties of consumer goods over time. Its modeling features include an endogenous hazard rate facing incumbent monopolists, the prevalence of research congestion, and the aggregate welfare importance of product differentiation. As a result, a patent’s effective life is endogenized and less than its legal life. The model is calibrated to a glo...

  6. Modeling of Craniofacial Anatomy, Variation, and Growth

    DEFF Research Database (Denmark)

    Thorup, Signe Strann

    The topic of this thesis is automatic analysis of craniofacial images with respect to changes due to growth and surgery, inter-subject variation and intracranial volume estimation. The methods proposed contribute to the knowledge about specific craniofacial anomalies, as well as provide a tool...... for detailed analyses for clinical and research purposes. Most of the applications in this thesis rely on non-rigid image registration by the means of warping one image into the coordinate system of another image. This warping results in a deformation field that describes the anatomical correspondence between......, thus creating a personalized atlas. The knowledge built into the atlas is e.g. location of anatomical regions and landmarks of importance to surgery planning and evaluation or population studies. With these correspondences, various analyses could be carried out e.g. quantification of growth, inter...

  7. Modelling the Growth of Swine Flu

    Science.gov (United States)

    Thomson, Ian

    2010-01-01

    The spread of swine flu has been a cause of great concern globally. With no vaccine developed as yet, (at time of writing in July 2009) and given the fact that modern-day humans can travel speedily across the world, there are fears that this disease may spread out of control. The worst-case scenario would be one of unfettered exponential growth.…

  8. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    Energy Technology Data Exchange (ETDEWEB)

    Jinsong Liu [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2006-04-15

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

  9. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jinsong [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2006-04-15

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

  10. Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

    International Nuclear Information System (INIS)

    Jinsong Liu

    2006-04-01

    Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10 5 years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10 5 years

  11. On Latent Growth Models for Composites and Their Constituents.

    Science.gov (United States)

    Hancock, Gregory R; Mao, Xiulin; Kher, Hemant

    2013-09-01

    Over the last decade and a half, latent growth modeling has become an extremely popular and versatile technique for evaluating longitudinal change and its determinants. Most common among the models applied are those for a single measured variable over time. This model has been extended in a variety of ways, most relevant for the current work being the multidomain and the second-order latent growth models. Whereas the former allows for growth function characteristics to be modeled for multiple outcomes simultaneously, with the degree of growth characteristics' relations assessed within the model (e.g., cross-domain slope factor correlations), the latter models growth in latent outcomes, each of which has effect indicators repeated over time. But what if one has an outcome that is believed to be formative relative to its indicator variables rather than latent? In this case, where the outcome is a composite of multiple constituents, modeling change over time is less straightforward. This article provides analytical and applied details for simultaneously modeling growth in composites and their constituent elements, including a real data example using a general computer self-efficacy questionnaire.

  12. Stochastic process corrosion growth models for pipeline reliability

    International Nuclear Information System (INIS)

    Bazán, Felipe Alexander Vargas; Beck, André Teófilo

    2013-01-01

    Highlights: •Novel non-linear stochastic process corrosion growth model is proposed. •Corrosion rate modeled as random Poisson pulses. •Time to corrosion initiation and inherent time-variability properly represented. •Continuous corrosion growth histories obtained. •Model is shown to precisely fit actual corrosion data at two time points. -- Abstract: Linear random variable corrosion models are extensively employed in reliability analysis of pipelines. However, linear models grossly neglect well-known characteristics of the corrosion process. Herein, a non-linear model is proposed, where corrosion rate is represented as a Poisson square wave process. The resulting model represents inherent time-variability of corrosion growth, produces continuous growth and leads to mean growth at less-than-one power of time. Different corrosion models are adjusted to the same set of actual corrosion data for two inspections. The proposed non-linear random process corrosion growth model leads to the best fit to the data, while better representing problem physics

  13. Modeling Root Growth, Crop Growth and N Uptake of Winter Wheat Based on SWMS_2D: Model and Validation

    Directory of Open Access Journals (Sweden)

    Dejun Yang

    Full Text Available ABSTRACT Simulations for root growth, crop growth, and N uptake in agro-hydrological models are of significant concern to researchers. SWMS_2D is one of the most widely used physical hydrologically related models. This model solves equations that govern soil-water movement by the finite element method, and has a public access source code. Incorporating key agricultural components into the SWMS_2D model is of practical importance, especially for modeling some critical cereal crops such as winter wheat. We added root growth, crop growth, and N uptake modules into SWMS_2D. The root growth model had two sub-models, one for root penetration and the other for root length distribution. The crop growth model used was adapted from EU-ROTATE_N, linked to the N uptake model. Soil-water limitation, nitrogen limitation, and temperature effects were all considered in dry-weight modeling. Field experiments for winter wheat in Bouwing, the Netherlands, in 1983-1984 were selected for validation. Good agreements were achieved between simulations and measurements, including soil water content at different depths, normalized root length distribution, dry weight and nitrogen uptake. This indicated that the proposed new modules used in the SWMS_2D model are robust and reliable. In the future, more rigorous validation should be carried out, ideally under 2D situations, and attention should be paid to improve some modules, including the module simulating soil N mineralization.

  14. Applied model for the growth of the daytime mixed layer

    DEFF Research Database (Denmark)

    Batchvarova, E.; Gryning, Sven-Erik

    1991-01-01

    numerically. When the mixed layer is shallow or the atmosphere nearly neutrally stratified, the growth is controlled mainly by mechanical turbulence. When the layer is deep, its growth is controlled mainly by convective turbulence. The model is applied on a data set of the evolution of the height of the mixed...... layer in the morning hours, when both mechanical and convective turbulence contribute to the growth process. Realistic mixed-layer developments are obtained....

  15. Non-rigid image registration using bone growth model

    DEFF Research Database (Denmark)

    Bro-Nielsen, Morten; Gramkow, Claus; Kreiborg, Sven

    1997-01-01

    Non-rigid registration has traditionally used physical models like elasticity and fluids. These models are very seldom valid models of the difference between the registered images. This paper presents a non-rigid registration algorithm, which uses a model of bone growth as a model of the change...... between time sequence images of the human mandible. By being able to register the images, this paper at the same time contributes to the validation of the growth model, which is based on the currently available medical theories and knowledge...

  16. Phase-field model of eutectic growth

    International Nuclear Information System (INIS)

    Karma, A.

    1994-01-01

    A phase-field model which describes the solidification of a binary eutectic alloy with a simple symmetric phase diagram is introduced and the sharp-interface limit of this model is explored both analytically and numerically

  17. Balanced growth path solutions of a Boltzmann mean field game model for knowledge growth

    KAUST Repository

    Burger, Martin

    2016-11-18

    In this paper we study balanced growth path solutions of a Boltzmann mean field game model proposed by Lucas and Moll [15] to model knowledge growth in an economy. Agents can either increase their knowledge level by exchanging ideas in learning events or by producing goods with the knowledge they already have. The existence of balanced growth path solutions implies exponential growth of the overall production in time. We prove existence of balanced growth path solutions if the initial distribution of individuals with respect to their knowledge level satisfies a Pareto-tail condition. Furthermore we give first insights into the existence of such solutions if in addition to production and knowledge exchange the knowledge level evolves by geometric Brownian motion.

  18. A smart growth evaluation model based on data envelopment analysis

    Science.gov (United States)

    Zhang, Xiaokun; Guan, Yongyi

    2018-04-01

    With the rapid spread of urbanization, smart growth (SG) has attracted plenty of attention from all over the world. In this paper, by the establishment of index system for smart growth, data envelopment analysis (DEA) model was suggested to evaluate the SG level of the current growth situation in cities. In order to further improve the information of both radial direction and non-radial detection, we introduced the non-Archimedean infinitesimal to form C2GS2 control model. Finally, we evaluated the SG level in Canberra and identified a series of problems, which can verify the applicability of the model and provide us more improvement information.

  19. Studying historical occupational careers with multilevel growth models

    Directory of Open Access Journals (Sweden)

    Wiebke Schulz

    2010-10-01

    Full Text Available In this article we propose to study occupational careers with historical data by using multilevel growth models. Historical career data are often characterized by a lack of information on the timing of occupational changes and by different numbers of observations of occupations per individual. Growth models can handle these specificities, whereas standard methods, such as event history analyses can't. We illustrate the use of growth models by studying career success of men and women, using data from the Historical Sample of the Netherlands. The results show that the method is applicable to male careers, but causes trouble when analyzing female careers.

  20. Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

    Science.gov (United States)

    Alvaro, J J; Clausen, S

    2010-03-01

    The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.

  1. Modeling growth from weaning to maturity in beef cattle breeds

    Science.gov (United States)

    To better understand growth trajectory and maturity differences between beef breeds, three models – Brody, spline, and quadratic – were fit to cow growth data, and resulting parameter estimates were evaluated for 3 breed categories – British, continental, and Brahman-influenced. The data were weight...

  2. Modeling growth of Clostridium perfringens in pea soup during cooling

    NARCIS (Netherlands)

    Jong, de A.E.I.; Beumer, R.R.; Zwietering, M.H.

    2005-01-01

    Clostridium perfringens is a pathogen that mainly causes food poisoning outbreaks when large quantities of food are prepared. Therefore, a model was developed to predict the effect of different cooling procedures on the growth of this pathogen during cooling of food: Dutch pea soup. First, a growth

  3. Evaluating the Predictive Value of Growth Prediction Models

    Science.gov (United States)

    Murphy, Daniel L.; Gaertner, Matthew N.

    2014-01-01

    This study evaluates four growth prediction models--projection, student growth percentile, trajectory, and transition table--commonly used to forecast (and give schools credit for) middle school students' future proficiency. Analyses focused on vertically scaled summative mathematics assessments, and two performance standards conditions (high…

  4. Modelling growth curves of Nigerian indigenous normal feather ...

    African Journals Online (AJOL)

    This study was conducted to predict the growth curve parameters using Bayesian Gompertz and logistic models and also to compare the two growth function in describing the body weight changes across age in Nigerian indigenous normal feather chicken. Each chick was wing-tagged at day old and body weights were ...

  5. A Schumpeterian Model of Entrepreneurship, Innovation, and Regional Economic Growth

    NARCIS (Netherlands)

    Batabyal, A.; Nijkamp, P.

    2012-01-01

    The authors provide the first theoretical analysis of a one-sector, discrete-time, Schumpeterian model of growth in a regional economy in which consumers are risk neutral, there is no population growth, monopolistic entrepreneurs produce intermediate goods, and a single consumption good is produced

  6. A grain boundary sliding model for cavitation, crack growth and ...

    African Journals Online (AJOL)

    A model is presented for cavity growth, crack propagation and fracture resulting from grain boundary sliding (GBS) during high temperature creep deformation. The theory of cavity growth by GBS was based on energy balance criteria on the assumption that the matrix is sufficiently plastic to accommodate misfit strains ...

  7. Incorporating H2 Dynamics and Inhibition into a Microbially Based Methanogenesis Model for Restored Wetland Sediments

    Science.gov (United States)

    Pal, David; Jaffe, Peter

    2015-04-01

    Estimates of global CH4 emissions from wetlands indicate that wetlands are the largest natural source of CH4 to the atmosphere. In this paper, we propose that there is a missing component to these models that should be addressed. CH4 is produced in wetland sediments from the microbial degradation of organic carbon through multiple fermentation steps and methanogenesis pathways. There are multiple sources of carbon for methananogenesis; in vegetated wetland sediments, microbial communities consume root exudates as a major source of organic carbon. In many methane models propionate is used as a model carbon molecule. This simple sugar is fermented into acetate and H2, acetate is transformed to methane and CO2, while the H2 and CO2 are used to form an additional CH4 molecule. The hydrogenotrophic pathway involves the equilibrium of two dissolved gases, CH4 and H2. In an effort to limit CH4 emissions from wetlands, there has been growing interest in finding ways to limit plant transport of soil gases through root systems. Changing planted species, or genetically modifying new species of plants may control this transport of soil gases. While this may decrease the direct emissions of methane, there is little understanding about how H2 dynamics may feedback into overall methane production. The results of an incubation study were combined with a new model of propionate degradation for methanogenesis that also examines other natural parameters (i.e. gas transport through plants). This presentation examines how we would expect this model to behave in a natural field setting with changing sulfate and carbon loading schemes. These changes can be controlled through new plant species and other management practices. Next, we compare the behavior of two variations of this model, with or without the incorporation of H2 interactions, with changing sulfate, carbon loading and root volatilization. Results show that while the models behave similarly there may be a discrepancy of nearly

  8. Hybrid modeling of microbial exopolysaccharide (EPS) production: The case of Enterobacter A47.

    Science.gov (United States)

    Marques, Rodolfo; von Stosch, Moritz; Portela, Rui M C; Torres, Cristiana A V; Antunes, Sílvia; Freitas, Filomena; Reis, Maria A M; Oliveira, Rui

    2017-03-20

    Enterobacter A47 is a bacterium that produces high amounts of a fucose-rich exopolysaccharide (EPS) from glycerol residue of the biodiesel industry. The fed-batch process is characterized by complex non-linear dynamics with highly viscous pseudo-plastic rheology due to the accumulation of EPS in the culture medium. In this paper, we study hybrid modeling as a methodology to increase the predictive power of models for EPS production optimization. We compare six hybrid structures that explore different levels of knowledge-based and machine-learning model components. Knowledge-based components consist of macroscopic material balances, Monod type kinetics, cardinal temperature and pH (CTP) dependency and power-law viscosity models. Unknown dependencies are set to be identified by a feedforward artificial neural network (ANN). A semiparametric identification schema is applied resorting to a data set of 13 independent fed-batch experiments. A parsimonious hybrid model was identified that describes the dynamics of the 13 experiments with the same parameterization. The final model is specific to Enterobacter A47 but can be easily extended to other microbial EPS processes. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. A size-structured model of bacterial growth and reproduction.

    Science.gov (United States)

    Ellermeyer, S F; Pilyugin, S S

    2012-01-01

    We consider a size-structured bacterial population model in which the rate of cell growth is both size- and time-dependent and the average per capita reproduction rate is specified as a model parameter. It is shown that the model admits classical solutions. The population-level and distribution-level behaviours of these solutions are then determined in terms of the model parameters. The distribution-level behaviour is found to be different from that found in similar models of bacterial population dynamics. Rather than convergence to a stable size distribution, we find that size distributions repeat in cycles. This phenomenon is observed in similar models only under special assumptions on the functional form of the size-dependent growth rate factor. Our main results are illustrated with examples, and we also provide an introductory study of the bacterial growth in a chemostat within the framework of our model.

  10. Microbial Performance of Food Safety Control and Assurance Activities in a Fresh Produce Processing Sector Measured Using a Microbial Assessment Scheme and Statistical Modeling

    DEFF Research Database (Denmark)

    Njage, Patrick Murigu Kamau; Sawe, Chemutai Tonui; Onyango, Cecilia Moraa

    2017-01-01

    assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies. Generalized linear mixed models and correlated random-effects joint models for multivariate clustered...... the maximum safety level for environmental samples. Escherichia coli was detected in five of the six CSLs, including the final product. Among the processing-environment samples, the hand or glove swabs of personnel revealed a higher level of predicted contamination with E. coli, and 80% of the factories were...... of contamination with coliforms in water at the inlet than in the final rinse water. Four (80%) of the five assessed processors had poor to unacceptable counts of Enterobacteriaceae on processing surfaces. Personnel-, equipment-, and product-related hygiene measures to improve the performance of preventive...

  11. Selection, calibration, and validation of models of tumor growth.

    Science.gov (United States)

    Lima, E A B F; Oden, J T; Hormuth, D A; Yankeelov, T E; Almeida, R C

    2016-11-01

    This paper presents general approaches for addressing some of the most important issues in predictive computational oncology concerned with developing classes of predictive models of tumor growth. First, the process of developing mathematical models of vascular tumors evolving in the complex, heterogeneous, macroenvironment of living tissue; second, the selection of the most plausible models among these classes, given relevant observational data; third, the statistical calibration and validation of models in these classes, and finally, the prediction of key Quantities of Interest (QOIs) relevant to patient survival and the effect of various therapies. The most challenging aspects of this endeavor is that all of these issues often involve confounding uncertainties: in observational data, in model parameters, in model selection, and in the features targeted in the prediction. Our approach can be referred to as "model agnostic" in that no single model is advocated; rather, a general approach that explores powerful mixture-theory representations of tissue behavior while accounting for a range of relevant biological factors is presented, which leads to many potentially predictive models. Then representative classes are identified which provide a starting point for the implementation of OPAL, the Occam Plausibility Algorithm (OPAL) which enables the modeler to select the most plausible models (for given data) and to determine if the model is a valid tool for predicting tumor growth and morphology ( in vivo ). All of these approaches account for uncertainties in the model, the observational data, the model parameters, and the target QOI. We demonstrate these processes by comparing a list of models for tumor growth, including reaction-diffusion models, phase-fields models, and models with and without mechanical deformation effects, for glioma growth measured in murine experiments. Examples are provided that exhibit quite acceptable predictions of tumor growth in laboratory

  12. Gompertzian stochastic model with delay effect to cervical cancer growth

    International Nuclear Information System (INIS)

    Mazlan, Mazma Syahidatul Ayuni binti; Rosli, Norhayati binti; Bahar, Arifah

    2015-01-01

    In this paper, a Gompertzian stochastic model with time delay is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of cervical cancer growth. Low values of Mean-Square Error (MSE) of Gompertzian stochastic model with delay effect indicate good fits

  13. Gompertzian stochastic model with delay effect to cervical cancer growth

    Energy Technology Data Exchange (ETDEWEB)

    Mazlan, Mazma Syahidatul Ayuni binti; Rosli, Norhayati binti [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia); Bahar, Arifah [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor and UTM Centre for Industrial and Applied Mathematics (UTM-CIAM), Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor (Malaysia)

    2015-02-03

    In this paper, a Gompertzian stochastic model with time delay is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via Levenberg-Marquardt optimization method of non-linear least squares. We apply Milstein scheme for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of cervical cancer growth. Low values of Mean-Square Error (MSE) of Gompertzian stochastic model with delay effect indicate good fits.

  14. Life in Ice: Microbial Growth Dynamics and Greenhouse Gas Production During Winter in a Thermokarst Bog Revealed by Stable Isotope Probing Targeted Metagenomics

    Science.gov (United States)

    Blazewicz, S.; White, R. A., III; Tas, N.; Euskirchen, E. S.; Mcfarland, J. W.; Jansson, J.; Waldrop, M. P.

    2016-12-01

    Permafrost contains a reservoir of frozen C estimated to be twice the size of the current atmospheric C pool. In response to changing climate, permafrost is rapidly warming which could result in widespread seasonal thawing. When permafrost thaws, soils that are rich in ice and C often transform into thermokarst wetlands with anaerobic conditions and significant production of atmospheric CH4. While most C flux research in recently thawed permafrost concentrates on the few summer months when seasonal thaw has occurred, there is mounting evidence that sizeable portions of annual CO2 and CH4 efflux occurs over winter or during a rapid burst of emissions associated with seasonal thaw. A potential mechanism for such efflux patterns is microbial activity in frozen soils over winter where gasses produced are partially trapped within ice until spring thaw. In order to better understand microbial transformation of soil C to greenhouse gas over winter, we applied stable isotope probing (SIP) targeted metagenomics combined with process measurements and field flux data to reveal activities of microbial communities in `frozen' soil from an Alaskan thermokarst bog. Field studies revealed build-up of CO2 and CH4 in frozen soils suggesting that microbial activity persisted throughout the winter in soils poised just below the freezing point. Laboratory incubations designed to simulate in-situ winter conditions (-1.5 °C and anaerobic) revealed continuous CH4 and CO2 production. Strikingly, the quantity of CH4 produced in 6 months in frozen soil was equivalent to approximately 80% of CH4 emitted during the 3 month summer `active' season. Heavy water SIP targeted iTag sequencing revealed growing bacteria and archaea in the frozen anaerobic soil. Growth was primarily observed in two bacterial phyla, Firmicutes and Bacteroidetes, suggesting that fermentation was likely the major C mineralization pathway. SIP targeted metagenomics facilitated characterization of the primary metabolic

  15. Development and validation of a stochastic model for potential growth of Listeria monocytogenes in naturally contaminated lightly preserved seafood.

    Science.gov (United States)

    Mejlholm, Ole; Bøknæs, Niels; Dalgaard, Paw

    2015-02-01

    A new stochastic model for the simultaneous growth of Listeria monocytogenes and lactic acid bacteria (LAB) was developed and validated on data from naturally contaminated samples of cold-smoked Greenland halibut (CSGH) and cold-smoked salmon (CSS). During industrial processing these samples were added acetic and/or lactic acids. The stochastic model was developed from an existing deterministic model including the effect of 12 environmental parameters and microbial interaction (O. Mejlholm and P. Dalgaard, Food Microbiology, submitted for publication). Observed maximum population density (MPD) values of L. monocytogenes in naturally contaminated samples of CSGH and CSS were accurately predicted by the stochastic model based on measured variability in product characteristics and storage conditions. Results comparable to those from the stochastic model were obtained, when product characteristics of the least and most preserved sample of CSGH and CSS were used as input for the existing deterministic model. For both modelling approaches, it was shown that lag time and the effect of microbial interaction needs to be included to accurately predict MPD values of L. monocytogenes. Addition of organic acids to CSGH and CSS was confirmed as a suitable mitigation strategy against the risk of growth by L. monocytogenes as both types of products were in compliance with the EU regulation on ready-to-eat foods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Characteristics of bacterial and fungal growth in plastic bottled beverages under a consuming condition model.

    Science.gov (United States)

    Watanabe, Maiko; Ohnishi, Takahiro; Araki, Emiko; Kanda, Takashi; Tomita, Atsuko; Ozawa, Kazuhiro; Goto, Keiichi; Sugiyama, Kanji; Konuma, Hirotaka; Hara-Kudo, Yukiko

    2014-01-01

    Microbial contamination in unfinished beverages can occur when drinking directly from the bottle. Various microorganisms, including foodborne pathogens, are able to grow in these beverages at room temperature or in a refrigerator. In this study, we elucidated the characteristics of microorganism growth in bottled beverages under consuming condition models. Furthermore, we provide insight into the safety of partially consumed bottled beverages with respect to food hygiene. We inoculated microorganisms, including foodborne pathogens, into various plastic bottled beverages and analysed the dynamic growth of microorganisms as well as bacterial toxin production in the beverages. Eight bottled beverage types were tested in this study, namely green tea, apple juice drink, tomato juice, carbonated drink, sport drink, coffee with milk, isotonic water and mineral water, and in these beverages several microorganism types were used: nine bacteria including three toxin producers, three yeasts, and five moulds. Following inoculation, the bottles were incubated at 35°C for 48 h for bacteria, 25°C for 48 h for yeasts, and 25°C for 28 days for moulds. During the incubation period, the number of bacteria and yeasts and visible changes in mould-growth were determined over time. Our results indicated that combinations of the beverage types and microorganism species correlated with the degree of growth. Regarding factors that affect the growth and toxin-productivity of microorganisms in beverages, it is speculated that the pH, static/shaking culture, temperature, additives, or ingredients, such as carbon dioxide or organic matter (especially of plant origin), may be important for microorganism growth in beverages. Our results suggest that various types of unfinished beverages have microorganism growth and can include food borne pathogens and bacterial toxins. Therefore, our results indicate that in terms of food hygiene it is necessary to consume beverages immediately after opening

  17. A new model for simulating growth in fish

    Directory of Open Access Journals (Sweden)

    Johannes Hamre

    2014-01-01

    Full Text Available A real dynamic population model calculates change in population sizes independent of time. The Beverton & Holt (B&H model commonly used in fish assessment includes the von Bertalanffy growth function which has age or accumulated time as an independent variable. As a result the B&H model has to assume constant fish growth. However, growth in fish is highly variable depending on food availability and environmental conditions. We propose a new growth model where the length increment of fish living under constant conditions and unlimited food supply, decreases linearly with increasing fish length until it reaches zero at a maximal fish length. The model is independent of time and includes a term which accounts for the environmental variation. In the present study, the model was validated in zebrafish held at constant conditions. There was a good fit of the model to data on observed growth in Norwegian spring spawning herring, capelin from the Barents Sea, North Sea herring and in farmed coastal cod. Growth data from Walleye Pollock from the Eastern Bering Sea and blue whiting from the Norwegian Sea also fitted reasonably well to the model, whereas data from cod from the North Sea showed a good fit to the model only above a length of 70 cm. Cod from the Barents Sea did not grow according to the model. The last results can be explained by environmental factors and variable food availability in the time under study. The model implicates that the efficiency of energy conversion from food decreases as the individual animal approaches its maximal length and is postulated to represent a natural law of fish growth.

  18. Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

    Directory of Open Access Journals (Sweden)

    Thomas J Moutinho

    Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

  19. Fracture Mechanical Markov Chain Crack Growth Model

    DEFF Research Database (Denmark)

    Gansted, L.; Brincker, Rune; Hansen, Lars Pilegaard

    1991-01-01

    propagation process can be described by a discrete space Markov theory. The model is applicable to deterministic as well as to random loading. Once the model parameters for a given material have been determined, the results can be used for any structure as soon as the geometrical function is known....

  20. Impacts of radiation exposure on the experimental microbial ecosystem: a particle-based model simulation approach

    International Nuclear Information System (INIS)

    Doi, M.; Tanaka, N.; Fuma, S.; Kawabata, Z.

    2004-01-01

    Well-designed experimental model ecosystem could be a simple reference of the actual environment and complex ecological systems. For ecological toxicity test of radiation and other environmental toxicants, we investigated and aquatic microbial ecosystem (closed microcosm) in the test tube with initial substrates,autotroph flagellate algae (Euglena, G.), heterotroph ciliate protozoa (Tetrahymena T.) and saprotroph bacteria (E, coli). These species organizes by itself to construct the ecological system, that keeps the sustainable population dynamics for more than 2 years after inoculation only by adding light diurnally and controlling temperature at 25 degree Celsius. Objective of the study is to develop the particle-based computer simulation by reviewing interactions among microbes and environment, and analyze the ecological toxicities of radiation on the microcosm by replicating experimental results in the computer simulation. (Author) 14 refs

  1. Modeling of microbial gas generation: application to the eastern Mediterranean “Biogenic Play”

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, M.; Dubille, M.; Montadert, L.

    2016-07-01

    Biogenic gas is becoming increasingly important as an exploration target in the petroleum industry because it occurs in geologically predictable circumstances and in large quantities at shallow depths as free gas or gas hydrates. As accumulations of biogenic gas result in a subtle synchronization between early generation and early trapping, we integrated a macroscopic model of microbial gas generation within a 3D basin and petroleum system forward simulator. The macroscopic model is based on a microscopic model, which consists in a 1D sedimentary column that accounts for sedimentation, compaction, Darcy flow and Diffusion flow. The organic carbon is the only non-soluble element considered in this version of the model. The dissolved elements are O2, SO4 2-, H2, CH3COOH, and CH4. Methane is dissolved in water or present as a free phase if its concentration exceeds its solubility at given pressure and temperature. In this microscopic model, the transformation of substrate into biomass is described through a set of logistic equations coupled with the transport equations (advection and diffusion). Based on the microscopic considerations we developed the macroscopic model of low maturity/biogenic gas generation in which hydrocarbons are generated through first order kinetic reactions at low maturity. This macroscopic model is adapted to petroleum system modeling at basin scale with TemisFlow®, which aims to understand and predict hydrocarbon generation, migration, and accumulation. It is composed of: i) A source rock criteria which allow defining the biogenic gas source rocks potential and ii) A kinetic model of methane generation. The previous model has been successfully applied on different basins such as the Carupano Basin from the offshore Venezuela, the Magdalena Delta (offshore Colombia) and the offshore Vietnam where direct observations of low-maturity gas were available. Furthermore, it has been applied in the offshore Lebanon in order to check the viability of

  2. Real-time monitoring of a microbial electrolysis cell using an electrical equivalent circuit model.

    Science.gov (United States)

    Hussain, S A; Perrier, M; Tartakovsky, B

    2018-04-01

    Efforts in developing microbial electrolysis cells (MECs) resulted in several novel approaches for wastewater treatment and bioelectrosynthesis. Practical implementation of these approaches necessitates the development of an adequate system for real-time (on-line) monitoring and diagnostics of MEC performance. This study describes a simple MEC equivalent electrical circuit (EEC) model and a parameter estimation procedure, which enable such real-time monitoring. The proposed approach involves MEC voltage and current measurements during its operation with periodic power supply connection/disconnection (on/off operation) followed by parameter estimation using either numerical or analytical solution of the model. The proposed monitoring approach is demonstrated using a membraneless MEC with flow-through porous electrodes. Laboratory tests showed that changes in the influent carbon source concentration and composition significantly affect MEC total internal resistance and capacitance estimated by the model. Fast response of these EEC model parameters to changes in operating conditions enables the development of a model-based approach for real-time monitoring and fault detection.

  3. Modeling Microbial Processes in EPIC to Estimate Greenhouse Gas Emissions from soils

    Science.gov (United States)

    Schwab, D. E.; Izaurralde, R. C.; McGill, W. B.; Williams, J. R.; Schmid, E.

    2009-12-01

    Emissions of trace gases (CO2, N2O and CH4) to the atmosphere from managed terrestrial ecosystems have been contributing significantly to the warming of Earth. Trace gas production is dominated by biospheric processes. An improved knowledge of the soil-plant-atmosphere interface is of key importance for understanding trace gas dynamics. In soils, microbial metabolism plays a key role in the release or uptake of trace gases. Here we present work on the biophysical and biogeochemical model EPIC (Environmental Policy/Integrated Climate) to extend its capabilities to simulate CO2 and N2O fluxes in managed and unmanaged ecosystems. Emphasis will be given to recently developed, microbially-based, denitrification and nitrification modules. The soil-atmosphere exchange of trace gases can be measured by using various equipments, but often these measurements exhibit extreme space-time variability. We use hourly time steps to account for the variability induced by small changes in environmental conditions. Soils are often studied as macroscopic systems, although their functions are predominantly controlled at a microscopic level; i.e. the level of the microorganisms. We include these processes to the extent that these are known and can be quantitatively described. We represent soil dynamics mathematically with routines for gas diffusion, Michael Menten processes, electron budgeting and other processes such as uptake and transformations. We hypothesize that maximization of energy capture form scarce substrates using energetic favorable reactions drives evolution and that competitive advantage can result by depriving a competitor from a substrate. This Microbe Model changes concepts of production of N-containing trace gases; it unifies understanding of N oxidation and reduction, predicts production and evolution of trace gases and is consistent with observations of anaerobic ammonium oxidation.

  4. Mediation Analysis in a Latent Growth Curve Modeling Framework

    Science.gov (United States)

    von Soest, Tilmann; Hagtvet, Knut A.

    2011-01-01

    This article presents several longitudinal mediation models in the framework of latent growth curve modeling and provides a detailed account of how such models can be constructed. Logical and statistical challenges that might arise when such analyses are conducted are also discussed. Specifically, we discuss how the initial status (intercept) and…

  5. Growth models for Pinus patula in Angola | Delgado-Matas ...

    African Journals Online (AJOL)

    This study developed growth models for Pinus patula Schiede ex Schltdl. et Cham. for the Central Highlands of Angola for simulating the development of stand characteristics. The model set included dominant height, individual-tree diameter increment, individual-tree height and self-thinning models. The study was based ...

  6. Regression models for linking patterns of growth to a later outcome: infant growth and childhood overweight

    Directory of Open Access Journals (Sweden)

    Andrew K. Wills

    2016-04-01

    Full Text Available Abstract Background Regression models are widely used to link serial measures of anthropometric size or changes in size to a later outcome. Different parameterisations of these models enable one to target different questions about the effect of growth, however, their interpretation can be challenging. Our objective was to formulate and classify several sets of parameterisations by their underlying growth pattern contrast, and to discuss their utility using an expository example. Methods We describe and classify five sets of model parameterisations in accordance with their underlying growth pattern contrast (conditional growth; being bigger v being smaller; becoming bigger and staying bigger; growing faster v being bigger; becoming and staying bigger versus being bigger. The contrasts are estimated by including different sets of repeated measures of size and changes in size in a regression model. We illustrate these models in the setting of linking infant growth (measured on 6 occasions: birth, 6 weeks, 3, 6, 12 and 24 months in weight-for-height-for-age z-scores to later childhood overweight at 8y using complete cases from the Norwegian Childhood Growth study (n = 900. Results In our expository example, conditional growth during all periods, becoming bigger in any interval and staying bigger through infancy, and being bigger from birth were all associated with higher odds of later overweight. The highest odds of later overweight occurred for individuals who experienced high conditional growth or became bigger in the 3 to 6 month period and stayed bigger, and those who were bigger from birth to 24 months. Comparisons between periods and between growth patterns require large sample sizes and need to consider how to scale associations to make comparisons fair; with respect to the latter, we show one approach. Conclusion Studies interested in detrimental growth patterns may gain extra insight from reporting several sets of growth pattern

  7. Models of the Economic Growth and their Relevance

    Directory of Open Access Journals (Sweden)

    Nicolae MOROIANU

    2012-06-01

    Full Text Available Until few years ago, the economic growth was something perfect normal, part of an era marked by the transformation speed. Normality itself has been transformed and we currently are influenced by other rules, unknown yet, which should answer the question: “How do we return to the economic growth?” The economic growth and the models aiming to solve this problem concern the economic history even since its beginnings. In this paper we would like to find out what is the relevance that the well-known macroeconomic models still have and which might be their applicability level in a framework created by a black swan event type.

  8. Modeling truck traffic volume growth congestion.

    Science.gov (United States)

    2009-05-01

    Modeling of the statewide transportation system is an important element in understanding issues and programming of funds to thwart potential congestion. As Alabama grows its manufacturing economy, the number of heavy vehicles traversing its highways ...

  9. Another brick in the cell wall: biosynthesis dependent growth model.

    Directory of Open Access Journals (Sweden)

    Adelin Barbacci

    Full Text Available Expansive growth of plant cell is conditioned by the cell wall ability to extend irreversibly. This process is possible if (i a tensile stress is developed in the cell wall due to the coupling effect between turgor pressure and the modulation of its mechanical properties through enzymatic and physicochemical reactions and if (ii new cell wall elements can be synthesized and assembled to the existing wall. In other words, expansive growth is the result of coupling effects between mechanical, thermal and chemical energy. To have a better understanding of this process, models must describe the interplay between physical or mechanical variable with biological events. In this paper we propose a general unified and theoretical framework to model growth in function of energy forms and their coupling. This framework is based on irreversible thermodynamics. It is then applied to model growth of the internodal cell of Chara corallina modulated by changes in pressure and temperature. The results describe accurately cell growth in term of length increment but also in term of cell pectate biosynthesis and incorporation to the expanding wall. Moreover, the classical growth model based on Lockhart's equation such as the one proposed by Ortega, appears as a particular and restrictive case of the more general growth equation developed in this paper.

  10. Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

    NARCIS (Netherlands)

    Rajilic-Stojanovic, M.; Maathuis, A.; Heilig, G.H.J.; Venema, K.; Vos, de W.M.; Smidt, H.

    2010-01-01

    A high-density phylogenetic microarray targeting small subunit rRNA (SSU rRNA) sequences of over 1000 microbial phylotypes of the human gastrointestinal tract, the HITChip, was used to assess the impact of faecal inoculum preparation and operation conditions on an in vitro model of the human large

  11. Phosphorus status and microbial community of paddy soil with the growth of annual ryegrass (Lolium multiflorum Lam.) under different phosphorus fertilizer treatments*

    Science.gov (United States)

    Guo, Hai-chao; Wang, Guang-huo

    2009-01-01

    Annual ryegrass (Lolium multiflorum Lam.) was grown in paddy soil in pots under different phosphorus (P) fertilizer treatments to investigate changes of P fractions and microbial community of the soil. The treatments included Kunyang phosphate rock (KPR) applications at 50 mg P/kg (KPR50) and 250 mg P/kg (KPR250), mono-calcium phosphate (MCP) application at 50 mg P/kg (MCP50), and the control without P application. The results showed that KPR50, KPR250, and MCP50 applications significantly increased the dry weight of the ryegrass by 13%, 38%, and 55%, and increased P uptake by 19%, 135%, and 324%, respectively. Compared with MCP50, the relative effectiveness of KPR50 and KPR250 treatments in ryegrass production was about 23% and 68%, respectively. After one season of ryegrass growth, the KPR50, KPR250, and MCP50 applications increased soil-available P by 13.4%, 26.8%, and 55.2%, respectively. More than 80% of the applied KPR-P remained as HCl-P fraction in the soil. Phospholipid fatty acid (PLFA) analysis showed that the total and bacterial PLFAs were significantly higher in the soils with KPR250 and MCP50 treatments compared with KPR50 and control. The latter had no significant difference in the total or bacterial PLFAs. The KPR50, KPR250, and MCP50 treatments increased fungal PLFA by 69%, 103%, and 69%, respectively. Both the principal component analysis and the cluster analysis of the PLFA data suggest that P treatments altered the microbial community composition of the soils, and that P availability might be an important contributor to the changes in the microbial community structure during the ryegrass growth in the paddy soils. PMID:19817001

  12. Deterministic three-half-order kinetic model for microbial degradation of added carbon substrates in soil

    International Nuclear Information System (INIS)

    Brunner, W.; Focht, D.D.

    1984-01-01

    The kinetics of mineralization of carbonaceous substrates has been explained by a deterministic model which is applicable to either growth or nongrowth conditions in soils. The mixed-order nature of the model does not require a priori decisions about reaction order, discontinuity period of lag or stationary phase, or correction for endogenous mineralization rates. The integrated equation is simpler than the integrated form of the Monod equation because of the following: (i) only two, rather than four, interdependent constants have to be determined by nonlinear regression analysis, (ii) substrate or product formation can be expressed explicitly as a function of time, (iii) biomass concentration does not have to be known, and (iv) the required initial estimate for the nonlinear regression analysis can be easily obtained from a linearized form rather than from an interval estimate of a differential equation. 14 CO 2 evolution data from soil have been fitted to the model equation. All data except those from irradiated soil gave us better fits by residual sum of squares (RSS) by assuming growth in soil was linear (RSS =0.71) as opposed to exponential (RSS = 2.87). The underlying reasons for growth (exponential versus linear), no growth, and relative degradation rates of substrates are consistent with the basic mechanisms from which the model is derived. 21 references

  13. An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.

    Science.gov (United States)

    Macías-Díaz, J E; Macías, Siegfried; Medina-Ramírez, I E

    2013-12-01

    In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Quadratic tracer dynamical models tobacco growth

    International Nuclear Information System (INIS)

    Qiang Jiyi; Hua Cuncai; Wang Shaohua

    2011-01-01

    In order to study the non-uniformly transferring process of some tracer dosages, we assume that the absorption of some tracer by tobacco is a quadratic function of the tracer quantity of the tracer in the case of fast absorption, whereas the exclusion of the tracer from tobacco is a linear function of the tracer quantity in the case of slow exclusion, after the tracer is introduced into tobacco once at zero time. A single-compartment quadratic dynamical model of Logistic type is established for the leaves of tobacco. Then, a two-compartment quadratic dynamical model is established for leaves and calms of the tobacco. Qualitative analysis of the models shows that the tracer applied to the leaves of the tobacco is excluded finally; however, the tracer stays at the tobacco for finite time. Two methods are also given for computing the parameters in the models. Finally, the results of the models are verified by the 32 P experiment for the absorption of tobacco. (authors)

  15. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

    Science.gov (United States)

    Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

    2017-04-07

    Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

  16. Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity

    Directory of Open Access Journals (Sweden)

    L. Vanysacker

    2013-01-01

    Full Text Available Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development.

  17. Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity

    Science.gov (United States)

    Vanysacker, L.; Denis, C.; Declerck, P.; Piasecka, A.; Vankelecom, I. F. J.

    2013-01-01

    Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development. PMID:23986906

  18. Multi-scale individual-based model of microbial and bioconversion dynamics in aerobic granular sludge.

    Science.gov (United States)

    Xavier, Joao B; De Kreuk, Merle K; Picioreanu, Cristian; Van Loosdrecht, Mark C M

    2007-09-15

    Aerobic granular sludge is a novel compact biological wastewater treatment technology for integrated removal of COD (chemical oxygen demand), nitrogen, and phosphate charges. We present here a multiscale model of aerobic granular sludge sequencing batch reactors (GSBR) describing the complex dynamics of populations and nutrient removal. The macro scale describes bulk concentrations and effluent composition in six solutes (oxygen, acetate, ammonium, nitrite, nitrate, and phosphate). A finer scale, the scale of one granule (1.1 mm of diameter), describes the two-dimensional spatial arrangement of four bacterial groups--heterotrophs, ammonium oxidizers, nitrite oxidizers, and phosphate accumulating organisms (PAO)--using individual based modeling (IbM) with species-specific kinetic models. The model for PAO includes three internal storage compounds: polyhydroxyalkanoates (PHA), poly phosphate, and glycogen. Simulations of long-term reactor operation show how the microbial population and activity depends on the operating conditions. Short-term dynamics of solute bulk concentrations are also generated with results comparable to experimental data from lab scale reactors. Our results suggest that N-removal in GSBR occurs mostly via alternating nitrification/denitrification rather than simultaneous nitrification/denitrification, supporting an alternative strategy to improve N-removal in this promising wastewater treatment process.

  19. Modeling and simulation of Si crystal growth from melt

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lijun; Liu, Xin; Li, Zaoyang [National Engineering Research Center for Fluid Machinery and Compressors, School of Energy and Power Engineering, Xi' an Jiaotong University, Xi' an, Shaanxi 710049 (China); Miyazawa, Hiroaki; Nakano, Satoshi; Kakimoto, Koichi [Research Institute for Applied Mechanics, Kyushu University, Kasuga 816-8580 (Japan)

    2009-07-01

    A numerical simulator was developed with a global model of heat transfer for any crystal growth taking place at high temperature. Convective, conductive and radiative heat transfers in the furnace are solved together in a conjugated way by a finite volume method. A three-dimensional (3D) global model was especially developed for simulation of heat transfer in any crystal growth with 3D features. The model enables 3D global simulation be conducted with moderate requirement of computer resources. The application of this numerical simulator to a CZ growth and a directional solidification process for Si crystals, the two major production methods for crystalline Si for solar cells, was introduced. Some typical results were presented, showing the importance and effectiveness of numerical simulation in analyzing and improving these kinds of Si crystal growth processes from melt. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  20. Growth Curve Models and Applications : Indian Statistical Institute

    CERN Document Server

    2017-01-01

    Growth curve models in longitudinal studies are widely used to model population size, body height, biomass, fungal growth, and other variables in the biological sciences, but these statistical methods for modeling growth curves and analyzing longitudinal data also extend to general statistics, economics, public health, demographics, epidemiology, SQC, sociology, nano-biotechnology, fluid mechanics, and other applied areas.   There is no one-size-fits-all approach to growth measurement. The selected papers in this volume build on presentations from the GCM workshop held at the Indian Statistical Institute, Giridih, on March 28-29, 2016. They represent recent trends in GCM research on different subject areas, both theoretical and applied. This book includes tools and possibilities for further work through new techniques and modification of existing ones. The volume includes original studies, theoretical findings and case studies from a wide range of app lied work, and these contributions have been externally r...

  1. Soil biochemical properties and microbial resilience in agroforestry systems: effects on wheat growth under controlled drought and flooding conditions.

    Science.gov (United States)

    Rivest, David; Lorente, Miren; Olivier, Alain; Messier, Christian

    2013-10-01

    Agroforestry is increasingly viewed as an effective means of maintaining or even increasing crop and tree productivity under climate change while promoting other ecosystem functions and services. This study focused on soil biochemical properties and resilience following disturbance within agroforestry and conventional agricultural systems and aimed to determine whether soil differences in terms of these biochemical properties and resilience would subsequently affect crop productivity under extreme soil water conditions. Two research sites that had been established on agricultural land were selected for this study. The first site included an 18-year-old windbreak, while the second site consisted in an 8-year-old tree-based intercropping system. In each site, soil samples were used for the determination of soil nutrient availability, microbial dynamics and microbial resilience to different wetting-drying perturbations and for a greenhouse pot experiment with wheat. Drying and flooding were selected as water stress treatments and compared to a control. These treatments were initiated at the beginning of the wheat anthesis period and maintained over 10 days. Trees contributed to increase soil nutrient pools, as evidenced by the higher extractable-P (both sites), and the higher total N and mineralizable N (tree-based intercropping site) found in the agroforestry compared to the conventional agricultural system. Metabolic quotient (qCO2) was lower in the agroforestry than in the conventional agricultural system, suggesting higher microbial substrate use efficiency in agroforestry systems. Microbial resilience was higher in the agroforestry soils compared to soils from the conventional agricultural system (windbreak site only). At the windbreak site, wheat growing in soils from agroforestry system exhibited higher aboveground biomass and number of grains per spike than in conventional agricultural system soils in the three water stress treatments. At the tree

  2. Benchmark data set for wheat growth models

    DEFF Research Database (Denmark)

    Asseng, S; Ewert, F.; Martre, P

    2015-01-01

    The data set includes a current representative management treatment from detailed, quality-tested sentinel field experiments with wheat from four contrasting environments including Australia, The Netherlands, India and Argentina. Measurements include local daily climate data (solar radiation, max...... analysis with 26 models and 30 years (1981-2010) for each location, for elevated atmospheric CO2 and temperature changes, a heat stress sensitivity analysis at anthesis, and a sensitivity analysis with soil and crop management variations and a Global Climate Model end-century scenario....

  3. A mathematical model of microalgae growth in cylindrical photobioreactor

    Science.gov (United States)

    Bakeri, Noorhadila Mohd; Jamaian, Siti Suhana

    2017-08-01

    Microalgae are unicellular organisms, which exist individually or in chains or groups but can be utilized in many applications. Researchers have done various efforts in order to increase the growth rate of microalgae. Microalgae have a potential as an effective tool for wastewater treatment, besides as a replacement for natural fuel such as coal and biodiesel. The growth of microalgae can be estimated by using Geider model, which this model is based on photosynthesis irradiance curve (PI-curve) and focused on flat panel photobioreactor. Therefore, in this study a mathematical model for microalgae growth in cylindrical photobioreactor is proposed based on the Geider model. The light irradiance is the crucial part that affects the growth rate of microalgae. The absorbed photon flux will be determined by calculating the average light irradiance in a cylindrical system illuminated by unidirectional parallel flux and considering the cylinder as a collection of differential parallelepipeds. Results from this study showed that the specific growth rate of microalgae increases until the constant level is achieved. Therefore, the proposed mathematical model can be used to estimate the rate of microalgae growth in cylindrical photobioreactor.

  4. Modelling breast cancer tumour growth for a stable disease population.

    Science.gov (United States)

    Isheden, Gabriel; Humphreys, Keith

    2017-01-01

    Statistical models of breast cancer tumour progression have been used to further our knowledge of the natural history of breast cancer, to evaluate mammography screening in terms of mortality, to estimate overdiagnosis, and to estimate the impact of lead-time bias when comparing survival times between screen detected cancers and cancers found outside of screening programs. Multi-state Markov models have been widely used, but several research groups have proposed other modelling frameworks based on specifying an underlying biological continuous tumour growth process. These continuous models offer some advantages over multi-state models and have been used, for example, to quantify screening sensitivity in terms of mammographic density, and to quantify the effect of body size covariates on tumour growth and time to symptomatic detection. As of yet, however, the continuous tumour growth models are not sufficiently developed and require extensive computing to obtain parameter estimates. In this article, we provide a detailed description of the underlying assumptions of the continuous tumour growth model, derive new theoretical results for the model, and show how these results may help the development of this modelling framework. In illustrating the approach, we develop a model for mammography screening sensitivity, using a sample of 1901 post-menopausal women diagnosed with invasive breast cancer.

  5. Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Fred Brokman; John Selker; Mark Rockhold

    2004-01-26

    While numerous techniques exist for remediation of contaminant plumes in groundwater or near the soil surface, remediation methods in the deep vadose zone are less established due to complex transport dynamics and sparse microbial populations. There is a lack of knowledge on how physical and hydrologic features of the vadose zone control microbial growth and colonization in response to nutrient delivery during bioremediation. Yet pollution in the vadose zone poses a serious threat to the groundwater resources lying deeper in the sediment. While the contaminants may be slowly degraded by native microbial communities, microbial degradation rates rarely keep pace with the spread of the pollutant. It is crucial to increase indigenous microbial degradation in the vadose zone to combat groundwater contamination.

  6. Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Brockman, Fred J.; Selker, John S.; Rockhold, Mark L.

    2004-10-31

    Executive Summary - While numerous techniques exist for remediation of contaminant plumes in groundwater or near the soil surface, remediation methods in the deep vadose zone are less established due to complex transport dynamics and sparse microbial populations. There is a lack of knowledge on how physical and hydrologic features of the vadose zone control microbial growth and colonization in response to nutrient delivery during bioremediation. Yet pollution in the vadose zone poses a serious threat to the groundwater resources lying deeper in the sediment. While the contaminants may be slowly degraded by native microbial communities, microbial degradation rates rarely keep pace with the spread of the pollutant. It is crucial to increase indigenous microbial degradation in the vadose zone to combat groundwater contamination...

  7. A mathematical model of the growth of uterine myomas.

    Science.gov (United States)

    Chen, C Y; Ward, J P

    2014-12-01

    Uterine myomas or fibroids are common, benign smooth muscle tumours that can grow to 10  cm or more in diameter and are routinely removed surgically. They are typically slow- growing, well-vascularised, spherical tumours that, on a macro-scale, are a structurally uniform, hard elastic material. We present a multi-phase mathematical model of a fully vascularised myoma growing within a surrounding elastic tissue. Adopting a continuum approach, the model assumes the conservation of mass and momentum of four phases, namely cells/collagen, extracellular fluid, arterial and venous phases. The cell/collagen phase is treated as a poro-elastic material, based on a linear stress-strain relationship, and Darcy's law is applied to describe flow in the extracellular fluid and the two vascular phases. The supply of extracellular fluid is dependent on the capillary flow rate and mean capillary pressure expressed in terms of the arterial and venous pressures. Cell growth and division is limited to the myoma domain and dependent on the local stress in the material. The resulting model consists of a system of nonlinear partial differential equations with two moving boundaries. Numerical solutions of the model successfully reproduce qualitatively the clinically observed three-phase "fast-slow-fast" growth profile that is typical for myomas. The results suggest that this growth profile requires stress-induced resistance to growth by the surrounding tissue and a switch-like cell growth response to stress. Analysis of large-time solutions reveal that while there is a functioning vasculature throughout the myoma, exponential growth results, otherwise power-law growth is predicted. An extensive survey of the effect of parameters on model solutions is also presented, and in particular, the enhanced growth caused by factors such as oestrogen is predicted by the model.

  8. Non-linear Growth Models in Mplus and SAS

    Science.gov (United States)

    Grimm, Kevin J.; Ram, Nilam

    2013-01-01

    Non-linear growth curves or growth curves that follow a specified non-linear function in time enable researchers to model complex developmental patterns with parameters that are easily interpretable. In this paper we describe how a variety of sigmoid curves can be fit using the Mplus structural modeling program and the non-linear mixed-effects modeling procedure NLMIXED in SAS. Using longitudinal achievement data collected as part of a study examining the effects of preschool instruction on academic gain we illustrate the procedures for fitting growth models of logistic, Gompertz, and Richards functions. Brief notes regarding the practical benefits, limitations, and choices faced in the fitting and estimation of such models are included. PMID:23882134

  9. Small Business Training Models for Community Growth.

    Science.gov (United States)

    Jellison, Holly M., Ed.

    Nine successful community college programs for small business management training are described in this report in terms of their college and economic context, purpose, offerings, delivery modes, operating and marketing strategies, community outreach, support services, faculty and staff, evaluation, and future directions. The model programs are…

  10. Explorative analysis of microbes, colloids and gases together with microbial modelling. Site description model SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Hallbeck, Lotta; Pedersen, Karsten (Microbial Analytics Sweden AB, Goeteborg (Sweden))

    2008-08-15

    The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on available primary data from the extended data freeze L2.3 (Nov 2007). This report focuses on microbiology, colloids and gases. Several methods must be used to characterise active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of

  11. Explorative analysis of microbes, colloids and gases together with microbial modelling. Site description model SDM-Site Laxemar

    International Nuclear Information System (INIS)

    Hallbeck, Lotta; Pedersen, Karsten

    2008-08-01

    The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on available primary data from the extended data freeze L2.3 (Nov 2007). This report focuses on microbiology, colloids and gases. Several methods must be used to characterise active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of

  12. Reserve growth in oil pools of Alberta : model and forecast

    Energy Technology Data Exchange (ETDEWEB)

    Verma, M.; Cook, T. [United States Geological Survey, Denver, CO (United States). Central Region

    2010-09-15

    This paper presented a reserve growth study that was conducted on oil pools in Alberta, Canada. Historical oil reserve data were evaluated to assess the potential for future reserve growth in both pools and fields, and reserve growth models and functions were developed to better forecast hydrocarbon volumes. The study also considered the sensitivity of reserve growth to such factors as pool size, porosity, and oil gravity. From 1960 to 2005, the reported known recoverable oil in Alberta, excluding the Athabasca oil sands and including only pools with adequate data, increased from 4.2 to 13.9 billion barrels of oil (BBO). New discoveries contributed 3.7 BBO and reserve growth added 6 BBO. Most reserve growth occurred in pools with more than 125,000 barrels of oil. Light-oil pools account for most of the total known oil volume and consequently showed the lowest growth. Pools with greater than 30 percent porosity grew more than pools with lower porosity reservoirs. Oil field growth was found to be almost twice that of pool growth, possibly because the analysis evaluated fields with two or more pools discovered in different years. The growth in oil volumes in Alberta pools is projected to be about 454 million barrels of oil in the period from 2006 to 2010. Over a 25-year period, the cumulative reserve growth in Alberta oil pools was substantially lower than other major petroleum-producing regions, but the growth at the field level compares well. 8 refs., 2 tabs., 9 figs.

  13. Capacity of Albit® Plant Growth Stimulator for Mitigating Side-effects of Pesticides on Soil Microbial Respiration

    Directory of Open Access Journals (Sweden)

    Natalia N. Karpun

    2017-11-01

    Full Text Available Microorganisms give an early and integrated measure of soil functioning. In particular, soil microbial respiration is recommended for monitoring soil quality. The present study aims to determine the capacity of Albit® (poly-β-hydroxybutyrate, PHB to reduce the detrimental effects of pesticides on soil microbial respiration. The effects of three conventional pesticides (deltamethrin, dithianon, and difenoconazole on basal respiration (BR and substrate-induced respiration (SIR were assessed in the presence and absence of Albit®. The studied pesticides caused negative impacts on soil functioning, reducing BR and SIR. Applications of Albit® increased BR and SIR, and both BR and SIR were kept similar to the control when pesticides were applied with Albit®. PHB, an active ingredient of Albit®, is known to increase beneficial microflora in the rhizosphere due to its regulatory activity on indigenous microorganisms. Thus, more studies should be carried out under different edaphoclimatic conditions to study the benefits of Albit® applications along with pesticides in order to mitigate their side effects on soil microbial functioning.

  14. The effect of hysteresis on microbial activity in computer simulation models

    NARCIS (Netherlands)

    Whitmore, A.P.; Heinen, M.

    1999-01-01

    Microbial activity in soils depends on the status or the soil water, which is expressed by pressure head (h) or water content (θ). There is no unique relationship between θ and h because moisture relations exhibit hysteresis. For convenience microbial activity has usually been related to the main

  15. Populational Growth Models Proportional to Beta Densities with Allee Effect

    Science.gov (United States)

    Aleixo, Sandra M.; Rocha, J. Leonel; Pestana, Dinis D.</