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Sample records for microbial growth determination

  1. Solutes determine the temperature windows for microbial survival and growth

    PubMed Central

    Chin, Jason P.; Megaw, Julianne; Magill, Caroline L.; Nowotarski, Krzysztof; Williams, Jim P.; Bhaganna, Prashanth; Linton, Mark; Patterson, Margaret F.; Underwood, Graham J. C.; Mswaka, Allen Y.; Hallsworth, John E.

    2010-01-01

    Microbial cells, and ultimately the Earth's biosphere, function within a narrow range of physicochemical conditions. For the majority of ecosystems, productivity is cold-limited, and it is microbes that represent the failure point. This study was carried out to determine if naturally occurring solutes can extend the temperature windows for activity of microorganisms. We found that substances known to disorder cellular macromolecules (chaotropes) did expand microbial growth windows, fungi preferentially accumulated chaotropic metabolites at low temperature, and chemical activities of solutes determined microbial survival at extremes of temperature as well as pressure. This information can enhance the precision of models used to predict if extraterrestrial and other hostile environments are able to support life; furthermore, chaotropes may be used to extend the growth windows for key microbes, such as saprotrophs, in cold ecosystems and manmade biomes. PMID:20404182

  2. Determination of Microbial Growth by Protein Assay in an Air-Cathode Single Chamber Microbial Fuel Cell.

    PubMed

    Li, Na; Kakarla, Ramesh; Moon, Jung Mi; Min, Booki

    2015-07-01

    Microbial fuel cells (MFCs) have gathered attention as a novel bioenergy technology to simultaneously treat wastewater with less sludge production than the conventional activated sludge system. In two different operations of the MFC and aerobic process, microbial growth was determined by the protein assay method and their biomass yields using real wastewater were compared. The biomass yield on the anode electrode of the MFC was 0.02 g-COD-cell/g- COD-substrate and the anolyte planktonic biomass was 0.14 g-COD-cell/g-COD-substrate. An MFC without anode electrode resulted in the biomass yield of 0.07 ± 0.03 g-COD-cell/g-COD-substrate, suggesting that oxygen diffusion from the cathode possibly supported the microbial growth. In a comparative test, the biomass yield under aerobic environment was 0.46 ± 0.07 g-COD-cell/g-COD-substrate, which was about 3 times higher than the total biomass value in the MFC operation.

  3. Scaling and optimal synergy: Two principles determining microbial growth in complex media

    NASA Astrophysics Data System (ADS)

    Massucci, Francesco Alessandro; Guimerà, Roger; Nunes Amaral, Luís A.; Sales-Pardo, Marta

    2015-06-01

    High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that nutrients are used so as to maximize growth, these reconstructions enable us to predict microbial growth. Although such predictions are generally accurate, these approaches do not give insights on how different nutrients are used to produce growth, and thus are difficult to generalize to new media or to different organisms. Here, we propose a systems-level phenomenological model of metabolism inspired by the virial expansion. Our model predicts biomass production given the nutrient uptakes and a reduced set of parameters, which can be easily determined experimentally. To validate our model, we test it against in silico simulations and experimental measurements of growth, and find good agreement. From a biological point of view, our model uncovers the impact that individual nutrients and the synergistic interaction between nutrient pairs have on growth, and suggests that we can understand the growth maximization principle as the optimization of nutrient synergies.

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

    NASA Astrophysics Data System (ADS)

    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

  5. Development of a multi-classification neural network model to determine the microbial growth/no growth interface.

    PubMed

    Fernández-Navarro, Francisco; Valero, Antonio; Hervás-Martínez, César; Gutiérrez, Pedro A; García-Gimeno, Rosa M; Zurera-Cosano, Gonzalo

    2010-07-15

    Boundary models have been recognized as useful tools to predict the ability of microorganisms to grow at limiting conditions. However, at these conditions, microbial behaviour can vary, being difficult to distinguish between growth or no growth. In this paper, the data from the study of Valero et al. [Valero, A., Pérez-Rodríguez, F., Carrasco, E., Fuentes-Alventosa, J.M., García-Gimeno, R.M., Zurera, G., 2009. Modelling the growth boundaries of Staphylococcus aureus: Effect of temperature, pH and water activity. International Journal of Food Microbiology 133 (1-2), 186-194] belonging to growth/no growth conditions of Staphylococcus aureus against temperature, pH and a(w) were divided into three categorical classes: growth (G), growth transition (GT) and no growth (NG). Subsequently, they were modelled by using a Radial Basis Function Neural Network (RBFNN) in order to create a multi-classification model that was able to predict the probability of belonging at one of the three mentioned classes. The model was developed through an over sampling procedure using a memetic algorithm (MA) in order to balance in part the size of the classes and to improve the accuracy of the classifier. The multi-classification model, named Smote Memetic Radial Basis Function (SMRBF) provided a quite good adjustment to data observed, being able to correctly classify the 86.30% of training data and the 82.26% of generalization data for the three observed classes in the best model. Besides, the high number of replicates per condition tested (n=30) produced a smooth transition between growth and no growth. At the most stringent conditions, the probability of belonging to class GT was higher, thus justifying the inclusion of the class in the new model. The SMRBF model presented in this study can be used to better define microbial growth/no growth interface and the variability associated to these conditions so as to apply this knowledge to a food safety in a decision-making process.

  6. New microbial growth factor

    NASA Technical Reports Server (NTRS)

    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. Prediction of Competitive Microbial Growth.

    PubMed

    Fujikawa, Hiroshi

    2016-01-01

     Prediction of competitive microbial growth is becoming important for microbial food safety. There would be two approaches to predict competitive microbial growth with mathematical models. The first approach is the development of a growth model for competitive microbes. Among several candidates for the competition model considered, the combination of the primary growth model of the new logistic (NL) model and the competition model of the Lotka-Vorttera (LV) model showed the best performance in predicting microbial competitive growth in the mixed culture of two species. This system further successfully predicted the growth of three competitive species in mixed culture. The second approach is the application of the secondary model especially for the parameter of the maximum cell population in the primary growth model. The combination of the NL model and a polynomial model for the maximum population successfully predicted Salmonella growth in raw ground beef. This system further successfully predicted Salmonella growth in beef at various initial concentrations and temperatures. The first approach requires microbial growth data in monoculture for analysis. The second approach to the prediction of competitive growth from the viewpoint of microbial food safety would be more suitable for practical application.

  8. Teaching Microbial Growth by Simulation.

    ERIC Educational Resources Information Center

    Ruiz, A. Fernandez; And Others

    1989-01-01

    Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

  9. Modeling microbial growth and dynamics.

    PubMed

    Esser, Daniel S; Leveau, Johan H J; Meyer, Katrin M

    2015-11-01

    Modeling has become an important tool for widening our understanding of microbial growth in the context of applied microbiology and related to such processes as safe food production, wastewater treatment, bioremediation, or microbe-mediated mining. Various modeling techniques, such as primary, secondary and tertiary mathematical models, phenomenological models, mechanistic or kinetic models, reactive transport models, Bayesian network models, artificial neural networks, as well as agent-, individual-, and particle-based models have been applied to model microbial growth and activity in many applied fields. In this mini-review, we summarize the basic concepts of these models using examples and applications from food safety and wastewater treatment systems. We further review recent developments in other applied fields focusing on models that explicitly include spatial relationships. Using these examples, we point out the conceptual similarities across fields of application and encourage the combined use of different modeling techniques in hybrid models as well as their cross-disciplinary exchange. For instance, pattern-oriented modeling has its origin in ecology but may be employed to parameterize microbial growth models when experimental data are scarce. Models could also be used as virtual laboratories to optimize experimental design analogous to the virtual ecologist approach. Future microbial growth models will likely become more complex to benefit from the rich toolbox that is now available to microbial growth modelers.

  10. Conditioning biomass for microbial growth

    DOEpatents

    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.

  11. Well having inhibited microbial growth

    DOEpatents

    Lee, Brady D.; Dooley, Kirk J.

    2006-08-15

    The invention includes methods of inhibiting microbial growth in a well. A packing material containing a mixture of a first material and an antimicrobial agent is provided to at least partially fill a well bore. One or more access tubes are provided in an annular space around a casing within the well bore. The access tubes have a first terminal opening located at or above a ground surface and have a length that extends from the first terminal opening at least part of the depth of the well bore. The access tubes have a second terminal opening located within the well bore. An antimicrobial material is supplied into the well bore through the first terminal opening of the access tubes. The invention also includes well constructs.

  12. A thermodynamic theory of microbial growth

    PubMed Central

    Desmond-Le Quéméner, Elie; Bouchez, Théodore

    2014-01-01

    Our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. In particular, the link between energy balances and growth dynamics is still not understood. Here we demonstrate a microbial growth equation relying on an explicit theoretical ground sustained by Boltzmann statistics, thus establishing a relationship between microbial growth rate and available energy. The validity of our equation was then questioned by analyzing the microbial isotopic fractionation phenomenon, which can be viewed as a kinetic consequence of the differences in energy contents of isotopic isomers used for growth. We illustrate how the associated theoretical predictions are actually consistent with recent experimental evidences. Our work links microbial population dynamics to the thermodynamic driving forces of the ecosystem, which opens the door to many biotechnological and ecological developments. PMID:24522260

  13. A thermodynamic theory of microbial growth.

    PubMed

    Desmond-Le Quéméner, Elie; Bouchez, Théodore

    2014-08-01

    Our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. In particular, the link between energy balances and growth dynamics is still not understood. Here we demonstrate a microbial growth equation relying on an explicit theoretical ground sustained by Boltzmann statistics, thus establishing a relationship between microbial growth rate and available energy. The validity of our equation was then questioned by analyzing the microbial isotopic fractionation phenomenon, which can be viewed as a kinetic consequence of the differences in energy contents of isotopic isomers used for growth. We illustrate how the associated theoretical predictions are actually consistent with recent experimental evidences. Our work links microbial population dynamics to the thermodynamic driving forces of the ecosystem, which opens the door to many biotechnological and ecological developments.

  14. Substrate and nutrient limitation regulating microbial growth in soil

    NASA Astrophysics Data System (ADS)

    Bååth, Erland

    2015-04-01

    Microbial activity and growth in soil is regulated by several abiotic factors, including temperature, moisture and pH as the most important ones. At the same time nutrient conditions and substrate availability will also determine microbial growth. Amount of substrate will not only affect overall microbial growth, but also affect the balance of fungal and bacterial growth. The type of substrate will also affect the latter. Furthermore, according to Liebig law of limiting factors, we would expect one nutrient to be the main limiting one for microbial growth in soil. When this nutrient is added, the initial second liming factor will become the main one, adding complexity to the microbial response after adding different substrates. I will initially describe different ways of determining limiting factors for bacterial growth in soil, especially a rapid method estimating bacterial growth, using the leucine incorporation technique, after adding C (as glucose), N (as ammonium nitrate) and P (as phosphate). Scenarios of different limitations will be covered, with the bacterial growth response compared with fungal growth and total activity (respiration). The "degree of limitation", as well as the main limiting nutrient, can be altered by adding substrate of different stoichiometric composition. However, the organism group responding after alleviating the nutrient limitation can differ depending on the type of substrate added. There will also be situations, where fungi and bacteria appear to be limited by different nutrients. Finally, I will describe interactions between abiotic factors and the response of the soil microbiota to alleviation of limiting factors.

  15. 21 CFR 866.2560 - Microbial growth monitor.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbial growth monitor. 866.2560 Section 866...) 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...

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

    PubMed

    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.

  17. Microbial Growth under Supercritical CO2

    PubMed Central

    Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B.

    2015-01-01

    Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface. PMID:25681188

  18. Microbial growth under supercritical CO2.

    PubMed

    Peet, Kyle C; Freedman, Adam J E; Hernandez, Hector H; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B; Thompson, Janelle R

    2015-04-01

    Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface.

  19. Oxygen transfer phenomena in 48-well microtiter plates: determination by optical monitoring of sulfite oxidation and verification by real-time measurement during microbial growth.

    PubMed

    Kensy, Frank; Zimmermann, Hartmut F; Knabben, Ingo; Anderlei, Tibor; Trauthwein, Harald; Dingerdissen, Uwe; Büchs, Jochen

    2005-03-20

    Oxygen limitation is one of the most frequent problems associated with the application of shaking bioreactors. The gas-liquid oxygen transfer properties of shaken 48-well microtiter plates (MTPs) were analyzed at different filling volumes, shaking diameters, and shaking frequencies. On the one hand, an optical method based on sulfite oxidation was used as a chemical model system to determine the maximum oxygen transfer capacity (OTR(max)). On the other hand, the Respiration Activity Monitoring System (RAMOS) was applied for online measurement of the oxygen transfer rate (OTR) during growth of the methylotropic yeast Hansenula polymorpha. A proportionality constant between the OTR(max) of the biological system and the OTR(max) of the chemical system were indicated from these data, offering the possibility to transform the whole set of chemical data to biologically relevant conditions. The results exposed "out of phase" shaking conditions at a shaking diameter of 1 mm, which were confirmed by theoretical consideration with the phase number (Ph). At larger shaking diameters (2-50 mm) the oxygen transfer rate in MTPs shaken at high frequencies reached values of up to 0.28 mol/L/h, corresponding to a volumetric mass transfer coefficient (k(L)a) of 1,600 1/h. The specific mass transfer area (a) increases exponentially with the shaking frequency up to values of 2,400 1/m. On the contrary, the mass transfer coefficient (k(L)) is constant at a level of about 0.15 m/h over a wide range of shaking frequencies and shaking diameters. However, at high shaking frequencies, when the complete liquid volume forms a thin film on the cylindric wall of the well, the mass transfer coefficient (k(L)) increases linearly to values of up to 0.76 m/h. Essentially, the present investigation demonstrates that the 48-well plate outperforms the 96-well MTP and shake flasks at widely used operating conditions with respect to oxygen supply. The 48-well plates emerge, therefore, as an excellent

  20. Influence of substrate and microbial interaction on efficiency of rumen microbial growth.

    PubMed

    Demeyer, D; Van Nevel, C

    1986-01-01

    Microbial N produced in the rumen and flowing to the duodenum (Ni) is related to the total amount of OM fermented or apparently digested in the rumen (OMf). This relationship, best expressed as microbial N yield (gNi/kgOMf), is affected mainly by the physical and chemical properties of feed carbohydrates and the amounts ingested. These factors influence yields at three levels of increasing complexity: Bacterial fermentation within one compartment following the continuous culture model. Fermentation pattern as such does not seem to affect yields. High fermentation rates are associated with lactate production, low methane production and transient polysaccharide synthesis. These effects induce acidification and lower yields, partly compensated by faster growth. Protozoal action, determined by the presence of sequestration spaces provided mainly by roughage diets. The presence of protozoa depresses microbial N yield but allows more complete fibre digestion. Compartmentation and differential passage. With roughage diets, optimal microbial N yield seems to require well developed microbial compartmentation, involving a large proportion of microbes in a large-particle pool with a slow turnover, balanced by a small proportion in liquid, small-particle pools with a fast turnover. Such a situation is associated with long roughage feeding. It is hypothesized that microbial N yields in the rumen may vary between two extremes which are associated with the feeding of long roughage on the one hand or with concentrate (starch) feeding on the other.

  1. An autocatalytic kinetic model for describing microbial growth during fermentation.

    PubMed

    Ibarz, Albert; Augusto, Pedro E D

    2015-01-01

    The mathematical modelling of the behaviour of microbial growth is widely desired in order to control, predict and design food and bioproduct processing, stability and safety. This work develops and proposes a new semi-empirical mathematical model, based on an autocatalytic kinetic, to describe the microbial growth through its biomass concentration. The proposed model was successfully validated using 15 microbial growth patterns, covering the three most important types of microorganisms in food and biotechnological processing (bacteria, yeasts and moulds). Its main advantages and limitations are discussed, as well as the interpretation of its parameters. It is shown that the new model can be used to describe the behaviour of microbial growth.

  2. Interspecies interactions are an integral determinant of microbial community dynamics

    PubMed Central

    Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  3. Nanomechanical sensors for single microbial cell growth monitoring

    NASA Astrophysics Data System (ADS)

    Maloney, Niall; Lukacs, Gyongyi; Jensen, Jason; Hegner, Martin

    2014-06-01

    A nanomechanical technique for rapid real time detection and monitoring of microorganism growth will significantly reduce costs and diagnosis times in industrial and clinical settings. Owing to their label free detection mechanism and unprecedented sensitivity to the mass and elastic modulus of biological structures, dynamically operated cantilever arrays provide an opportunity to rapidly detect and track the evolution of microbial growth. Here we report the monitoring of the growth of single Aspergillus niger spores via the multimode response of microcantilevers. The fungal hyphal structure affects the cantilevers' nanomechanical properties as it propagates along the sensor. We demonstrate, for the first time, the mapping of cellular events with great accuracy using a cantilever frequency response. Imaging of growth conditions on the cantilever, which is performed in parallel, allows for verification of these results. Theoretical comparison and finite element modelling confirm experimental findings and allow for determination of the hyphal elastic modulus.A nanomechanical technique for rapid real time detection and monitoring of microorganism growth will significantly reduce costs and diagnosis times in industrial and clinical settings. Owing to their label free detection mechanism and unprecedented sensitivity to the mass and elastic modulus of biological structures, dynamically operated cantilever arrays provide an opportunity to rapidly detect and track the evolution of microbial growth. Here we report the monitoring of the growth of single Aspergillus niger spores via the multimode response of microcantilevers. The fungal hyphal structure affects the cantilevers' nanomechanical properties as it propagates along the sensor. We demonstrate, for the first time, the mapping of cellular events with great accuracy using a cantilever frequency response. Imaging of growth conditions on the cantilever, which is performed in parallel, allows for verification of these

  4. Bioflumology: Microbial mat growth in flumes

    NASA Astrophysics Data System (ADS)

    Airo, A.; Weigert, S.; Beck, C.

    2014-04-01

    The emergence of oxygenic photosynthesis resulted in a transformational change of Earth's geochemical cycles and the subsequent evolution of life. However, it remains vigorously debated when this metabolic ability had evolved in cyanobacteria. This is largely because studies of Archean microfossil morphology, molecular biomarkers, and isotopic characteristics are frequently ambiguous. However, the high degree of morphological similarities between modern photosynthetic and Archean fossil mats has been interpreted to indicate phototactic microbial behavior or oxygenic photosynthesis. In order to better evaluate the relationship between mat morphology and metabolism, we here present a laboratory set-up for conducting month-long experiments in several sterilizable circular flumes designed to allow single-species cyanobacterial growth under adjustable fluid-flow conditions and protected from contamination.

  5. Biologically-motivated system identification: application to microbial growth modeling.

    PubMed

    Yan, Jinyao; Deller, J R

    2014-01-01

    This paper presents a new method for identification of system models that are linear in parametric structure, but arbitrarily nonlinear in signal operations. The strategy blends traditional system identification methods with three modeling strategies that are not commonly employed in signal processing: linear-time-invariant-in-parameters models, set-based parameter identification, and evolutionary selection of the model structure. This paper reports recent advances in the theoretical foundation of the methods, then focuses on the operation and performance of the approach, particularly the evolutionary model determination. The method is applied to the modeling of microbial growth by Monod Kinetics.

  6. Detecting differential growth of microbial populations with Gaussian process regression

    PubMed Central

    Tonner, Peter D.; Darnell, Cynthia L.; Engelhardt, Barbara E.; Schmid, Amy K.

    2017-01-01

    Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form. Extensions to these models are required to quantify the effects of perturbations, which often exhibit nonstandard growth curves. Rather than assume specific functional forms for experimental perturbations, we developed a general and robust model of microbial population growth curves using Gaussian process (GP) regression. GP regression modeling of high-resolution time-series growth data enables accurate quantification of population growth and allows explicit control of effects from other covariates such as genetic background. This framework substantially outperforms commonly used microbial population growth models, particularly when modeling growth data from environmentally stressed populations. We apply the GP growth model and develop statistical tests to quantify the differential effects of environmental perturbations on microbial growth across a large compendium of genotypes in archaea and yeast. This method accurately identifies known transcriptional regulators and implicates novel regulators of growth under standard and stress conditions in the model archaeal organism Halobacterium salinarum. For yeast, our method correctly identifies known phenotypes for a diversity of genetic backgrounds under cyclohexamide stress and also detects previously unidentified oxidative stress sensitivity across a subset of strains. Together, these results demonstrate that the GP models are interpretable, recapitulating biological knowledge of growth response while providing new insights into the relevant parameters affecting microbial population growth. PMID:27864351

  7. Minimal models of growth and decline of microbial populations.

    PubMed

    Juška, Alfonsas

    2011-01-21

    Dynamics of growth and decline of microbial populations were analysed and respective models were developed in this investigation. Analysis of the dynamics was based on general considerations concerning the main properties of microorganisms and their interactions with the environment which was supposed to be affected by the activity of the population. Those considerations were expressed mathematically by differential equations or systems of the equations containing minimal sets of parameters characterizing those properties. It has been found that: (1) the factors leading to the decline of the population have to be considered separately, namely, accumulation of metabolites (toxins) in the medium and the exhaustion of resources; the latter have to be separated again into renewable ('building materials') and non-renewable (sources of energy); (2) decline of the population is caused by the exhaustion of sources of energy but no decline is predicted by the model because of the exhaustion of renewable resources; (3) the model determined by the accumulation of metabolites (toxins) in the medium does not suggest the existence of a separate 'stationary phase'; (4) in the model determined by the exhaustion of energy resources the 'stationary' and 'decline' phases are quite discernible; and (5) there is no symmetry in microbial population dynamics, the decline being slower than the rise. Mathematical models are expected to be useful in getting insight into the process of control of the dynamics of microbial populations. The models are in agreement with the experimental data.

  8. Microbial growth and transport in saturated and unsaturated porous media

    NASA Astrophysics Data System (ADS)

    Hron, Pavel; Jost, Daniel; Bastian, Peter; Ippisch, Olaf

    2014-05-01

    There is a considerable ongoing effort aimed at understanding the behavior of microorganisms in porous media. Microbial activity is of significant interest in various environmental applications such as in situ bioremediation, protection of drinking water supplies and for subsurface geochemistry in general. The main limiting factors for bacterial growth are the availability of electron acceptors, nutrients and bio-available water. The capillary fringe, defined - in a wider sense than usual - as the region of the subsurface above the groundwater table, but still dominated by capillary rise, is a region where all these factors are abundantly available. It is thus a region where high microbial activity is to be expected. In a research unit 'Dynamic Capillary Fringes - A Multidisciplinary Approach (DyCap)' founded by the German Research Foundation (DFG), the growth of microorganisms in the capillary fringe was studied experimentally and with numerical simulations. Processes like component transport and diffusion, exchange between the liquid phase and the gas phase, microbial growth and cell attachment and detachment were incorporated into a numerical simulator. The growth of the facultative anaerobic Escherichia coli as a function of nutrient availability and oxygen concentration in the liquid phase is modeled with modified Monod-type models and modifications for the switch between aerobic and anaerobic growth. Laboratory batch experiments with aqueous solutions of bacteria have been carried out under various combinations of oxygen concentrations in the gas phase and added amounts of dissolved organic carbon to determine the growth model parameters by solution of a parameter estimation problem. For the transport of bacteria the adhesion to phase boundaries is also very important. As microorganisms are transported through porous media, they are removed from the pore fluid by physicochemical filtration (attachment to sediment grain surfaces) or are adhering to gas

  9. Crabgrass (Digitaria sanguinalis) allelochemicals that interfere with crop growth and the soil microbial community.

    PubMed

    Zhou, Bin; Kong, Chui-Hua; Li, Yong-Hua; Wang, Peng; Xu, Xiao-Hua

    2013-06-05

    Three chemicals, veratric acid, maltol, and (−)-loliolide, were isolated from crabgrass and their structures were identified by spectroscopic analysis. The chemicals were detected in crabgrass root exudates and rhizosphere soils, and their concentrations ranged from 0.16 to 8.10 μg/g. At an approximate concentration determined in crabgrass root exudates, all chemicals significantly inhibited the growth of wheat, maize, and soybean and reduced soil microbial biomass carbon. Phospholipid fatty acid profiling showed that veratric acid, maltol, and (−)-loliolide affected the signature lipid biomarkers of soil bacteria, actinobacteria, and fungi, resulting in changes in soil microbial community structures. There were significant relationships between crop growth and soil microbes under the chemicals' application. Chemical-specific changes in the soil microbial community generated negative feedback on crop growth. The results suggest that veratric acid, maltol, and (−)-loliolide released from crabgrass may act as allelochemicals interfering with crop growth and the soil microbial community.

  10. General calibration of microbial growth in microplate readers

    PubMed Central

    Stevenson, Keiran; McVey, Alexander F.; Clark, Ivan B. N.; Swain, Peter S.; Pilizota, Teuta

    2016-01-01

    Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under different nutritional or stress environments, to characterization of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions, and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements. PMID:27958314

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

    EPA Science Inventory

    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...

  12. Probabilistic Model of Microbial Cell Growth, Division, and Mortality ▿

    PubMed Central

    Horowitz, Joseph; Normand, Mark D.; Corradini, Maria G.; Peleg, Micha

    2010-01-01

    After a short time interval of length δt during microbial growth, an individual cell can be found to be divided with probability Pd(t)δt, dead with probability Pm(t)δt, or alive but undivided with the probability 1 − [Pd(t) + Pm(t)]δt, where t is time, Pd(t) expresses the probability of division for an individual cell per unit of time, and Pm(t) expresses the probability of mortality per unit of time. These probabilities may change with the state of the population and the habitat's properties and are therefore functions of time. This scenario translates into a model that is presented in stochastic and deterministic versions. The first, a stochastic process model, monitors the fates of individual cells and determines cell numbers. It is particularly suitable for small populations such as those that may exist in the case of casual contamination of a food by a pathogen. The second, which can be regarded as a large-population limit of the stochastic model, is a continuous mathematical expression that describes the population's size as a function of time. It is suitable for large microbial populations such as those present in unprocessed foods. Exponential or logistic growth with or without lag, inactivation with or without a “shoulder,” and transitions between growth and inactivation are all manifestations of the underlying probability structure of the model. With temperature-dependent parameters, the model can be used to simulate nonisothermal growth and inactivation patterns. The same concept applies to other factors that promote or inhibit microorganisms, such as pH and the presence of antimicrobials, etc. With Pd(t) and Pm(t) in the form of logistic functions, the model can simulate all commonly observed growth/mortality patterns. Estimates of the changing probability parameters can be obtained with both the stochastic and deterministic versions of the model, as demonstrated with simulated data. PMID:19915038

  13. Spotsizer: High-throughput quantitative analysis of microbial growth

    PubMed Central

    Jeffares, Daniel C.; Arzhaeva, Yulia; Bähler, Jürg

    2017-01-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license. PMID:27712582

  14. Spotsizer: High-throughput quantitative analysis of microbial growth.

    PubMed

    Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

    2016-10-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

  15. Microbial contamination and growth in total parenteral nutrition solutions.

    PubMed

    Lawrence, J; Turner, M; Gilbert, P

    1988-04-01

    TPN bags (196) and giving sets were subjected to microbiological examination following administration within a busy nutrition ward. Of these, five (2.6%) were found to be contaminated with coagulase-negative Gram-positive cocci. In all but one instance the contamination was restricted to the terminal ends of the giving sets rather than to the nutrition bag itself. Isolation of micro-organisms from the ward environment suggested that the contamination had arisen extrinsically during the setting up of the infusions. Isolates from the contaminated products, together with type species of Escherichia coli and Candida albicans, were examined with respect to their growth requirements and used to challenge four TPN formulations. Growth and survival of the organisms was monitored for up to 21 days. In all instances significant numbers of organisms were recovered after 72 h. Significant growth of the Staphylococcal isolate and C. albicans occurred over the initial 48-72 h incubation, this appeared to be greater in extent for the lipid-containing formulations. The temperature of storage of the formulation was the major determining factor for microbial growth and survival. No survivors were recovered, however, from any formulation after 21 days.

  16. Impact of UV disinfection on microbially available phosphorus, organic carbon, and microbial growth in drinking water.

    PubMed

    Lehtola, Markku J; Miettinen, Ilkka T; Vartiainen, Terttu; Rantakokko, Panu; Hirvonen, Arja; Martikainen, Pertti J

    2003-03-01

    UV irradiation at a wavelength of 253.7 nm (UV(254)) is commonly used for drinking water disinfection. UV radiation is known to convert organically combined phosphorus to orthophosphate and to degrade natural organic matter. We studied if UV disinfection increases the amount of microbially available forms of organic carbon and phosphorus in drinking waters with different characteristics, and if these changes in water chemical quality could enhance the microbial growth in drinking water. The UV(254) dose (15-50 mWs/cm(2)) used in waterworks reduced the concentration of assimilable organic carbon and the sum of the molecular size fractions. The release of microbially available phosphorus needed higher doses (204 mWs/cm(2)) of UV(254) radiation. Of bacteria in drinking water, 90% were inactivated with UV(254)-irradiation doses below 50 mWs/cm(2). A high dose (501 mWs/cm(2)) of UV(254) radiation inhibited the microbial growth in water.

  17. Microbial growth and physiology in space - A review

    NASA Technical Reports Server (NTRS)

    Cioletti, Louis A.; Mishra, S. K.; Pierson, Duane L.

    1991-01-01

    An overview of microbial behavior in closed environments is given with attention to data related to simulated microgravity and actual space flight. Microbes are described in terms of antibiotic sensitivity, subcellular structure, and physiology, and the combined effects are considered of weightlessness and cosmic radiation on human immunity to such microorganisms. Space flight results report such effects as increased phage induction, accelerated microbial growth rates, and the increased risk of disease communication and microbial exchange aboard confining spacecraft. Ultrastructural changes are also noted in the nuclei, cell membranes, and cytoplasmic streaming, and it appears that antibiotic sensitivity is reduced under both actual and simulated conditions of spaceflight.

  18. Estimating phosphorus availability for microbial growth in an emerging landscape

    USGS Publications Warehouse

    Schmidt, S.K.; Cleveland, C.C.; Nemergut, D.R.; Reed, S.C.; King, A.J.; Sowell, P.

    2011-01-01

    Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5 years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was < 1 μg/g of microbial-available P in recently de-glaciated soils in both years of this study. These estimates fell well below estimates of available soil P obtained using traditional extraction procedures. Our results give both theoretical and practical insights into the kinetics of C and P utilization in young soils, as well as show changes in microbial P availability during early stages of soil development.

  19. Microbial Growth, Water Flow, and Solute Transport in Unsaturated Porous Media

    NASA Astrophysics Data System (ADS)

    Yarwood, R. R.; Rockhold, M. L.; Niemet, M. R.; Bottomley, P. J.; Selker, J. S.

    2004-05-01

    We present an investigation that studied interactions between microbial growth, water flow, and solute transport in variably saturated porous media. The experimental system provided for continuous, noninvasive observation of microbial activity, while simultaneously monitoring water content and solute flow paths in a two-dimensional porous matrix. The spatial and temporal development of microbial colonization by a Pseudomonas fluorescens bacterium was monitored by induction of a bioluminescent phenotype. A model was developed that allowed quantification of population density from bioluminescence measurements. Liquid saturation was quantified from the transmission of light through the system, and solute flow paths were determined with a dye tracer. Dramatic changes in microbial colonization were observed, including upward migration against flow. This migration was particularly interesting because it cannot be explained by passive transport. Bacterial growth and accumulation significantly impacted the hydrologic properties of the media, including apparent desaturation within the colonized region, diversion of flow around the colonized region, and lowering of the capillary fringe height.

  20. Optimization of biomass composition explains microbial growth-stoichiometry relationships

    USGS Publications Warehouse

    Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

    2011-01-01

    Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

  1. Optimization of biomass composition explains microbial growth-stoichiometry relationships.

    PubMed

    Franklin, Oskar; Hall, Edward K; Kaiser, Christina; Battin, Tom J; Richter, Andreas

    2011-02-01

    Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

  2. A New Sensitive Bioassay for Determination of Microbially Available Phosphorus in Water

    PubMed Central

    Lehtola, Markku J.; Miettinen, Ilkka T.; Vartiainen, Terttu; Martikainen, Pertti J.

    1999-01-01

    The content of assimilable organic carbon has been proposed to control the growth of microbes in drinking water. However, recent results have shown that there are regions where it is predominantly phosphorus which determines the extent of microbial growth in drinking waters. Even a very low concentration of phosphorus (below 1 μg of P liter−1) can promote extensive microbial growth. We present here a new sensitive method to determine microbially available phosphorus concentrations in water down to 0.08 μg of P liter−1. The method is a bioassay in which the analysis of phosphorus in a water sample is based on maximum growth of Pseudomonas fluorescens P17 when the energy supply and inorganic nutrients, with the exception of phosphorus, do not limit bacterial growth. Maximum growth (CFU) in the water sample is related to the concentration of phosphorus with the factor 373,200 ± 9,400 CFU/μg of PO4-P. A linear relationship was found between cell growth and phosphorus concentration between 0.05 to 10 μg of PO4-P liter−1. The content of microbially available phosphorus in Finnish drinking waters varied from 0.1 to 10.2 μg of P liter−1 (median, 0.60 μg of P liter−1). PMID:10223996

  3. Dynamic speckle study of microbial growth

    NASA Astrophysics Data System (ADS)

    Vincitorio, F. M.; Mulone, C.; Marcuzzi, P. A.; Budini, N.; Freyre, C.; Lopez, A. J.; Ramil, A.

    2015-08-01

    In this work we present a characterization of yeast dynamic speckle activity during growth in an isolated agar culture medium. We found that it is possible to detect the growth of the microorganisms even before they turn out to be visible. By observing the time evolution of the speckle activity at different regions of the culture medium we could extract a map of the growth process, which served to analyze how the yeast develops and spreads over the agar's medium. An interesting point of this study concerns with the influence of the laser light on the yeast growth rate. We have found that yeast finds hard to develop at regions with higher laser light illumination, although we used a synchronous system to capture the speckle pattern. The results obtained in this work would serve us as a starting point to fabricate a detector of growing microorganism colonies, with obvious interesting applications in diverse areas.

  4. [A membrane filter sampling method for determining microbial air pollution].

    PubMed

    Cherneva, P; Kiranova, A

    1996-01-01

    The method is a contribution in the evaluation of the exposition and the control of the standards for organic powders. The method concerns the sample-taking procedure and the analysis-making technique for determining of the concentration of the microbial pollution of the air. It is based on filtering of some amount of air through a membrane filter which is then processed for cultivating of microbial colonies on its surface. The results are obtained in number of microbial colonies per unit of air. The method presents opportunity to select and vary the filtered volume of air, to determine the respirable fraction, to determine the personal exposition, as well as for the simultaneous determining of the microbial pollution together with other important parameters of the particle pollutants of the air (metal, fibre and others).

  5. Kinetics of microbial growth on pentachlorophenol.

    PubMed Central

    Klecka, G M; Maier, W J

    1985-01-01

    Batch and fed-batch experiments were conducted to examine the kinetics of pentachlorophenol utilization by an enrichment culture of pentachlorophenol-degrading bacteria. The Haldane modification of the Monod equation was found to describe the relationship between the specific growth rate and substrate concentration. Analysis of the kinetic parameters indicated that the maximum specific growth rate and yield coefficients are low, with values of 0.074 h-1 and 0.136 g/g, respectively. The Monod constant (Ks) was estimated to be 60 micrograms/liter, indicating a high affinity of the microorganisms for the substrate. However, high concentrations (KI = 1,375 micrograms/liter) were shown to be inhibitory for metabolism and growth. These kinetic parameters can be used to define the optimal conditions for the removal of pentachlorophenol in biological treatment systems. PMID:3977315

  6. [Development of a predictive program for microbial growth under various temperature conditions].

    PubMed

    Fujikawa, Hiroshi; Yano, Kazuyoshi; Morozumi, Satoshi; Kimura, Bon; Fujii, Tateo

    2006-12-01

    A predictive program for microbial growth under various temperature conditions was developed with a mathematical model. The model was a new logistic model recently developed by us. The program predicts Escherichia coli growth in broth, Staphylococcus aureus growth and its enterotoxin production in milk, and Vibrio parahaemolyticus growth in broth at various temperature patterns. The program, which was built with Microsoft Excel (Visual Basic Application), is user-friendly; users can easily input the temperature history of a test food and obtain the prediction instantly on the computer screen. The predicted growth and toxin production can be important indices to determine whether a food is microbiologically safe or not. This program should be a useful tool to confirm the microbial safety of commercial foods.

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

    EPA Science Inventory

    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...

  8. Effect on Microbial Growth of a New Skin Protectant Formulation.

    PubMed

    Stoffel, Joseph; Bernatchez, Stéphanie F

    2017-03-01

    Objective: Evaluate the effect of a new investigational skin protectant formulation on the growth of various microorganisms in vitro. Approach: An in vitro laboratory assay with various species of gram-positive bacteria, gram-negative bacteria, and yeast grown on agar plates was used to verify that a new investigational product used for the management of incontinence-associated dermatitis (IAD) does not support microbial growth. Results: The investigational product did not support the growth of all organisms tested for 48 h in these assays. The results demonstrate the barrier properties of this investigational formulation against bacteria and yeast that are relevant to incontinent patients. Innovation: IAD accompanied by skin damage is difficult to manage with currently available products. A new skin protectant that can be applied as a liquid and polymerizes into a breathable film in situ even in the presence of exudate (as shown previously) has been developed and tested to ensure that it does not support microbial growth. Conclusion: This work verifies that this new product does not support microbial growth in vitro using organisms relevant for the intended application.

  9. Effect on Microbial Growth of a New Skin Protectant Formulation

    PubMed Central

    Stoffel, Joseph; Bernatchez, Stéphanie F.

    2017-01-01

    Objective: Evaluate the effect of a new investigational skin protectant formulation on the growth of various microorganisms in vitro. Approach: An in vitro laboratory assay with various species of gram-positive bacteria, gram-negative bacteria, and yeast grown on agar plates was used to verify that a new investigational product used for the management of incontinence-associated dermatitis (IAD) does not support microbial growth. Results: The investigational product did not support the growth of all organisms tested for 48 h in these assays. The results demonstrate the barrier properties of this investigational formulation against bacteria and yeast that are relevant to incontinent patients. Innovation: IAD accompanied by skin damage is difficult to manage with currently available products. A new skin protectant that can be applied as a liquid and polymerizes into a breathable film in situ even in the presence of exudate (as shown previously) has been developed and tested to ensure that it does not support microbial growth. Conclusion: This work verifies that this new product does not support microbial growth in vitro using organisms relevant for the intended application. PMID:28289552

  10. Microbial physiology and ecology of slow growth.

    PubMed Central

    Koch, A L

    1997-01-01

    The uptake capabilities of the cell have evolved to permit growth at very low external nutrient concentrations. How are these capabilities controlled when the substrate concentrations are not extremely low and the uptake systems could import substrate much more rapidly than the metabolic capabilities of the cell might be able to handle? To answer this question, earlier theories for the kinetics of uptake through the cell envelope and steady-state systems of metabolic enzymes are discussed and a computer simulation is presented. The problems to the cell of fluctuating levels of nutrient and too much substrate during continuous culture are discussed. Too much substrate can lead to oligotrophy, substrate-accelerated death, entry into the viable but not culturable state, and lactose killing. The relationship between uptake and growth is considered. Finally, too little substrate may lead to catastrophic attempts at mounting molecular syntheses that cannot be completed. PMID:9293184

  11. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin.

    PubMed

    Kim, Hyeun Bum; Borewicz, Klaudyna; White, Bryan A; Singer, Randall S; Sreevatsan, Srinand; Tu, Zheng Jin; Isaacson, Richard E

    2012-09-18

    Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production.

  12. Effects of Spatial Localization on Microbial Consortia Growth.

    PubMed

    Venters, Michael; Carlson, Ross P; Gedeon, Tomas; Heys, Jeffrey J

    2017-01-01

    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.

  13. Effects of Spatial Localization on Microbial Consortia Growth

    PubMed Central

    Venters, Michael; Carlson, Ross P.; Gedeon, Tomas

    2017-01-01

    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. PMID:28045924

  14. Determination of cyanide using a microbial sensor

    SciTech Connect

    Nakanishi, Keijiro; Ikebukuro, Kazunori; Karube, Isao

    1996-08-01

    A microbial cyanide sensor was prepared, consisting of immobilized Saccharomyces cerevisiae and an oxygen electrode. When the electrode was inserted into a solution containing glucose, the respiration activity of the microorganisms increased. The change in the respiration activity is monitored with the oxygen electrode. When cyanide is added to the sample solution, the electron transport chain reaction of the respiration system in the mitochondria is inhibited, resulting in a decrease in respiration. The inhibition is caused by cyanide binding with respiration enzymes such as the cytochrome oxidase complex in the mitochondrial inner membrane. Therefore, the cyanide concentration can be measured from the change in the respiration rate. When the sensor was applied to a batch system at pH 8.0 and 30{degrees}C, the cyanide calibration curve showed linearity in the concentration range between 0.3 pM and 150 {mu}m CN{sup -}. 13 refs., 8 figs., 1 tab.

  15. Microbial growth curves: what the models tell us and what they cannot.

    PubMed

    Peleg, Micha; Corradini, Maria G

    2011-12-01

    Most of the models of microbial growth in food are Empirical algebraic, of which the Gompertz model is the most notable, Rate equations, mostly variants of the Verhulst's logistic model, or Population Dynamics models, which can be deterministic and continuous or stochastic and discrete. The models of the first two kinds only address net growth and hence cannot account for cell mortality that can occur at any phase of the growth. Almost invariably, several alternative models of all three types can describe the same set of experimental growth data. This lack of uniqueness is by itself a reason to question any mechanistic interpretation of growth parameters obtained by curve fitting alone. As argued, all the variants of the Verhulst's model, including the Baranyi-Roberts model, are empirical phenomenological models in a rate equation form. None provides any mechanistic insight or has inherent advantage over the others. In principle, models of all three kinds can predict non-isothermal growth patterns from isothermal data. Thus a modeler should choose the simplest and most convenient model for this purpose. There is no reason to assume that the dependence of the "maximum specific growth rate" on temperature, pH, water activity, or other factors follows the original or modified versions of the Arrhenius model, as the success of Ratkowsky's square root model testifies. Most sigmoid isothermal growth curves require three adjustable parameters for their mathematical description and growth curves showing a peak at least four. Although frequently observed, there is no theoretical reason that these growth parameters should always rise and fall in unison in response to changes in external conditions. Thus quantifying the effect of an environmental factor on microbial growth require that all the growth parameters are addressed, not just the "maximum specific growth rate." Different methods to determine the "lag time" often yield different values, demonstrating that it is a

  16. Bioelectrochemical system accelerates microbial growth and degradation of filter paper.

    PubMed

    Sasaki, Kengo; Hirano, Shin-Ichi; Morita, Masahiko; Sasaki, Daisuke; Matsumoto, Norio; Ohmura, Naoya; Igarashi, Yasuo

    2011-01-01

    Bioelectrochemical reactors (BERs) with a cathodic working potential of -0.6 or -0.8 V more efficiently degraded cellulosic material, i.e., filter paper (57.4-74.1% in 3 days and 95.9-96.3% in 7 days) than did control reactors without giving exogenous potential (15.4% in 3 days and 64.2% in 7 days). At the same time, resultant conversions to methane and carbon dioxide in cathodic working chamber of BERs by application of electrochemical reduction in 3 days of operation were larger than control reactors. However, cumulative methane production in cathodic BERs was similar to those in control reactors after 7 days of operation. Microscopic observation and 16S rRNA gene analysis showed that microbial growth in the entire consortium was higher after 2 days of operation of cathodic BERs as compared with the control reactors. In addition, the number of methanogenic 16S rRNA gene copies in cathodic BERs was higher than in control reactors. Moreover, archaeal community structures constructed in cathodic BERs consisted of hydrogenotrophic methanogen-related organisms and differed from those in control reactors after 2 days of operation. Specifically, the amount of Methanothermobacter species in cathodic BERs was higher within archaeal communities than in those control reactors after 2 days of operation. Electrochemical reduction may be effective for accelerating microbial growth in the start-up period and thereby increasing microbial treatment of cellulosic waste and methane production.

  17. INVESTIGATING THE EFFECT OF MICROBIAL GROWTH AND BIOFILM FORMATION ON SEISMIC WAVE PROPAGATION IN SEDIMENT

    EPA Science Inventory

    Previous laboratory investigations have demonstrated that the seismic methods are sensitive to microbially-induced changes in porous media through the generation of biogenic gases and biomineralization. The seismic signatures associated with microbial growth and biofilm formation...

  18. Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica.

    PubMed

    Sumner, D Y; Jungblut, A D; Hawes, I; Andersen, D T; Mackey, T J; Wall, K

    2016-11-01

    Microbial pinnacles in ice-covered Lake Vanda, McMurdo Dry Valleys, Antarctica, extend from the base of the ice to more than 50 m water depth. The distribution of microbial communities, their photosynthetic potential, and pinnacle morphology affects the local accumulation of biomass, which in turn shapes pinnacle morphology. This feedback, plus environmental stability, promotes the growth of elaborate microbial structures. In Lake Vanda, all mats sampled from greater than 10 m water depth contained pinnacles with a gradation in size from <1-mm-tall tufts to pinnacles that were centimeters tall. Small pinnacles were cuspate, whereas larger ones had variable morphology. The largest pinnacles were up to ~30 cm tall and had cylindrical bases and cuspate tops. Pinnacle biomass was dominated by cyanobacteria from the morphological and genomic groups Leptolyngbya, Phormidium, and Tychonema. The photosynthetic potential of these cyanobacterial communities was high to depths of several millimeters into the mat based on PAM fluorometry, and sufficient light for photosynthesis penetrated ~5 mm into pinnacles. The distribution of photosynthetic potential and its correlation to pinnacle morphology suggests a working model for pinnacle growth. First, small tufts initiate from random irregularities in prostrate mat. Some tufts grow into pinnacles over the course of ~3 years. As pinnacles increase in size and age, their interiors become colonized by a more diverse community of cyanobacteria with high photosynthetic potential. Biomass accumulation within this subsurface community causes pinnacles to swell, expanding laminae thickness and creating distinctive cylindrical bases and cuspate tops. This change in shape suggests that pinnacle morphology emerges from a specific distribution of biomass accumulation that depends on multiple microbial communities fixing carbon in different parts of pinnacles. Similarly, complex patterns of biomass accumulation may be reflected in the

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

    NASA Astrophysics Data System (ADS)

    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

  20. Modeling of a compost biofilter incorporating microbial growth

    SciTech Connect

    Morgenroth, E.; Schroeder, E.D.; Chang, D.P.Y.; Scow, K.M.

    1995-11-01

    Biofiltration of air streams is gaining acceptance as an air pollution control technology. Biofilters are advantageous because of low operating costs and low energy requirements. Biofilters are advantageous for the removal of biodegradable pollutants at low concentrations. In this paper steady state and dynamic models for biofilters are presented. Analytical steady state models are useful for design purposes. The effects of changing operating conditions on removal efficiency and elimination capacity can be predicted. Dynamic models give a better representation of processes in a biofilter. A dynamic biofilter model incorporating microbial growth was developed. The dynamic model accounts for higher organism density at the inlet due to higher substrate concentrations.

  1. Perception and regulatory principles of microbial growth control.

    PubMed

    Khonsari, Armin S; Kollmann, Markus

    2015-01-01

    Fast growth represents an effective strategy for microbial organisms to survive in competitive environments. To accomplish this task, cells must adapt their metabolism to changing nutrient conditions in a way that maximizes their growth rate. However, the regulation of the growth related metabolic pathways can be fundamentally different among microbes. We therefore asked whether growth control by perception of the cell's intracellular metabolic state can give rise to higher growth than by direct perception of extracellular nutrient availability. To answer this question, we created a simplified dynamical computer model of a cellular metabolic network whose regulation was inferred by an optimization approach. We used this model for a competing species experiment, where a species with extracellular nutrient perception competes against one with intracellular nutrient perception by evaluating their respective average growth rate. We found that the intracellular perception is advantageous under situations where the up and down regulation of pathways cannot follow the fast changing nutrient availability in the environment. In this case, optimal regulation ignores any other nutrients except the most preferential ones, in agreement with the phenomenon of catabolite repression in prokaryotes. The corresponding metabolic pathways remain activated, despite environmental fluctuations. Therefore, the cell can take up preferential nutrients as soon as they are available without any prior regulation. As a result species that rely on intracellular perception gain a relevant fitness advantage in fluctuating nutrient environments, which enables survival by outgrowing competitors.

  2. Development of a program to fit data to a new logistic model for microbial growth.

    PubMed

    Fujikawa, Hiroshi; Kano, Yoshihiro

    2009-06-01

    Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.

  3. Impact of Metal Pollution and Thlaspi caerulescens Growth on Soil Microbial Communities▿

    PubMed Central

    Epelde, Lur; Becerril, José M.; Kowalchuk, George A.; Deng, Ye; Zhou, Jizhong; Garbisu, Carlos

    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 to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and Thlaspi caerulescens growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip). T. caerulescens proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg−1 (dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while T. caerulescens growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg−1 and 250 mg Cd kg−1 (DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with T. caerulescens and to gain insight into the effects of metal pollution on soilborne microbial communities. PMID:20935131

  4. Effects of dilution on dissolved oxygen depletion and microbial populations in the biochemical oxygen demand determination.

    PubMed

    Seo, Kyo Seong; Chang, Ho Nam; Park, Joong Kon; Choo, Kwang-Ho

    2007-09-01

    The biochemical oxygen demand (BOD) value is still a key parameter that can determine the level of organics, particularly the content of biodegradable organics in water. In this work, the effects of sample dilution, which should be done inevitably to get appropriate dissolved oxygen (DO) depletion, on the measurement of 5-day BOD (BOD(5)), was investigated with and without seeding using natural and synthetic water. The dilution effects were also evaluated for water samples taken in different seasons such as summer and winter because water temperature can cause a change in the types of microbial species, thus leading to different oxygen depletion profiles during BOD testing. The predation phenomenon between microbial cells was found to be dependent on the inorganic nutrients and carbon sources, showing a change in cell populations according to cell size after 5-day incubation. The dilution of water samples for BOD determination was linked to changes in the environment for microbial growth such as nutrition. The predation phenomenon between microbial cells was more important with less dilution. BOD(5) increased with the specific amount of inorganic nutrient per microbial mass when the natural water was diluted. When seeding was done for synthetic water samples, the seed volume also affected BOD due to the rate of organic uptake by microbes. BOD(5) increased with the specific bacterial population per organic source supplied at the beginning of BOD measurement. For more accurate BOD measurements, specific guidelines on dilution should be established.

  5. Microbial growth and macromolecular synthesis in the northwestern Atlantic Ocean

    SciTech Connect

    Cuhel, R.L.; Jannasch, H.W.; Taylor, C.D.

    1983-01-01

    Simultaneous time-course measurements of /sup 35/SO/sub 4//sup 2 -/, /sup 32/PO/sup 43 -/, /sup 15/NH/sub 4//sup +/, and (/sup 14/C)acetate, glucose, and glutamate uptake were made at three stations in the northwestern Atlantic Ocean, using water samples taken from well below the euphotic zone. Marked deviations from linearity were observed in 14 of the 15 cases. At the two most inshore stations uptake of /sup 15/NH/sub 4//sup +/ or incorporation of /sup 35/SO/sub 4//sup 2 -/ into protein was undetectable for 16-30 h, followed by very rapid increases in the rates of activity. The sudden burst of SO/sub 4//sup 2 -/and NH/sub 4//sup +/ uptake was accompanied by a major increase in the incorporation of /sup 32/P into RNA and lipid fractions of the microbial population at a continental slope station. At a station in Sargasso Sea, all substrates were taken up without lag. Extended incubations led to a growth plateau which may be a measure of the total biologically labile organic nutrient supply. In all cases tested, chloramphenicol severely restricted uptake. One of the inshore stations was revisited a year later with similar results. The combined data demonstrate the utility of using inorganic nutrient uptake and subcellular incorporation patterns to measure microbial growth and metabolism and stress the necessity of time-course rather than end-point incubations.

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

    NASA Astrophysics Data System (ADS)

    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

  7. Optimising Microbial Growth with a Bench-Top Bioreactor

    ERIC Educational Resources Information Center

    Baker, A. M. R.; Borin, S. L.; Chooi, K. P.; Huang, S. S.; Newgas, A. J. S.; Sodagar, D.; Ziegler, C. A.; Chan, G. H. T.; Walsh, K. A. P.

    2006-01-01

    The effects of impeller size, agitation and aeration on the rate of yeast growth were investigated using bench-top bioreactors. This exercise, carried out over a six-month period, served as an effective demonstration of the importance of different operating parameters on cell growth and provided a means of determining the optimisation conditions…

  8. Impact of Microbial Growth on Subsurface Perfluoroalkyl Acid Transport

    NASA Astrophysics Data System (ADS)

    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.

  9. EFFECT OF TEMPERATURE ON THE C ISOTOPIC VALUE OF MICROBIAL LIPIDS APPLIED TO DETERMINE C USAGE IN MICROBIAL COMMUNITIES

    EPA Science Inventory

    The combination of compound specific stable isotopic analysis with phospholipid fatty acid (PLFAS) analysis is useful in determining the source of organic carbon used by groups of a microbial community. Determination of the effect of certain environmental parameters is important ...

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

    NASA Astrophysics Data System (ADS)

    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 aestivummicrobial growth rates directly (N limitation) and indirectly (changing the quantity of fine roots). So, 50% decrease in N fertilization caused the overall increase or decrease of microbial growth rates depending on plant species. The μ-value increase was lower for microorganisms growing on yeast 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

  11. Teaching the Microbial Growth Curve Concept Using Microalgal Cultures and Flow Cytometry

    ERIC Educational Resources Information Center

    Forget, Nathalie; Belzile, Claude; Rioux, Pierre; Nozais, Christian

    2010-01-01

    The microbial growth curve is widely studied within microbiology classes and bacteria are usually the microbial model used. Here, we describe a novel laboratory protocol involving flow cytometry to assess the growth dynamics of the unicellular microalgae "Isochrysis galbana." The algal model represents an appropriate alternative to…

  12. Inhibition of microbial growth on air cathodes of single chamber microbial fuel cells by incorporating enrofloxacin into the catalyst layer.

    PubMed

    Liu, Weifeng; Cheng, Shaoan; Sun, Dan; Huang, Haobin; Chen, Jie; Cen, Kefa

    2015-10-15

    The inevitable growth of aerobic bacteria on the surface of air cathodes is an important factor reducing the performance stability of air cathode single-chamber membrane-free microbial fuel cells (MFCs). Thus searching for effective methods to inhibit the cathodic microbial growth is critical for the practical application of MFCs. In this study, enrofloxacin (ENR), a broad spectrum fluoroquinolone antibiotic, was incorporated into the catalyst layer of activated carbon air cathodes (ACACs) to inhibit the cathodic microbial growth. The biomass content on ACACs was substantially reduced by 60.2% with ENR treatment after 91 days of MFCs operation. As a result of the inhibited microbial growth, the oxygen reduction catalytic performance of the ENR treated ACACs was much stable compared to the fast performance decline of the untreated control. Consequently, a quite stable electricity production was obtained for the MFCs with the ENR treated ACACs, in contrast with a 22.5% decrease in maximum power density of the MFCs with the untreated cathode. ENR treatment of ACACs showed minimal effects on the anode performance. These results indicate that incorporating antibiotics into ACACs should be a simple and effective strategy to inhibit the microbial growth and improve the long-term stability of the performance of air cathode and the electricity production of MFCs.

  13. The role of microbial signals in plant growth and development

    PubMed Central

    Ortíz-Castro, Randy; Contreras-Cornejo, Hexon Angel; Macías-Rodríguez, Lourdes

    2009-01-01

    Plant growth and development involves a tight coordination of the spatial and temporal organization of cell division, cell expansion and cell differentiation. Orchestration of these events requires the exchange of signaling molecules between the root and shoot, which can be affected by both biotic and abiotic factors. The interactions that occur between plants and their associated microorganisms have long been of interest, as knowledge of these processes could lead to the development of novel agricultural applications. Plants produce a wide range of organic compounds including sugars, organic acids and vitamins, which can be used as nutrients or signals by microbial populations. On the other hand, microorganisms release phytohormones, small molecules or volatile compounds, which may act directly or indirectly to activate plant immunity or regulate plant growth and morphogenesis. In this review, we focus on recent developments in the identification of signals from free-living bacteria and fungi that interact with plants in a beneficial way. Evidence has accumulated indicating that classic plant signals such as auxins and cytokinins can be produced by microorganisms to efficiently colonize the root and modulate root system architecture. Other classes of signals, including N-acyl-L-homoserine lactones, which are used by bacteria for cell-to-cell communication, can be perceived by plants to modulate gene expression, metabolism and growth. Finally, we discuss the role played by volatile organic compounds released by certain plant growth-promoting rhizobacteria in plant immunity and developmental processes. The picture that emerges is one in which plants and microbes communicate themselves through transkingdom signaling systems involving classic and novel signals. PMID:19820333

  14. The role of microbial signals in plant growth and development.

    PubMed

    Ortíz-Castro, Randy; Contreras-Cornejo, Hexon Angel; Macías-Rodríguez, Lourdes; López-Bucio, José

    2009-08-01

    Plant growth and development involves a tight coordination of the spatial and temporal organization of cell division, cell expansion and cell differentiation. Orchestration of these events requires the exchange of signaling molecules between the root and shoot, which can be affected by both biotic and abiotic factors. The interactions that occur between plants and their associated microorganisms have long been of interest, as knowledge of these processes could lead to the development of novel agricultural applications. Plants produce a wide range of organic compounds including sugars, organic acids and vitamins, which can be used as nutrients or signals by microbial populations. On the other hand, microorganisms release phytohormones, small molecules or volatile compounds, which may act directly or indirectly to activate plant immunity or regulate plant growth and morphogenesis. In this review, we focus on recent developments in the identification of signals from free-living bacteria and fungi that interact with plants in a beneficial way. Evidence has accumulated indicating that classic plant signals such as auxins and cytokinins can be produced by microorganisms to efficiently colonize the root and modulate root system architecture. Other classes of signals, including N-acyl-L-homoserine lactones, which are used by bacteria for cell-to-cell communication, can be perceived by plants to modulate gene expression, metabolism and growth. Finally, we discuss the role played by volatile organic compounds released by certain plant growth-promoting rhizobacteria in plant immunity and developmental processes. The picture that emerges is one in which plants and microbes communicate themselves through transkingdom signaling systems involving classic and novel signals.

  15. Kraft mill residues effects on Monterey pine growth and soil microbial activity.

    PubMed

    Jordan, Miguel; Sánchez, Miguel Angel; Padilla, Leandro; Céspedes, Ricardo; Osses, Miguel; González, Bernardo

    2002-01-01

    The production of bleached Kraft pulp generates inorganic and organic residues that are usually deposited on the soil surface or land-filled. Studies conducted to address the impact of these wastes on the environment are scarce. In this work, Monterey pine (Pinus radiata D. Don), an important tree for pulping, was evaluated for germination and development under greenhouse conditions in forest soils exposed to solid residues of the cellulose industry using the Kraft process. Soils exposed to 10 to 60% ashes, 10 to 70% fly ashes, or 10 to 30% dregs allowed substantial seed germination and seedling growth. In contrast, soils exposed to low proportions of brown rejects, grits, or a mixture of all these residues were detrimental for germination, plant growth, or both. The strongest negative effect (no germination) was observed with as low as 10% grits. The changes in pH and/or water content caused by solid wastes did not correlate with detrimental effects observed in various soil-residue combinations. No significant changes in the microbial community of soils exposed to these solid residues were observed by determination of culturable counts, or by terminal-restriction fragment length polymorphism analysis of the microbial community DNA. The presence of organic residues did not affect the ability of the soil microbial community to remove typical pulp bleaching chloroaromatics. However, inorganic wastes strongly decreased the removal of such compounds.

  16. Impact of microbial growth on water flow and solute transport in unsaturated porous media

    NASA Astrophysics Data System (ADS)

    Yarwood, R. R.; Rockhold, M. L.; Niemet, M. R.; Selker, J. S.; Bottomley, P. J.

    2006-10-01

    A novel analytical method was developed that permitted real-time, noninvasive measurements of microbial growth and associated changes in hydrodynamic properties in porous media under unsaturated flowing conditions. Salicylate-induced, lux gene-based bioluminescence was used to quantify the temporal and spatial development of colonization over a 7-day time course. Water contents were determined daily by measuring light transmission through the system. Hydraulic flow paths were determined daily by pulsing a bromophenol blue dye solution through the colonized region of the sand. Bacterial growth and accumulation had a significant impact on the hydraulic properties of the porous media. Microbial colonization caused localized drying within the colonized zone, with decreases in saturation approaching 50% of antecedent values, and a 25% lowering of the capillary fringe height. Flow was retarded within the colonized zone and diverted around it concurrent with the expansion of the colonized zone between days 3 and 6. The location of horizontal dispersion corresponded with the cell densities of 1-3 × 109 cells g-1 dry sand. The apparent solute velocity through the colonized region was reduced from 0.41 cm min-1 (R2 = 0.99) to 0.25 cm min-1 (R2 = 0.99) by the sixth day of the experiment, associated with population densities that would occupy approximately 7% of the available pore space within the colonized region. Changes in the extent of colonization occurred over the course of the experiment, including upward migration against flow. The distribution of cells was not determined by water flow alone, but rather by a dynamic interaction between water flow and microbial growth. This experimental system provides rich data sets for the testing of conceptualizations expressed through numerical modeling.

  17. Impact of microbial growth on water flow and solute transport in unsaturated porous media

    SciTech Connect

    Yarwood, R. R.; Rockhold, M. L.; Niemet, M. R.; Selker, John S.; Bottomley, Peter J.

    2006-10-05

    A novel analytical method was developed that permitted real-time, noninvasive measurements of microbial growth and associated changes in hydrodynamic properties in porous media under unsaturated flowing conditions. Salicylate-induced, lux gene-based bioluminescence was used to quantify the temporal and spatial development of colonization over a seven day time course. Water contents were determined daily by measuring light transmission through the system. Hydraulic flow paths were determined daily by pulsing a bromophenol blue dye solution through the colonized region of the sand. Bacterial growth and accumulation had a significant impact on the hydraulic properties of the porous media. Microbial colonization caused localized drying within the colonized zone, with decreases in saturation approaching 50% of antecedent values, and a 25% lowering of the capillary fringe height. Flow was retarded within the colonized zone and diverted around it. The apparent solute velocity through the colonized region was reduced from 0.41 cm min 1 (R2 = 0.99) to 0.25 cm min 1 (R2 = 0.99) by the sixth day of the experiment, associated with maximum population densities that would occupy about 7% of the available pore space within the colonized region. Changes in the extent of colonization occurred over the course of the experiment, including upward migration against flow. The distribution of cells was not determined by water flow alone, but rather by a dynamic interaction between water flow and microbial growth. This experimental system provides rich data sets for the testing of conceptualizations expressed through numerical modeling.

  18. Exploring the optimum conditions for maximizing the microbial growth of Candida intermedia by response surface methodology.

    PubMed

    Yönten, Vahap; Aktaş, Nahit

    2014-01-01

    Exploring optimum and cost-efficient medium composition for microbial growth of Candida intermedia Y-1981 yeast culture growing on whey was studied by applying a multistep response surface methodology. In the first step, Plackett-Burman (PB) design was utilized to determine the most significant fermentation medium factors on microbial growth. The medium temperature, sodium chloride and lactose concentrations were determined as the most important factors. Subsequently, the optimum combinations of the selected factors were explored by steepest ascent (SA) and central composite design (CCD). The optimum values for lactose and sodium chloride concentrations and medium temperature were found to be 18.4 g/L, 0.161 g/L, and 32.4°C, respectively. Experiments carried out at the optimum conditions revealed a maximum specific growth rate of 0.090 1/hr; 42% of total lactose removal was achieved in 24 h of fermentation time. The obtained results were finally verified with batch reactor experiments carried out under the optimum conditions evaluated.

  19. Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters.

    PubMed

    Adadi, Roi; Volkmer, Benjamin; Milo, Ron; Heinemann, Matthias; Shlomi, Tomer

    2012-01-01

    Identifying the factors that determine microbial growth rate under various environmental and genetic conditions is a major challenge of systems biology. While current genome-scale metabolic modeling approaches enable us to successfully predict a variety of metabolic phenotypes, including maximal biomass yield, the prediction of actual growth rate is a long standing goal. This gap stems from strictly relying on data regarding reaction stoichiometry and directionality, without accounting for enzyme kinetic considerations. Here we present a novel metabolic network-based approach, MetabOlic Modeling with ENzyme kineTics (MOMENT), which predicts metabolic flux rate and growth rate by utilizing prior data on enzyme turnover rates and enzyme molecular weights, without requiring measurements of nutrient uptake rates. The method is based on an identified design principle of metabolism in which enzymes catalyzing high flux reactions across different media tend to be more efficient in terms of having higher turnover numbers. Extending upon previous attempts to utilize kinetic data in genome-scale metabolic modeling, our approach takes into account the requirement for specific enzyme concentrations for catalyzing predicted metabolic flux rates, considering isozymes, protein complexes, and multi-functional enzymes. MOMENT is shown to significantly improve the prediction accuracy of various metabolic phenotypes in E. coli, including intracellular flux rates and changes in gene expression levels under different growth rates. Most importantly, MOMENT is shown to predict growth rates of E. coli under a diverse set of media that are correlated with experimental measurements, markedly improving upon existing state-of-the art stoichiometric modeling approaches. These results support the view that a physiological bound on cellular enzyme concentrations is a key factor that determines microbial growth rate.

  20. Factors Limiting Microbial Growth and Activity at a Proposed High-Level Nuclear Repository, Yucca Mountain, Nevada

    PubMed Central

    Kieft, T. L.; Kovacik, W. P.; 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(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-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(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) 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. PMID:16535670

  1. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species.

    PubMed

    Narang, A

    1998-07-05

    There is a similarity between the metabolic dynamics of a microbial species growing on a mixture of two substrates and the dynamics of growth of two competing populations. Specifically, the enzymes catalyzing the uptake and catabolism of substrates exhibit phenomena analogous to extinction and coexistence."Extinction" of the enzymes associated with one of the substrates results in sequential utilization of the substrates (diauxie) (Monod, 1942). "Coexistence" of the enzymes associated with the substrates results in simultaneous utilization of the substrates (Egli, 1995). Here, we formulate a simple model that shows the basis for this dynamical similarity: The equations describing the evolution of the enzyme levels are dynamical analogs of the Lotka-Volterra model for two competing species. The analogy suggests ways of capturing the experimentally observed preculture-dependent growth patterns, i.e., growth patterns that vary depending on the physiological state of the preculture.

  2. Dynamics of microbial growth and coexistence on variably saturated rough surfaces.

    PubMed

    Long, Tao; Or, Dani

    2009-08-01

    The high degree of microbial diversity found in soils is attributed to the highly heterogeneous pore space and the dynamic aqueous microenvironments. Previous studies have shown that spatial and temporal variations in aqueous diffusion pathways play an important role in shaping microbial habitats and biological activity in unsaturated porous media. A new modeling framework was developed for the quantitative description of diffusion-dominated microbial interactions focusing on competitive growth of two microbial species inhabiting partially saturated rough surfaces. Surface heterogeneity was represented by patches with different porosities and water retention properties, yielding heterogeneous distribution of water contents that varies with changes in relative humidity or soil matric potential. Nutrient diffusion and microbial growth on the variably hydrated and heterogeneous surface was modeled using a hybrid method that combines a reaction diffusion method for nutrient field with individual based model for microbial growth and expansion. The model elucidated the effects of hydration dynamics and heterogeneity on nutrient fluxes and mobility affecting microbial population growth, expansion, and coexistence at the microscale. In contrast with single species dominance under wet conditions, results demonstrated prolonged coexistence of two competing species under drier conditions where nutrient diffusion and microbial movement were both limited. The uneven distribution of resources and diffusion pathways in heterogeneous surfaces highlighted the importance of position in the landscape for survival that may compensate for competitive disadvantages conferred by physiological traits. Increased motility was beneficial for expansion and survival. Temporal variations in hydration conditions resulted in fluctuations in microbial growth rate and population size. Population growth dynamics of the dominant species under wet-dry cycles were similar to growth under average value

  3. Biochar and microbial signaling: production conditions determine effects on microbial communication.

    PubMed

    Masiello, Caroline A; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R; Rudgers, Jennifer A; Wagner, Daniel S; Zygourakis, Kyriacos; Silberg, Jonathan J

    2013-10-15

    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m(2)/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m(2)/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.

  4. Biochar and microbial signaling: production conditions determine effects on microbial communication

    PubMed Central

    Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.

    2013-01-01

    Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell-cell communication varied, with the biochar prepared at 700°C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300°C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops. PMID:24066613

  5. [Biofilm--short characteristic of microbial growth related to drinking water distribution systems].

    PubMed

    Szczotko, Maciej

    2007-01-01

    General information about drinking water biofilms containing few steps biofilm forming process, microorganisms' short characterization and potential risk related to microbial presence in water installations has been presented. A part of review concerns European Acceptance Scheme (EAS) basis and current methods applied for assessment of susceptibility of materials contacting with drinking water to microbial growth.

  6. Soil degradation and amendment effects on soil properties, microbial communities, and plant growth

    NASA Astrophysics Data System (ADS)

    Gebhardt, M.; Fehmi, J. S.; Rasmussen, C.; Gallery, R. E.

    2015-12-01

    Human activities that disrupt soil properties are fundamentally changing ecosystems. Soil degradation, caused by anthropogenic disturbance can decrease microbial abundance and activity, leading to changes in nutrient availability, soil organic matter, and plant establishment. The addition of amendments to disturbed soils have the potential ameliorate these negative consequences. We studied the effects of soil degradation, via an autoclave heat shock method, and the addition of amendments (biochar and woodchips) on microbial activity, soil carbon and nitrogen availability, microbial biomass carbon and nitrogen content, and plant growth of ten plant species native to the semi-arid southwestern US. Relative to non-degraded soils, microbial activity, measured via extracellular enzyme assays, was significantly lower for all seven substrates assayed. These soils also had significantly lower amounts of carbon assimilated into microbial biomass but no change in microbial biomass nitrogen. Soil degradation had no effect on plant biomass. Amendments caused changes in microbial activity: biochar-amended soils had significant increases in potential activity with five of the seven substrates measured; woodchip amended soils had significant increases with two. Soil carbon increased with both amendments but this was not reflected in a significant change in microbial biomass carbon. Biochar-amended soils had increases in soil nitrogen availability but neither amendment caused changes in microbial biomass nitrogen. Biochar amendments had no significant effect on above- or belowground plant biomass while woodchips significantly decreased aboveground plant biomass. Results show that soil degradation decreases microbial activity and changes nutrient dynamics, but these are not reflected in changes in plant growth. Amendments provide nutrient sources and change soil pore space, which cause microbial activities to fluctuate and may, in the case of woodchips, increase plant drought

  7. Survival and growth of potential microbial contaminants in severe environments.

    PubMed

    Hawrylewicz, E J; Hagen, C A; Ehrlich, R

    1966-01-01

    Studies conducted in our laboratory have established that a number of potential soil microbes could survive a simulated Martian environment. In view of the uncertainty of the Martian environment and the importance of noncontamination of extraterrestrial bodies, studies were performed with common soil microbes to determine the minimal environment necessary to produce a complete growth cycle. The effects of diurnal temperature cycling (+25 degrees C to -65 degrees C) and of limiting concentrations of moisture and oxygen on spore germination, vegetative growth and sporulation of Bacillus cereus and B. subtilis have been determined. The results indicated that diurnally temperature-cycled heat-shocked spores of B. cereus in the simulated Martian atmosphere: 1) survived when the moisture concentration was < or = 4%; 2) germinated but became nonviable when the moisture concentration was > 4 < 8%; 3) germinated with subsequent vegetative growth when a) the moisture concentration was > or = 8%, and b) the concentration was > or = 6% and the partial pressure of oxygen was 15 mm; 4) sporulated when the moisture concentration was > or = 6% and the partial pressure of oxygen was 15 mm. Similar data for heat-shocked spores of B. subtilis in the simulated Martian atmosphere, diurnally temperature-cycled, indicated that the spores: 1) survived when the moisture concentration was > or = 6%; 2) germinated but became nonviable when the moisture concentration was > 1 < 4%; 3) germinated with subsequent vegetative growth when the moisture concentration was > or = 8%; 4) sporulated when the moisture concentration was > or = 6% and the partial pressure of oxygen was > or = 10 mm. Preliminary studies with B. cereus and B. subtilis spores produced in the simulated Martian environment and reintroduced into this environment indicated that vegetative cell growth and sporulation were normal. These data are discussed with regard to the probability of contamination of extraterrestrial bodies.

  8. Carbon nanotubes as plant growth regulators: effects on tomato growth, reproductive system, and soil microbial community.

    PubMed

    Khodakovskaya, Mariya V; Kim, Bong-Soo; Kim, Jong Nam; Alimohammadi, Mohammad; Dervishi, Enkeleda; Mustafa, Thikra; Cernigla, Carl E

    2013-01-14

    Multi-walled carbon nanotubes (CNTs) can affect plant phenotype and the composition of soil microbiota. Tomato plants grown in soil supplemented with CNTs produce two times more flowers and fruit compared to plants grown in control soil. The effect of carbon nanotubes on microbial community of CNT-treated soil is determined by denaturing gradient gel electrophoresis and pyrosequencing analysis. Phylogenetic analysis indicates that Proteobacteria and Bacteroidetes are the most dominant groups in the microbial community of soil. The relative abundances of Bacteroidetes and Firmicutes are found to increase, whereas Proteobacteria and Verrucomicorbia decrease with increasing concentration of CNTs. The results of comparing diversity indices and species level phylotypes (OTUs) between samples showed that there is not a significant affect on bacterial diversity.

  9. Maximising electricity production by controlling the biofilm specific growth rate in microbial fuel cells.

    PubMed

    Ledezma, Pablo; Greenman, John; Ieropoulos, Ioannis

    2012-08-01

    The aim of this work is to study the relationship between growth rate and electricity production in perfusion-electrode microbial fuel cells (MFCs), across a wide range of flow rates by co-measurement of electrical output and changes in population numbers by viable counts and optical density. The experiments hereby presented demonstrate, for the first time to the authors' knowledge, that the anodic biofilm specific growth rate can be determined and controlled in common with other loose matrix perfusion systems. Feeding with nutrient-limiting conditions at a critical flow rate (50.8 mL h(-1)) resulted in the first experimental determination of maximum specific growth rate μ(max) (19.8 day(-1)) for Shewanella spp. MFC biofilms, which is considerably higher than those predicted or assumed via mathematical modelling. It is also shown that, under carbon-energy limiting conditions there is a strong direct relationship between growth rate and electrical power output, with μ(max) coinciding with maximum electrical power production.

  10. Control of Microbial Growth in Alginate/Polydopamine Core/Shell Microbeads.

    PubMed

    Kim, Beom Jin; Park, Taegyun; Park, So-Young; Han, Sang Woo; Lee, Hee-Seung; Kim, Yang-Gyun; Choi, Insung S

    2015-10-01

    Microbial microencapsulation not only protects microorganisms from harmful environments by physically isolating them from the outside media but also has the potential to tailor the release profile of the encapsulated cells. However, the microbial release has not yet been controlled tightly, leading to undesired detrimental exposure of microorganisms to the outside. In this work, we suggest a simple method for controlling the cell release by suppressing the microbial growth in the microbeads. Alginate microbeads, encapsulating yeast cells, were coated with ultrathin but robust polydopamine shells, and the resulting core/shell structures effectively reduced the growth rate, while maintaining the cell viability.

  11. Application of the new logistic model to microbial growth prediction in food.

    PubMed

    Fujikawa, Hiroshi

    2011-06-01

    Recently a microbial growth model, the new logistic model, which could precisely describe and predict microbial growth at various patterns of temperature, was developed by the author (Biocontrol Science, 15, 75-80, 2010). The author shows several software programs developed with the model in this review. First, a program that analyzes microbial growth data and generates growth curves fitted to the model was developed. Second, a growth prediction program for Escherichia coli, Staphylococcus aureus, and Vibrio paraheamolyticus [corrected] exposed at various patterns of temperature was made based on experimental data. For V. paraheamolyticus [corrected] a program for bacterial growth under environmental conditions including temperature, salt concentration, and pH was developed. These programs are available free at the Japan Food Industry Center. Furthermore, a method to estimate the temperature at various points on or inside a food exposed to a given temperature was developed by using the measured temperatures of two points on the surface of the food and the heat conduction law. Combining this method with the growth model, a system that predicts microbial growth in a food exposed to various temperature patterns was made. This system could be a prototype of an alert system for microbial food safety.

  12. Growth-altering microbial interactions are responsive to chemical context

    PubMed Central

    2017-01-01

    Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed dynamic and responsive to local chemical context. PMID:28319121

  13. Growth-altering microbial interactions are responsive to chemical context.

    PubMed

    Liu, Angela; Archer, Anne M; Biggs, Matthew B; Papin, Jason A

    2017-01-01

    Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. We present a novel workflow for inferring microbial interactions that integrates semi-automated image analysis with a colony stamping mechanism, with the overall effect of improving throughput and reproducibility of colony interaction assays. We apply our approach to infer interactions among bacterial species associated with the normal lung microbiome, and how those interactions are altered by the presence of benzo[a]pyrene, a carcinogenic compound found in cigarettes. We found that the presence of this single compound changed the interaction network, demonstrating that microbial interactions are indeed dynamic and responsive to local chemical context.

  14. 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.

    PubMed

    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

  15. Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that el...

  16. Microbial Protein-Antigenome Determination (MAD) Technology: A Proteomics-Based Strategy for Rapid Identification of Microbial Targets of Host Humoral Immune Responses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Immunogenic, pathogen-specific proteins have excellent potential for development of novel management modalities. Here, we describe an innovative application of proteomics called Microbial protein-Antigenome Determination (MAD) Technology for rapid identification of native microbial proteins that eli...

  17. Inhibition of microbial growth by carbon nanotube networks

    NASA Astrophysics Data System (ADS)

    Olivi, Massimiliano; Zanni, Elena; de Bellis, Giovanni; Talora, Claudio; Sarto, Maria Sabrina; Palleschi, Claudio; Flahaut, Emmanuel; Monthioux, Marc; Rapino, Stefania; Uccelletti, Daniela; Fiorito, Silvana

    2013-09-01

    In the last years carbon nanotubes have attracted increasing attention for their potential applications in the biomedical field as diagnostic and therapeutic nano tools. Here we investigate the antimicrobial activity of different fully characterized carbon nanotube types (single walled, double walled and multi walled) on representative pathogen species: Gram-positive Staphylococcus aureus, Gram-negative Pseudomonas aeruginosa and the opportunistic fungus Candida albicans. Our results show that all the carbon nanotube types possess a highly significant antimicrobial capacity, even though they have a colony forming unit capacity and induction of oxidative stress in all the microbial species to a different extent. Moreover, scanning electron microscopy analysis revealed that the microbial cells were wrapped or entrapped by carbon nanotube networks. Our data taken together suggest that the reduced capacity of microbial cells to forming colonies and their oxidative response could be related to the cellular stress induced by the interactions of pathogens with the CNT network.

  18. Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment.

    PubMed

    Cabrol, Léa; Quéméneur, Marianne; Misson, Benjamin

    2017-02-01

    Sodium azide (NaN3) was evaluated as inhibitor of microbial growth and activity in marine sediment resuspensions by monitoring the abundance of free-living and sessile bacteria using both flow cytometry and qPCR methods. Results show that 50mM of NaN3 strongly inhibits bacterial growth under natural and enriched resource conditions.

  19. Comparison of Primary Models to Predict Microbial Growth by the Plate Count and Absorbance Methods.

    PubMed

    Pla, María-Leonor; Oltra, Sandra; Esteban, María-Dolores; Andreu, Santiago; Palop, Alfredo

    2015-01-01

    The selection of a primary model to describe microbial growth in predictive food microbiology often appears to be subjective. The objective of this research was to check the performance of different mathematical models in predicting growth parameters, both by absorbance and plate count methods. For this purpose, growth curves of three different microorganisms (Bacillus cereus, Listeria monocytogenes, and Escherichia coli) grown under the same conditions, but with different initial concentrations each, were analysed. When measuring the microbial growth of each microorganism by optical density, almost all models provided quite high goodness of fit (r(2) > 0.93) for all growth curves. The growth rate remained approximately constant for all growth curves of each microorganism, when considering one growth model, but differences were found among models. Three-phase linear model provided the lowest variation for growth rate values for all three microorganisms. Baranyi model gave a variation marginally higher, despite a much better overall fitting. When measuring the microbial growth by plate count, similar results were obtained. These results provide insight into predictive microbiology and will help food microbiologists and researchers to choose the proper primary growth predictive model.

  20. Comparison of Primary Models to Predict Microbial Growth by the Plate Count and Absorbance Methods

    PubMed Central

    Pla, María-Leonor; Oltra, Sandra; Esteban, María-Dolores; Andreu, Santiago; Palop, Alfredo

    2015-01-01

    The selection of a primary model to describe microbial growth in predictive food microbiology often appears to be subjective. The objective of this research was to check the performance of different mathematical models in predicting growth parameters, both by absorbance and plate count methods. For this purpose, growth curves of three different microorganisms (Bacillus cereus, Listeria monocytogenes, and Escherichia coli) grown under the same conditions, but with different initial concentrations each, were analysed. When measuring the microbial growth of each microorganism by optical density, almost all models provided quite high goodness of fit (r2 > 0.93) for all growth curves. The growth rate remained approximately constant for all growth curves of each microorganism, when considering one growth model, but differences were found among models. Three-phase linear model provided the lowest variation for growth rate values for all three microorganisms. Baranyi model gave a variation marginally higher, despite a much better overall fitting. When measuring the microbial growth by plate count, similar results were obtained. These results provide insight into predictive microbiology and will help food microbiologists and researchers to choose the proper primary growth predictive model. PMID:26539483

  1. Microbial Biofilm Growth on Irradiated, Spent Nuclear Fuel Cladding

    SciTech Connect

    S.M. Frank

    2009-02-01

    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 × 103 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.

  2. Prediction of microbial growth in mixed culture with a competition model.

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

    Prediction of microbial growth in mixed culture was studied with a competition model that we had developed recently. The model, which is composed of the new logistic model and the Lotka-Volterra model, is shown to successfully describe the microbial growth of two species in mixed culture using Staphylococcus aureus, Escherichia coli, and Salmonella. With the parameter values of the model obtained from the experimental data on monoculture and mixed culture with two species, it then succeeded in predicting the simultaneous growth of the three species in mixed culture inoculated with various cell concentrations. To our knowledge, it is the first time for a prediction model for multiple (three) microbial species to be reported. The model, which is not built on any premise for specific microorganisms, may become a basic competition model for microorganisms in food and food materials.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2013-07-01

    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 15N to differentiate between microbial N that had been assimilated from the leaf substrate (enriched with 15N) or immobilized from the water (natural abundance 15N:14N) in five Appalachian streams ranging in ambient NO3(-)N concentrations from about 5 to 900 microg NO3(-)N/L. Ambient NO3(-) concentration increased sugar maple decomposition rate but did not influence the proportion of microbial N derived from substrate or exogenous pools. Instead, these proportions were strongly influenced by the percentage of detrital ash-free dry mass (AFDM) remaining. Substrate-derived N made up a large proportion of the microbial N after the first 24 h in all streams. Detrital and microbial isotopic 15N signatures approached that of the water as decomposition progressed in all streams, suggesting that exogenous N may be the predominant source of N for meeting microbial requirements even when exogenous N concentrations are low. Our results support predictions of more rapid decomposition of organic matter in response to increased N availability and highlight the tight coupling of processes driving microbial N cycling and organic matter decomposition.

  5. Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories

    NASA Astrophysics Data System (ADS)

    Chen, Ruirui; Senbayram, Mehmet; Blagodatsky, Sergey; Dittert, Klaus; Lin, Xiangui; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2014-05-01

    The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural 13C labelling adding C4-sucrose or C4-maize straw to C3-soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects - microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K-strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β-glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r-strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K- and r-strategists were beneficial for priming effects, with an increasing contribution of K-selected species under N limitation. Thus, the priming phenomenon described in 'microbial N mining' theory can be ascribed to K-strategists. In contrast, 'stoichiometric decomposition' theory, that is, accelerated OM

  6. Determining potential for microbial atrazine degradation in agricultural drainage ditches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Passage of agricultural runoff through vegetated drainage ditches has been shown to reduce the amount of pesticides, such as atrazine, exiting agricultural watersheds. Previous studies found that microbial communities in soil from fields treated with atrazine display enhanced rates of atrazine degr...

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

    PubMed

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E

    2015-01-01

    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 by describing microbial-plants and microbial-microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use.

  8. Thermodynamics of Microbial Growth Coupled to Metabolism of Glucose, Ethanol, Short-Chain Organic Acids, and Hydrogen ▿ †

    PubMed Central

    Roden, Eric E.; Jin, Qusheng

    2011-01-01

    A literature compilation demonstrated a linear relationship between microbial growth yield and the free energy of aerobic and anaerobic (respiratory and/or fermentative) metabolism of glucose, ethanol, formate, acetate, lactate, propionate, butyrate, and H2. This relationship provides a means to estimate growth yields for modeling microbial redox metabolism in soil and sedimentary environments. PMID:21216913

  9. Bioenergetic Limitations on Slow Microbial Growth in the Subsurface: What is the Burden of Maintenance on the Overall Energy Budget?

    NASA Astrophysics Data System (ADS)

    Smeaton, C. M.; Bajracharya, B. M.; Ridenour, C.; Van Cappellen, P.

    2014-12-01

    In low energy environments such as the subsurface, the minimum energy required to maintain cellular integrity and function (maintenance energy) may represent a significant fraction of the total energy available to microbial communities. However, traditional kinetic and thermodynamic models incorporating key microbial processes are often developed using data collected in nutrient rich growth media. In this study, slow microbial growth in the subsurface was simulated using a flow through bioreactor system in experiments designed to determine the maintenance energy requirement of the model subsurface bacterium Shewanella oneidensis. An existing bioreactor system (Applikon EZ-control®, 2.4 L) was modified to include a biomass retention filtration unit (retentostat) resulting in biomass accumulation over time. An artificial low-nutrient groundwater medium was optimized for slow S. oneidensis growth and was supplied and removed from the reactor at flow rates on the order of 1 mL min-1 with a dilution rate of 0.025 h-1. The retentostat was run under electron donor limited conditions with nitrate, a common groundwater contaminant, supplied at 0.025 mM h-1 and lactate supplied in excess at 0.125 mM h-1. Respiratory ammonification of nitrate by S. oneidensis and cell growth was monitored over time (40 days) and compared to parallel incubations in batch reactors. Initial rates of ammonification were similar in the bioreactor and batch reactors, however, optical density and ATP measurements showed slow yet increasing microbial growth over time (generation time = 17 days) in the retentostat. In contrast, cells in the batch reactors did not grow significantly and died within 2 weeks of inoculation. A maintenance energy demand was estimated (2.5 kJ C-mol biomass h-1) by fitting the biomass production rates to the van Verseveld equation. The low maintenance energy demand of S. oneidensis as compared to typical maintenance energies reported in the literature (>10 kJ C-mol biomass

  10. A mesoscopic stochastic model for the specific consumption rate in substrate-limited microbial growth

    PubMed Central

    2017-01-01

    The specific consumption rate of substrate, as well as the associated specific growth rate, is an essential parameter in the mathematical description of substrate-limited microbial growth. In this paper we develop a completely new kinetic model of substrate transport, based on recent knowledge on the structural biology of transport proteins, which correctly describes very accurate experimental results at near-zero substrate concentration values found in the literature, where the widespread Michaelis-Menten model fails. Additionally, our model converges asymptotically to Michaelis-Menten predictions as substrate concentration increases. Instead of the single active site enzymatic reaction of Michaelis-Menten type, the proposed model assumes a multi-site kinetics, simplified as an apparent all-or-none mechanism for the transport, which is controlled by means of the local substrate concentration in the close vicinity of the transport protein. Besides, the model also assumes that this local concentration is not equal to the mean substrate concentration experimentally determined in the culture medium. Instead, we propose that it fluctuates with a mostly exponential distribution of Weibull type. PMID:28187189

  11. Evaluation of the microbial growth response to inorganic nanoparticles

    PubMed Central

    Williams, Darryl N; Ehrman, Sheryl H; Pulliam Holoman, Tracey R

    2006-01-01

    In order to enhance the utilization of inorganic nanoparticles in biological systems, it is important to develop a fundamental understanding of the influence they have on cellular health and function. Experiments were conducted to test silica, silica/iron oxide, and gold nanoparticles for their effects on the growth and activity of Escherichia coli (E. coli). Transmission electron microscopy (TEM) and dynamic light scattering (DLS) were used to characterize the morphology and quantify size distribution of the nanoparticles, respectively. TEM was also used to verify the interactions between composite iron oxide nanoparticles and E. coli. The results from DLS indicated that the inorganic nanoparticles formed small aggregates in the growth media. Growth studies measured the influence of the nanoparticles on cell proliferation at various concentrations, showing that the growth of E. coli in media containing the nanoparticles indicated no overt signs of toxicity. PMID:16507102

  12. Development of a new logistic model for microbial growth in foods.

    PubMed

    Fujikawa, Hiroshi

    2010-09-01

    Mathematical models are essentially needed to quantitatively predict microbial growth in food products during their production and distribution. Recently we developed a new logistic model for microbial growth. The model is an extended logistic model, which shows a sigmoid curve on a semi-log plot. The model could precisely describe and predict bacterial growth at constant and dynamic temperatures in broth, on nutrient agar plates, and in pouched food. Prediction results with our model were very similar to those with the Baranyi model, which is well known worldwide. The model also predicted the amount of metabolites (toxins) that would be produced by a microorganism. Namely, with the growth model and the kinetics of staphylococcal enterotoxin A production, the amount of the toxins produced by Staphylococcus aureus in milk was successfully predicted. Our model could be a tool in the alert system and the quantitative risk assessment of harmful microbes in food.

  13. Evaluation of indirect impedance for measuring microbial growth in complex food matrices.

    PubMed

    Johnson, N; Chang, Z; Bravo Almeida, C; Michel, M; Iversen, C; Callanan, M

    2014-09-01

    The suitability of indirect impedance to accurately measure microbial growth in real food matrices was investigated. A variety of semi-solid and liquid food products were inoculated with Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Lactobacillus plantarum, Pseudomonas aeruginosa, Escherichia coli, Salmonella enteriditis, Candida tropicalis or Zygosaccharomyces rouxii and CO2 production was monitored using a conductimetric (Don Whitely R.A.B.I.T.) system. The majority (80%) of food and microbe combinations produced a detectable growth signal. The linearity of conductance responses in selected food products was investigated and a good correlation (R(2) ≥ 0.84) was observed between inoculum levels and times to detection. Specific growth rate estimations from the data were sufficiently accurate for predictive modeling in some cases. This initial evaluation of the suitability of indirect impedance to generate microbial growth data in complex food matrices indicates significant potential for the technology as an alternative to plating methods.

  14. Microbial Growth at Ultraslow Rates: Regulation and Genetic Stability.

    DTIC Science & Technology

    1983-03-01

    this taxonomic range of eubacteria , and the understanding we have gained of underlying biochemical and genetic machineries, it is clear that any...to eubacteria and whose effects on mu and Y, in fact, made the Monod-type equations invalid as soon as they were eluci- dated to the level reached by...growth parameters. Thus, we sought specifically: 1) to find if there was a pattern of growth behavior at slow rates common among eubacteria ; 2) to

  15. What is Growth? Concurrent determination of a bacterial population's many shades of growth

    NASA Astrophysics Data System (ADS)

    Lambert, Guillaume; Kussell, Edo

    2013-03-01

    One of the most exciting developments in the study of the physics of microbial life is the ability to precisely monitor stochastic variations of gene expression in individual cells. A fundamental question is whether these variations improve the long-term ability of a population to adapt to new environments. While variations in gene expression in bacteria are easily measured through the use of reporter systems such as green fluorescent proteins and its variants, precise determination of a cell's growth rate, and how it is influenced by its immediate environment, remains challenging. Here, we show that many conflicting and ambiguous definitions of bacterial growth can actually be used interchangeably in E. coli. Indeed, by monitoring small populations of E. coli bacteria inside a microfluidic device, we show that seemingly independent measurements of growth (elongation rate and the average division time, for instance) agree very precisely with one another. We combine these definitions with the population's length and age distribution to very precisely quantify the influence of temperature variations on a population's growth rate. We conclude by using coalescence theory to describe the evolution of a population's genetic structure over time.

  16. Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

    PubMed Central

    Giordano, Nils; Mairet, Francis; Gouzé, Jean-Luc

    2016-01-01

    Microbial physiology exhibits growth laws that relate the macromolecular composition of the cell to the growth rate. Recent work has shown that these empirical regularities can be derived from coarse-grained models of resource allocation. While these studies focus on steady-state growth, such conditions are rarely found in natural habitats, where microorganisms are continually challenged by environmental fluctuations. The aim of this paper is to extend the study of microbial growth strategies to dynamical environments, using a self-replicator model. We formulate dynamical growth maximization as an optimal control problem that can be solved using Pontryagin’s Maximum Principle. We compare this theoretical gold standard with different possible implementations of growth control in bacterial cells. We find that simple control strategies enabling growth-rate maximization at steady state are suboptimal for transitions from one growth regime to another, for example when shifting bacterial cells to a medium supporting a higher growth rate. A near-optimal control strategy in dynamical conditions is shown to require information on several, rather than a single physiological variable. Interestingly, this strategy has structural analogies with the regulation of ribosomal protein synthesis by ppGpp in the enterobacterium Escherichia coli. It involves sensing a mismatch between precursor and ribosome concentrations, as well as the adjustment of ribosome synthesis in a switch-like manner. Our results show how the capability of regulatory systems to integrate information about several physiological variables is critical for optimizing growth in a changing environment. PMID:26958858

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  18. Influence of different buffers (HEPES/MOPS) on keratinocyte cell viability and microbial growth.

    PubMed

    Dias, Kássia de Carvalho; Barbugli, Paula Aboud; Vergani, Carlos Eduardo

    2016-06-01

    This study assessed the effect of the buffers 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and 3-(N-morpholino) propanesulfonic acid (MOPS) on keratinocyte cell viability and microbial growth. It was observed that RPMI buffered with HEPES, supplemented with l-glutamine and sodium bicarbonate, can be used as a more suitable medium to promote co-culture.

  19. Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment.

    PubMed

    Lomstein, Bente Aa; Langerhuus, Alice T; D'Hondt, Steven; Jørgensen, Bo B; Spivack, Arthur J

    2012-03-18

    Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.

  20. Modeling microbial dynamics in heterogeneous environments: Growth on soil carbon sources

    SciTech Connect

    Resat, Haluk; Bailey, Vanessa L.; McCue, Lee Ann; Konopka, Allan

    2012-01-01

    We have developed a new hybrid model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment. The modeling framework can represent porous media such as soil. The individual based biological model can explicitly simulate microbial diversity, and cell metabolism is regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions and by the functional attributes of individual microbes. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences may suggest different functional roles for these two classes of microbes in cellulose utilization. Our model predicted an emergent behavior in which co-existence led to higher cellulose utilization efficiency and reduced stochasticity. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20 {micro}m size portions of the soil physical structure and in 111 {micro}m size soil aggregates with a random pore structure. Trends in dynamic properties were very similar at these two scales, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied.

  1. Kinetic model for microbial growth and desulphurisation with Enterobacter sp.

    PubMed

    Liu, Long; Guo, Zhiguo; Lu, Jianjiang; Xu, Xiaolin

    2015-02-01

    Biodesulphurisation was investigated by using Enterobacter sp. D4, which can selectively desulphurise and convert dibenzothiophene into 2-hydroxybiphenyl (2-HBP). The experimental values of growth, substrate consumption and product generation were obtained at 95 % confidence level of the fitted values using three models: Hinshelwood equation, Luedeking-Piret and Luedeking-Piret-like equations. The average error values between experimental values and fitted values were less than 10 %. These kinetic models describe all the experimental data with good statistical parameters. The production of 2-HBP in Enterobacter sp. was by "coupled growth".

  2. The effect of Triphala and Chlorhexidine mouthwash on dental plaque, gingival inflammation, and microbial growth

    PubMed Central

    Bajaj, Neeti; Tandon, Shobha

    2011-01-01

    The objective of this study was to ascertain the effects of a mouthwash prepared with Triphala on dental plaque, gingival inflammation, and microbial growth and compare it with commercially available Chlorhexidine mouthwash. This study was conducted after ethics committee approval and written consent from guardians (and assent from the children) were obtained. A total of 1431 students in the age group 8–12 years, belonging to classes fourth to seventh, were the subjects for this study. The Knowledge, Attitude and Practice (KAP) of the subjects was determined using a questionnaire. The students were divided into three groups namely, Group I (n = 457) using Triphala mouthwash (0.6%), Group II (n = 440) using Chlorhexidine mouthwash (0.1%) (positive control), and Group III (n = 412) using distilled water (negative control). The assessment was carried out on the basis of plaque scores, gingival scores, and the microbiological analysis (Streptococcus and lactobacilli counts). Statistical analysis for plaque and gingival scores was conducted using the paired sample t-test (for intragroup) and the Tukey's test (for intergroup conducted along with analysis of variance test). For the Streptococcus mutans and Lactobacillus counts, Wilcoxon and Mann–Whitney test were applied for intragroup and intergroup comparison, respectively. All the tests were carried out using the SPSS software. Both the Group I and Group II showed progressive decrease in plaque scores from baseline to the end of 9 months; however, for Group III increase in plaque scores from the baseline to the end of 9 months was noted. Both Group I and Group II showed similar effect on gingival health. There was inhibitory effect on microbial counts except Lactobacillus where Triphala had shown better results than Chlorhexidine. It was concluded that there was no significant difference between the Triphala and the Chlorhexidine mouthwash. PMID:21897640

  3. Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

    PubMed Central

    Zhao, Mengxin; Wu, Linwei; Gao, Qun; Wang, Feng; Wen, Chongqing; Wang, Mengmeng; Liang, Yuting; Zhou, Jizhong

    2016-01-01

    ABSTRACT Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty

  4. Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization.

    PubMed

    Zhao, Mengxin; Sun, Bo; Wu, Linwei; Gao, Qun; Wang, Feng; Wen, Chongqing; Wang, Mengmeng; Liang, Yuting; Hale, Lauren; Zhou, Jizhong; Yang, Yunfeng

    2016-01-01

    Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P < 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid

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

    PubMed

    Pineda, Lane; Chwalibog, Andrè; Sawosz, Ewa; Lauridsen, Charlotte; Engberg, Ricarda; Elnif, Jan; Hotowy, Anna; Sawosz, Filip; Gao, Yuhong; Ali, Abdalla; Moghaddam, Heshmat Sepehri

    2012-10-01

    This study evaluated the potential of silver nanoparticles (AgNano) as an antimicrobial growth-promoting supplement for broiler chickens. One hundred forty-four seven-day-old broiler chicks were distributed randomly to AgNano treatments at 0, 10 and 20 mg/kg (Control, Group AgNano10, and Group AgNano20, respectively) provided via the drinking water from day 7 to 36 post-hatching. Body weight and feed consumption were measured weekly. In addition, balance and respiration experiments were carried out to determine nitrogen (N) utilisation and energy retention. At days 22 and 36, blood samples 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 of broiler chickens. However, in Group AgNano10 N intake (p = 0.05) and retention (p = 0.03) was increased, but N excretion and efficiency of utilisation was not affected. The populations of bacteria in the intestinal samples were not affected by AgNano supplementation. The concentration of immunoglobulin (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 performance of chickens.

  6. Influence of heavy metals on microbial growth kinetics including lag time: mathematical modeling and experimental verification.

    PubMed

    Sengör, S Sevinç; Barua, Sutapa; Gikas, Petros; Ginn, Timothy R; Peyton, Brent; Sani, Rajesh K; Spycher, Nicolas F

    2009-10-01

    Heavy metals can significantly affect the kinetics of substrate biodegradation and microbial growth, including lag times and specific growth rates. A model to describe microbial metabolic lag as a function of the history of substrate concentration has been previously described by Wood et al. (Water Resour Res 31:553-563) and Ginn (Water Resour Res 35:1395-1408). In the present study, this model is extended by including the effect of heavy metals on metabolic lag by developing an inhibitor-dependent functional to account for the metabolic state of the microorganisms. The concentration of the inhibiting metal is explicitly incorporated into the functional. The validity of the model is tested against experimental data on the effects of zinc on Pseudomonas species isolated from Lake Coeur d'Alene sediments, Idaho, U.S.A., as well as the effects of nickel or cobalt on a mixed microbial culture collected from the aeration tank of a wastewater treatment plant in Athens, Greece. The simulations demonstrate the ability to incorporate the effect of metals on metabolism through lag, yield coefficient, and specific growth rates. The model includes growth limitation due to insufficient transfer of oxygen into the growth medium.

  7. Biological management of Sclerotinia sclerotiorum in pea using plant growth promoting microbial consortium.

    PubMed

    Jain, Akansha; Singh, Akanksha; Singh, Surendra; Singh, Harikesh Bahadur

    2015-08-01

    The beneficial plant-microbe interactions play crucial roles in protection against large number of plant pathogens causing disease. The present study aims to investigate the growth promoting traits induced by beneficial microbes namely Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27, and Bacillus subtilis BHHU100 treated singly and in combinations under greenhouse and field conditions to control Sclerotinia sclerotiorum. Plants treated with three microbe consortium enhanced plant growth maximally both in the presence and absence of the pathogen. Increase in plant length, total biomass, number of leaves, nodules and secondary roots, total chlorophyll and carotenoid content, and yield were recorded in plants treated with microbial consortia. Also, a decrease in plant mortality was observed in plants treated with microbial consortia in comparison to untreated control plants challenged with S. sclerotiorum. Furthermore, the decrease in disease of all the treatments can be associated with differential improvement of growth induced in pea.

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

    NASA Astrophysics Data System (ADS)

    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

  9. Growth dynamic of Naegleria fowleri in a microbial freshwater biofilm.

    PubMed

    Goudot, Sébastien; Herbelin, Pascaline; Mathieu, Laurence; Soreau, Sylvie; Banas, Sandrine; Jorand, Frédéric

    2012-09-01

    The presence of pathogenic free-living amoebae (FLA) such as Naegleria fowleri in freshwater environments is a potential public health risk. Although its occurrence in various water sources has been well reported, its presence and associated factors in biofilm remain unknown. In this study, the density of N. fowleri in biofilms spontaneously growing on glass slides fed by raw freshwater were followed at 32 °C and 42 °C for 45 days. The biofilms were collected with their substrata and characterized for their structure, numbered for their bacterial density, thermophilic free-living amoebae, and pathogenic N. fowleri. The cell density of N. fowleri within the biofilms was significantly affected both by the temperature and the nutrient level (bacteria/amoeba ratio). At 32 °C, the density remained constantly low (1-10 N. fowleri/cm(2)) indicating that the amoebae were in a survival state, whereas at 42 °C the density reached 30-900 N. fowleri/cm(2) indicating an active growth phase. The nutrient level, as well, strongly affected the apparent specific growth rate (μ) of N. fowleri in the range of 0.03-0.23 h(-1). At 42 °C a hyperbolic relationship was found between μ and the bacteria/amoeba ratio. A ratio of 10(6) to 10(7) bacteria/amoeba was needed to approach the apparent μ(max) value (0.23 h(-1)). Data analysis also showed that a threshold for the nutrient level of close to 10(4) bacteria/amoeba is needed to detect the growth of N. fowleri in freshwater biofilm. This study emphasizes the important role of the temperature and bacteria as prey to promote not only the growth of N. fowleri, but also its survival.

  10. Impacts of Microbial Growth on the Air Quality of the International Space Station

    NASA Technical Reports Server (NTRS)

    Macatangay, Ariel V.; Bruce, Rebekah J.

    2010-01-01

    An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples

  11. Impacts of Microbial Growth on the Air Quality of the International Space Station

    NASA Technical Reports Server (NTRS)

    Macatangay, Ariel V.; Bruce, Rebekah J.

    2009-01-01

    An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples.

  12. Methods for determining the abundance, diversity and activity of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Pereg, Lily

    2014-05-01

    The diversity and abundance of soil microbial communities play important roles in determining soil structure, quality and productivity. The past decade has seen an increase in the number and efficiency of methods for determining microbial diversity, abundance and function. Recognising that only a very small proportion of the soil microbial community can be cultured, most current studies use molecular techniques based on the 16S and 18S rRNA encoding sequences (DGGE, TRFLP, OFRG, ARISA, SSCP) as well as techniques based on the cellular composition of the microbes (PLFA composition). Recent developments include high-throughput sequencing and microarrays, representing major advances in microbial community analysis. While the diversity of microbes can be determined using DNA-based techniques, microbial activity changes under various conditions. Therefore, the analysis of soil function at any given time requires the analysis of gene expression using RNA-based techniques. Molecular techniques have tremendously advanced our knowledge in the field of soil microbiology, however, the limitations should not be underestimated. This presentation will critically review both the advantages and the limitations of techniques used in soil microbial analysis.

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

    PubMed

    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.

  14. Determining the nitrogen and oxygen isotope effects of microbial denitrification

    NASA Astrophysics Data System (ADS)

    Philp, C.; Martin, T. S.; Casciotti, K. L.

    2013-12-01

    The nitrogen cycle describes how nitrogen, a critical nutrient for life, moves throughout the ground, oceans, and atmosphere. An essential component of the nitrogen cycle is denitrification, in which bioavailable nitrogen is transformed into nitrous oxide and nitrogen gas and can no longer be harnessed by most organisms. We can further understand the importance of this nitrogen cycle process by examining the N and O isotope effects of microbial denitrification. We have cultured four denitrifying bacteria: P. stutzeri, P. putida, P. aureofaciens, and P. aeruginosa. After providing them with an initial amount of nitrite we tracked the rate at which each type of bacteria consumed the nitrite through a time series experiment. We then measured the N and O isotope ratios of the nitrite at each time point using a gas-source isotope ratio mass spectrometer. The subsequent isotope effects calculated using the Rayleigh equation provide an important tool for modeling denitrification in the environment.

  15. Adapting isostatic microbial growth parameters into non-isostatic models for use in dynamic ecosystems

    NASA Astrophysics Data System (ADS)

    Spangler, J.; Schulz, C. J.; Childers, G. W.

    2009-12-01

    Modeling microbial respiration and growth is an important tool for understanding many geochemical systems. The estimation of growth parameters relies on fitting experimental data to a selected model, such as the Monod equation or some variation, most often under batch or continuous culture conditions. While continuous culture conditions can be analogous to some natural environments, it often isn’t the case. More often, microorganisms are subject to fluctuating temperature, substrate concentrations, pH, water activity, and inhibitory compounds, to name a few. Microbial growth estimation under non-isothermal conditions has been possible through use of numerical solutions and has seen use in the field of food microbiology. In this study, numerical solutions were used to extend growth models under more non-isostatic conditions using momentary growth rate estimates. Using a model organism common in wastewater (Paracoccus denitrificans), growth and respiration rate parameters were estimated under varying static conditions (temperature, pH, electron donor/acceptor concentrations) and used to construct a non-isostatic growth model. After construction of the model, additional experiments were conducted to validate the model. These non-isostatic models hold the potential for allowing the prediction of cell biomass and respiration rates under a diverse array of conditions. By not restricting models to constant environmental conditions, the general applicability of the model can be greatly improved.

  16. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale.

    PubMed

    Bru, D; Ramette, A; Saby, N P A; Dequiedt, S; Ranjard, L; Jolivet, C; Arrouays, D; Philippot, L

    2011-03-01

    Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

  17. Quantitative Polymerase Chain Reaction for Microbial Growth Kinetics of Mixed Culture System.

    PubMed

    Cotto, Ada; Looper, Jessica K; Mota, Linda C; Son, Ahjeong

    2015-11-01

    Microbial growth kinetics is often used to optimize environmental processes owing to its relation to the breakdown of substrate (contaminants). However, the quantification of bacterial populations in the environment is difficult owing to the challenges of monitoring a specific bacterial population within a diverse microbial community. Conventional methods are unable to detect and quantify the growth of individual strains separately in the mixed culture reactor. This work describes a novel quantitative PCR (qPCR)-based genomic approach to quantify each species in mixed culture and interpret its growth kinetics in the mixed system. Batch experiments were performed for both single and dual cultures of Pseudomonas putida and Escherichia coli K12 to obtain Monod kinetic parameters (μmax and Ks). The growth curves and kinetics obtained by conventional methods (i.e., dry weight measurement and absorbance reading) were compared with that obtained by qPCR assay. We anticipate that the adoption of this qPCR-based genomic assay can contribute significantly to traditional microbial kinetics, modeling practice, and the operation of bioreactors, where handling of complex mixed cultures is required.

  18. Microbial growth and the effects of mild acidification and preservatives in refrigerated sweet potato puree.

    PubMed

    Pérez-Díaz, Ilenys M; Truong, Van-Den; Webber, Ashlee; McFeeters, Roger F

    2008-03-01

    Refrigerated sweet potato puree is a convenient form of sweet potato that can be used as an ingredient in formulated foods. The microbiology of refrigerated sweet potato puree during storage for up to 5 weeks was evaluated. Because the puree was made by comminuting steam-cooked sweet potatoes before refrigeration, no naturally occurring vegetative bacterial cells were detected during a 4-week period of refrigerated storage at 4 degrees C. However, if postprocessing microbial contamination of the puree were to occur, contaminating microorganisms such as Listeria monocytogenes could grow during refrigerated storage. The effects of acidification or the addition of potassium sorbate and sodium benzoate on a population of L. monocytogenes inoculated into refrigerated (4 degrees C) sweet potato puree were determined. Inoculation of the refrigerated puree with L. monocytogenes at 10(6) CFU/ml resulted in a 3-log increase after 3 weeks storage of nonsupplemented puree. Supplementation of the sweet potato puree with 0.06% (wt/vol) sorbic acid or benzoic acid plus mild acidification of the sweet potato puree with citric acid to pH 4.2 prevented growth of L. monocytogenes during storage at 4 degrees C.

  19. Structural effects of ionic liquids on microalgal growth inhibition and microbial degradation.

    PubMed

    Pham, Thi Phuong Thuy; Cho, Chul-Woong; Yun, Yeoung-Sang

    2016-03-01

    In the present study, we investigated structural effects of various ionic liquids (ILs) on microalgal growth inhibition and microbial biodegradability. For this, we tested pyridinium- and pyrrolidinium-based ILs with various alkyl chain lengths and bromide anion, and compared the toxicological effects with log EC50 values of imidazolium-based IL with the same alkyl chains and anion from literature. Comparing determined EC50 values of cationic moieties with the same alkyl chain length, pyridinium-based ILs were found to be slightly more toxic towards the freshwater green alga, Pseudokirchneriella subcapitata, than a series of pyrrolidinium and imidazolium except to 1-octyl-3-methylimidazolium bromide. Concerning the biodegradation study of 12 ILs using the activated sludge microorganisms, the results showed that the pyridinium derivatives except to 1-propyl-3-methylpyridinium cation were degraded. Whereas in case of imidazolium- and pyrrolidinium-based compounds, only n-hexyl and n-octyl substituted cations were fully degraded but no significant biodegradation was observed for the short chains (three and four alkyl chains).

  20. ATP monitoring technology for microbial growth control in potable water systems

    NASA Astrophysics Data System (ADS)

    Whalen, Patrick A.; Whalen, Philip J.; Cairns, James E.

    2006-05-01

    ATP (Adenosine Triphosphate) is the primary energy transfer molecule present in all living biological cells on Earth. ATP cannot be produced or maintained by anything but a living organism, and as such, its measurement is a direct indication of biological activity. The main advantage of ATP as a biological indicator is the speed of the analysis - from collecting the sample to obtaining the result, only minutes are required. The technology to measure ATP is already widely utilized to verify disinfection efficacy in the food industry and is also commonly applied in industrial water processes such as cooling water systems to monitor microbial growth and biocide applications. Research has indicated that ATP measurement technology can also play a key role in such important industries as potable water distribution and biological wastewater treatment. As will be detailed in this paper, LuminUltra Technologies has developed and applied ATP measurement technologies designed for any water type, and as such can provide a method to rapidly and accurately determine the level of biological activity in drinking water supplies. Because of its speed and specificity to biological activity, ATP measurement can play a key role in defending against failing drinking water quality, including those encountered during routine operation and also bioterrorism.

  1. Waste water derived electroactive microbial biofilms: growth, maintenance, and basic characterization.

    PubMed

    Gimkiewicz, Carla; Harnisch, Falk

    2013-12-29

    The growth of anodic electroactive microbial biofilms from waste water inocula in a fed-batch reactor is demonstrated using a three-electrode setup controlled by a potentiostat. Thereby the use of potentiostats allows an exact adjustment of the electrode potential and ensures reproducible microbial culturing conditions. During growth the current production is monitored using chronoamperometry (CA). Based on these data the maximum current density (jmax) and the coulombic efficiency (CE) are discussed as measures for characterization of the bioelectrocatalytic performance. Cyclic voltammetry (CV), a nondestructive, i.e. noninvasive, method, is used to study the extracellular electron transfer (EET) of electroactive bacteria. CV measurements are performed on anodic biofilm electrodes in the presence of the microbial substrate, i.e. turnover conditions, and in the absence of the substrate, i.e. nonturnover conditions, using different scan rates. Subsequently, data analysis is exemplified and fundamental thermodynamic parameters of the microbial EET are derived and explained: peak potential (Ep), peak current density (jp), formal potential (E(f)) and peak separation (ΔEp). Additionally the limits of the method and the state-of the art data analysis are addressed. Thereby this video-article shall provide a guide for the basic experimental steps and the fundamental data analysis.

  2. Waste Water Derived Electroactive Microbial Biofilms: Growth, Maintenance, and Basic Characterization

    PubMed Central

    Gimkiewicz, Carla; Harnisch, Falk

    2013-01-01

    The growth of anodic electroactive microbial biofilms from waste water inocula in a fed-batch reactor is demonstrated using a three-electrode setup controlled by a potentiostat. Thereby the use of potentiostats allows an exact adjustment of the electrode potential and ensures reproducible microbial culturing conditions. During growth the current production is monitored using chronoamperometry (CA). Based on these data the maximum current density (jmax) and the coulombic efficiency (CE) are discussed as measures for characterization of the bioelectrocatalytic performance. Cyclic voltammetry (CV), a nondestructive, i.e. noninvasive, method, is used to study the extracellular electron transfer (EET) of electroactive bacteria. CV measurements are performed on anodic biofilm electrodes in the presence of the microbial substrate, i.e. turnover conditions, and in the absence of the substrate, i.e. nonturnover conditions, using different scan rates. Subsequently, data analysis is exemplified and fundamental thermodynamic parameters of the microbial EET are derived and explained: peak potential (Ep), peak current density (jp), formal potential (Ef) and peak separation (ΔEp). Additionally the limits of the method and the state-of the art data analysis are addressed. Thereby this video-article shall provide a guide for the basic experimental steps and the fundamental data analysis. PMID:24430581

  3. A comparison of additional treatment processes to limit particle accumulation and microbial growth during drinking water distribution.

    PubMed

    Liu, G; Lut, M C; Verberk, J Q J C; Van Dijk, J C

    2013-05-15

    Water quality changes, particle accumulation and microbial growth occurring in pilot-scale water distribution systems fed with normally treated and additional treated groundwater were monitored over a period of almost one year. The treatment processes were ranked in the following order: nanofiltration (NF) > (better than) ultrafiltration (UF) > ion exchange (IEX) for limiting particle accumulation. A different order was found for limiting overall microbial growth: NF > IEX > UF. There were strong correlations between particle load and particle accumulation, and between nutrient load and microbial growth. It was concluded that particle accumulation can be controlled by reducing the particle load in water treatment plants; and the microbial growth can be better controlled by limiting organic nutrients rather than removing biomass in water treatment plants. The major focus of this study was on microbial growth. The results demonstrated that growth occurred in all types of treated water, including the phases of bulk water, biofilm and loose deposits. Considering the growth in different phases, similar growth in bulk water was observed for all treatments; NF strongly reduced growth both in loose deposits and in biofilm; UF promoted growth in biofilm, while strongly limiting growth in loose deposits. IEX had good efficiency in between UF and NF, limiting both growths in loose deposits and in biofilm. Significant growth was found in loose deposits, suggesting that loose deposit biomass should be taken into account for growth evaluation and/or prediction. Strong correlations were found between microbial growth and pressure drop in a membrane fouling simulator which proved that a membrane fouling simulator can be a fast growth predictor (within a week). Different results obtained by adenosine triphosphate and flow cytometry cell counts revealed that ATP can accurately describe both suspended and particle-associated biomass, and flow cytometry files of TCC measurements needs

  4. Methods for Facilitating Microbial Growth on Pulp Mill Waste Streams and Characterization of the Biodegradation Potential of Cultured Microbes

    PubMed Central

    Mathews, Stephanie L.; Ayoub, Ali S.; Pawlak, Joel; Grunden, Amy M.

    2013-01-01

    The kraft process is applied to wood chips for separation of lignin from the polysaccharides within lignocellulose for pulp that will produce a high quality paper. Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. However, the recalcitrant nature of the lignocellulose resources, its chemical derivatives that constitute the majority of available organic carbon within black liquor, and its basic pH present challenges to microbial biodegradation of this waste material. Methods for the collection and modification of black liquor for microbial growth are aimed at utilization of this pulp waste to convert the lignin, organic acids, and polysaccharide degradation byproducts into valuable chemicals. The lignocellulose extraction techniques presented provide a reproducible method for preparation of lignocellulose growth substrates for understanding metabolic capacities of cultured microorganisms. Use of gas chromatography-mass spectrometry enables the identification and quantification of the fermentation products resulting from the growth of microorganisms on pulping waste. These methods when used together can facilitate the determination of the metabolic activity of microorganisms with potential to produce fermentation products that would provide greater value to the pulping system and reduce effluent waste, thereby increasing potential paper milling profits and offering additional uses for black liquor. PMID:24378616

  5. Methods for facilitating microbial growth on pulp mill waste streams and characterization of the biodegradation potential of cultured microbes.

    PubMed

    Mathews, Stephanie L; Ayoub, Ali S; Pawlak, Joel; Grunden, Amy M

    2013-12-12

    The kraft process is applied to wood chips for separation of lignin from the polysaccharides within lignocellulose for pulp that will produce a high quality paper. Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. However, the recalcitrant nature of the lignocellulose resources, its chemical derivatives that constitute the majority of available organic carbon within black liquor, and its basic pH present challenges to microbial biodegradation of this waste material. Methods for the collection and modification of black liquor for microbial growth are aimed at utilization of this pulp waste to convert the lignin, organic acids, and polysaccharide degradation byproducts into valuable chemicals. The lignocellulose extraction techniques presented provide a reproducible method for preparation of lignocellulose growth substrates for understanding metabolic capacities of cultured microorganisms. Use of gas chromatography-mass spectrometry enables the identification and quantification of the fermentation products resulting from the growth of microorganisms on pulping waste. These methods when used together can facilitate the determination of the metabolic activity of microorganisms with potential to produce fermentation products that would provide greater value to the pulping system and reduce effluent waste, thereby increasing potential paper milling profits and offering additional uses for black liquor.

  6. DNA-based determination of microbial biomass suitable for frozen and alkaline soil samples

    NASA Astrophysics Data System (ADS)

    Semenov, Mikhail; Blagodatskaya, Evgeniya; Kogut, Boris; Kuzyakov, Yakov

    2015-04-01

    Microbial biomass is a sensitive indicator of changes due to soil management, long before other basic soil measures such as Corg or Ntot. Improvement of methods for determination of microbial biomass still remains relevant, and these methods should be correctly applicable for the soil samples being in various state. This study was designed to demonstrate the applicability of DNA-based determination of microbial biomass under conditions when the common basic approaches, namely chloroform fumigation-extraction (CFE) and substrate-induced respiration (SIR), are restricted by certain soil properties, experimental designs or research needs, e.g. in frozen, alkaline or carbonaceous soils. We compared microbial biomass determined by CFE, SIR and by DNA approaches in the range of neutral and slightly alkaline Chernozem and alkaline Calcisol of semi-arid climate. The samples of natural and agricultural ecosystems were taken throughout the soil profile from long-term static field experiments in the European part of Russia. Extraction and subsequent quantification of dsDNA revealed a strong agreement with SIR and CFE when analyzing the microbial biomass content in soils with pH below 8. The conversion factors (FDNA) from dsDNA to SIR-Cmic (5.10) and CFE-Cmic (4.41) were obtained by testing a range of the soil samples down to 1.5 m depth and indicated a good reproducibility of DNA-based estimations. In alkaline soils (pH > 8), CO2 retention due to alkaline pH and exchange with carbonates resulted in a strong underestimation of soil microbial biomass by SIR or even in the absence of any CO2 emission, especially at low absolute values of microbial biomass in subsoil. Correction of CO2 efflux by theoretical retention pH-dependent factors caused overestimation of SIR-biomass. In alkaline conditions, DNA extraction proved to be a reliable alternative for microbial biomass determination. Moreover, the DNA-based approach can serve as an excellent alternative enabling correct

  7. Soil pH determines microbial diversity and composition in the park grass experiment.

    PubMed

    Zhalnina, Kateryna; Dias, Raquel; de Quadros, Patricia Dörr; Davis-Richardson, Austin; Camargo, Flavio A O; Clark, Ian M; McGrath, Steve P; Hirsch, Penny R; Triplett, Eric W

    2015-02-01

    The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6-7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.

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

    PubMed Central

    Li, W K

    1984-01-01

    The uptake of [3H]glucose and a mixture of 3H-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 the specific growth rate and initial standing stock of the microbial assemblages. PMID:6696414

  9. On the feasibility of growth-coupled product synthesis in microbial strains.

    PubMed

    Klamt, Steffen; Mahadevan, Radhakrishnan

    2015-07-01

    Enforcing obligate coupling of growth with synthesis of a desired product has become a key principle for metabolic engineering of microbial production strains. Various methods from stoichiometric and constraint-based modeling have been developed to calculate intervention strategies by which a given microorganism can only grow if it synthesizes a desired compound as a mandatory by-product. However, growth-coupled synthesis is not necessarily feasible for every compound of a metabolic network and no rigorous criterion is currently known to test feasibility of coupled product and biomass formation (before searching for suitable intervention strategies). In this work, we show which properties a network must fulfill such that strain designs guaranteeing coupled biomass and product synthesis can exist at all. In networks without flux bounds, coupling is feasible if and only if an elementary mode exists that leads to formation of both biomass and product. Setting flux boundaries leads to more complicated inhomogeneous problems. Making use of the concept of elementary (flux) vectors, a generalization of elementary modes, a criterion for feasibility can also be derived for this situation. We applied our criteria to a metabolic model of Escherichia coli and determined for each metabolite, whether its net production can be coupled with biomass synthesis and calculated the maximal (guaranteed) coupling yield. The somewhat surprising result is that, under aerobic conditions, coupling is indeed possible for each carbon metabolite of the central metabolism. This also holds true for most metabolites under anaerobic conditions but consideration of ATP maintenance requirements implies infeasibility of coupling for certain compounds. On the other hand, ATP maintenance may also increase the maximal coupling yield for some metabolites. Overall, our work provides important insights and novel tools for a central problem of computational strain design.

  10. Dynamic mathematical model to predict microbial growth and inactivation during food processing.

    PubMed Central

    Van Impe, J F; Nicolaï, B M; Martens, T; De Baerdemaeker, J; Vandewalle, J

    1992-01-01

    Many sigmoidal functions to describe a bacterial growth curve as an explicit function of time have been reported in the literature. Furthermore, several expressions have been proposed to model the influence of temperature on the main characteristics of this growth curve: maximum specific growth rate, lag time, and asymptotic level. However, as the predictive value of such explicit models is most often guaranteed only at a constant temperature within the temperature range of microbial growth, they are less appropriate in optimization studies of a whole production and distribution chain. In this paper a dynamic mathematical model--a first-order differential equation--has been derived, describing the bacterial population as a function of both time and temperature. Furthermore, the inactivation of the population at temperatures above the maximum temperature for growth has been incorporated. In the special case of a constant temperature, the solution coincides exactly with the corresponding Gompertz model, which has been validated in several recent reports. However, the main advantage of this dynamic model is its ability to deal with time-varying temperatures, over the whole temperature range of growth and inactivation. As such, it is an essential building block in (time-saving) simulation studies to design, e.g., optimal temperature-time profiles with respect to microbial safety of a production and distribution chain of chilled foods. PMID:1444404

  11. Determination of the microbial origin of geosmin in Chinese liquor.

    PubMed

    Du, Hai; Xu, Yan

    2012-03-07

    Geosmin is the major cause of the common earthy off-flavor in light-aroma type Chinese liquor and, thus, highly detrimental to the aromatic quality. To find out its origin, the evolving process of geosmin in light-aroma type liquor making was monitored, and microbial analysis of Daqu containing geosmin was carried out. The results showed that geosmin appeared in all the fermented sorghums at different fermentation periods. About 57% geosmin in the fermented sorghums was distilled into liquor. During the distillation process, the peak of geosmin concentration appeared when alcohol content was 50-60% vol. More importantly, high geosmin content was observed during the Daqu-making process. Furthermore, five Streptomyces strains were isolated from different types of Daqu used for the fermentation of light-aroma type liquor. All of them produced only geosmin as the main volatile metabolite but no 2-methylisoborneol (2-MIB). It appears that microorganisms developing in Daqu are responsible for the presence of geosmin in liquor. Because of the relatively low detection threshold estimated at 110 ng/L in 46 vol % hydroalcoholic solution, the presence of geosmin in Daqu may pose a risk for Chinese liquor producers.

  12. Phenolic-rich leaf carbon fractions differentially influence microbial respiration and plant growth.

    PubMed

    Meier, Courtney L; Bowman, William D

    2008-11-01

    Phenolics can reduce soil nutrient availability, either indirectly by stimulating microbial nitrogen (N) immobilization or directly by enhancing physical protection within soil. Phenolic-rich plants may therefore negatively affect neighboring plant growth by restricting the N supply. We used a slow-growing, phenolic-rich alpine forb, Acomastylis rossii, to test the hypothesis that phenolic-rich carbon (C) fractions stimulate microbial population growth and reduce plant growth. We generated low-molecular-weight (LMW) fractions, tannin fractions, and total soluble C fractions from A. rossii and measured their effects on soil respiration and growth of Deschampsia caespitosa, a fast-growing, co-dominant grass. Fraction effects fell into two distinct categories: (1) fractions did not increase soil respiration and killed D. caespitosa plants, or (2) fractions stimulated soil respiration and reduced plant growth and plant N concentration while simultaneously inhibiting root growth. The LMW phenolic-rich fractions increased soil respiration and reduced plant growth more than tannins. These results suggest that phenolic compounds can inhibit root growth directly as well as indirectly affect growth by reducing pools of plant available N by stimulating soil microbes. Both mechanisms illustrate how below-ground phenolic effects may influence the growth of neighboring plants. We also examined patterns of foliar phenolic concentrations among populations of A. rossii across a natural productivity gradient (productivity was used as a proxy for competition intensity). Concentrations of some LMW phenolics increased significantly in more productive sites where A. rossii is a competitive equal with the faster growing D. caespitosa. Taken together, our results contribute important information to the growing body of evidence indicating that the quality of C moving from plants to soils can have significant effects on neighboring plant performance, potentially associated with phytoxic

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

    SciTech Connect

    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.

  14. Microbial Communities in Biofilms of an Acid Mine Drainage Site Determined by Phospholipid Analysis

    NASA Astrophysics Data System (ADS)

    Das Gupta, S.; Fang, J.

    2008-12-01

    Phospholipids were extracted to determine the microbial biomass and community structure of biofims from an acid mine drainage (AMD) at the Green Valley coal mine site (GVS) in western Indiana. The distribution of specific biomarkers indicated the presence of a variety of microorganisms. Phototrophic microeukaryotes, which include Euglena mutabilis, algae, and cyanobacteria were the most dominant organisms, as indicated by the presence of polyunsaturated fatty acids. The presence of terminally methyl branched fatty acids suggests the presence of Gram-positive bacteria, and the mid-methyl branched fatty acids indicates the presence of sulfate-reducing bacteria. Fungi appear to also be an important part of the AMD microbial communities as suggested by the presence of 18:2 fatty acid. The acidophilic microeukaryotes Euglena dominated the biofilm microbial communities. These microorganisms appear to play a prominent role in the formation and preservation of stromatolites and in releasing oxygen to the atmosphere by oxygenic photosynthesis. Thus, the AMD environment comprises a host of microorganisms spreading out within the phylogenetic tree of life. Novel insights on the roles of microbial consortia in the formation and preservation of stromatolites and the production of oxygen through photosynthesis in AMD systems may have significance in the understanding of the interaction of Precambrian microbial communities in environments that produced microbially-mediated sedimentary structures and that caused oxygenation of Earth's atmosphere.

  15. Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling

    PubMed Central

    Liu, Yiwen; Sun, Jing; Peng, Lai; Wang, Dongbo; Dai, Xiaohu; Ni, Bing-Jie

    2016-01-01

    Anaerobic ammonium oxidation (anammox) is known to autotrophically convert ammonium to dinitrogen gas with nitrite as the electron acceptor, but little is known about their released microbial products and how these are relative to heterotrophic growth in anammox system. In this work, we applied a mathematical model to assess the heterotrophic growth supported by three key microbial products produced by bacteria in anammox biofilm (utilization associated products (UAP), biomass associated products (BAP), and decay released substrate). Both One-dimensional and two-dimensional numerical biofilm models were developed to describe the development of anammox biofilm as a function of the multiple bacteria–substrate interactions. Model simulations show that UAP of anammox is the main organic carbon source for heterotrophs. Heterotrophs are mainly dominant at the surface of the anammox biofilm with small fraction inside the biofilm. 1-D model is sufficient to describe the main substrate concentrations/fluxes within the anammox biofilm, while the 2-D model can give a more detailed biomass distribution. The heterotrophic growth on UAP is mainly present at the outside of anammox biofilm, their growth on BAP (HetB) are present throughout the biofilm, while the growth on decay released substrate (HetD) is mainly located in the inner layers of the biofilm. PMID:27273460

  16. Plant growth in Arabidopsis is assisted by compost soil-derived microbial communities

    PubMed Central

    Carvalhais, Lilia C.; Muzzi, Frederico; Tan, Chin-Hong; Hsien-Choo, Jin; Schenk, Peer M.

    2013-01-01

    Plants in natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of roots and the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we examined Arabidopsis thaliana roots and shoots in the presence or absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect on Arabidopsis shoots in the presence of soil microbes compared to plants grown in microbe-free soil under otherwise identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also led to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in nitrogen uptake, oxidative stress/redox signaling, and salicylic acid (SA)-mediated plant defense while upregulating jasmonate (JA) signaling, cell wall organization/biosynthesis and photosynthesis. Multi-species analyses such as simultaneous transcriptional profiling of plants and their interacting microorganisms (metatranscriptomics) coupled to metagenomics may further increase our understanding of the intricate networks underlying plant-microbe interactions. PMID:23847639

  17. Soft deposits, the key site for microbial growth in drinking water distribution networks.

    PubMed

    Zacheus, O M; Lehtola, M J; Korhonen, L K; Martikainen, P J

    2001-05-01

    In this project we studied the microbiological quality of soft pipeline deposits removed from drinking water distribution networks during mechanical cleaning. Drinking water and deposit samples were collected from 16 drinking water distribution networks located at eight towns in different parts of Finland. Soft pipeline deposits were found to be the key site for microbial growth in the distribution networks. The microbial numbers in the soft deposits were significantly higher than numbers in running water. The highest microbial numbers were detected in the main deposit pushed ahead by the first swab. The deposits contained high numbers of heterotrophic bacteria, actinomycetes and fungi. Also coliform bacteria were often isolated from deposit samples. Manganese and copper in the deposits correlated negatively with the numbers of heterotrophic bacteria. After a year, the viable microbial numbers in the new deposits were almost as high as in the old deposits before the first mechanical cleaning. The bacterial biomass production was higher in the new than in the old deposits.

  18. The influence of six pharmaceuticals on freshwater sediment microbial growth incubated at different temperatures and UV exposures.

    PubMed

    Veach, Allison; Bernot, Melody J; Mitchell, James K

    2012-07-01

    Pharmaceutical compounds have been detected in freshwater for several decades. Once they enter the aquatic ecosystem, they may be transformed abiotically (i.e., photolysis) or biotically (i.e., microbial activity). To assess the influence of pharmaceuticals on microbial growth, basal salt media amended with seven pharmaceutical treatments (acetaminophen, caffeine, carbamazepine, cotinine, ibuprofen, sulfamethoxazole, and a no pharmaceutical control) were inoculated with stream sediment. The seven pharmaceutical treatments were then placed in five different culture environments that included both temperature treatments of 4, 25, 37°C and light treatments of continuous UV-A or UV-B exposure. Microbial growth in the basal salt media was quantified as absorbance (OD(550)) at 7, 14, 21, 31, and 48d following inoculation. Microbial growth was significantly influenced by pharmaceutical treatments (P < 0.01) and incubation treatments (P < 0.01). Colonial morphology of the microbial communities post-incubation identified selection of microbial and fungal species with exposure to caffeine, cotinine, and ibuprofen at 37°C; acetaminophen, caffeine, and cotinine at 25°C; and carbamazepine exposed to continuous UV-A. Bacillus and coccus cellular arrangements (1000X magnification) were consistently observed across incubation treatments for each pharmaceutical treatment although carbamazepine and ibuprofen exposures incubated at 25°C also selected spiral-shaped bacteria. These data indicate stream sediment microbial communities are influenced by pharmaceuticals though physiochemical characteristics of the environment may dictate microbial response.

  19. [Macrokinetic basis for the model of microbial growth in a limited volume under constant conditions with a single leading substrate].

    PubMed

    Gendugov, V M; Glazunov, G P

    2013-01-01

    Within the framework of the macrokinetic approach and continuum and chemical/biochemical gross reaction conceptions, an equation describing the complete dynamics of microbial growth and decline as function of a variable concentration of the leading substrate was deduced. This equation allows us to distinguish quantitatively and qualitatively the stages of microbial growth and the intervals of microbial tolerance to the initial concentration of the leading substrate. Adequacy of the model was confirmed by comparison with experimental dynamics of aerobic microorganisms in the samples of groundwater collected from a region polluted with uranium.

  20. Determination of carbon and nitrogen in microbial biomass of southern-Taiga soils by different methods

    NASA Astrophysics Data System (ADS)

    Makarov, M. I.; Malysheva, T. I.; Maslov, M. N.; Kuznetsova, E. Yu.; Menyailo, O. V.

    2016-06-01

    The results of methods for determining microbial biomass carbon vary in reproducibility among soils. The fumigation-extraction and substrate-induced respiration methods give similar results for Albic Luvisol and Gleyic Fluvisol, while the results of the rehydration method are reliably higher. In Histic Fluvisol, relatively similar results are obtained using the fumigation-extraction and rehydration methods, and the substrate-induced respiration method gives almost halved results. The seasonal dynamics of microbial biomass carbon also varies depending on the method used. The highest difference is typical for the warm period, when the concentrations found by the extraction and substrate-induced methods poorly agree between two out of three soils studied. The concentration of microbial biomass nitrogen is less sensitive to the analytical method: the differences between the results of the fumigation-extraction and rehydration methods are statistically insignificant in the all soils. To reveal stable relationships between the results of determining microbial carbon and the soil properties and analytical method, a large diversity of soils should be studied. This will allow for proposing of conversion factors for the recalculation of the obtained values to the concentrations of carbon and nitrogen in microbial biomass for different soils (or soil groups) and, hence, the more correct comparison of the results obtained by different methods.

  1. Growth performance of calves fed microbially enhanced soy protein in pelleted starters.

    PubMed

    Senevirathne, N D; Anderson, J L; Gibbons, W R; Clapper, J A

    2017-01-01

    Our objective was to determine effects of feeding calves pelleted starters with microbially enhanced (fungi-treated) soy protein (MSP) in replacement of soybean meal (SBM) with different milk replacers (MR). Thirty-six Holstein calves (2 d old; 24 females, 12 males) in individual hutches were used in a 12-wk randomized complete block design study. Treatments were (1) MSP pellets with MR formulated for accelerated growth (28% crude protein, 18% fat; MSPA), (2) SBM pellets with MR formulated for accelerated growth (SBMA), and (3) MSP pellets with conventional MR (20% crude protein, 20% fat; MSPC). Pellets were similar except for 23% MSP or 23% SBM (dry matter basis). Pellets and water were fed ad libitum throughout the study. Feeding rates of MR on a dry matter basis were 0.37kg twice daily during wk 1, 0.45kg twice daily during wk 2 to 5, and 0.45kg once daily during wk 6. Intakes were recorded daily. Body weights, frame size measurements, and jugular blood samples were collected 2 d every 2 wk at 3 h after the morning feeding. Fecal grab samples were collected 5 times per d for 3 d during wk 12 and then composited by calf for analysis of apparent total-tract digestibility of nutrients using acid detergent insoluble ash as an internal marker. Total and starter pellet dry matter intake were greatest for calves fed SBMA and least for MSPC. Calves had similar average daily gain among treatments, but there was a treatment by week interaction and during the last few weeks of the study calves on MSPC had less body weight compared with MSPA or SBMA. Gain-to-feed ratio was similar among treatments; however, there was a treatment by week interaction. Serum glucose was similar among treatments. Plasma urea nitrogen was greatest for calves fed MSPA and least for MSPC. Plasma concentrations of IGF-1 were greatest for calves fed SBMA. Plasma concentrations of triglycerides were greatest for calves fed MSPC. Plasma concentrations of β-hydroxybutyrate had a treatment by time

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

    PubMed

    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.

  3. Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition.

    PubMed

    Lautenschlager, Karin; Boon, Nico; Wang, Yingying; Egli, Thomas; Hammes, Frederik

    2010-09-01

    Drinking water quality is routinely monitored in the distribution network but not inside households at the point of consumption. Fluctuating temperatures, residence times (stagnation), pipe materials and decreasing pipe diameters can promote bacterial growth in buildings. To test the influence of stagnation in households on the bacterial cell concentrations and composition, water was sampled from 10 separate households after overnight stagnation and after flushing the taps. Cell concentrations, measured by flow cytometry, increased (2-3-fold) in all water samples after stagnation. This increase was also observed in adenosine tri-phosphate (ATP) concentrations (2-18-fold) and heterotrophic plate counts (4-580-fold). An observed increase in cell biovolume and ATP-per-cell concentrations furthermore suggests that the increase in cell concentrations was due to microbial growth. After 5 min flushing of the taps, cell concentrations and water temperature decreased to the level generally found in the drinking water network. Denaturing gradient gel electrophoresis also showed a change in the microbial composition after stagnation. This study showed that water stagnation in household pipes results in considerable microbial changes. While hygienic risk was not directly assessed, it emphasizes the need for the development of good material validation methods, recommendations and spot tests for in-house water installations. However, a simple mitigation strategy would be a short flushing of taps prior to use.

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

    PubMed Central

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E.

    2015-01-01

    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 by describing microbial–plants and microbial–microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use. PMID:25821453

  5. Microbial growth in the polar oceans - role of temperature and potential impact of climate change.

    PubMed

    Kirchman, David L; Morán, Xosé Anxelu G; Ducklow, Hugh

    2009-06-01

    Heterotrophic bacteria are the most abundant organisms on the planet and dominate oceanic biogeochemical cycles, including that of carbon. Their role in polar waters has been enigmatic, however, because of conflicting reports about how temperature and the supply of organic carbon control bacterial growth. In this Analysis article, we attempt to resolve this controversy by reviewing previous reports in light of new data on microbial processes in the western Arctic Ocean and by comparing polar waters with low-latitude oceans. Understanding the regulation of in situ microbial activity may help us understand the response of the Arctic Ocean and Antarctic coastal waters over the coming decades as they warm and ice coverage declines.

  6. Growth kinetics of an indigenous mixed microbial consortium during phenol degradation in a batch reactor.

    PubMed

    Saravanan, Pichiah; Pakshirajan, K; Saha, Prabirkumar

    2008-01-01

    Biodegradation of phenol by a mixed microbial culture, isolated from a sewage treatment plant, was investigated in batch shake flasks. A minimum concentration of 100 and a maximum of 800 mg 1(-1) of phenol in the media were adapted in the degradation study. The phenol degradation rate varied largely and was less than 10 mg l(-1)h(-1) at both extremes of the initial concentrations in the media. The degradation rate was maximum 15.7 mg l(-1)h(-1) at 400 mg l(-1) phenol. The culture followed substrate inhibition kinetics and the specific growth rate were fitted to Haldane and Han-Levenspiel models. Between the two models the Han-Levenspiel was found to be a better fit with a root mean square error of 0.0211. The biokinetics constants estimated using these models showed good potential of the mixed microbial culture in phenol degradation.

  7. Total soil DNA quantification as an alternative microbial biomass determination approach

    NASA Astrophysics Data System (ADS)

    Semenov, Mikhail

    2015-04-01

    Many studies on geographically widespread soils from arctic permafrost to arid and tropical soils, as well as those studies on extreme events, such as freezing-thawing and drying-rewetting of soils, require immediate freezing of soil after sampling. The two common basic approaches, such as chloroform fumigation-extraction (CFE) and substrate-induced respiration (SIR), however, are not applicable in frozen or dry soil samples due to a partial destruction of microbial cells during freezing-thawing and drying-rewetting. This calls for approaches enabling correct estimation of microbial biomass in frozen or dried soil samples. This study was aimed to compare commonly used SIR and CFE techniques with total soil DNA quantification and demonstrate the applicability of DNA-based determination of microbial biomass in carbonate-containing, slightly (Chernozem) and strongly alkaline (Calcisol) soils of semi-arid climates. The samples of natural and agricultural ecosystems were taken throughout the soil profile from long-term static field experiments in the European part of Russia. The linear regression between SIR-Cmic and total soil dsDNA for the Chernozem showed very strong correlation. From the regression equation, the conversion factor of 5.10 with R2 = 0.96 was obtained. The effect of CO2 retention at alkaline pH (>8) and low microbial biomass-C resulted in an inability to obtain any SIR-CO2 release at deeper horizons of Calcisol, i.e. the CO2 retention potential was higher that the CO2 evolution. As a consequence, the values of SIR-Cmic of Calcisol at the horizons with pH > 8.0 were strongly underestimated (by a factor of 2-3). This smoothed the differences in Cmic between soil horizons. Nevertheless, reliable dsDNA values obtained for these soils demonstrated well-pronounced changes in microbial biomass within soil profile. The CFE and DNA-based approaches showed a good correspondence, with R2 = 0.96 for both soil types. The CFE-Cmic to DNA-Cmic factor of 0

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Development of a competition model for microbial growth in mixed culture.

    PubMed

    Fujikawa, Hiroshi; Munakata, Kanako; Sakha, Mohammad Z

    2014-01-01

    A novel competition model for describing bacterial growth in mixed culture was developed in this study. Several model candidates were made with our logistic growth model that precisely describes the growth of a monoculture of bacteria. These candidates were then evaluated for the usefulness in describing growth of two competing species in mixed culture using Staphylococcus aureus, Escherichia coli, and Salmonella. Bacterial cells of two species grew at initial doses of 10(3), 10(4), and 10(5) CFU/g at 28ºC. Among the candidates, a model where the Lotka-Volterra model, a general competition model in ecology, was incorporated as a new term in our growth model was the best for describing all types of growth of two competitors in mixed culture. Moreover, the values for the competition coefficient in the model were stable at various combinations of the initial populations of the species. The Baranyi model could also successfully describe the above types of growth in mixed culture when it was coupled with the Gimenez and Dalgaard model. However, the values for the competition coefficients in the competition model varied with the conditions. The present study suggested that our model could be a basic model for describing microbial competition.

  10. GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

    EPA Science Inventory

    The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

  11. Colorimetric determination of catechol siderophores in microbial cultures.

    PubMed

    Rioux, C; Jordan, D C; Rattray, J B

    1983-08-01

    A highly sensitive spectrophotometric method for the selective detection of catechol compounds such as catechol siderophores (e.g., enterobactin) is described. The basis of the method involves the ability of the vicinal aromatic hydroxyl groups under acidic conditions to bring about a reduction of Fe3+ (from ferric ammonium citrate) to Fe2+. Detection of Fe2+ in the presence of Fe3+ is made with 1,10-phenanthroline under previously established conditions. The assay mixture is heated at 60 degrees C for 1 h to accelerate the development of color which is subsequently measured at 510 nm. The Beer-Lambert law is obeyed over the range of 0.16 to 60 microM 2,3-dihydroxybenzoic acid. Compared to the Arnow nitration method, the assay is more responsive, is approximately seven times more sensitive, and is effective with catechols substituted at positions 3 and 4. The method gives positive results with catechols such as DL-DOPA, L-dopamine, (+/-)-epinephrine, and DL-norepinephrine. Very rapid color development is obtained with ascorbic acid and p-diols, while m-diols are poorly detected. Low degrees of reactivity are shown by hydroxylamino and hydroxamate compounds. Phenolic, sulfydryl, indolyl, and quinonyl derivatives do not interfere with the reaction. The method has been adapted to determine catechol compounds in the culture medium of bacterial cells grown at different iron concentrations.

  12. Microbial growth and transport in porous media under denitrification conditions: experiments and simulations

    NASA Astrophysics Data System (ADS)

    Clement, T. P.; Peyton, B. M.; Skeen, R. S.; Jennings, D. A.; Petersen, J. N.

    1997-01-01

    Soil column experiments were conducted to study bacterial growth and transport in porous media under denitrifying conditions. The study used a denitrifying microbial consortium isolated from aquifer sediments sampled at the U.S. Department of Energy's Hanford site. One-dimensional, packed-column transport studies were conducted under two substrate loading conditions. A detailed numerical model was developed to predict the measured effluent cell and substrate concentration profiles. First-order attachment and detachment models described the interphase exchange processes between suspended and attached biomass. Insignificantly different detachment coefficient values of 0.32 and 0.43 day -1, respectively, were estimated for the high and low nitrate loading conditions (48 and 5 mg l -1 NO 3, respectively). Comparison of these values with those calculated from published data for aerobically growing organisms shows that the denitrifying consortium had lower detachment rate coefficients. This suggests that, similar to detachment rates in reactor-grown biofilms, detachment in porous media may increase with microbial growth rate. However, available literature data are not sufficient to confirm a specific analytical model for predicting this growth dependence.

  13. Soil microbial biomass and root growth in Bt and non-Bt cotton

    NASA Astrophysics Data System (ADS)

    Tan, D. K. Y.; Broughton, K.; Knox, O. G.; Hulugalle, N. R.

    2012-04-01

    The introduction of transgenic Bacillus thuringiensis (Bt) cotton (Gossypium hirsutum L.) has had a substantial impact on pest management in the cotton industry. While there has been substantial research done on the impact of Bt on the above-ground parts of the cotton plant, less is known about the effect of Bt genes on below ground growth of cotton and soil microbial biomass. The aim of this research was to test the hypothesis that Bt [Sicot 80 BRF (Bollgard II Roundup Ready Flex®)] and non-Bt [Sicot 80 RRF (Roundup Ready Flex®)] transgenic cotton varieties differ in root growth and root turnover, carbon indices and microbial biomass. A field experiment was conducted in Narrabri, north-western NSW. The experimental layout was a randomised block design and used minirhizotron and core break and root washing methods to measure cotton root growth and turnover during the 2008/09 season. Root growth in the surface 0-0.1 m of the soil was measured using the core break and root washing methods, and that in the 0.1 to 1 m depth was measured with a minirhizotron and an I-CAP image capture system. These measurements were used to calculate root length per unit area, root carbon added to the soil through intra-seasonal root death, carbon in roots remaining at the end of the season and root carbon potentially added to the soil. Microbial biomass was also measured using the ninhydrin reactive N method. Root length densities and length per unit area of non-Bt cotton were greater than Bt cotton. There were no differences in root turnover between Bt and non-Bt cotton at 0-1 m soil depth, indicating that soil organic carbon stocks may not be affected by cotton variety. Cotton variety did not have an effect on soil microbial biomass. The results indicate that while there are differences in root morphology between Bt and non-Bt cotton, these do not change the carbon turnover dynamics in the soil.

  14. A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction.

    PubMed

    Istok, J D; Park, M; Michalsen, M; Spain, A M; Krumholz, L R; Liu, C; McKinley, J; Long, P; Roden, E; Peacock, A D; Baldwin, B

    2010-03-01

    'Bioimmobilization' of redox-sensitive heavy metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In one approach, growth-limiting substrates are added to the subsurface to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated reductive precipitation ('bioreduction') of targeted contaminants. We present a theoretical framework for modeling this process that modifies conventional geochemical reaction path modeling to include thermodynamic descriptions for microbial growth and may be called biogeochemical reaction path modeling. In this approach, the actual microbial community is represented by a synthetic microbial community consisting of a collection of microbial groups; each with a unique growth equation that couples a specific pair of energy yielding redox reactions. The growth equations and their computed standard-state free energy yields are appended to the thermodynamic database used in conventional geochemical reaction path modeling, providing a direct coupling between chemical species participating in both microbial growth and geochemical reactions. To compute the biogeochemical reaction paths, growth substrates are reacted incrementally with the defined geochemical environment and the coupled equations are solved simultaneously to predict reaction paths that display changing microbial biomass, community composition (i.e. the fraction of total biomass in each microbial group), and the aqueous and mineral composition of the system, including aqueous speciation and oxidation state of the targeted contaminants. The approach, with growth equations derived from the literature using well-known bioenergetics principles, was used to predict the results of a laboratory microcosm experiment and an in situ field experiment that investigated the bioreduction of uranium. Predicted effects of ethanol or acetate addition on uranium

  15. Determining the safety of microbial cultures for consumption by humans and animals.

    PubMed

    Pariza, Michael W; Gillies, Kevin O; Kraak-Ripple, Sarah F; Leyer, Gregory; Smith, Amy B

    2015-10-01

    Fermented foods and feeds have been consumed for millennia, and microorganisms isolated from traditional fermentations have been used as probiotics. There is interest in developing new microbial cultures for these uses, but to date safety evaluation procedures have only been discussed in general terms. We propose a comprehensive approach for determining the safety of microbial cultures that lack an established history of safe use for their intended new applications. Three scenarios are considered: (1) substantially increased exposure to a culture that has an established record of safety in a more limited application; (2) a new strain without a history of safe use that was isolated from a food or feed that has a history of safe use; and (3) a new strain isolated from a non-food or non-feed source. Our safety evaluation process is based on scientific procedures and is in the form of a decision tree composed of 13 questions. Our decision tree for determining the safety of microbial cultures for consumption by humans or animals is modeled on previous decision trees that are used worldwide to evaluate the safety of microbial enzymes for use in human food or animal feed.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Effect of temperature on microbial growth rate-mathematical analysis: the Arrhenius and Eyring-Polanyi connections.

    PubMed

    Huang, Lihan; Hwang, Andy; Phillips, John

    2011-10-01

    The objective of this work is to develop a mathematical model for evaluating the effect of temperature on the rate of microbial growth. The new mathematical model is derived by combination and modification of the Arrhenius equation and the Eyring-Polanyi transition theory. The new model, suitable for both suboptimal and the entire growth temperature ranges, was validated using a collection of 23 selected temperature-growth rate curves belonging to 5 groups of microorganisms, including Pseudomonas spp., Listeria monocytogenes, Salmonella spp., Clostridium perfringens, and Escherichia coli, from the published literature. The curve fitting is accomplished by nonlinear regression using the Levenberg-Marquardt algorithm. The resulting estimated growth rate (μ) values are highly correlated to the data collected from the literature (R(2) = 0.985, slope = 1.0, intercept = 0.0). The bias factor (B(f) ) of the new model is very close to 1.0, while the accuracy factor (A(f) ) ranges from 1.0 to 1.22 for most data sets. The new model is compared favorably with the Ratkowsky square root model and the Eyring equation. Even with more parameters, the Akaike information criterion, Bayesian information criterion, and mean square errors of the new model are not statistically different from the square root model and the Eyring equation, suggesting that the model can be used to describe the inherent relationship between temperature and microbial growth rates. The results of this work show that the new growth rate model is suitable for describing the effect of temperature on microbial growth rate. Practical Application:  Temperature is one of the most significant factors affecting the growth of microorganisms in foods. This study attempts to develop and validate a mathematical model to describe the temperature dependence of microbial growth rate. The findings show that the new model is accurate and can be used to describe the effect of temperature on microbial growth rate in foods.

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

    PubMed

    Mejlholm, Ole; Kjeldgaard, Jette; Modberg, Anne; Vest, Mette Bohn; Bøknaes, Niels; Koort, Joanna; Björkroth, Johanna; Dalgaard, Paw

    2008-06-10

    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 studied. Different recipes were used to study the effect of preserving parameters (organic acids, pH and NaCl) on growth of microorganisms and shelf life at 7-8 degrees C or 12 degrees C. Particularly, brines with different concentrations of (i) benzoic, citric and sorbic acids or (ii) acetic, citric 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 of the industrially processed brined shrimp. In addition, shelf life of brined shrimp was affected by the types and concentrations of organic acids and by the storage temperature as expected. The effect of MAP was less pronounced. Eighty-two isolates from the spoilage microflora of brined shrimp were identified and they included 53 lactic acid bacteria, 6 coagulase negative Staphylococcus spp., 18 Pseudomonas fluorescens and 5 yeast isolates. After storage at 7 degrees C, P. fluorescens, Enterococcus-like isolates, E. malodoratus, Carnobacterium maltaromaticum, coagulase negative Staphylococcus spp. and Lactobacillus sakei constituted the dominating microflora of shrimp in brines that contained benzoic, citric and sorbic acids as preservatives. L. sakei dominated the

  20. Stochastic-Convective Transport with Nonlinear Reaction: Biodegradation With Microbial Growth

    NASA Astrophysics Data System (ADS)

    Ginn, T. R.; Simmons, C. S.; Wood, B. D.

    1995-01-01

    The representation of subsurface flow and reactive transport as an ensemble of one-dimensional stream tubes is extended to account for nonlinear biodegradation with coupled microbial growth. The Stochastic-convective reaction (SCR) model is derived for bioreaction of a single solute by a single class of microorganisms coupled with dynamic microbial growth. A new global variable, the integral of the solute degraded per unit length of system traversed, accounts for degradation. Dimensionless scaling and the method of characteristics are used to reduce the model, written for a single convecting reactor (stream tube), to a pair of coupled nonlinear functional equations for solute concentration and microbial biomass. Existence of a solution to the stream tube system is shown, both numerical and approximate analytical approaches to the solution are given, and example computations using both methods are presented. Conditions under which the stream tube solution is "canonical," or scalable to fit any permissible stream tube travel time function, arise from requirements for invariance (over the stream tube ensemble) of effective one-dimensional stream tubes used to represent transport along real stream tubes in three-dimensional space. Averaging of the stream tube solution over travel time and reaction properties representative of physical and chemical heterogeneities is described as a way to separate and upscale the processes of macrodispersion and microbiological reaction. The approach is exercised to simulate Monte Carlo average behavior of bioreactive transport in physically heterogeneous two-dimensional media. Results show that the method captures the ensemble average large-scale effects of the nonlinear reactions more accurately than done in the classical reactive convection-dispersion equation (CDR), even when the appropriate scale dependent dispersion coefficient is afforded to the CDR.

  1. Development and characterization of a novel immobilized microbial membrane for rapid determination of biochemical oxygen demand load in industrial waste-waters.

    PubMed

    Rastogi, Shikha; Kumar, Anil; Mehra, N K; Makhijani, S D; Manoharan, A; Gangal, V; Kumar, Rita

    2003-01-01

    The rapid determination of waste-water quality of waste-water treatment plants in terms of pollutional strength, i.e. biochemical oxygen demand (BOD) is difficult or even impossible using the chemical determination method. The present study reports the determination of BOD within minutes using microbial BOD sensors, as compared to the 5-day determination using the conventional method. Multiple criteria establish the basis for the development of a BOD biosensor useful for rapid and reliable BOD estimation in industrial waste-waters. Of these, preparation of a suitable novel immobilized microbial membrane used in conjunction with an apt transducer is discussed. As a result, a microbial biosensor based on a formulated, synergistic, pre-tested microbial consortium has been developed for the measurement of BOD load of various industrial waste-waters. The sensor showed maximum response in terms of current difference, when a cell concentration of 2.25 x 10(10) CFU, harvested in their log phase of growth were utilized for microbial membrane construction. The sensor showed a stability of 180 days when the prepared membranes were stored at a temperature of 4 degrees C in 50 mM phosphate buffer of pH 6.8. The reusability of the immobilized membranes was up to 200 cycles without appreciable loss of their response characteristics. A linear relationship between the current change and a glucose-glutamic acid (GAA) concentration up to 60 mg l(-1) was observed (r=0.999). The lower detection limit was 1.0 mg l(-1) BOD. The sensor response was reproducible within +/-5% of the mean in a series of ten samples having 44 mg l(-1) BOD using standard a GGA solution. When used for the BOD estimation of industrial waste-waters, a relatively good agreement was found between the two methods, i.e. 5-day BOD and that measured by the developed microbial sensor.

  2. MediaDB: a database of microbial growth conditions in defined media.

    PubMed

    Richards, Matthew A; Cassen, Victor; Heavner, Benjamin D; Ajami, Nassim E; Herrmann, Andrea; Simeonidis, Evangelos; Price, Nathan D

    2014-01-01

    Isolating pure microbial cultures and cultivating them in the laboratory on defined media is used to more fully characterize the metabolism and physiology of organisms. However, identifying an appropriate growth medium for a novel isolate remains a challenging task. Even organisms with sequenced and annotated genomes can be difficult to grow, despite our ability to build genome-scale metabolic networks that connect genomic data with metabolic function. The scientific literature is scattered with information about defined growth media used successfully for cultivating a wide variety of organisms, but to date there exists no centralized repository to inform efforts to cultivate less characterized organisms by bridging the gap between genomic data and compound composition for growth media. Here we present MediaDB, a manually curated database of defined media that have been used for cultivating organisms with sequenced genomes, with an emphasis on organisms with metabolic network models. The database is accessible online, can be queried by keyword searches or downloaded in its entirety, and can generate exportable individual media formulation files. The data assembled in MediaDB facilitate comparative studies of organism growth media, serve as a starting point for formulating novel growth media, and contribute to formulating media for in silico investigation of metabolic networks. MediaDB is freely available for public use at https://mediadb.systemsbiology.net.

  3. Microbial competition in porous environments can select against rapid biofilm growth.

    PubMed

    Coyte, Katharine Z; Tabuteau, Hervé; Gaffney, Eamonn A; Foster, Kevin R; Durham, William M

    2017-01-10

    Microbes often live in dense communities called biofilms, where competition between strains and species is fundamental to both evolution and community function. Although biofilms are commonly found in soil-like porous environments, the study of microbial interactions has largely focused on biofilms growing on flat, planar surfaces. Here, we use microfluidic experiments, mechanistic models, and game theory to study how porous media hydrodynamics can mediate competition between bacterial genotypes. Our experiments reveal a fundamental challenge faced by microbial strains that live in porous environments: cells that rapidly form biofilms tend to block their access to fluid flow and redirect resources to competitors. To understand how these dynamics influence the evolution of bacterial growth rates, we couple a model of flow-biofilm interaction with a game theory analysis. This investigation revealed that hydrodynamic interactions between competing genotypes give rise to an evolutionarily stable growth rate that stands in stark contrast with that observed in typical laboratory experiments: cells within a biofilm can outcompete other genotypes by growing more slowly. Our work reveals that hydrodynamics can profoundly affect how bacteria compete and evolve in porous environments, the habitat where most bacteria live.

  4. Impact of growth conditions on susceptibility of five microbial species to alkaline stress.

    PubMed

    Brändle, Nathalie; Zehnder, Matthias; Weiger, Roland; Waltimo, Tuomas

    2008-05-01

    The effects of different growth conditions on the susceptibility of five taxa to alkaline stress were investigated. Enterococcus faecalis ATCC 29212, Streptococcus sobrinus OMZ 176, Candida albicans ATCC 90028, Actinomyces naeslundii ATCC 12104, and Fusobacterium nucleatum ATCC 10953 were grown as planktonic cells, allowed to adhere to dentin for 24 hours, grown as monospecies or multispecies biofilms on dentin under anaerobic conditions with a serum-enriched nutrient supply at 37 degrees C for 5 days. In addition, suspended biofilm microorganisms and 5-day old planktonic multispecies cultures were used. Microbial recovery upon direct exposure to saturated calcium hydroxide solution (pH 12.5) for 10 and 100 minutes was compared with control exposure to physiologic saline. Planktonic microorganisms were most susceptible; only E. faecalis and C. albicans survived in saturated solution for 10 minutes, the latter also for 100 minutes. Dentin adhesion was the major factor in improving the resistance of E. faecalis and A. naeslundii to calcium hydroxide, whereas the multispecies context in a biofilm was the major factor in promoting resistance of S. sobrinus to the disinfectant. In contrast, the C. albicans response to calcium hydroxide was not influenced by the growth condition. Adherence to dentin and interspecies interactions in a biofilm appear to differentially affect the sensitivity of microbial species to calcium hydroxide.

  5. Effect of antimony on the microbial growth and the activities of soil enzymes.

    PubMed

    An, Youn-Joo; Kim, Minjin

    2009-02-01

    The effects of antimony (Sb) on microbial growth inhibition and activities of soil enzymes were investigated in the present study. Test bacterial species were Escherichia coli, Bacillus subtilis and Streptococcus aureus. Among the microorganisms tested, S. aureus was the most sensitive. The 50% effects on the inhibition of specific growth rate of E. coli, B. subtilis, and, S. aureus were 555, 18.4, and 15.8 mg Sb L(-1), respectively. A silt loam soil was amended with antimony and incubated in a controlled condition. Microbial activities of dehydrogenase, acid phosphatase (P cycle), arylsulfatase (S cycle), beta-glucosidase (C cycle), urease (N cycle), and fluorescein diacetate hydrolase in soil were measured. Activities of urease and dehydrogenase were related with antimony and can be an early indication of antimony contamination. The maximum increase in soil urease activity by antimony was up to 168% after 3d compared with the control. The activities of other four enzymes (acid phosphatase, fluorescein diacetate hydrolase, arylsulfatase and ss-glucosidase) were less affected by antimony. This study suggested that antimony affects nitrogen cycle in soil by changing urease activity under the neutral pH, however, soil enzyme activities may not be a good protocol due to their complex response patterns to antimony pollution.

  6. Electrooptical Analysis of Microbial Cell Suspensions forDetermination of Antibiotic Resistance.

    PubMed

    Guliy, Olga I; Bunin, Victor D; Korzhenevich, Vyacheslav I; Volkov, Alexey A; Ignatov, Oleg V

    2016-12-01

    The effects of ampicillin; kanamycin, chloramphenicol, and tetracycline on electrophysical characteristics of cells of sensitive (ampicillin; kanamycin, chloramphenicol) and resistant (ampicillin; kanamycin, chloramphenicol, tetracycline) Escherichia coli strains were studied. Under the action of antibiotics sensitive and resistant E. coli strains acquire different electro-optical properties. Changes in suspension-orientational spectra, that are observed under the action of ampicillin; kanamycin, chloramphenicol, and tetracycline can be used in determination of antibiotic resistance of the studied bacterial strains. In our opinion, the methods of microbial suspension electro-optical analysis can be used in microbiology, mеdicinе, veterinary, and are an effective tool for solving the problems connected with determination of microbial cell antibiotic resistance.

  7. Microbial biodiversity in cheese consortia and comparative Listeria growth on surfaces of uncooked pressed cheeses.

    PubMed

    Callon, Cécile; Retureau, Emilie; Didienne, Robert; Montel, Marie-Christine

    2014-03-17

    The study set out to determine how changes in the microbial diversity of a complex antilisterial consortium from the surface of St-Nectaire cheese modify its antilisterial activities. On the basis of the microbial composition of a natural complex consortium named TR15 (Truefood consortium 15), three new consortia of different species and strain compositions were defined: TR15-SC (58 isolates from TR15 collection), TR15-M (pools of isolates from selective counting media) and TR15-BHI (pools of isolates from BHI medium). Their antilisterial activities on the surfaces of uncooked pressed cheese made with pasteurised milk were compared with the activity of complex consortium TR15 and a control cheese inoculated only with starter culture (Streptococcus thermophilus, Lactobacillus delbrueckii). The natural consortium TR15 was the most inhibitory, followed by reconstituted consortium TR15-BHI. The dynamics of the cheese rind microbial flora were monitored by counting on media and by isolate identification using 16S rDNA sequencing and direct 16S rDNA Single Strand Conformation Polymorphism analysis. The combination of these methods showed that rind with natural consortium TR15 had greater microbial diversity and different microbial dynamics than cheese rinds with reconstituted consortia. Cheese rind with the natural consortium showed higher citrate consumption and the highest concentrations of lactic and acetic acids, connected with high levels of lactic acid bacteria such as Carnobacterium maltaromaticum, Vagococcus fluvialis, Enterococcus gilvus, Leuconostoc mesenteroides, Brochothrix thermosphacta and Lactococcus lactis, ripening bacteria such as Arthrobacter nicotianae/arilaitensis, and Gram negative bacteria (Pseudomonas psychrophila and Enterobacter spp.). The highest L. monocytogenes count was on rind with TR15-M and was positively associated with the highest pH value, high succinic and citric acid contents, and the highest levels of Marinilactibacillus

  8. The influence of microbial associations on germination of wheat seeds and growth of seedlings under impact of zinc salts

    NASA Astrophysics Data System (ADS)

    Somova, L. A.; Pechurkin, N. S.

    2009-04-01

    The life support systems (LSS) for long-term missions are to use cycling-recycling systems, including biological recycling. Higher plants are the traditional regenerator of air and producer of food. They should be used in many successive generations of their reproduction in LSS. Studies of influence of microbial associations on germination of wheat seeds and on growth of seedlings under impact of heavy metals are necessary because of migration of heavy metals in LSS. Microbial associations are able to stimulate growth of plants, to protect them from pathogenic organisms and from toxicity of heavy metal salts. The goal of this work was to investigate effect of microbial associations on the germination of wheat seeds and on the growth of seedlings under impact of different concentrations of ZnSO4. The results of investigations showed that:Zinc salt had an adverse effect on germination of wheat seeds, beginning with concentrations of 8 MPC (Maximum Permissible Concentration) and higher.Microbial associations (concentrations -104 to 107 cells/ml) were able to decrease (partly or completely) the adverse effect of ZnSO4 on germination of wheat seeds.Concentrations (104-107 cells/ml) of microbial associations were able to decrease partly the adverse effect of zinc salts (intervals: from 1 to 32 MP?) on the growth and development of wheat plantlets during heterotrophic phase.The root system of plants was more sensitive to the adverse effect of ZnSO4 than shoots of plants.

  9. A theoretical study of the thermodynamics of microbial growth using Saccharomyces cerevisiae and a different free energy equation.

    PubMed

    Battley, Edwin H

    2013-06-01

    Microbial growth is a biological process that has been previously treated as a chemical reaction operating in accord with the Gibbs free energy equation, Delta G = Delta H-T Delta S. The heat of yeast growth was the first to be measured, in 1856, by direct calorimetry of a large wine vat. Until then there was a tendency for biologists to continue with the old notion that the energy change accompanying the growth of microorganisms was reflected in the amount of heat that was produced during this process. The application of chemical thermodynamics to systems involving microbial growth did not occur until much later. The full application of the Gibbs equation to microbial growth did not take place until the experimental measurement of yeast cell entropy was made in 1997 Further investigations then showed that the quantity of thermal energy for solid substances represented by TS was twice that of the quantity of thermal energy represented by Qab that is experimentally necessary to raise T of a substance from 0/K to T/K. Since there can only be one value for this, the use of the equation Delta X = Delta H-Delta Qab was investigated with respect to microbial growth, and is described in this review.

  10. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids. Part I: effects on growth performance, microbial populations, and immune status.

    PubMed

    Walsh, M C; Rostagno, M H; Gardiner, G E; Sutton, A L; Richert, B T; Radcliffe, J S

    2012-01-01

    Pigs (n = 88) weaned at 19 ± 2 d of age were used in a 14-d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on growth, immune status, Salmonella infection and shedding, and intestinal microbial populations after intranasal inoculation of Salmonella Typhimurium (10(10) cfu/pig). Pigs were challenged with Salmonella 6 d after commencement of water treatments. Treatments were 1) control diet; 2) control diet + DFM (Enterococcus faecium, Bacillus subtilis, and Bacillus licheniformis) in drinking water at 10(9) cfu/L for each strain of bacteria; 3) control diet + an organic acid-based blend (predominantly propionic, acetic, and benzoic acid) in drinking water at 2.58 mL/L; and 4) control diet + 55 mg/kg of carbadox. Serum samples were taken on d 6, 8, 10, and 14 for determination of tumor necrosis factor α (TNFα) concentrations. Fecal samples were taken on d 0, 5, 7, and 11 for determination of Salmonella shedding and enumeration of coliforms. Pigs were euthanized on d 6, 8, 10, and 14. Intestinal and cecal tissue and digesta and mesenteric lymph nodes were sampled and analyzed for Salmonella. Duodenal, jejunal, and ileal mucosal scrapings were sampled for measurement of mucosal TNFα concentrations. Water delivery of DFM prevented a decline in ADG on d 2 to 6 postchallenge compared with the negative control (P < 0.05). Coliform counts tended to be greater (P = 0.09) in the cecum of the DFM treatment group on d 2 postinfection compared with the negative control and acid treatment groups. However, Salmonella prevalence in the feces, gastrointestinal tract, or lymph nodes was not affected by water delivery of acids or DFM. Serum and mucosal TNFα concentrations were not affected by treatment throughout the study with the exception of ileal concentrations on d 4 postchallenge, which were greater in the negative control group compared with all other treatments (P < 0.05). The in-feed antibiotic was the only treatment that

  11. Determinate Root Growth and Meristem Maintenance in Angiosperms

    PubMed Central

    Shishkova, S.; Rost, T. L.; Dubrovsky, J. G.

    2008-01-01

    Background The difference between indeterminate and determinate growth in plants consists of the presence or absence of an active meristem in the fully developed organ. Determinate root growth implies that the root apical meristem (RAM) becomes exhausted. As a consequence, all cells in the root tip differentiate. This type of growth is widely found in roots of many angiosperm taxa and might have evolved as a developmental adaptation to water deficit (in desert Cactaceae), or low mineral content in the soil (proteoid roots in various taxa). Scope and Conclusions This review considers the mechanisms of determinate root growth to better understand how the RAM is maintained, how it functions, and the cellular and genetic bases of these processes. The role of the quiescent centre in RAM maintenance and exhaustion will be analysed. During root ageing, the RAM becomes smaller and its organization changes; however, it remains unknown whether every root is truly determinate in the sense that its RAM becomes exhausted before senescence. We define two types of determinate growth: constitutive where determinacy is a natural part of root development; and non-constitutive where determinacy is induced usually by an environmental factor. Determinate root growth is proposed to include two phases: the indeterminate growth phase, when the RAM continuously produces new cells; and the termination growth phase, when cell production gradually decreases and eventually ceases. Finally, new concepts regarding stem cells and a stem cell niche are discussed to help comprehend how the meristem is maintained in a broad taxonomic context. PMID:17954472

  12. Determination of microbial carbon sources and cycling during remediation of petroleum hydrocarbon impacted soil using natural abundance (14)C analysis of PLFA.

    PubMed

    Cowie, Benjamin R; Greenberg, Bruce M; Slater, Gregory F

    2010-04-01

    In a petroleum impacted land-farm soil in Sarnia, Ontario, compound-specific natural abundance radiocarbon analysis identified biodegradation by the soil microbial community as a major pathway for hydrocarbon removal in a novel remediation system. During remediation of contaminated soils by a plant growth promoting rhizobacteria enhanced phytoremediation system (PEPS), the measured Delta(14)C of phospholipid fatty acid (PLFA) biomarkers ranged from -793 per thousand to -897 per thousand, directly demonstrating microbial uptake and utilization of petroleum hydrocarbons (Delta(14)C(PHC) = -1000 per thousand). Isotopic mass balance indicated that more than 80% of microbial PLFA carbon was derived from petroleum hydrocarbons (PHC) and a maximum of 20% was obtained from metabolism of more modern carbon sources. These PLFA from the contaminated soils were the most (14)C-depleted biomarkers ever measured for an in situ environmental system, and this study demonstrated that the microbial community in this soil was subsisting primarily on petroleum hydrocarbons. In contrast, the microbial community in a nearby uncontaminated control soil maintained a more modern Delta(14)C signature than total organic carbon (Delta(14)C(PLFA) = +36 per thousand to -147 per thousand, Delta(14)C(TOC) = -148 per thousand), indicating preferential consumption of the most modern plant-derived fraction of soil organic carbon. Measurements of delta(13)C and Delta(14)C of soil CO(2) additionally demonstrated that mineralization of PHC contributed to soil CO(2) at the contaminated site. The CO(2) in the uncontaminated control soil exhibited substantially more modern Delta(14)C values, and lower soil CO(2) concentrations than the contaminated soils, suggesting increased rates of soil respiration in the contaminated soils. In combination, these results demonstrated that biodegradation in the soil microbial community was a primary pathway of petroleum hydrocarbon removal in the PEPS system. This study

  13. Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO2

    NASA Astrophysics Data System (ADS)

    Nie, Ming; Bell, Colin; Wallenstein, Matthew D.; Pendall, Elise

    2015-03-01

    Increased plant productivity and decreased microbial respiratory C loss can potentially mitigate increasing atmospheric CO2, but we currently lack effective means to achieve these goals. Soil microbes may play critical roles in mediating plant productivity and soil C/N dynamics under future climate scenarios of elevated CO2 (eCO2) through optimizing functioning of the root-soil interface. By using a labeling technique with 13C and 15N, we examined the effects of plant growth-promoting Pseudomonas fluorescens on C and N cycling in the rhizosphere of a common grass species under eCO2. These microbial inoculants were shown to increase plant productivity. Although strong competition for N between the plant and soil microbes was observed, the plant can increase its capacity to store more biomass C per unit of N under P. fluorescens addition. Unlike eCO2 effects, P. fluorescens inoculants did not change mass-specific microbial respiration and accelerate soil decomposition related to N cycling, suggesting these microbial inoculants mitigated positive feedbacks of soil microbial decomposition to eCO2. The potential to mitigate climate change by optimizing soil microbial functioning by plant growth-promoting Pseudomonas fluorescens is a prospect for ecosystem management.

  14. Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO₂.

    PubMed

    Nie, Ming; Bell, Colin; Wallenstein, Matthew D; Pendall, Elise

    2015-03-18

    Increased plant productivity and decreased microbial respiratory C loss can potentially mitigate increasing atmospheric CO₂, but we currently lack effective means to achieve these goals. Soil microbes may play critical roles in mediating plant productivity and soil C/N dynamics under future climate scenarios of elevated CO₂ (eCO₂) through optimizing functioning of the root-soil interface. By using a labeling technique with (13)C and (15)N, we examined the effects of plant growth-promoting Pseudomonas fluorescens on C and N cycling in the rhizosphere of a common grass species under eCO₂. These microbial inoculants were shown to increase plant productivity. Although strong competition for N between the plant and soil microbes was observed, the plant can increase its capacity to store more biomass C per unit of N under P. fluorescens addition. Unlike eCO₂ effects, P. fluorescens inoculants did not change mass-specific microbial respiration and accelerate soil decomposition related to N cycling, suggesting these microbial inoculants mitigated positive feedbacks of soil microbial decomposition to eCO₂. The potential to mitigate climate change by optimizing soil microbial functioning by plant growth-promoting Pseudomonas fluorescens is a prospect for ecosystem management.

  15. Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO2

    PubMed Central

    Nie, Ming; Bell, Colin; Wallenstein, Matthew D.; Pendall, Elise

    2015-01-01

    Increased plant productivity and decreased microbial respiratory C loss can potentially mitigate increasing atmospheric CO2, but we currently lack effective means to achieve these goals. Soil microbes may play critical roles in mediating plant productivity and soil C/N dynamics under future climate scenarios of elevated CO2 (eCO2) through optimizing functioning of the root-soil interface. By using a labeling technique with 13C and 15N, we examined the effects of plant growth-promoting Pseudomonas fluorescens on C and N cycling in the rhizosphere of a common grass species under eCO2. These microbial inoculants were shown to increase plant productivity. Although strong competition for N between the plant and soil microbes was observed, the plant can increase its capacity to store more biomass C per unit of N under P. fluorescens addition. Unlike eCO2 effects, P. fluorescens inoculants did not change mass-specific microbial respiration and accelerate soil decomposition related to N cycling, suggesting these microbial inoculants mitigated positive feedbacks of soil microbial decomposition to eCO2. The potential to mitigate climate change by optimizing soil microbial functioning by plant growth-promoting Pseudomonas fluorescens is a prospect for ecosystem management. PMID:25784647

  16. Growth rate determinations from radiocarbon in bamboo corals (genus Keratoisis)

    NASA Astrophysics Data System (ADS)

    Farmer, Jesse R.; Robinson, Laura F.; Hönisch, Bärbel

    2015-11-01

    Radiocarbon (14C) measurements are an important tool for determining growth rates of bamboo corals, a cosmopolitan group of calcitic deep-sea corals. Published growth rate estimates for bamboo corals are highly variable, with potential environmental or ecological drivers of this variability poorly constrained. Here we systematically investigate the application of 14C for growth rate determinations in bamboo corals using 55 14C dates on the calcite and organic fractions of six bamboo corals (identified as Keratoisis sp.) from the western North Atlantic Ocean. Calcite 14C measurements on the distal surface of these corals and five previously published bamboo corals exhibit a strong one-to-one relationship with the 14C of dissolved inorganic carbon (DI14C) in ambient seawater (r2=0.98), confirming the use of Keratoisis sp. calcite 14C as a proxy for seawater 14C activity. Radial growth rates determined from 14C age-depth regressions, 14C plateau tuning and bomb 14C reference chronologies range from 12 to 78 μm y-1, in general agreement with previously published radiometric growth rates. We document potential biases to 14C growth rate determinations resulting from water mass variability, bomb radiocarbon, secondary infilling (ontogeny), and growth rate nonlinearity. Radial growth rates for Keratoisis sp. specimens do not correlate with ambient temperature, suggesting that additional biological and/or environmental factors may influence bamboo coral growth rates.

  17. Elemental Economy: microbial strategies for optimizing growth in the face of nutrient limitation

    PubMed Central

    Merchant, Sabeeha S.; Helmann, John D.

    2014-01-01

    Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility at 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. PMID:22633059

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

    PubMed

    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.

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

    PubMed

    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.

  20. Fractional differential equations based modeling of microbial survival and growth curves: model development and experimental validation.

    PubMed

    Kaur, A; Takhar, P S; Smith, D M; Mann, J E; Brashears, M M

    2008-10-01

    A fractional differential equations (FDEs)-based theory involving 1- and 2-term equations was developed to predict the nonlinear survival and growth curves of foodborne pathogens. It is interesting to note that the solution of 1-term FDE leads to the Weibull model. Nonlinear regression (Gauss-Newton method) was performed to calculate the parameters of the 1-term and 2-term FDEs. The experimental inactivation data of Salmonella cocktail in ground turkey breast, ground turkey thigh, and pork shoulder; and cocktail of Salmonella, E. coli, and Listeria monocytogenes in ground beef exposed at isothermal cooking conditions of 50 to 66 degrees C were used for validation. To evaluate the performance of 2-term FDE in predicting the growth curves-growth of Salmonella typhimurium, Salmonella Enteritidis, and background flora in ground pork and boneless pork chops; and E. coli O157:H7 in ground beef in the temperature range of 22.2 to 4.4 degrees C were chosen. A program was written in Matlab to predict the model parameters and survival and growth curves. Two-term FDE was more successful in describing the complex shapes of microbial survival and growth curves as compared to the linear and Weibull models. Predicted curves of 2-term FDE had higher magnitudes of R(2) (0.89 to 0.99) and lower magnitudes of root mean square error (0.0182 to 0.5461) for all experimental cases in comparison to the linear and Weibull models. This model was capable of predicting the tails in survival curves, which was not possible using Weibull and linear models. The developed model can be used for other foodborne pathogens in a variety of food products to study the destruction and growth behavior.

  1. Modeling the utilization of starch by activated sludge for simultaneous substrate storage and microbial growth.

    PubMed

    Karahan, Ozlem; van Loosdrecht, Mark C M; Orhon, Derin

    2006-05-05

    This paper presents a mechanistic model incorporating microbial growth on external substrate with simultaneous formation of storage biopolymers (activated sludge model for growth and storage-ASMGS) for the utilization of starch by activated sludge. Model description and calibration utilized experimental data of an SBR fed with particulate native potato starch (NPS) and soluble starch (SolS) selected as model substrates. The fate of starch was monitored in a cycle together with glycogen and oxygen uptake rate (OUR) profiles. In the experiments, glycogen formation was significantly lower than predicted by total conversion of starch to glycogen, justifying the need to account for primary growth on starch. The proposed model basically modified Activated Sludge Model No.3 (ASM3), to include adsorption of starch, its hydrolysis and simultaneous growth and glycogen formation using the hydrolysis products, which was mainly maltose. Model simulations indicated hydrolysis of the adsorbed starch as the rate limiting process. The proposed model calibrated well the fate of all major model components, namely, starch, glycogen, and OUR. Particulate NPS and SolS were hydrolyzed with similar rates; however, primary and secondary growth processes on SolS were more efficient, with higher yields, due to the more easily utilizable products of SolS, both in terms of extracellular hydrolysis and of stored poly-glucose. Modeling with ASM3, assuming starch as either readily or slowly biodegradable, did not provide an equally acceptable fit for the glycogen and OUR curves; supporting the need to consider primary growth together with storage as defined in the proposed model.

  2. Prospecting cold deserts of north western Himalayas for microbial diversity and plant growth promoting attributes.

    PubMed

    Yadav, Ajar Nath; Sachan, Shashwati Ghosh; Verma, Priyanka; Saxena, Anil Kumar

    2015-06-01

    Microbial communities in different samples collected from cold deserts of north western Himalayas, India, were analyzed using 16S rRNA gene sequencing and phospholipid fatty acids (PLFA) analysis. A total of 232 bacterial isolates were characterized employing 16S rDNA-Amplified Ribosomal DNA Restriction Analysis with the three restriction endonucleases Alu I, Msp I and Hae III, which led to formation of 29-54 groups for the different sites, adding up to169 groups. 16S rRNA gene based phylogenetic analysis, revealed that 82 distinct species of 31 different genera, belonged to four phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. PLFA profiling was performed for concerned samples which gave an estimate of microbial communities without cultivating the microorganisms. PLFA analysis led to characterization of diverse group of microbes in different samples such as gram-negative, gram-positive bacteria, actinomycetes, cyanobacteria, anaerobic bacteria, sulphate reducing bacteria and fungi. The representative strains were screened for their plant growth promoting attributes, which included production of ammonia, HCN, gibberellic acid, IAA and siderophore; solubilization of phosphorus and activity of ACC deaminase. In vitro antifungal activity assay was performed against Rhizoctonia solani and Macrophomina phaseolina. Cold adapted microorganisms may serve as inoculants for crops growing under cold climatic conditions. To our knowledge, this is the first report for the presence of Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus tylopili and Pseudomonas cedrina in cold deserts and exhibit multifunctional PGP attributes at low temperatures.

  3. Determination of the feasibility of using open path FTIR to monitor levels of 3-methylfuran and 1-octen-3-ol for the purpose of detecting microbial contamination in indoor environments

    SciTech Connect

    Olive, Brent

    1996-03-01

    Studies have shown that the presence of microbial growth correlates with health complaints associated with sick building syndrome. Microbial growth may be found in damp places within a building, and may be dispersed to other areas if present in the HVAC system. Certain individuals may be especially sensitive to the presence of these microorganisms, and may experience adverse reactions at extremely low concentrations. Unfortunately, the source of the problem may not be discovered because many times the microbial growth is not visible. However, there are some volatile organic compounds that are given off by certain microorganisms which may be used to determine the presence of microbial contamination. 3-Methylfuran is an excellent indicator of growing fungi. It is produced by a majority of fungi, and can be used as an indicator of ongoing growth. 1-Octen-3-ol is also produced by a number of fungi, and has been used in the past as an indicator of such. These two compounds and many other volatiles given off by microorganisms have been termed microbial volatile organic compounds (MVOCs). Many of these compounds are commonly found in indoor air, and thus, may be present even when there is not microbial contamination.

  4. Microbial-enzymatic-hybrid biological fuel cell with optimized growth conditions for Shewanella oneidensis DSP-10.

    PubMed

    Roy, Jared N; Luckarift, Heather R; Sizemore, Susan R; Farrington, Karen E; Lau, Carolin; Johnson, Glenn R; Atanassov, Plamen

    2013-07-10

    In this work we present a biological fuel cell fabricated by combining a Shewanella oneidensis microbial anode and a laccase-modified air-breathing cathode. This concept is devised as an extension to traditional biochemical methods by incorporating diverse biological catalysts with the aim of powering small devices. In preparing the biological fuel cell anode, novel hierarchical-structured architectures and biofilm configurations were investigated. A method for creating an artificial biofilm based on encapsulating microorganisms in a porous, thin film of silica was compared with S. oneidensis biofilms that were allowed to colonize naturally. Results indicate comparable current and power densities for artificial and natural biofilm formations, based on growth characteristics. As a result, this work describes methods for creating controllable and reproducible bio-anodes and demonstrates the versatility of hybrid biological fuel cells.

  5. Well constructions with inhibited microbial growth and methods of antimicrobial treatment in wells

    DOEpatents

    Lee, Brady D.; Dooley, Kirk J.

    2004-11-02

    The invention includes methods of inhibiting microbial growth in a well. A packing material containing a mixture of a first material and an antimicrobial agent is provided to at least partially fill a well bore. One or more access tubes are provided in an annular space around a casing within the well bore. The access tubes have a first terminal opening located at or above a ground surface and have a length that extends from the first terminal opening at least part of the depth of the well bore. The access tubes have a second terminal opening located within the well bore. An antimicrobial material is supplied into the well bore through the first terminal opening of the access tubes. The invention also includes well constructs.

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

    PubMed

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

    2014-05-15

    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 (Fe1+xS). 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 (Fe3S4) when the free sulfide concentration was 29.3mM. Furthermore, sufficient free Fe(2+) led to the additional formation of vivianite [Fe3(PO4)2·8(H2O)]. 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.

  7. Artificial Selection for Determinate Growth Habit in Soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, while Glycine soja, the wild progenitor of soybean, is indeterminate. Indeterminate (Dt1) and determina...

  8. Temperature dependence of metabolic rates for microbial growth, maintenance, and survival

    PubMed Central

    Price, P. Buford; Sowers, Todd

    2004-01-01

    Our work was motivated by discoveries of prokaryotic communities that survive with little nutrient in ice and permafrost, with implications for past or present microbial life in Martian permafrost and Europan ice. We compared the temperature dependence of metabolic rates of microbial communities in permafrost, ice, snow, clouds, oceans, lakes, marine and freshwater sediments, and subsurface aquifer sediments. Metabolic rates per cell fall into three groupings: (i) a rate, μg(T), for growth, measured in the laboratory at in situ temperatures with minimal disturbance of the medium; (ii) a rate, μm(T), sufficient for maintenance of functions but for a nutrient level too low for growth; and (iii) a rate, μs(T), for survival of communities imprisoned in deep glacial ice, subsurface sediment, or ocean sediment, in which they can repair macromolecular damage but are probably largely dormant. The three groups have metabolic rates consistent with a single activation energy of ≈110 kJ and that scale as μg(T):μm(T):μs(T) ≈ 106:103:1. There is no evidence of a minimum temperature for metabolism. The rate at -40°C in ice corresponds to ≈10 turnovers of cellular carbon per billion years. Microbes in ice and permafrost have metabolic rates similar to those in water, soil, and sediment at the same temperature. This finding supports the view that, far below the freezing point, liquid water inside ice and permafrost is available for metabolism. The rate μs(T) for repairing molecular damage by means of DNA-repair enzymes and protein-repair enzymes such as methyltransferase is found to be comparable to the rate of spontaneous molecular damage. PMID:15070769

  9. Determination of Listeria monocytogenes Growth during Mushroom Production and Distribution

    PubMed Central

    Leong, Dara; Alvarez-Ordóñez, Avelino; Guillas, Floriane; Jordan, Kieran

    2013-01-01

    In the EU, food is considered safe with regard to Listeria monocytogenes if its numbers do not exceed 100 CFU/g throughout the shelf-life of the food. Therefore, it is important to determine if a food supports growth of L. monocytogenes. Challenge studies to determine the ability of a food to support growth of L. monocytogenes are essential as predictive modelling often overestimates the growth ability of L. monocytogenes. The aim of this study was to determine if growth of L. monocytogenes was supported during the production and distribution of mushrooms. A three-strain mixture of L. monocytogenes was inoculated onto three independent batches of whole mushrooms, sliced mushrooms, mushroom casing and mushroom substrate at a concentration of about 100–1000 CFU/g. The batches were incubated at potential abuse temperatures, as a worst case scenario, and at intervals during storage L. monocytogenes numbers, % moisture and pH were determined. The results showed that the sliced and whole mushrooms had the ability to support growth, while mushroom casing allowed survival but did not support growth. Mushroom substrate showed a rich background microflora that grew on Listeria selective media and this hindered enumeration of L. monocytogenes. In the case of this study, Combase predictions were not always accurate, indicating that challenge studies may be a necessary part of growth determination of L. monocytogenes. PMID:28239137

  10. Microbial growth in dry grain food (Sunsik) beverages prepared with water, milk, soymilk, or honey-water.

    PubMed

    Jung, Jin-Ho; Lee, Sun-Young

    2010-05-01

    This study was conducted to investigate the growth of microorganisms, including pathogenic bacteria such as Cronobacter sakazakii and Bacillus cereus, in Sunsik beverages made of water, milk, soymilk, or honey-water during storage at room temperature. Prepared Sunsik beverages were stored at room temperature and the growth of total aerobic counts, Escherichia coli/coliforms, and yeast and mold were measured. Also, samples inoculated with a cocktail of C. sakazakii or B. cereus spores were stored at room temperature and their growths were determined during storage. Populations of total aerobic counts and coliforms significantly increased with increasing storage time at room temperature, which resulted in higher than 8 log and 7 log after 24 h in all samples except for the honey-water sample, respectively. Levels of total aerobic counts and coliforms were significantly lower in the honey-water sample than in the other samples after 6 and 9 h of storage, respectively. Initial populations of C. sakazakii and B. cereus ranged from 0 to 1 log CFU/mL, respectively, and these populations significantly increased with increasing storage time at room temperature. Therefore, populations of C. sakazakii and B. cereus were approximately 7 to 8 log CFU/mL after 24 h of storage. However, after 12 and 9 h of storage, there were significant differences in levels of C. sakazakii and B. cereus between the honey-water sample and the other samples, respectively. Based on these results, the addition of honey can inhibit microbial growth in Sunsik beverages; however, the best way to avoid pathogen infection would be to consume Sunsik beverages as soon as possible after preparation.

  11. Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture.

    PubMed

    Grunert, Oliver; Reheul, Dirk; Van Labeke, Marie-Christine; Perneel, Maaike; Hernandez-Sanabria, Emma; Vlaeminck, Siegfried E; Boon, Nico

    2016-05-01

    Vegetables and fruits are an important part of a healthy food diet, however, the eco-sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N-fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.

  12. Reduced growth of Listeria monocytogenes in two model cheese microcosms is not associated with individual microbial strains.

    PubMed

    Imran, Muhammad; Bré, Jean-Michel; Guéguen, Marielle; Vernoux, Jean-Paul; Desmasures, Nathalie

    2013-02-01

    Two model antilisterial microbial communities consisting of two yeasts, two Gram positive and two Gram negative bacteria, and originating from Livarot cheese smear were previously designed. They were used in the present study to analyse the impact of microbial population dynamics on growth of Listeria monocytogenes in cheese microcosm. Specific culture media and PCR primers were developed for simultaneous culture-dependent and real-time PCR quantification of strains belonging to Marinomonas sp., Paenibacillus sp., Staphylococcus equorum, Arthrobacter arilaitensis, Pseudomonas putida, Serratia liquefaciens, Candida natalensis, and Geotrichum candidum, in cheese microcosms. All strains were enumerated after 3, 5, 8 and 14 days at 15 °C. They established well at high counts in all cheese microcosms. Growth dynamics for all strains in presence of L. monocytogenes WSLC 1685 were compared to those of microbial communities obtained by omitting in turn one of the six members of the initial community. The growth of the microbial strains was neither markedly disturbed by Listeria presence nor by the removal of each strain in turn. Furthermore, these communities had a significant reducing effect on growth of L. monocytogenes independently of pH, as confirmed by mathematical modelling. A barrier effect was observed, that could be explained by specific competition for nutrients.

  13. Biogeochemistry of Stinking Springs, Utah. Part II: Microbial Diversity and Photo- and Chemo-Autotrophic Growth Rates in a Layered Microbial Mat

    NASA Astrophysics Data System (ADS)

    Monteverde, D.; Metzger, J. G.; Bournod, C.; Kelly, H.; Johnson, H.; Sessions, A. L.; Osburn, M.; Shapiro, R. S.; Rideout, J.; Johnston, D. T.; Stevenson, B.; Stamps, B. W.; Vuono, D.; Hanselmann, K.; Spear, J. R.

    2013-12-01

    Layered microbial mats have garnered attention for their high phylogenetic diversity and exploitation of geochemical gradients often on the mm scale. However, despite their novelty and implications for early life diversification, little is known about layered microbial mat growth rates or the interdependence of the microbial communities within the system. Stinking Springs, a warm, sulfidic, saline spring northeast of the Great Salt Lake, serves as our test-site to investigate some of these questions. Stinking Springs undergoes downstream changes in pH (6.59-8.14), sulfide (527μM - below detection), sulfate (13-600μM), TCO2 (7.77-3.71mM), and temperature (40-21°C) along its ~150m flow path. The first 10m of discharge is channelized, beyond that, the spring supports a 10 to 40mm-thick layered microbial mat covering ~40% of the total spring runoff area. The mat was divided into four texturally-distinct layers which were each analyzed for 16S rRNA, lipid abundance, and bicarbonate and acetate uptake rates in addition to standard microscopy analyses. 16S rRNA analyses confirmed high taxa diversity within each layer, which varied significantly in taxa makeup such that no single phylum dominated the abundance (>33%) in more than one mat layer. The taxonomic diversity tended to increase with mat depth, a similar finding to other studies on layered microbial mats. A mat sampling transect across 16 meters showed that layer taxonomic diversity was conserved horizontally for all four mat layers, which implies mat depth has a larger control on diversity than physical or chemical parameters. Microscopy indicated the presence of diatoms in all layers which was confirmed by lipid abundance of sterols and long-branch fatty acid methyl esters. Incubation experiments were conducted in light and dark conditions over 24 hours with separate 13C-tagged bicarbonate and acetate additions. Heterotrophic growth rates (acetate uptake; 0.03-0.65%/day) were higher than autotrophic growth

  14. An evaluation of microbial growth and corrosion of 316L SS in glycol/seawater mixtures.

    PubMed

    Lee, Jason S; Ray, Richard I; Lowe, Kristine L; Jones-Meehan, Joanne; Little, Brenda J

    2003-04-01

    Glycol/seawater mixtures containing > 50% glycol inhibit corrosion of 316L stainless steel and do not support bacterial growth. The results indicate bacteria are able to use low concentrations of glycol (10%) as a growth medium, but bacterial growth decreased with increasing glycol concentration. Pitting potential, determined by anodic polarization, was used to evaluate susceptibility of 316L SS to corrosion in seawater-contaminated glycol. Mixture containing a minimum concentration of 50% propylene glycol-based coolant inhibited pitting corrosion. A slightly higher minimum concentration (55%) was needed for corrosion protection in ethylene glycol mixtures.

  15. An evaluation of microbial growth and corrosion of 316L SS in glycol/seawater mixtures

    NASA Technical Reports Server (NTRS)

    Lee, Jason S.; Ray, Richard I.; Lowe, Kristine L.; Jones-Meehan, Joanne; Little, Brenda J.

    2003-01-01

    Glycol/seawater mixtures containing > 50% glycol inhibit corrosion of 316L stainless steel and do not support bacterial growth. The results indicate bacteria are able to use low concentrations of glycol (10%) as a growth medium, but bacterial growth decreased with increasing glycol concentration. Pitting potential, determined by anodic polarization, was used to evaluate susceptibility of 316L SS to corrosion in seawater-contaminated glycol. Mixture containing a minimum concentration of 50% propylene glycol-based coolant inhibited pitting corrosion. A slightly higher minimum concentration (55%) was needed for corrosion protection in ethylene glycol mixtures.

  16. Feedbacks between flow, sediment motion and microbial growth on sand bars initiate and shape elongated stromatolite mounds

    NASA Astrophysics Data System (ADS)

    Mariotti, G.; Perron, J. T.; Bosak, T.

    2014-07-01

    Elongated stromatolites are often used as indicators of current direction and shoreline orientation, especially in paleoenvironmental reconstructions. However, mechanisms that create shore-parallel, m-scale elongated stromatolite mounds in carbonate sand are not well understood. We propose that this geometry is initiated by microbial growth on the parts of sand bars that experience low wave-induced bed shear stresses. We test this idea by growing microbial mats on carbonate sand bars in a laboratory wave tank. Cyanobacterial mats grow on the bar runnels, where sediment motion is negligible, but are absent from the bar ridges, where the waves generate migrating ripples. When microbially-promoted lithification reinforces and preserves this initial pattern, elongated stromatolites should initiate in the runnels of sand bars, with long wavelengths (5-100 m) and small width-to-wavelength ratios (∼0.3). These dimensions are consistent with modern shore-parallel stromatolites in Hamelin Pool, Western Australia, and with patterns of microbial colonization in other sandy sediments. This model of elongated stromatolite mounds can inform paleoenvironmental reconstructions by clarifying and quantifying feedbacks among waves, sediment transport and microbial growth.

  17. Microbial colonization and growth on metal sulfides and other mineral surfaces

    NASA Technical Reports Server (NTRS)

    Caldwell, D.; Sundquist, A. R.; Lawrence, J.; Doyle, A. P.

    1985-01-01

    To determine whether a bacterial film forms on sulfur minerals in situ, various sulfur containing and other minerals were incubated in Penitencia Creek. The rate of cell growth and attachment within the surface microenvironment of mineral surfaces was also determined. To determine whether surfaces enriched with soluble sulfur substrates (cysteine, glutathione, thioglycolate, sulfite, and thiosulfate) increased the rate of growth or attachment of natural communities, membrane enrichments were incubated. These rates were determined as described by Caldwell et al. (1981, 1983). The growth of Pseudomonas fluorescens, a heterotrophic sulfur oxidizer, was studied in batch cell suspensions and in continuous culture. In batch culture the cells were oxygen limited (growth rate 0.33 per hour under oxygen limitations and 0.52 per hour when vigorously aerated). Growth within the film was glucose limited. Several behavioral phenomena were observed for cells growing within the hydrodynamic boundary layer. Despite a flow of 10 cm per second in the environment, the bacteria were able to move freely in both directions within the hydrodynamic boundary layer.

  18. Ruminal fermentation, microbial growth and amino acid flow in single-flow continuous culture fermenters fed a diet containing olive leaves.

    PubMed

    Molina-Alcaide, E; Martín-García, A I; Moumen, A; Carro, M D

    2010-04-01

    Six single-flow continuous culture fermenters were used to determine fermentation profile, microbial growth and amino acid (AA) flow promoted by olive leaves supplemented with barley grains and faba beans (OLSUP), and alfalfa hay (AH). Two incubation runs were carried out with three fermenters inoculated with ruminal fluid from wethers and three from goats. The inoculum source did not affect (p = 0.059 to 0.980) any of the parameters. Daily volatile fatty acid (VFA) production and carbohydrate digestibility were greater (p = 0.009 and 0.024, respectively) for AH, therefore the pH values were lower (p = 0.015) than for OLSUP. Acetate was greater (p < 0.001) and isobutyrate, isovalerate and caproate lower (p < 0.001 to 0.006) for AH with greater acetate/propionate (p = 0.014) and 'VFA/digested carbohydrate' (p = 0.026) ratios. Daily microbial N flow and efficiency were greater (p = 0.016 and p = 0.041) for diet AH. Individual AA flows were greater (p < 0.001 to 0.016) for AH, but microbial essential AA proportion was greater for OLSUP (p = 0.015). The results indicate that OLSUP promoted lower bacterial growth and AA flow than AH, which could have been partially due to a limitation of N availability to ruminal microbes.

  19. Real-time optical monitoring of microbial growth using optimal combination of light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Kobayashi, Ken-ichi; Yamada, Takeshi; Hiraishi, Akira; Nakauchi, Shigeki

    2012-12-01

    We developed a real-time optical monitoring system consisting of a monochrome complementary metal-oxide semiconductor (CMOS) camera and two light-emitting diodes (LEDs) with a constant temperature incubator for the rapid detection of microbial growth on solid media. As a target organism, we used Alicyclobacillus acidocaldarius, which is an acidophilic thermophilic endospore-forming bacterium able to survive in pasteurization processes and grow in acidic drink products such as apple juice. This bacterium was cultured on agar medium with a redox dye applied to improve detection sensitivity. On the basis of spectroscopic properties of the colony, medium, and LEDs, an optimal combination of two LED illuminations was selected to maximize the contrast between the colony and medium areas. We measured A. acidocaldarius and Escherichia coli at two different dilution levels using these two LEDs. From the results of time-course changes in the number of detected pixels in the detection images, a similar growth rate was estimated amongst the same species of microbes, regardless of the dilution level. This system has the ability to detect a colony of approximately 26 μm in diameter in a detection image, and it can be interpreted that the size corresponds to less than 20 μm diameter in visual inspection.

  20. Syntrophic growth on formate: a new microbial niche in anoxic environments.

    PubMed

    Dolfing, Jan; Jiang, Bo; Henstra, Anne M; Stams, Alfons J M; Plugge, Caroline M

    2008-10-01

    Anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. The interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. Contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. Since formate is a direct substrate for methanogens, a niche for microorganisms that grow by the conversion of formate to hydrogen plus bicarbonate--or vice versa--may seem unlikely. Here we report experimental evidence for growth on formate by syntrophic communities of (i) Moorella sp. strain AMP in coculture with a thermophilic hydrogen-consuming Methanothermobacter species and of (ii) Desulfovibrio sp. strain G11 in coculture with a mesophilic hydrogen consumer, Methanobrevibacter arboriphilus AZ. In pure culture, neither Moorella sp. strain AMP, nor Desulfovibrio sp. strain G11, nor the methanogens grow on formate alone. These results imply the existence of a previously unrecognized microbial niche in anoxic environments.

  1. Influence of packaging conditions on natural microbial population growth of endive.

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

    The influence of three packaging conditions, i.e., unmodified atmosphere packaging (UAP), passive modified atmosphere packaging (MAP), and active MAP, on the natural microbial population growth of endive was investigated at 20 degrees C. For UAP, endive was placed in macroperforated oriented polypropylene pouches that maintained gas composition close to that of air (21 kPa O2 and 0 kPa CO2) but also limited superficial product dehydration. For MAP, endive was placed in low-density polyethylene pouches that induced a 3 kPa O2 and 5 kPa CO2 equilibrium atmosphere composition. Steady state was reached after 25 h of storage with an oxygen absorbing packet (active MAP) compared with 100 h without the packet (passive MAP) and was maintained for 200 h. After 312 h of storage, both active and passive MAP reduced total aerobic mesophile, yeast, and mold population growth compared with endive in UAP. Active MAP accelerated and improved the inhibition of Pseudomonas spp. and Enterobacteriaceae, respectively, probably because of the rapid O2 depletion during the transition period. A shift in the Enterobacteriaceae subpopulation from Rhanella aquatilis to Enterobacter agglomerans was observed for both passive and active MAP.

  2. Carbon tetrachloride degradation: Effect of microbial growth substrate and vitamin B{sub 12} content

    SciTech Connect

    Zou, S.; Stensel, H.D.; Ferguson, J.F.

    2000-05-01

    Microbial degradation kinetics of carbon tetrachloride (CT) under reducing conditions were investigated for different cultures, fed with 1,2-propanediol, dextrose, propionalde-hyde, or acetate and nitrate, in the anaerobic step of an anaerobic/aerobic operation sequence. Methanogenesis was inhibited due to the aerobic step. CT biodegradation rates followed first-order kinetics with respect to CT concentration and biomass and were not affected by the presence of growth substrate. CT degradation rates increased linearly with higher intracellular vitamin B{sub 12} content. The culture fed 1,2-propanediol had the highest vitamin B{sub 12} content, which was 3.8, 4.7, and 16 times that of the propionaldehyde-,dextrose-, and acetate-fed cultures, respectively, and its first-order degradation rate constant was 2.8, 4.5, 6.0 times that for those cultures, respectively. No CT degradation occurred with culture liquid, suggesting that intracellular factors were responsible for CT degradation. The propanediol culture was able to sustain a constant CT degradation rate for a 16-day test period without substrate addition. Compared to a propanediol-fed culture grown only under anaerobic conditions, the propanediol culture grown under the sequential anaerobic/aerobic condition resulted in more biomass growth and a greater CT degradation rate per unit of propanediol fed, although its CT degradation rate per unit of biomass was lower.

  3. Stabilising metal(loid)s in soil with iron and aluminium-based products: microbial, biochemical and plant growth impact.

    PubMed

    Garau, Giovanni; Silvetti, Margherita; Castaldi, Paola; Mele, Elena; Deiana, Pietrino; Deiana, Salvatore

    2014-06-15

    Four iron and aluminium-based products, including red mud (RM), hematite (Fe2O3), an iron-rich water treatment residual (Fe-WTR) and amorphous Al hydroxide (Al-OH), were evaluated for their effectiveness at stabilising As and heavy metals (i.e. Cd, Cu, Pb, Zn) in a circumneutral contaminated soil [As (2105 mg kg(-1)), Cd (18 mg kg(-1)), Cu (264 mg kg(-1)), Pb (710 mg kg(-1)), Zn (522 mg kg(-1))]. Treatment impacts on soil microbial and biochemical features (i.e. microbial biomass-C, microbial counts, 16S rRNA PCR-TTGE of culturable bacteria, dehydrogenase, urease and β-glucosidase activity, Biolog derived parameters-AWCD and richness) as well as bean (Phaseolus vulgaris) and wheat (Triticum vulgare) growth were also assessed. After 6 months equilibration, all the amendments (application rate 3% w/w) but RM reduced labile As while only Al-OH reduced the concentration of water-soluble heavy metals. Despite the highest bioavailability of contaminants, most of the soil microbial and biochemical features monitored (i.e. microbial biomass-C, total bacterial counts, dehydrogenase activity and AWCD) were significantly higher in the RM-soil. Bean germination was completely inhibited in RM-soil while wheat growth was similar to that of the control. The Al-OH treatment was best overall, promoting microbial abundance, diversity and activity while increasing bean and wheat growth and reducing As accumulated in plant shoots. Results suggest that Al-OH is a suitable candidate for field evaluations while the use of RM in the remediation of circumneutral or subalkaline contaminated soils should be reconsidered.

  4. Ileal MUC2 gene expression and microbial population, but not growth performance and immune response, are influenced by in ovo injection of probiotics in broiler chickens.

    PubMed

    Majidi-Mosleh, A; Sadeghi, A A; Mousavi, S N; Chamani, M; Zarei, A

    2017-02-01

    1. The objective of present study was to evaluate the effects of intra-amniotic injection of different probiotic strains (Bacillus subtilis, Enterococcus faecium and Pediococcus acidilactici) on the intestinal MUC2 gene expression, microbial population, growth performance and immune response in broiler chicken. 2. In a completely randomised design, different probiotic strains were injected into the amniotic fluid of the 480 live embryos (d 18 of incubation), with 4 treatments and 5 replicates. Ileal MUC2 gene expression, microbial profile, growth performance and immune response were determined. 3. Injection of probiotic strains, especially B. subtilis, had significant effect on expression of the MUC2 on d 21 of incubation and d 3 post-hatch, but not on d 19 of incubation. 4. Injection of the probiotic strains decreased significantly the Escherichia coli population and increased the lactic acid bacteria population during the first week post-hatch. 5. Inoculation of probiotics had no significant effect on antibody titres against Newcastle disease virus, antibody titres against sheep red blood cell and cell-mediated immune response of chickens compared to control. 6. In ovo injection of the probiotic strains had no significant effect on growth performance of broiler chickens. 7. It was concluded that injection of probiotic bacteria especially B. subtilis into the amniotic fluid has a beneficial effect on ileal MUC2 gene expression and bacteria population during the first week post-hatch, but has no effect on growth performance and immune response in broiler chickens.

  5. [Influence of Mirabilis jalapa Linn. Growth on the Microbial Community and Petroleum Hydrocarbon Degradation in Petroleum Contaminated Saline-alkali Soil].

    PubMed

    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

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

    PubMed

    Józefiak, Damian; Kierończyk, Bartosz; Juśkiewicz, Jerzy; Zduńczyk, Zenon; Rawski, Mateusz; Długosz, Jakub; Sip, Anna; Højberg, Ole

    2013-01-01

    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 supplement

  7. Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar

    PubMed Central

    Jaiswal, Amit K.; Elad, Yigal; Paudel, Indira; Graber, Ellen R.; Cytryn, Eddie; Frenkel, Omer

    2017-01-01

    Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar. PMID:28287177

  8. Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar.

    PubMed

    Jaiswal, Amit K; Elad, Yigal; Paudel, Indira; Graber, Ellen R; Cytryn, Eddie; Frenkel, Omer

    2017-03-13

    Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar.

  9. [Determination of Azospirillum Brasilense Cells With Bacteriophages via Electrooptical Analysis of Microbial Suspensions].

    PubMed

    Gulii, O I; Karavayeva, O A; Pavlii, S A; Sokolov, O I; Bunin, V D; Ignatov, O V

    2015-01-01

    The dependence-of changes in the electrooptical properties of Azospirillum brasilense cell suspension Sp7 during interaction with bacteriophage ΦAb-Sp7 on the number and time of interactions was studied. Incubation of cells with bacteriophage significantly changed the electrooptical signal within one minute. The selective effect of bacteriophage ΦAb on 18 strains of bacteria of the genus Azospirillum was studied: A. amazonense Ami4, A. brasilense Sp7, Cd, Sp107, Sp245, Jm6B2, Brl4, KR77, S17, S27, SR55, SR75, A. halopraeferans Au4, A. irakense KBC1, K A3, A. lipoferum Sp59b, SR65 and RG20a. We determined the limit of reliable determination of microbial cells infected with bacteriophage: - 10(4) cells/mL. The presence of foreign cell cultures of E. coli B-878 and E. coli XL-1 did not complicate the detection of A brasilense Sp7 cells with the use of bacteriophage ΦAb-Sp7. The results demonstrated that bacteriophage (ΦAb-Sp7 can be used for the detection of Azospirillum microbial cells via t electrooptical analysis of cell suspensions.

  10. Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

    PubMed

    Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

    2017-02-01

    Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory.

  11. Influence of microbial growth in the redox potential of fermented cucumbers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commonly, pH measurements are used during the production of fermented cucumbers to indirectly monitor growth of lactic acid bacteria (LAB) and acid production. Redox potential (Eh) measurements, which are determined by the flux of electrons in a system, could serve as a more accurate tool to monitor...

  12. Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

    NASA Astrophysics Data System (ADS)

    Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2015-04-01

    Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS < ATS = rhizospheric soils < NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg

  13. An integrated model for predictive microbiology and simultaneous determination of lag phase duration and exponential growth rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new mechanistic growth model was developed to describe microbial growth under isothermal conditions. The development of the mathematical model was based on the fundamental phenomenon of microbial growth, which is normally a three-stage process that includes lag, exponential, and stationary phases...

  14. Population growth rate and its determinants: an overview.

    PubMed Central

    Sibly, Richard M; Hone, Jim

    2002-01-01

    We argue that population growth rate is the key unifying variable linking the various facets of population ecology. The importance of population growth rate lies partly in its central role in forecasting future population trends; indeed if the form of density dependence were constant and known, then the future population dynamics could to some degree be predicted. We argue that population growth rate is also central to our understanding of environmental stress: environmental stressors should be defined as factors which when first applied to a population reduce population growth rate. The joint action of such stressors determines an organism's ecological niche, which should be defined as the set of environmental conditions where population growth rate is greater than zero (where population growth rate = r = log(e)(N(t+1)/N(t))). While environmental stressors have negative effects on population growth rate, the same is true of population density, the case of negative linear effects corresponding to the well-known logistic equation. Following Sinclair, we recognize population regulation as occurring when population growth rate is negatively density dependent. Surprisingly, given its fundamental importance in population ecology, only 25 studies were discovered in the literature in which population growth rate has been plotted against population density. In 12 of these the effects of density were linear; in all but two of the remainder the relationship was concave viewed from above. Alternative approaches to establishing the determinants of population growth rate are reviewed, paying special attention to the demographic and mechanistic approaches. The effects of population density on population growth rate may act through their effects on food availability and associated effects on somatic growth, fecundity and survival, according to a 'numerical response', the evidence for which is briefly reviewed. Alternatively, there may be effects on population growth rate of

  15. DETERMINATION OF MICROBIAL COMMUNITY STRUCTURE IN UNTREATED WASTEWATER FROM DIFFERENT GEOGRAPHIC LOCALES

    EPA Science Inventory

    Microbial sewage communities consist of a combination of human faecal microorganisms and urban infrastructure-derived microbes originating from infiltration of rainwater and stormwater inputs. Together these different sources of microbial diversity form a unique population struc...

  16. Effect of dietary alginic acid on juvenile tilapia (Oreochromis niloticus) intestinal microbial balance, intestinal histology and growth performance.

    PubMed

    Merrifield, Daniel L; Harper, Glenn M; Mustafa, Sanaa; Carnevali, Oliana; Picchietti, Simona; Davies, Simon J

    2011-04-01

    The aim of the present study was to assess the effect of a commercial alginic acid source (Ergosan) on tilapia Oreochromis niloticus intestinal microbial balance, intestinal morphology, and growth parameters. Fish were fed a basal control diet or the basal diet plus a source of alginic acid (5 g kg(-1) Ergosan; Schering-Plough Aquaculture, UK) for 9 weeks. At the end of the trial, light and electron microscopy demonstrated that the morphology of the intestinal tract at the gross and ultra-structural level was not affected by dietary alginic acid inclusion. Both groups of fish displayed healthy, normal morphology with no signs of disease, cell or tissue damage. Intestinal epithelial leucocyte infiltration was not affected by dietary alginic acid. Molecular bacterial profiles derived from PCR-DGGE illustrated highly similar microbial communities (both within the lumen and associated with the intestinal mucosa) in the respective treatment groups. Microbial ecological parameters (e.g. species diversity and richness) also remained unaffected. Although not significant, trends towards elevated survival and body protein content were observed in the alginic acid-fed fish. These results are suggestive that alginic acid does not adversely impact the indigenous gastrointestinal microbial balance and subsequently does not impact upon the epithelial brush border integrity. Validation of non-detrimental impacts of immunostimulatory products on gastric microbiota and epithelial integrity should be pursued in future studies as maintaining microbial balance and epithelial integrity is essential for proper gut functionality.

  17. Supplementation of direct-fed microbials as an alternative to antibiotic on growth performance, immune response, cecal microbial population, and ileal morphology of broiler chickens.

    PubMed

    Salim, H M; Kang, H K; Akter, N; Kim, D W; Kim, J H; Kim, M J; Na, J C; Jong, H B; Choi, H C; Suh, O S; Kim, W K

    2013-08-01

    An experiment was conducted to investigate the supplementation of direct-fed microbials (DFM) as an alternative to antibiotics on growth performance, immune response, cecal microbial population, and ileal morphology of broiler chickens. A total of 800 one-day-old male broiler chicks (Ross × Ross) were randomly allotted to 4 dietary treatments with 4 replicate pens per treatment (50 birds/replicate pen). The 4 dietary treatments fed for 35 d were a corn-soybean meal basal diet (control); control plus 0.1% virginiamycin, as an antibiotic growth promoter (AGP); control plus 0.1% direct-fed microbials that contained Lactobacillus reuteri (DFM 1); and control plus 0.1% direct-fed microbials that contained a mixture of L. reuteri, Bacillus subtilis, and Saccharomyces cerevisiae (DFM 2). Results showed that dietary AGP and DFM supplementation significantly increased (P < 0.05) the BW gain of broilers during 0 to 21 d. The feed intake was reduced, whereas the feed conversion was improved significantly when birds were fed DFM 2 at 0 to 7 d of age. The white blood cell and monocyte levels were significantly higher in the DFM 2 group compared with the control. In addition, feeding DFM significantly (P < 0.05) increased the plasma immunoglobulin levels where a higher level was observed in DFM 2 compared with those of the other treatments. Neither DFM nor AGP treatments affected the cecal Lactobacillus and Salmonella content; however, cecal Escherichia coli content significantly decreased in broiler chickens fed DFM and AGP. The ileal villus height, and width and total thickness of muscularis externa were significantly increased when birds were fed DFM compared with AGP and control. These results indicate that the dietary supplementation of DFM increases the growth performance of birds at an early age, stimulates the immune response, decreases the number of E. coli, and improves the ileal morphology of broiler chickens. Thus, DFM that contained a mixture of several beneficial

  18. Temperature and humidity measurements within desert barchan sand dunes, relation to dune aeolian mobility and microbial growth

    NASA Astrophysics Data System (ADS)

    Louge, Michel; Hay, Anthony; Richer, Renee; Valance, Alexandre; Ould el Moctar, Ahmed; Xu, Jin; Abdul-Majid, Sara

    2013-04-01

    We present diurnal variations of temperature and humidity profiles below the surface of hyper-arid aeolian crescent-shaped "barchan" dunes in Qatar and Mauritania, measured using a thermal probe and a new ultra-sensitive capacitance instrument that we developed for this purpose. We also report long-term measurements from a probe sunk on the downwind avalanche face of a mobile Qatar barchan, recording temperature and humidity until it emerged on the upwind slope 15 months later. We interpret the data by modeling heat and moisture transfer at the surface in terms of measured net surface radiation, wind, and atmospheric conditions. We demonstrate the presence of microbes on sand grains within these mobile dunes using microscopic observations, fluorescence counts, metagenomic sequencing, and C12/C13 isotope analysis of carbon dioxide sampled below the surface. By determining how water activity grows with moisture adsorbed on these sands, we delimit regions within the dune where our instruments recorded humidity conducive to microbial growth. Finally, we compare the mobility of two adjacent Mauritania barchans having distinct surface grain size, shape, and depth humidity profiles. Armored by large grains on its surface, the smaller dune was more oblong. As a result, it lacked flow recirculation in its wake, trapped less aeolian sand downwind, and was much less mobile than its smaller size would suggest. This slower mobility led to greater humidity and cohesion at depth than the larger dune exposed to the same atmospheric and wind conditions.

  19. Deep-water microbialites of the Mesoproterozoic Dismal Lakes Group: microbial growth, lithification, and implications for coniform stromatolites.

    PubMed

    Bartley, J K; Kah, L C; Frank, T D; Lyons, T W

    2015-01-01

    Offshore facies of the Mesoproterozoic Sulky Formation, Dismal Lakes Group, arctic Canada, preserve microbialites with unusual morphology. These microbialites grew in water depths greater than several tens of meters and correlate with high-relief conical stromatolites of the more proximal September Lake reef complex. The gross morphology of these microbial facies consists of ridge-like vertical supports draped by concave-upward, subhorizontal elements, resulting in tent-shaped cuspate microbialites with substantial primary void space. Morphological and petrographic analyses suggest a model wherein penecontemporaneous upward growth of ridge elements and development of subhorizontal draping elements initially resulted in a buoyantly supported, unlithified microbial form. Lithification began via precipitation within organic elements during microbialite growth. Mineralization either stabilized or facilitated collapse of initially neutrally buoyant microbialite forms. Microbial structures and breccias were then further stabilized by precipitation of marine herringbone cement. During late-stage diagenesis, remaining void space was occluded by ferroan dolomite cement. Cuspate microbialites are most similar to those found in offshore facies of Neoarchean carbonate platforms and to unlithified, buoyantly supported microbial mats in modern ice-covered Antarctic lakes. We suggest that such unusual microbialite morphologies are a product of the interaction between motile and non-motile communities under nutrient-limiting conditions, followed by early lithification, which served to preserve the resultant microbial form. The presence of marine herringbone cement, commonly associated with high dissolved inorganic carbon (DIC), low O2 conditions, also suggests growth in association with reducing environments at or near the seafloor or in conjunction with a geochemical interface. Predominance of coniform stromatolite forms in the Proterozoic--across a variety of depositional

  20. An Overview on Novel Microbial Determination Methods in Pharmaceutical and Food Quality Control

    PubMed Central

    Nemati, Mahboob; Hamidi, Aliasghar; Maleki Dizaj, Solmaz; Javaherzadeh, Vahid; Lotfipour, Farzaneh

    2016-01-01

    Traditional microbiological methods tend to be labor-intensive and time-consuming. Rapid and novel methods in microbiological tests provide more sensitive, precise and reproducible results compared with conventional methods. In microbiology, the most rapid testing methods belong to the field of biotechnology such as PCR, ELISA, ATP bioluminescence and etc. Nevertheless impedance microbiology, biosensors and analytical procedures to determine microbial constituents are of significance. The present review article was conducted using internet databases and related scientific literatures and articles that provide information on developments in the rapid methods in microbiology. The main focus is on the application of rapid methods in microbial quality control of pharmaceutical products. Reviewed literature showed that rapid methods and automation in microbiology is an advanced area for studying and applying of improved methods in the early detection, and characterization of microorganisms and their products in food, pharmaceutical and cosmetic industrials as well as environmental monitoring and clinical applications. It can be concluded that rapid methods and automation in microbiology should continue as potent and efficient technologies to develop the novel tests to be performed in the future because of the ever-increasing concerns about the safety of food and pharmaceutical products. However the main issues to be considered are the scale up of developed methods and the regulatory requirements. PMID:27766214

  1. A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities.

    PubMed

    Bell, Tisza A S; Prithiviraj, Bharath; Wahlen, Brad D; Fields, Matthew W; Peyton, Brent M

    2015-01-01

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal "crop." In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (∼9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. The characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass productivity in an open

  2. A lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities

    DOE PAGES

    Bell, Tisza A.S.; Prithiviraj, Bharath; Wahlen, Brad D.; ...

    2016-01-07

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal “crop.” In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (~9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgarismore » and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. As a result, the characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass

  3. Association between fertilizer-mediated changes in microbial communities and Aedes albopictus growth and survival.

    PubMed

    Muturi, Ephantus J; Ramirez, Jose L; Rooney, Alejandro P; Dunlap, Chris

    2016-12-01

    Contamination of aquatic habitats with anthropogenic nutrients has been associated with an increase in mosquito larval populations but the underlying mechanisms remain poorly understood. We examined the individual and combined effects of two synthetic fertilizers (ammonium sulfate and potassium chloride) on Aedes albopictus survival, development time, and sex ratio. The bacterial and fungal communities of water samples from different fertilizer treatments were also characterized by MiSeq sequencing of the 16S rRNA gene (bacteria) and internal transcribed spacer 1 (fungi) and their relationship with mosquito survival and development determined. Mosquitoes from ammonium sulfate treatment had significantly lower survival rates and longer development times compared to those from control, potassium chloride or a mixture of the two fertilizers. Fertilizer treatment had no significant effects on Ae. albopictus sex ratio although ammonium sulfate treatment tended to be more biased towards males relative to the other treatments. There were no significant effects of fertilizer treatment on fungal communities. However, potassium chloride treatments had lower bacterial diversity compared to the other treatments and the bacterial community structure of control and potassium chloride treatments differed significantly from that of ammonium sulfate and a mixture of the two fertilizers. Microbial composition but not diversity was significantly associated with mosquito survival and development. These findings suggest that anthropogenic nutrients can have a profound impact on mosquito survival and development. In addition to any potential direct effects on mosquito physiology, our results suggest that fertilizers can act indirectly by disrupting the microbial communities that provide a critical food resource for mosquito larvae.

  4. A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities

    PubMed Central

    Bell, Tisza A. S.; Prithiviraj, Bharath; Wahlen, Brad D.; Fields, Matthew W.; Peyton, Brent M.

    2016-01-01

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal “crop.” In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (∼9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. The characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass productivity in an

  5. Bioprospecting for microbial products that affect ice crystal formation and growth.

    PubMed

    Christner, Brent C

    2010-01-01

    At low temperatures, some organisms produce proteins that affect ice nucleation, ice crystal structure, and/or the process of recrystallization. Based on their ice-interacting properties, these proteins provide an advantage to species that commonly experience the phase change from water to ice or rarely experience temperatures above the melting point. Substances that bind, inhibit or enhance, and control the size, shape, and growth of ice crystals could offer new possibilities for a number of agricultural, biomedical, and industrial applications. Since their discovery more than 40 years ago, ice nucleating and structuring proteins have been used in cryopreservation, frozen food preparation, transgenic crops, and even weather modification. Ice-interacting proteins have demonstrated commercial value in industrial applications; however, the full biotechnological potential of these products has yet to be fully realized. The Earth's cold biosphere contains an almost endless diversity of microorganisms to bioprospect for microbial compounds with novel ice-interacting properties. Microorganisms are the most appropriate biochemical factories to cost effectively produce ice nucleating and structuring proteins on large commercial scales.

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed

    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.

  9. Microbial colonization of a closed growth chamber during hydroponic cultivation of lettuce.

    PubMed

    Koenig, D W; Bruce, R J; Molina, T C; Barta, D J; Pierson, D L

    1997-01-01

    The goal of this study was to characterize sessile and planktonic microbiota that developed during two successive hydroponic cultures of lettuce in a closed chamber system. Coupons of polyvinyl chloride (PVC) placed in the nutrient solution lines were removed periodically, as were samples of the nutrient solutions and condensate from the air-handling system. The bacteria and fungi present on the coupons and in fluid samples were enumerated by direct plate counts. Disinfecting the hydroponic system with 0.1% hypochlorite and 0.1 N nitric acid reduced the bacterial densities in biofilm samples from 1 x 10(7) CFU/10 cm2 to 1 x 10(1) CFU/10 cm2 and eliminated culturable fungi; Staphylococcus sp., Pseudomonas sp., and Micrococcus sp. survived this procedure. Bacterial and fungal concentrations in all samples returned to predisinfection levels after 2 days of plant growth. Pseudomonas and Acremonium predominated both before and after disinfection. Fungal concentrations never exceeded 7 x 10(2) CFU/10 cm2. The coupon microbiota differed from that of the rhizoplane at harvest. Overall, the greatest numbers of species were found on the rhizoplane samples collected during the second crop. The microbial community changed little during individual crops or between successive crops. Diversity indices remained relatively constant for all samples.

  10. Study to determine the aquatic biological effects on the Solid Rocket Booster (SRB). [technique for monitoring marine microbial fouling

    NASA Technical Reports Server (NTRS)

    Colwell, R. R.; Zachary, A.

    1979-01-01

    The surface of the reusable solid rocket boosters (SRB), which are jettisoned from the Shuttle Orbiter to parachute in the sea, are studied for colonization by marine life. Techniques for monitoring the marine microbial fouling of SRB materials are presented. An assessment of the nature and degree of the biofouling expected on the SRB materials in the recovery zone is reported. A determination of the degree and the effects of seasonal variation occurring on microbial fouling in the retrieval zone waters is made. The susceptibility of the SRB parachute recovery system to microbial fouling and biodeterioration is investigated. The development of scanning electron microscopy and epifluorescence microscopic observation techniques for rapid assessment of microbial fouling is discussed.

  11. Determination of relative growth rates of natural quartz crystals

    PubMed

    Ihinger; Zink

    2000-04-20

    Although the theory describing crystal growth in the geological environment is well established, there are few quantitative studies that delimit the absolute time involved in the growth of natural crystals. The actual mechanisms responsible for the variation in size and shape of individual crystal faces are, in fact, not well understood. Here we describe a micro-infrared spectroscopic study of a single, gem-quality quartz crystal that allows us to measure the size, shape and relative growth rate of each of the crystal faces that are active throughout its growth history. We demonstrate that the abundances of hydrogen-bearing impurities can serve as 'speedometers' to monitor the growth rate of advancing crystal faces. Our technique can be applied to crystals from a variety of geological environments to determine their growth histories. Within the electronics industry, the technique might facilitate the production of defect-free synthetic crystals required for high-quality resonators and, ultimately, might allow determination of the absolute time involved in geological processes such as the crystallization of magmas, fluid flow in metamorphism and the sealing of open cracks in earthquake rupture zones.

  12. Effect of pretreatments on microbial growth and sensory properties of dry-salted olives.

    PubMed

    Değirmencioğlu, Nurcan; Gürbüz, Ozan; Değirmencioğlu, Ali; Yildiz, Semanur

    2014-09-01

    The effect of various washing solutions (acetic acid, lactic acid, and chlorine dioxide) and NaCl concentrations (2.5, 5.0, and 10.0%) on the stability of dry-salted olives (cultivars Gemlik and Edincik) during storage was studied. Vacuum-packed olives were stored at 4°C for 7 months and monitored for microbiological changes that occurred in the dry-salted olives during the dry-salting process and for their stability during storage. Microbial populations were enumerated using pour plating (for aerobic plate counts) and spread plating (for counts of lactic acid bacteria and yeasts and molds). Aerobic plate counts were <2.5 log CFU/g for olive samples washed in chlorine dioxide at all NaCl concentrations. At 4°C, the population of yeasts and molds increased steadily during the shelf life in Gemlik olive samples washed with all of the solutions, except chlorine dioxide, whereas yeast and mold counts in Edincik olives decreased depending on the increase in salt concentration. Therefore, different combinations of organic acids, NaCl, and vacuum packaging can be successfully used to control the growth of yeasts and molds in these olives. The combination of vacuum sealing (with a 10-ppm chlorine dioxide wash) and storage at 4°C was the most effective approach for controlling the growth of lactic acid bacteria and yeasts and molds. Members of the sensory panel considered saltiness to be appropriate at 2.5 and 5.0% NaCl. Softness and bitterness scores increased with reduced NaCl concentrations, but rancidity and hardness scores increased as NaCl concentration increased.

  13. Predictive microbiology models vs. modeling microbial growth within Listeria monocytogenes risk assessment: what parameters matter and why.

    PubMed

    Pouillot, Régis; Lubran, Meryl B

    2011-06-01

    Predictive microbiology models are essential tools to model bacterial growth in quantitative microbial risk assessments. Various predictive microbiology models and sets of parameters are available: it is of interest to understand the consequences of the choice of the growth model on the risk assessment outputs. Thus, an exercise was conducted to explore the impact of the use of several published models to predict Listeria monocytogenes growth during food storage in a product that permits growth. Results underline a gap between the most studied factors in predictive microbiology modeling (lag, growth rate) and the most influential parameters on the estimated risk of listeriosis in this scenario (maximum population density, bacterial competition). The mathematical properties of an exponential dose-response model for Listeria accounts for the fact that the mean number of bacteria per serving and, as a consequence, the highest achievable concentrations in the product under study, has a strong influence on the estimated expected number of listeriosis cases in this context.

  14. Microbial enrichment of a novel growing substrate and its effect on plant growth.

    PubMed

    Trifonova, R; Postma, J; Schilder, M T; van Elsas, J D

    2009-10-01

    The quality of torrefied grass fibers (TGF) as a new potting soil ingredient was tested in a greenhouse experiment. TGF was colonized with previously selected microorganisms. Four colonization treatments were compared: (1) no inoculants, (2) the fungus Coniochaeta ligniaria F/TGF15 alone, (3) the fungus followed by inoculation with two selected bacteria, and (4) the fungus with seven selected bacteria. Cultivation-based and DNA-based methods, i.e., PCR-DGGE and BOX-PCR, were applied to assess the bacterial and fungal communities established in the TGF. Although colonization was not performed under sterile conditions, all inoculated strains were recovered from TGF up to 26 days incubation. Stable fungal and bacterial populations of 10(8) and 10(9) CFU/g TGF, respectively, were reached. As a side effect of the torrefaction process that aimed at the chemical stabilization of grass fibers, potentially phytotoxic compounds were generated. These phytotoxic compounds were cold-extracted from the fibers and analyzed by gas chromatography mass spectrometry. Four of 15 target compounds that had previously been found in the extract of TGF were encountered, namely phenol, 2-methoxyphenol, benzopyran-2-one, and tetrahydro-5,6,7,7a-benzofuranone. The concentration of these compounds decreased significantly during incubation. The colonized TGF was mixed with peat (P) in a range of 100%:0%, 50%:50%, 20%:80%, and 0%:100% TGF/P (w/w), respectively, to assess suitability for plant growth. Germination of tomato seeds was assessed three times, i.e., with inoculated TGF that had been incubated for 12, 21, and 26 days. In these tests, 90-100% of the seeds germinated in 50%:50% and 20%:80% TGF/P, whereas on average only 50% of the seeds germinated in pure TGF. Germination was not improved by the microbial inoculants. However, plant fresh weight as well as leaf area of 28-day-old tomato plants were significantly increased in all treatments where C. ligniaria F/TGF15 was inoculated compared

  15. [Mitigating the repress of cinnamic acid to cucumber growth by microbial strain].

    PubMed

    Yu, Guo-hui; Xie, Yin-hua; Chen, Yan-hong; Chen, Yuan-feng; Cheng, Ping

    2006-12-01

    Cucumber is one of the most important vegetable species. Its continuous planting has become a common practice demand in many areas of China, but an obstacle from continuous planting made sustainable production of this crop to be prohibited. The self-toxic effect was considered as an important negative factor to continuous cropping cucumber. And cinnamic acid was found to be the main substance to cause self-toxic. Strain Ha8, which isolated from waste water estuary in Zhuhai city and has been authenticated as Cellulosimicrobium cellulans, was found to be able to degrade cinnamic acid, benzoic acid, paraaminobenzoic acid and phenol. Its biologic degrading rate to cinnamic acid was 64.1% and its total degrading rate to cinnamic acid was 79.32% . Therefore, strain Ha8 was used to mitigate the growth stress of cucumber caused by cinnamic acid in the research. In the experiment by hydroponic culturing method, it was found that the stem length, root length, stem weight, leaf weight, root weight, numbers of flower and harvest weight of cucumbers were lower than those untreated ones when added 2micromol/L or 10micromol/L cinnamic acid in culturing solution. But when added 10(7)cfu/L of strain Ha8 and 2micromol/L or 10micromol/L cinnamic acid in same culturing solution, these parameters were higher than those treated only by 2mircomol/L or 10micromol/L cinnamic acid. The result shown that strain Ha8 could mitigate the self-toxic effect caused by cinnamic acid. In edaphic culturing experiments, it was found that organic fertilizer mixed with strain Ha8 could mitigate the growth stress of cucumber caused by 100mg/kg cinnamic acid. When added 3mg/kg sterilized organic fertilizer with strain Ha8 (> or = 10(6)cfu/g dry organic fertilizer) in the culturing soil, the result was satisfied. This treatment could not only improve the growth of cucumber, enhance their root dehydrogenase activity and output, promote their nutrition absorption rate, but also adjust the microbial groups in

  16. Effect of zinc on growth performance, gut morphometry, and cecal microbial community in broilers challenged with Salmonella enterica serovar typhimurium.

    PubMed

    Shao, Yuxin; Lei, Zhao; Yuan, Jianmin; Yang, Ying; Guo, Yuming; Zhang, Bingkun

    2014-12-01

    To evaluate the effects of supplemental zinc on growth performance, gut morphometry, and the cecal microbial community in broilers challenged with Salmonella typhimurium, 180, 1-day-old male Cobb 500 broiler chicks were randomly assigned to 3 treatments with ten replicates for a 42 day experiment. The 3 treatments were: unchallenged, S. typhimurium-challenged, and S. typhimurium-challenged with 120 mg/kg of zinc supplementation in the diet. Salmonella infection caused a reduction in body-weight gain and feed intake, disrupted the intestinal structure by decreasing the villus-height/crypt-depth ratio of the ileum and increasing the apoptotic index of ileal epithelial cells. Moreover, the cecal microbial community was altered by Salmonella infection, as demonstrated by a reduced number of Lactobacillus and total bacteria. Dietary zinc supplementation improved growth performance by increasing the body-weight gain and feed intake in the challenged broilers. In addition, zinc repaired intestinal injury by reducing the apoptotic index of ileal epithelial cells, enhancing villus height and the villus-height/crypt-depth ratio of the ileum, and the proliferation index of ileal epithelial cells. Finally, zinc regulated the cecal microbial community by increasing the number of total bacteria and beneficial Lactobacillus bacteria, and reducing the number of Salmonella. The results indicated that dietary zinc supplementation improved growth performance, intestinal morphology, and intestinal microbiota in S. typhimurium-challenged broilers.

  17. Organic and inorganic fertilizer effect on soil CO2 flux, microbial biomass, and growth of Nigella sativa L.

    NASA Astrophysics Data System (ADS)

    Salehi, Aliyeh; Fallah, Seyfollah; Sourki, Ali Abasi

    2017-01-01

    Cattle manure has a high carbon/nitrogen ratio and may not decompose; therefore, full-dose application of urea fertilizer might improve biological properties by increasing manure decomposition. This study aimed to investigate the effect of combining cattle manure and urea fertilizer on soil CO2 flux, microbial biomass carbon, and dry matter accumulation during Nigella sativa L. (black cumin) growth under field conditions. The treatments were control, cattle manure, urea, different levels of split and full-dose integrated fertilizer. The results showed that integrated application of cattle manure and chemical fertilizer significantly increased microbial biomass carbon by 10%, soil organic carbon by 2.45%, total N by 3.27%, mineral N at the flowering stage by 7.57%, and CO2 flux by 9% over solitary urea application. Integrated application increased microbial biomass carbon by 10% over the solitary application and the full-dose application by 5% over the split application. The soil properties and growth parameters of N. sativa L. benefited more from the full-dose application than the split application of urea. Cattle manure combined with chemical fertilizer and the full-dose application of urea increased fertilizer efficiency and improved biological soil parameters and plant growth. This method decreased the cost of top dressing urea fertilizer and proved beneficial for the environment and medicinal plant health.

  18. The effect of salt reduction on sensory quality and microbial growth in hotdog sausages, bacon, ham and salami.

    PubMed

    Aaslyng, Margit Dall; Vestergaard, Christian; Koch, Anette Granly

    2014-01-01

    Sodium chloride (NaCl) is a multi-functional ingredient used to inhibit microbial growth and to ensure good texture and taste in processed meat. This study showed how moderately (22-25%) and greatly (43-50%) reduction of NaCl affected yield, sensory quality and microbial growth in hotdog sausages, bacon, cooked cured ham and salami. In greatly reduced products, the yield was reduced by 8% in sausages and 6% in ham, whereas the yield in bacon and salami remained unaffected. The microbial growth was generally not affected by reducing the content of NaCl to 2.0% in sausages, 2.3% in bacon, 1.7% in ham and 6.3% in salami (aqueous phase). Salt taste, juiciness and texture were the sensory parameters most affected by the NaCl reduction. In sausages and ham, reduction from 2.2% to 1.7% and from 2.3% to 1.3% (w/w), respectively, did not alter the sensory properties. In contrast, the sensory properties of bacon and salami were significantly affected already after a moderately reduction.

  19. Interaction of growth-determining systems with gravity

    NASA Astrophysics Data System (ADS)

    Merkys, A.; Laurinavičius, R.; Bendoraityté, D.; Švegždiené, D.; Rupainiené, O.

    The experiments have been carried out with lettuce shoots on board the Salyut-7 orbital station, the Kosmos-1667 biological satellite and under ground conditions at 180° plant inversion. By means of the centrifuge Biogravistat-1M the threshold value of gravitational sensitivity of lettuce shoots has been determined on board the Salyut-7 station. It was found to be equal to 2.9 × 10-3g for hypocotyls and 1.5 × 10-4g for roots. The following results have been received in the experiment performed on board the Kosmos-1667 satellite: a) under microgravity the proliferation of the meristem cells and the growth of roots did not differ from the control; b) the growth of hypocotyls in length was significantly enhanced in microgravity; c) under microgravity transverse growth of hypocotyls (increase in cross sectional area) was significantly increased due to enhancement of cortical parenchyma cell growth. At 180° inversion in Earth's gravity root extension growth and rate of cell division in the root apical meristem were decreased. The determination of DNA-fuchsin value in the nuclei of the cell root apexes showed that inversion affected processess of the cell cycle preceeding cytokinesis.

  20. Mapping and determinism of soil microbial community distribution across an agricultural landscape

    PubMed Central

    Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

    2015-01-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

  1. Intrauterine growth restriction: effects of physiological fetal growth determinants on diagnosis.

    PubMed

    Haram, Kjell; Søfteland, Eirik; Bukowski, Radek

    2013-01-01

    The growth of the fetus, which is strongly associated with the outcome of pregnancy, reflects interplay of several physiological and pathological factors. The assessment of fetal growth is based on comparison of birthweight (BW) or estimated fetal weight (EFW) to standards which define reference ranges at a spectrum of gestational ages. Most birthweight standards do not take into account effects of physiological determinants of fetal growth. Additionally, gestational age in many standards is based on the menstrual history and is often inaccurate. Fetal growth norms should be based on an early ultrasound estimate of gestational age. Customized standards, which have included only ultrasound-dated pregnancies, seem to be superior to population-based birthweight norms in predicting perinatal mortality and morbidity. Adjustment for individual variation in customized growth curves reduces false-positive diagnosis of IUGR and may lead to a very significant reduction in intervention for suspected IUGR. Customized growth potential identifies better the risk for adverse outcome than the currently used national standards, but customized charts may fail in detecting growth-restricted stillbirth. An individual's birthweight is the sum of physiological and pathological influences operating during pregnancy. Growth potential norms are a better discriminator of aberrations of fetal growth than population, ultrasound, and customized norms.

  2. Intrauterine Growth Restriction: Effects of Physiological Fetal Growth Determinants on Diagnosis

    PubMed Central

    Haram, Kjell

    2013-01-01

    The growth of the fetus, which is strongly associated with the outcome of pregnancy, reflects interplay of several physiological and pathological factors. The assessment of fetal growth is based on comparison of birthweight (BW) or estimated fetal weight (EFW) to standards which define reference ranges at a spectrum of gestational ages. Most birthweight standards do not take into account effects of physiological determinants of fetal growth. Additionally, gestational age in many standards is based on the menstrual history and is often inaccurate. Fetal growth norms should be based on an early ultrasound estimate of gestational age. Customized standards, which have included only ultrasound-dated pregnancies, seem to be superior to population-based birthweight norms in predicting perinatal mortality and morbidity. Adjustment for individual variation in customized growth curves reduces false-positive diagnosis of IUGR and may lead to a very significant reduction in intervention for suspected IUGR. Customized growth potential identifies better the risk for adverse outcome than the currently used national standards, but customized charts may fail in detecting growth-restricted stillbirth. An individual's birthweight is the sum of physiological and pathological influences operating during pregnancy. Growth potential norms are a better discriminator of aberrations of fetal growth than population, ultrasound, and customized norms. PMID:23864862

  3. Chrysen-2-ol derivative from West Indian Wood Nettle Laportea aestuans (L.) Chew inhibits oxidation and microbial growth in vitro

    PubMed Central

    Oloyede, Ganiyat K.; Oyelola, Martha S.

    2013-01-01

    Bio-active compounds present in West Indian Wood Nettle Laportea aestuans (L.) Chew (Urticaceae), used in ethno medicine as antioxidant and antimicrobial were studied. The aim of this research work was to isolate and characterize the bio-active compounds in the n-hexane fraction of L. aestuans, determine the toxicity and subject it to in-vitro antimicrobial and free radical scavenging activities. The chemical constituents were isolated by gradient elution column chromatographic technique and Ultra Violet/visible (UV), Infrared (IR) and Nuclear Magnetic Resonance (NMR) spectroscopies were used for structural elucidation. The free radical scavenging activity of the isolate was assessed using three methods; scavenging effect on 2,2-diphenyl-1-picrylhydrazyl radical (DPPH), hydroxyl radical generated from hydrogen peroxide and ferric thiocynate method. Antimicrobial screening was done by agar well diffusion method while toxicity was determined by Brine shrimp lethality test. Structures were proposed for the white crystalline solids isolated; (4E)-3,6-dimethylhep-4-en-3-ol (AB) and 1,2,3,4,4a,4b,5,6,6a,7,8,9,10,10a,10b,11-hexadecahydro-1,1,6a,10b-tetramethyl-7-((E)-4,7-dimethyloct-5-enyl) chrysen-2-ol (AC). Percentage yield of AC was 91.2 and was non-toxic with LC50 (µg/ml) value of 1581233000.0. AC significantly scavenged free radical at 0.0625 mg/ml in the DPPH (64.73 %) and hydrogen peroxide (99.22 %) tests. It also showed 65.23 % inhibition at 1.0 mg/ml in the ferric thiocyanate test. AC also inhibited microbial growth significantly when compared with gentamicin and tioconazole which are antibacterial and antifungal standards respectively. The presence of Chrysen-2-ol derivative in L. aestuans which was non-toxic and possessed significant antimicrobial and antioxidant activities supports its ethno medicinal application. PMID:27092035

  4. Chrysen-2-ol derivative from West Indian Wood Nettle Laportea aestuans (L.) Chew inhibits oxidation and microbial growth in vitro.

    PubMed

    Oloyede, Ganiyat K; Oyelola, Martha S

    2013-01-01

    Bio-active compounds present in West Indian Wood Nettle Laportea aestuans (L.) Chew (Urticaceae), used in ethno medicine as antioxidant and antimicrobial were studied. The aim of this research work was to isolate and characterize the bio-active compounds in the n-hexane fraction of L. aestuans, determine the toxicity and subject it to in-vitro antimicrobial and free radical scavenging activities. The chemical constituents were isolated by gradient elution column chromatographic technique and Ultra Violet/visible (UV), Infrared (IR) and Nuclear Magnetic Resonance (NMR) spectroscopies were used for structural elucidation. The free radical scavenging activity of the isolate was assessed using three methods; scavenging effect on 2,2-diphenyl-1-picrylhydrazyl radical (DPPH), hydroxyl radical generated from hydrogen peroxide and ferric thiocynate method. Antimicrobial screening was done by agar well diffusion method while toxicity was determined by Brine shrimp lethality test. Structures were proposed for the white crystalline solids isolated; (4E)-3,6-dimethylhep-4-en-3-ol (AB) and 1,2,3,4,4a,4b,5,6,6a,7,8,9,10,10a,10b,11-hexadecahydro-1,1,6a,10b-tetramethyl-7-((E)-4,7-dimethyloct-5-enyl) chrysen-2-ol (AC). Percentage yield of AC was 91.2 and was non-toxic with LC50 (µg/ml) value of 1581233000.0. AC significantly scavenged free radical at 0.0625 mg/ml in the DPPH (64.73 %) and hydrogen peroxide (99.22 %) tests. It also showed 65.23 % inhibition at 1.0 mg/ml in the ferric thiocyanate test. AC also inhibited microbial growth significantly when compared with gentamicin and tioconazole which are antibacterial and antifungal standards respectively. The presence of Chrysen-2-ol derivative in L. aestuans which was non-toxic and possessed significant antimicrobial and antioxidant activities supports its ethno medicinal application.

  5. How do Gradients in Mineralogy and Nutrient Availability Alter Links between Microbial Growth Efficiency and Soil Carbon Storage?

    NASA Astrophysics Data System (ADS)

    Cusack, D. F.; Reed, S.; Wieder, W. R.; Taylor, P.; Cleveland, C. C.; Chadwick, O.; Vitousek, P.

    2013-12-01

    Our understanding of the terrestrial carbon (C) balance depends on understanding how C is (1) partitioned by heterotrophic microbes to biomass vs. respiration (i.e. growth efficiency), and (2) stabilized and stored in soils. Microbial growth efficiency may also strongly influence soil C stabilization if microbial biomass is a dominant source of C to organo-mineral associations. We hypothesized that natural variation in nutrient availability, as well as addition of scarce nutrients, may alter growth efficiency such that soil C storage on mineral surfaces increases without increasing C losses via heterotrophic respiration. We predicted that nutrient poor sites with relatively high reactive mineral availability (i.e. not C-saturated) have the largest potential to store new microbial biomass C. To test our hypothesis we used a microbial radionuclide-labeling technique combined with long- and short-term nutrient additions to follow C through soils that vary in mineral composition and background nutrient availability. We collected mineral soils (0-10 cm depth) from 8 Hawaiian sites that provided maximum variation in nutrient availability, reactive mineral content, and background soil C. Soils were sieved, pooled by site, and homogenized prior to a laboratory addition of radio (14C)-labeled sucrose, including nitrogen (N) and/or phosphorus (P) additions in full factorial design. We followed the 14C into microbial biomass growth, into soil mineral fractions, and into 14C-respiration (CO2) over 24 hours. We say effects of laboratory fertilization and ecosystem conditions on microbial growth efficiency and C losses via CO2. Across the 8 diverse soils, the full addition of 14C-sucrose+NP increased cumulative loss of 14C-CO2 relative to addition of 14C-sucrose alone (p<0.05), with the effect becoming more pronounced over the course of the experiment. Addition of 14C-sucrose with one additional nutrient (N or P) did not increase 14C-CO2 across the 8 soils relative to 14C

  6. Probiotics: determinants of survival and growth in the gut.

    PubMed

    Bezkorovainy, A

    2001-02-01

    Bifidobacteria and lactobacilli are purportedly beneficial to human health and are called probiotics. Their survival during passage through the human gut, when administered in fermented milk products, has been investigated intensely in recent years. Well-controlled, small-scale studies on diarrhea in both adults and infants have shown that probiotics are beneficial and that they survive in sufficient numbers to affect gut microbial metabolism. Survival rates have been estimated at 20-40% for selected strains, the main obstacles to survival being gastric acidity and the action of bile salts. Although it is believed that the maximum probiotic effect can be achieved if the organisms adhere to intestinal mucosal cells, there is no evidence that exogenously administered probiotics do adhere to the mucosal cells. Instead, they seem to pass into the feces without having adhered or multiplied. Thus, to obtain a continuous exogenous probiotic effect, the probiotic culture must be ingested continually. Certain exogenously administered substances enhance the action of both exogenous and endogenous probiotics. Human milk contains many substances that stimulate the growth of bifidobacteria in vitro and also in the small intestine of infants; however, it is unlikely that they function in the colon. However, lactulose and certain fructose-containing compounds, called prebiotics, are not digested in the small intestine but pass into the cecum unchanged, where they are selectively utilized by probiotics. Beneficial effects may thus accrue from exogenously administered probiotics, often administered with prebiotics, or by endogenous bifidobacteria and lactobacilli, whose metabolic activity and growth may also be enhanced by the administration of prebiotics.

  7. Impact of initial biofilm growth on the anode impedance of microbial fuel cells.

    PubMed

    Ramasamy, Ramaraja P; Ren, Zhiyong; Mench, Matthew M; Regan, John M

    2008-09-01

    Electrochemical impedance spectroscopy (EIS) was used to study the behavior of a microbial fuel cell (MFC) during initial biofilm growth in an acetate-fed, two-chamber MFC system with ferricyanide in the cathode. EIS experiments were performed both on the full cell (between cathode and anode) as well as on individual electrodes. The Nyquist plots of the EIS data were fitted with an equivalent electrical circuit to estimate the contributions of various intrinsic resistances to the overall internal MFC impedance. During initial development of the anode biofilm, the anode polarization resistance was found to decrease by over 70% at open circuit and by over 45% at 27 microA/cm(2), and a simultaneous increase in power density by about 120% was observed. The exchange current density for the bio-electrochemical reaction on the anode was estimated to be in the range of 40-60 nA/cm(2) for an immature biofilm after 5 days of closed circuit operation, which increased to around 182 nA/cm(2) after more than 3 weeks of operation and stable performance in an identical parallel system. The polarization resistance of the anode was 30-40 times higher than that of the ferricyanide cathode for the conditions tested, even with an established biofilm. For a two-chamber MFC system with a Nafion 117 membrane and an inter-electrode spacing of 15 cm, the membrane and electrolyte solution dominate the ohmic resistance and contribute to over 95% of the MFC internal impedance. Detailed EIS analyses provide new insights into the dominant kinetic resistance of the anode bio-electrochemical reaction and its influence on the overall power output of the MFC system, even in the high internal resistance system used in this study. These results suggest that new strategies to address this kinetic constraint of the anode bio-electrochemical reactions are needed to complement the reduction of ohmic resistance in modern designs.

  8. A lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities

    SciTech Connect

    Bell, Tisza A.S.; Prithiviraj, Bharath; Wahlen, Brad D.; Fields, Matthew W.; Peyton, Brent M.

    2016-01-07

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal “crop.” In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (~9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. As a result, the characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to

  9. Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli

    PubMed Central

    2014-01-01

    Background Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement quality. A key challenge has been how to enhance measurement quality without sacrificing throughput. Results We developed a new high-throughput measurement system, termed Colony-live. Here we show that Colony-live provides accurate measurement of three growth values (lag time of growth (LTG), maximum growth rate (MGR), and saturation point growth (SPG)) by visualizing colony growth over time. By using a new normalization method for colony growth, Colony-live gives more precise and accurate growth values than the conventional method. We demonstrated the utility of Colony-live by measuring growth values for the entire Keio collection of Escherichia coli single-gene knockout mutants. By using Colony-live, we were able to identify subtle growth defects of single-gene knockout mutants that were undetectable by the conventional method quantified by fixed time-point camera imaging. Further, Colony-live can reveal genes that influence the length of the lag-phase and the saturation point of growth. Conclusions Measurement quality is critical to achieving the resolution required to identify unique phenotypes among a diverse range of phenotypes. Sharing high-quality genome-wide datasets should benefit many researchers who are interested in specific gene functions or the architecture of cellular systems. Our Colony-live system provides a new powerful tool to accelerate accumulation of knowledge of microbial growth phenotypes. PMID:24964927

  10. Microbial growth fluctuating in response to solar-terrestrial activity variations.

    PubMed

    Voychuk, S I; Gromozova, E N

    2012-01-01

    Populations of microorganisms display fluctuations in the variable physiological and biochemical properties during cultivation under constant laboratory conditions. A series of explanations were proposed for this phenomenon, and different factors were studied as possible regulators. It was found that such fluctuations possess cosmic rhythms, but no factor(s) were proposed that could sufficiently explain and predict the magnitude of changes that happened on a daily basis in the long-term experiments. In this study we investigated specific growth rate fluctuations of Saccharomyces cerevisiae yeasts that were marked daily during cultivation under constant conditions. The effects of different solar and terrestrial factors were then analysed. The significant correlation indices were found for growth rate fluctuations against solar wind speed and the number of flares M on the Sun. These two factors determined the cyclic nature of the growth rate fluctuations, and thus its general course of increase or decrease. The effects of several other factors (Flares C number, planetary A index variation, and changes in the atmospheric factors such as temperature and humidity) and their two-way interactions were significant in producing an equation to describe the magnitude of changes of the yeast's growth parameters. The R2 of the equation achieved 91% and adjusted R2 was 78%. It is obvious that temperature and humidity are the factors that cannot directly influence the yeast populations under laboratory conditions and thus we suppose that they only reflect modifications of the really important factor(s) that take place in the Earth's atmosphere. We have concluded that different solar and terrestrial factors are responsible for the fluctuations in the daily kinetic parameters of the yeast growth.

  11. Effects of feeding corn silage inoculated with microbial additives on the ruminal fermentation, microbial protein yield, and growth performance of lambs.

    PubMed

    Basso, F C; Adesogan, A T; Lara, E C; Rabelo, C H S; Berchielli, T T; Teixeira, I A M A; Siqueira, G R; Reis, R A

    2014-12-01

    This study aimed to examine the effects of feeding corn silage inoculated without or with either Lactobacillus buchneri (LB) alone or a combination of LB and Lactobacillus plantarum (LBLP) on the apparent digestibility, ruminal fermentation, microbial protein synthesis, and growth performance of lambs. Thirty Santa Inês×Dorper crossbred intact males lambs weighing 20.4±3.8 kg were blocked by weight into 10 groups. Lambs in each group were randomly assigned to 1 of the following 3 dietary treatments: untreated (Control), LB, and LBLP silage. Lambs were fed experimental diets for 61 d. The apparent digestibility was indirectly estimated from indigestible NDF measured on d 57 to 59. Spot urine samples were collected from all animals on d 59 to estimate microbial protein synthesis. Lambs were slaughtered for carcass evaluation on d 61 when they weighed 32.4±5.2 kg. Six additional ruminally cannulated Santa Inês×Dorper crossbred wethers weighing 40.5±1.8 kg were used to examine dietary effects on ruminal fermentation. Average daily gain was increased when lambs were fed LBLP silage (P<0.05) but not LB silage. The LBLP silage had the highest (P<0.05) lactic acid concentration and both inoculated silages had greater acetic acid concentrations than the Control silage (P<0.05). Inoculation of corn silage increased intakes of DM, OM, CP, NDF, total carbohydrate (CHO), and GE by the lambs but decreased digestibility of DM, OM, CP, total and nonstructural carbohydrates, and concentration of GE and ME. (P<0.05). Nevertheless, lambs fed inoculated silages had greater microbial N supply than those on the Control treatment (P<0.05). The acetate to propionate ratio was lower in ruminal fluid of wethers in LBLP treatment than LB and Control treatment (P<0.05) and ruminal pH tended to be greater in LB lambs than in LBLP and Control wethers (P<0.10). Finally, the inoculation with both bacteria combined enhanced the silage fermentation. The intakes of DM, OM, CP, NDF, and GE

  12. Comparison of Tunable Diode Laser Absorption Spectroscopy and Isothermal Micro-calorimetry for Non-invasive Detection of Microbial Growth in Media Fills

    PubMed Central

    Brueckner, David; Roesti, David; Zuber, Ulrich Georg; Schmidt, Rainer; Kraehenbuehl, Stefan; Bonkat, Gernot; Braissant, Olivier

    2016-01-01

    Two methods were investigated for non-invasive microbial growth-detection in intact glass vials as possible techniques for automated inspection of media-filled units. Tunable diode laser absorption spectroscopy (TDLAS) was used to determine microbially induced changes in O2 and CO2 concentrations within the vial headspaces. Isothermal microcalorimetry (IMC) allowed the detection of metabolic heat production. Bacillus subtilis and Streptococcus salivarius were chosen as test organisms. Parameters as robustness, sensitivity, comparability and time to detection (TtD) were evaluated to assess method adequacy. Both methods robustly detected growth of the tested microorganisms within less than 76 hours using an initial inoculum of <10CFU. TDLA turned out to be less sensitive than TDLA and IMC, as some false negative results were observed. Compared to the visual media-fill examination of spiked samples, the investigated techniques were slightly slower regarding TtD. Although IMC showed shorter TtD than TDLAS the latter is proposed for automating the media-fill inspection, as larger throughput can be achieved. For routine use either TDLA or a combination of TDLA and TDLA should be considered. IMC may be helpful for replacing the sterility assessment of commercial drug products before release. PMID:27282661

  13. Interventions for control of Salmonella: clearance of microbial growth from rubber picker fingers.

    PubMed

    Arnold, J W; Yates, I E

    2009-06-01

    A study was conducted to determine if a surface material with antimicrobial properties combined with an effective disinfectant could achieve total clearance of bacterial contamination. Before beginning the project, new rubber picker fingers collected from 3 processing facilities were tested for endogenous microflora. Five species of bacteria common to soil and human handling were present: Bacillus amyloliquefaciens, Bacillus cereus/thuringiensis, Staphylococcus epidermidis, Staphylococcus hominis ssp. novobiosepticus, and Staphylococcus intermedius. In separate experiments, new (unused) rubber picker fingers from 3 manufacturers were exposed to broiler carcass rinses, and the kinetics of bacterial attachment to finger material was determined. Turbidity of the bacterial suspensions at varying dilutions containing picker finger sections was compared hourly with controls to evaluate inhibition. New rubber finger material from the 3 manufacturers significantly inhibited bacterial growth (P < 0.05), without the aid of antibacterial additives. We improved an assay for screening disinfectants against growth of pathogens and determined the activity of 5 disinfectant compounds. Two of the compounds were most effective against Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, Salmonella Enteritidis, and Escherichia coli, and one of the compounds was selected for further study with Salmonella Enteritidis. Scanning electron microscopy confirmed the levels of Salmonella Enteritidis before and after treatment. The most effective compound was nontoxic and completely cleared Salmonella Enteritidis contamination from the rubber picker finger surface.

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

    PubMed

    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.

  15. PAIRED-CITY STUDY TO DETERMINE THE CONTRIBUTION OF SOURCE WATER TYPE TO THE ENDEMIC LEVEL OF MICROBIAL DISEASE

    EPA Science Inventory

    Paired-City Study to Determine the Contribution of Source Water Type to the Endemic Level of Microbial Disease

    F Frost PhD, T Kunde MPH, L Harter PhD, T Muller MS, GF Craun PE MPH, RL Calderon MPH PhD

    ABSTRACT

    Context: The effectiveness of current drinking...

  16. Microbial trench-based optofluidic system for reagentless determination of phenolic compounds.

    PubMed

    Sanahuja, David; Giménez-Gómez, Pablo; Vigués, Núria; Ackermann, Tobias Nils; Guerrero-Navarro, Alfons Eduard; Pujol-Vila, Ferran; Sacristán, Jordi; Santamaria, Nidia; Sánchez-Contreras, María; Díaz-González, María; Mas, Jordi; Muñoz-Berbel, Xavier

    2015-04-07

    Phenolic compounds are one of the main contaminants of soil and water due to their toxicity and persistence in the natural environment. Their presence is commonly determined with bulky and expensive instrumentation (e.g. chromatography systems), requiring sample collection and transport to the laboratory. Sample transport delays data acquisition, postponing potential actions to prevent environmental catastrophes. This article presents a portable, miniaturized, robust and low-cost microbial trench-based optofluidic system for reagentless determination of phenols in water. The optofluidic system is composed of a poly(methyl methacrylate) structure, incorporating polymeric optical elements and miniaturized discrete auxiliary components for optical transduction. An electronic circuit, adapted from a lock-in amplifier, is used for system control and interfering ambient light subtraction. In the trench, genetically modified bacteria are stably entrapped in an alginate hydrogel for quantitative determination of model phenol catechol. Alginate is also acting as a diffusion barrier for compounds present in the sample. Additionally, the superior refractive index of the gel (compared to water) confines the light in the lower level of the chip. Hence, the optical readout of the device is only altered by changes in the trench. Catechol molecules (colorless) in the sample diffuse through the alginate matrix and reach bacteria, which degrade them to a colored compound. The absorbance increase at 450 nm reports the presence of catechol simply, quickly (~10 min) and quantitatively without addition of chemical reagents. This miniaturized, portable and robust optofluidic system opens the possibility for quick and reliable determination of environmental contamination in situ, thus mitigating the effects of accidental spills.

  17. Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

    PubMed Central

    Perrotta, Allison R.; Kumaraswamy, Rajkumari; Bastidas-Oyanedel, Juan R.; Alm, Eric J.

    2017-01-01

    The sustainable recovery of resources from wastewater streams can provide many social and environmental benefits. A common strategy to recover valuable resources from wastewater is to harness the products of fermentation by complex microbial communities. In these fermentation bioreactors high microbial community diversity within the inoculum source is commonly assumed as sufficient for the selection of a functional microbial community. However, variability of the product profile obtained from these bioreactors is a persistent challenge in this field. In an attempt to address this variability, the impact of inoculum on the microbial community structure and function within the bioreactor was evaluated using controlled laboratory experiments. In the course of this work, sequential batch reactors were inoculated with three complex microbial inocula and the chemical and microbial compositions were monitored by HPLC and 16S rRNA amplicon analysis, respectively. Microbial community dynamics and chemical profiles were found to be distinct to initial inoculate and highly reproducible. Additionally we found that the generation of a complex volatile fatty acid profile was not specific to the diversity of the initial microbial inoculum. Our results suggest that the composition of the original inoculum predictably contributes to bioreactor community structure and function. PMID:28196102

  18. Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor.

    PubMed

    Perrotta, Allison R; Kumaraswamy, Rajkumari; Bastidas-Oyanedel, Juan R; Alm, Eric J; Rodríguez, Jorge

    2017-01-01

    The sustainable recovery of resources from wastewater streams can provide many social and environmental benefits. A common strategy to recover valuable resources from wastewater is to harness the products of fermentation by complex microbial communities. In these fermentation bioreactors high microbial community diversity within the inoculum source is commonly assumed as sufficient for the selection of a functional microbial community. However, variability of the product profile obtained from these bioreactors is a persistent challenge in this field. In an attempt to address this variability, the impact of inoculum on the microbial community structure and function within the bioreactor was evaluated using controlled laboratory experiments. In the course of this work, sequential batch reactors were inoculated with three complex microbial inocula and the chemical and microbial compositions were monitored by HPLC and 16S rRNA amplicon analysis, respectively. Microbial community dynamics and chemical profiles were found to be distinct to initial inoculate and highly reproducible. Additionally we found that the generation of a complex volatile fatty acid profile was not specific to the diversity of the initial microbial inoculum. Our results suggest that the composition of the original inoculum predictably contributes to bioreactor community structure and function.

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

    PubMed Central

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

    2017-01-01

    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. PMID:28367963

  20. Determining microbial products and identifying molecular targets in the human microbiome.

    PubMed

    Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, Curtis

    2014-11-04

    Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.

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

    PubMed Central

    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

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

    PubMed

    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.

  3. Effect of silver nano-particles on soil microbial growth, activity and community diversity in a sandy loam soil.

    PubMed

    Samarajeewa, A D; Velicogna, J R; Princz, J I; Subasinghe, R M; Scroggins, R P; Beaudette, L A

    2017-01-01

    Silver nano-particles (AgNPs) are widely used in a range of consumer products as a result of their antimicrobial properties. Given the broad spectrum of uses, AgNPs have the potential for being released to the environment. As a result, environmental risks associated with AgNPs need to be assessed to aid in the development of regulatory guidelines. Research was performed to assess the effects of AgNPs on soil microbial activity and diversity in a sandy loam soil with an emphasis on using a battery of microbial tests involving multiple endpoints. The test soil was spiked with PVP coated (0.3%) AgNPs at the following concentrations of 49, 124, 287, 723 and 1815 mg Ag kg(-1) dry soil. Test controls included an un-amended soil; soil amended with PVP equivalent to the highest PVP concentration of the coated AgNP; and soil amended with humic acid, as 1.8% humic acid was used as a suspension agent for the AgNPs. The impact on soil microbial community was assessed using an array of tests including heterotrophic plate counting, microbial respiration, organic matter decomposition, soil enzyme activity, biological nitrification, community level physiological profiling (CLPP), Ion Torrent™ DNA sequencing and denaturing gradient gel electrophoresis (DGGE). An impact on microbial growth, activity and community diversity was evident from 49 to 1815 mg kg(-1) with the median inhibitory concentrations (IC50) as low as 20-31 mg kg(-1) depending on the test. AgNP showed a notable impact on microbial functional and genomic diversity. Emergence of a silver tolerant bacterium was observed at AgNP concentrations of 49-287 mg kg(-1) after 14-28 days of incubation, but not detectable at 723 and 1815 mg kg(-1). The bacterium was identified as Rhodanobacter sp. The study highlighted the effectiveness of using multiple microbial endpoints for inclusion to the environmental risk assessment of nanomaterials.

  4. Metagenomic Profiling of Microbial Composition and Antibiotic Resistance Determinants in Puget Sound

    PubMed Central

    Port, Jesse A.; Wallace, James C.; Griffith, William C.; Faustman, Elaine M.

    2012-01-01

    Human-health relevant impacts on marine ecosystems are increasing on both spatial and temporal scales. Traditional indicators for environmental health monitoring and microbial risk assessment have relied primarily on single species analyses and have provided only limited spatial and temporal information. More high-throughput, broad-scale approaches to evaluate these impacts are therefore needed to provide a platform for informing public health. This study uses shotgun metagenomics to survey the taxonomic composition and antibiotic resistance determinant content of surface water bacterial communities in the Puget Sound estuary. Metagenomic DNA was collected at six sites in Puget Sound in addition to one wastewater treatment plant (WWTP) that discharges into the Sound and pyrosequenced. A total of ∼550 Mbp (1.4 million reads) were obtained, 22 Mbp of which could be assembled into contigs. While the taxonomic and resistance determinant profiles across the open Sound samples were similar, unique signatures were identified when comparing these profiles across the open Sound, a nearshore marina and WWTP effluent. The open Sound was dominated by α-Proteobacteria (in particular Rhodobacterales sp.), γ-Proteobacteria and Bacteroidetes while the marina and effluent had increased abundances of Actinobacteria, β-Proteobacteria and Firmicutes. There was a significant increase in the antibiotic resistance gene signal from the open Sound to marina to WWTP effluent, suggestive of a potential link to human impacts. Mobile genetic elements associated with environmental and pathogenic bacteria were also differentially abundant across the samples. This study is the first comparative metagenomic survey of Puget Sound and provides baseline data for further assessments of community composition and antibiotic resistance determinants in the environment using next generation sequencing technologies. In addition, these genomic signals of potential human impact can be used to guide

  5. [Accelerated determination of microbial sensitivity to antibiotics and chemotherapeutic preparations by serial dilutions using the peroxidase test].

    PubMed

    Fel'dman, Iu M; Leĭbman, E T

    1980-02-01

    A rapid method for determination of microbial sensitivity to antibiotics and chemotherapeutic drugs with the use of the peroxidase test is described. The procedure takes 6 hours. Peroxidase is determined by a change in the color of the methyl-para-amino phenol sulfate solution added to the broth culture in 6 hours (simultaneously with hydrogen peroxide). The peroxidase test provides detection of the microbe multiplication even when no turbidity is observed.

  6. [Parameter determination of algae growth based on ecological tank experiment].

    PubMed

    Pang, Yong; Ding, Ling; Gao, Guang

    2005-05-01

    A dynamic simulation experiment of algae in an ecological tank was performed at the Taihu Laboratory for Lake Ecosystem Research. During the experiment, water from Taihu Lake was infused into the ecological tank and samples were taken continually to observe algae growth under varying conditions, such as temperature, sunlight and nutrients. Based on the experiment, an algae growth model, considering nitrogen and phosphorus cycle, was developed by using the advanced PHREEQC model. After that, a detailed calibration and validation of parameters in the model were done on the basis of experimental results. The least square method was used to determine the optimal set of parameters. The calculated values of algae and nutrient concentrations show fairly satisfying fittness with measured data.

  7. The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.

    PubMed

    Selma, María V; Romo-Vaquero, María; García-Villalba, Rocío; González-Sarrías, Antonio; Tomás-Barberán, Francisco A; Espín, Juan C

    2016-04-01

    We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.

  8. Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

    PubMed Central

    Sanchez, Alvaro; Gore, Jeff

    2013-01-01

    The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate

  9. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries.

    PubMed

    Goodman, Andrew L; Wu, Meng; Gordon, Jeffrey I

    2011-11-17

    Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq is based on a modified mariner transposon containing MmeI sites at its ends, allowing cleavage at chromosomal sites 16-17 bp from the inserted transposon. Genomic regions adjacent to the transposons are amplified by linear PCR with a biotinylated primer. Products are bound to magnetic beads, digested with MmeI and barcoded with sample-specific linkers appended to each restriction fragment. After limited PCR amplification, fragments are sequenced using a high-throughput instrument. The sequence of each read can be used to map the location of a transposon in the genome. Read count measures the relative abundance of that mutant in the population. Solid-phase library preparation makes this protocol rapid (18 h), easy to scale up, amenable to automation and useful for a variety of samples. A protocol for characterizing libraries of transposon mutant strains clonally arrayed in a multiwell format is provided.

  10. Batch growth kinetics of an indigenous mixed microbial culture utilizing m-cresol as the sole carbon source.

    PubMed

    Saravanan, Pichiah; Pakshirajan, K; Saha, Prabirkumar

    2009-02-15

    An indigenous mixed microbial culture, isolated from a sewage treatment plant located in Guwahati was used to study biodegradation of m-cresol in batch shake flasks. m-Cresol concentration in the growth media was varied from 100mg/L to 900mg/L. The degradation kinetics was found to follow a three-half-order model at all initial m-cresol concentrations with regression values greater than 0.97. A maximum observed specific degradation rate of 0.585h(-1) was observed at 200mg/L m-cresol concentration in the medium. In the range of m-cresol concentrations used in the study, specific growth rate of the culture and specific degradation rates were observed to follow substrate inhibition kinetics. These two rates were fitted to kinetic models of Edward, Haldane, Luong, Han-Levenspiel, and Yano-Koga that are used to explain substrate inhibition on growth of microbial culture. Out of these models Luong and Han-Levenspiel models fitted the experimental data best with lowest root mean square error values. Biokinetic constants estimated from these two models showed good potential of the indigenous mixed culture in degrading m-cresol in wastewaters.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    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 °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.

  12. Effects of Monotypic and Binary Mixtures of Metal Oxide Nanoparticles on Microbial Growth in Sandy Soil Collected from Artificial Recharge Sites

    PubMed Central

    Ko, Kyung-Seok; Ha, Kyoochul; Kong, In Chul

    2015-01-01

    The potential effects of monotypic and binary metal oxide nanoparticles (NPs, ZnO, NiO, Co3O4 and TiO2) on microbial growth were evaluated in sandy soil collected from artificial recharge sites. Microbial growth was assessed based on adenosine triphosphate (ATP) content, dehydrogenase activity (DHA), and viable cell counts (VCC). Microbial growth based on ATP content and VCC showed considerable differences depending on NP type and concentration, whereas DHA did not significantly change. In general, ZnO NPs showed the strongest effect on microbial growth in all measurements, showing an EC50 value of 10.9 mg/L for ATP content. The ranking (EC50) of NPs based on their effect on microbial growth assessed by ATP content and VCC was ZnO > Co3O4 > NiO > TiO2. Upon exposure to binary NP mixtures, synergistic and additive modes of action were observed for ATP content and VCC, respectively. The ranges of observed (P(O)) and expected (P(E)) activity were 83%–92% and 78%–82% of the control (p-value 0.0010) based on ATP content and 78%–95% and 72%–94% of the control (p-value 0.8813) based on VCC under the tested conditions, respectively. The results indicate that the effects of NP mixtures on microbial growth in the sandy soil matrix were as great, or greater, than those of single NPs. Therefore, understanding the effects of single NPs and NP mixtures is essential for proper ecological risk assessment. Additionally, these findings demonstrate that the evaluation of NP effects may be profoundly influenced by the method of microbial growth measurement. PMID:26610489

  13. An Apple Fruit Fermentation (AFF) Treatment Improves the Composition of the Rhizosphere Microbial Community and Growth of Strawberry (Fragaria × ananassa Duch 'Benihoppe') Seedlings.

    PubMed

    Zhang, Jie; Pang, Hui; Ma, Mengxia; Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong

    2016-01-01

    Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth.

  14. An Apple Fruit Fermentation (AFF) Treatment Improves the Composition of the Rhizosphere Microbial Community and Growth of Strawberry (Fragaria × ananassa Duch ‘Benihoppe’) Seedlings

    PubMed Central

    Bu, Yufen; Shao, Wei; Huang, Weijing; Ji, Qianlong; Yao, Yuncong

    2016-01-01

    Plant growth can be promoted by the application of apple fruit fermentation (AFF), despite unclear of the underlying mechanisms, the effects involved in AFF on rhizosphere microorganisms have been hypothesized. We investigated the consequences of applying AFF alone or in combination with Bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA were performed to determine AFF effects on rhizosphere. Moreover, the growth index and antioxidant enzyme activities were determined 30 days after treatments. We identified five dominant bacteria in AFF: Coprinus atramentarius, Bacillus megaterium, Bacillus licheniformis, Weissella and B. subtilis. The greatest number of bacterial species were observed in the rhizosphere of control matrix (water treated), and the lowest diversity appeared in the rhizosphere soil treated with 108 cfu/mL B. licheniformis alone. Combining AFF plus B. licheniformis in one treatment resulted in the largest leaf area, plant height, root length, plant weight, and the markedly higher activities of antioxidant enzymes. We conclude that a combination of AFF plus B. licheniformis treatment to matrix can increase antioxidant enzymes activities in strawberry seedlings, optimize the status of rhizosphere microbial, and promote plant growth. PMID:27755580

  15. Condensing heat exchanger microbial growth and control study-phase 2

    SciTech Connect

    Marsh, R.W.; Caron, M.E.; Metselaar, C.; Steele, J.

    1993-12-31

    The Space Station Temperature and Humidity Control Condensing Heat Exchangers will be utilized to collect and remove atmospheric water vapor generated by the metabolic and hygienic activity of crew members. The porous hydrophillic coating within the heat exchangers will always be wet. Cabin air will continuously flow through the heat exchangers during system operation which makes them a potential site for microbial colonization. This paper summarizes the findings form an ongoing study which evaluates biofilm formation on wet hydrophilic coated panels compared to panels to which microbial control measures have have been applied. The control measures evaluated are an antimicrobial agent within the coating and periodic drying.

  16. LIPID ANALYSIS TO DETERMINE THE EFFECT OF A SOURCE REMEDIAL TECHNOLOGY IN MICROBIAL ECOLOGY

    EPA Science Inventory

    Microbial community structures and related changes in the subsurface environment were investigated following in situ chemical oxidation (ISCO) treatment at Launch Complex 34, Cape Canaveral Air Station, Florida. The site has dense non-aqueous phase (DNAPL) concentrations of TCE ...

  17. Biofilm feeding: Microbial colonization of food promotes the growth of a detritivorous arthropod

    PubMed Central

    Horváthová, Terézia; Babik, Wiesław; Bauchinger, Ulf

    2016-01-01

    Abstract Feeding on plant material is common among animals, but how different animals overcome the dietary deficiencies imposed by this feeding strategy is not well understood. Microorganisms are generally considered to play a vital role in the nutritional ecology of plant feeding animals. Commonly microbes living inside animal bodies are considered more important, but recent studies suggest external microbes significantly shape plant-feeding strategies in invertebrates. Here we investigate how external microbes that typically form biofilm on primary plant material affect growth rates in a terrestrial isopod species Porcellio scaber. We experimentally manipulated the amount of biofilm on three different primary diet sources and quantified growth and survival of individuals that fed on food with either a small or large amount of biofilm. In addition, we tested how dietary manipulation shapes the composition of bacterial communities in the gut. The presence of visible biofilm significantly affected the growth of isopods: individuals that fed on the primary diet source with a large amount of biofilm gained more mass than individuals feeding on a diet with marginal biofilm. Diet also significantly affected the bacterial gut community. The primary diet source mainly determined the taxonomic composition of the bacterial community in the isopod gut, whereas the amount of biofilm affected the relative abundance of bacterial taxa. Our study suggests that terrestrial isopods may cope with low-quality plant matter by feeding on biofilm, with decomposition of plant material by organisms outside of the feeding organism (here a terrestrial isopod) probably playing a major role. Future investigations may be directed towards the primary diet source, plant matter, and the secondary diet source, biofilm, and should assess if both components are indeed uptaken in detritivorous species. PMID:27110187

  18. Effect of reduced barometric pressure on water availability related to microbial growth.

    PubMed

    Hawrylewicz, E J; Hagen, C; Tolkacz, V; Ehrlich, R

    1967-01-01

    Data obtained from Mariner IV indicate that the barometric pressure on Mars is considerably lower than previously estimated. Current estimates from Mariner IV indicate a range from 4 to 7 mb and by near infrared spectroscopy 33-56 mb. Inasmuch as the pressure has a marked influence on availability of water, this should affect the existence of Martian life. At the maximum temperatures recorded on Mars, namely 25 degrees C, a barometric pressure of 30 mb is required for the retention of free water. The lower pressure, 4 mb, would suggest that the moisture is present as a vapor above the freezing point and consequently it is not available for utilizing by living cells. The lower estimates of barometric pressure also inversely affect the carbon dioxide concentration in the Martian atmosphere. Our previous studies have demonstrated that spores of Bacillus cereus survive, germinate and grow in a simulated Martian environment (2.4% CO2, 98 mb) supplemented with moisture. The studies described in this paper were designed to determine the effect of low barometric pressures (10 to 98 mb Hg) and high concentrations of carbon dioxide (37 to 100%) in the simulated Martian environment on survival and growth of B cereus. The organism was inoculated into a felsite-limonite soil at 8% moisture level. The temperature cycles used were 8 hr at -65 degrees C and 16 hr at 25 degrees C, or 20 hr at -65 degrees C and 4 hr at 25 degrees C. The data suggest that the organism after achieving maximum growth in the simulated Martian environment (2.4% CO2, 98 mb) immediately enters into the growth phase upon reinoculation into fresh soil. These data reflect upon the possibility of contamination through air movements. Based upon currently available Martian environmental data, the probability of contamination of Mars by terrestrial micro-organisms will be discussed.

  19. A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.

    PubMed

    Zarecki, Raphy; Oberhardt, Matthew A; Reshef, Leah; Gophna, Uri; Ruppin, Eytan

    2014-07-01

    Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.

  20. Characterization of microbial growth on processing equipment by electrochemical impedance spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial activity that leads to the formation of biofilms on process equipment can accelerate corrosion, reduce heat transfer rates, and generally decrease process efficiencies. Additional concerns arise in the food and pharma industries where product quality and safety are a high priority. Followi...

  1. Influence of lead acetate on soil microbial biomass and community structure in two different soils with the growth of Chinese cabbage (Brassica chinensis).

    PubMed

    Liao, Min; Chen, Cheng-Li; Zeng, Lu-Sheng; Huang, Chang-Yong

    2007-01-01

    A greenhouse pot experiment was conducted to evaluate the impact of different concentrations of lead acetate on soil microbial biomass and community structure during growth of Chinese cabbage (Brassica chinensis) in two different soils. The field soils were used for a small pot, short-term 60-day growth chamber study. The soils were amended with different Pb concentrations, ranging from 0 to 900mgkg(-1) soil. The experimental design was a 2 soilx2 vegetation/non-vegetationx6 treatments (Pb)x3 replicate factorial experiment. At 60 days the study was terminated and soils were analyzed for microbial parameters, namely, microbial biomass, basal respiration and PLFAs. The results indicated that the application of Pb at lower concentrations (100 and 300mgkg(-1)) as lead acetate resulted in a slight increase in soil microbial biomass, whereas Pb concentrations >500mgkg(-1) caused an immediate gradual significant decline in biomass. However, the degree of impact on soil microbial biomass and basal respiration by Pb was related to management (plant vegetation) or the contents of clay and organic matter in soils. The profiles of 21 phospholipid fatty acids (PLFAs) were used to assess whether observed changes in functional microbial parameters were accompanied by changes in the composition of the microbial communities after Pb application at 0, 300 and 900mg Pbkg(-1) soil. The results of principal component analyses (PCA) indicated that there were significant increases in fungi biomarkers of 18:3omega6c, 18:1omega9c and a decrease in cy17:0, which is an indicator of gram-negative bacteria for the high levels of Pb treatments In a word, soil microbial biomass and community structure, therefore, may be sensitive indicators reflecting environmental stress in soil-Pb-plant system. However, further studies will be needed to better understand how these changes in microbial community structure might actually impact soil microbial community function.

  2. Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification.

    PubMed

    Theisen, C Harwood; Sumner, D Y; Mackey, T J; Lim, D S S; Brady, A L; Slater, G F

    2015-07-01

    Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from in situ mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth

  3. Soil biochemical properties and microbial resilience in agroforestry systems: effects on wheat growth under controlled drought and flooding conditions.

    PubMed

    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

  4. Effects of Agaricus lilaceps fairy rings on soil aggregation and microbial community structure in relation to growth stimulation of western wheatgrass (Pascopyrum smithii) in Eastern Montana rangeland.

    PubMed

    Caesar-Tonthat, The Can; Espeland, Erin; Caesar, Anthony J; Sainju, Upendra M; Lartey, Robert T; Gaskin, John F

    2013-07-01

    Stimulation of plant productivity caused by Agaricus fairy rings has been reported, but little is known about the effects of these fungi on soil aggregation and the microbial community structure, particularly the communities that can bind soil particles. We studied three concentric zones of Agaricus lilaceps fairy rings in Eastern Montana that stimulate western wheatgrass (Pascopyrum smithii): outside the ring (OUT), inside the ring (IN), and stimulated zone adjacent to the fungal fruiting bodies (SZ) to determine (1) soil aggregate proportion and stability, (2) the microbial community composition and the N-acetyl-β-D-glucosaminidase activity associated with bulk soil at 0-15 cm depth, (3) the predominant culturable bacterial communities that can bind to soil adhering to wheatgrass roots, and (4) the stimulation of wheatgrass production. In bulk soil, macroaggregates (4.75-2.00 and 2.00-0.25 mm) and aggregate stability increased in SZ compared to IN and OUT. The high ratio of fungal to bacteria (fatty acid methyl ester) and N-acetyl-β-D-glucosaminidase activity in SZ compared to IN and OUT suggest high fungal biomass. A soil sedimentation assay performed on the predominant isolates from root-adhering soil indicated more soil-binding bacteria in SZ than IN and OUT; Pseudomonas fluorescens and Stenotrophomonas maltophilia isolates predominated in SZ, whereas Bacillus spp. isolates predominated in IN and OUT. This study suggests that growth stimulation of wheatgrass in A. lilaceps fairy rings may be attributed to the activity of the fungus by enhancing soil aggregation of bulk soil at 0-15 cm depth and influencing the amount and functionality of specific predominant microbial communities in the wheatgrass root-adhering soil.

  5. Determination and improvement of microbial safety of wheat sprouts with chemical sanitizers.

    PubMed

    Tornuk, Fatih; Ozturk, Ismet; Sagdic, Osman; Yetim, Hasan

    2011-04-01

    In this study, total aerobic mesophilic bacteria (TAMB), total coliform (TC), yeasts and moulds (YM), and Escherichia coli, Salmonella, and Staphylococcus aureus counts of wheat seeds and sprouts germinated for 9 days under different relative humidity (RH) (90% and 95%) and temperatures (18 °C, 20 °C, and 22 °C) were determined. The disinfection capabilities of sodium hypochlorite (NaOCl) (100, 200, and 400 ppm) and hydrogen peroxide (H(2)O(2)) (3% and 6%) on wheat seeds/sprouts were also investigated. It has been found that native TAMB, TC, YM, and E. coli population significantly increased (p<0.05) with the germination; however, no Salmonella and S. aureus were detected on the seeds and/or sprouts. Again, increasing the temperature and RH resulted in a rapid proliferation of microorganisms. On the other hand, E. coli population could be completely eliminated by the treatment of different concentrations of NaOCl or H(2)O(2) before the germination of wheat seeds. Again, increasing the NaOCl and H(2)O(2) concentrations resulted in additional reductions of TAMB, TC, and YM population; and the highest reductions in sprouts were observed when the seed was soaked in 400 ppm NaOCl for 30 minutes followed by tap water wash and germination for 9 days. Population reduction of 1.46 log colony-forming unit (cfu)/g of TAMB, 1.97 log cfu/g of YM, and 0.84 log cfu/g of TC in sprouts was achieved when compared with the control. The chemical sanitization did not negatively affect the germination capability of the seeds. Therefore, soaking the seeds in 400 ppm of NaOCl for 30 minutes followed by a germination environment of 18 °C and 90% RH was found to be the most appropriate germination condition for wheat sprouts with reduced microbial population.

  6. Enhanced growth of halophyte plants in biochar-amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation.

    PubMed

    Zheng, Hao; Wang, Xiao; Chen, Lei; Wang, Zhenyu; Xia, Yang; Zhang, Yipeng; Wang, Hefang; Luo, Xianxiang; Xing, Baoshan

    2017-03-27

    Soil health is essential and irreplaceable for plant growth and global food production, which has been threatened by climate change and soil degradation. Degraded coastal soils are urgently required to reclaim using new sustainable technologies. Interest in applying biochar to improve soil health and promote crop yield has rapidly increased because of its multiple benefits. However, effects of biochar addition on the saline-sodic coastal soil health and halophyte growth were poorly understood. Response of two halophytes, Sesbania (Sesbania cannabina) and Seashore mallow (Kosteletzkya virginica), to the individual or co-application of biochar and inorganic fertilizer into a coastal soil was investigated using a 52-day pot experiment. The biochar alone or co-application stimulated the plant growth (germination, root development, biomass), primarily attributed to the enhanced nutrients availability from the biochar-improved soil health. Additionally, the promoted microbial activities and bacterial community shift towards the beneficial taxa (e.g., Pseudomonas and Bacillus) in the rhizosphere also contributed to the enhanced plant growth and biomass. Our findings showed the promising significance because biochar added at an optimal level (≤5%) could be a feasible option to reclaim the degraded coastal soil, enhance plant growth and production, and increase soil health and food security.

  7. Range expansions transition from pulled to pushed waves as growth becomes more cooperative in an experimental microbial population

    PubMed Central

    Yurtsev, Eugene Anatoly; Korolev, Kirill S.; Gore, Jeff

    2016-01-01

    Range expansions are becoming more frequent due to environmental changes and rare long-distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intraspecific cooperativity. For noncooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher [Fisher RA (1937) Ann Eugen 7(4):355–369] and Skellam [Skellam JG (1951) Biometrika 38(1-2):196–218], suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, that is, controlled by growth and dispersal in the bulk as well as in the front. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution. PMID:27185918

  8. Slow pyrolysis of poultry litter and pine woody biomass: impact of chars and bio-oils on microbial growth.

    PubMed

    Das, K C; Garcia-Perez, M; Bibens, B; Melear, N

    2008-06-01

    Accidental or prescribed fires in forests and in cultivated fields, as well as primitive charcoal production practices, are responsible for the release of large amounts of gases, char and condensable organic molecules into the environment. This paper describes the impact of condensable organic molecules and chars resulting from the slow pyrolysis of poultry litter, pine chips and pine pellets on the growth of microbial populations in soil and water. The proximate and elemental analyses as well as the content of proteins, cellulose, hemicellulose, lignin, and ash for each of these bio-materials are reported. The yields and some properties of char and condensable liquids are also documented. The behavior of microbial populations in soil and water is followed through respiration studies. It was found that biological activity was highest when aqueous fractions from poultry litter were applied in water. Cumulative oxygen consumption over a 120-h period was highest in the aqueous phases from poultry litter coarse fraction (1.82 mg/g). On average the oxygen consumption when oily fractions from poultry litter were applied represented 44 to 62% of that when aqueous fractions were applied. Pine chip and pine pellet derived liquids and chars produced respiration activity that were an order of magnitude lower than that of poultry litter liquid fractions. These results suggest that the growth observed is due to the effect of protein-derived molecules.

  9. Development of a fast and reliable method for the assessment of microbial colonization and growth on textiles by DNA quantification.

    PubMed

    Teufel, Linda; Schuster, K Christian; Merschak, Petra; Bechtold, Thomas; Redl, Bernhard

    2008-01-01

    There is a lack of relevant methods to assess the colonization of textiles by skin bacteria because present methods are mainly culture-based procedures. Therefore, the goal of this study was to develop a fast and sensitive culture-independent procedure for the quantification of microbial colonization and growth on textiles. We have established a suitable protocol to use DNA quantification as a reliable method for in vitroand in vivoinvestigations of textiles. For DNA extraction, a two-step procedure comprising treatment of the textile with a solution containing Triton X-100 and lysozyme for 1 h and a successive treatment by SDS and proteinase K for 2 h turned out to be most efficient. DNA extracted from textiles and fabrics was than quantified with the highly sensitive PicoGreen fluorescent dye. In vitrochallenge tests demonstrated a strong correlation between numbers of bacteria on textiles and amount of DNA extracted from textiles. Therefore, this method was used to compare different materials after in vivotrials for assessment of their susceptibility for microbial colonization and growth.

  10. Dimensionless parameters to summarize the influence of microbial growth and inhibition on the bioremediation of groundwater contaminants.

    PubMed

    Mohamed, M; Hatfield, K

    2011-09-01

    Monod expressions are preferred over zero- and first-order decay expressions in modeling contaminants biotransformation in groundwater because they better represent complex conditions. However, the wide-range of values reported for Monod parameters suggests each case-study is unique. Such uniqueness restricts the usefulness of modeling, complicates an interpretation of natural attenuation and limits the utility of a bioattenuation assessment to a small number of similar cases. In this paper, four Monod-based dimensionless parameters are developed that summarize the effects of microbial growth and inhibition on groundwater contaminants. The four parameters represent the normalized effective microbial growth rate (η), the normalized critical contaminant/substrate concentration (S*), the critical contaminant/substrate inhibition factor (N), and the bioremediation efficacy (η*). These parameters enable contaminated site managers to assess natural attenuation or augmented bioremediation at multiple sites and then draw comparisons between disparate remediation activities, sites and target contaminants. Simulations results are presented that reveal the sensitivity of these dimensionless parameters to Monod parameters and varying electron donor/acceptor loads. These simulations also show the efficacy of attenuation (η*) varying over space and time. Results suggest electron donor/acceptor amendments maintained at relative concentrations S* between 0.5 and 1.5 produce the highest remediation efficiencies. Implementation of the developed parameters in a case study proves their usefulness.

  11. Effect of nitrogen gas packaging on the quality and microbial growth of fresh-cut vegetables under low temperatures.

    PubMed

    Koseki, Shigenobu; Itoh, Kazuhiko

    2002-02-01

    Nitrogen (N2) gas packaging for fresh-cut vegetables (lettuce and cabbage) has been examined as a means of modified atmosphere packaging (MAP) for extending the shelf life of cut vegetables. Gas composition in enclosed packages that contained cut vegetables and were filled with 100% N2 had an oxygen (O2) concentration of 1.2 to 5.0% and a carbon dioxide (CO2) concentration of 0.5 to 3.5% after 5 days of storage. An atmosphere of low concentrations of O2 and high CO2 conditions occurred naturally in the package filled with N2 gas. Degradation of cut vegetables in terms of appearance was delayed by N2 gas packaging. Because of this effect, the appearance of fresh-cut vegetables packaged with N2 gas remained acceptable at temperatures below 5 degrees C after 5 days. Treatment with acidic electrolyzed water (AcEW) contributed to the acceptability of the vegetables' appearance at 5 and 10 degrees C in the air-packaging system. N2 gas packaging did not significantly affect the growth of microbial populations (total aerobic bacteria, coliform bacteria, Bacillus cereus, and psychrotrophic bacteria) in or on cut vegetables at 1, 5, and 10 degrees C for 5 days. Microbial growth in or on the cut vegetables was inhibited at 1 degrees C for 5 days regardless of atmospheric conditions.

  12. Determination of the amount of protein and amino acids extracted from the microbial protein (SCP) of lignocellulosic wastes.

    PubMed

    Ahmadi, A R; Ghoorchian, H; Hajihosaini, R; Khanifar, J

    2010-04-15

    With the increasing world population, the use of lignocellulosic wastes for production of microbial protein as animal feed becomes a necessity of our time. In order to verify the most productive protein, the amount of protein and amino acid extracted from Single Cell Protein (SCP) needs to be determined by an effective method. In this study Microbial protein was produced by treatment of wheat straw with Pleurotus florida; with heat at 100 degrees C and NaOH 2% as substrate by solid state fermentation. Concentration of protein was 62.8% per 100 g of dried microbial protein. Then the extracted protein hydrolyzed with HCl 6 Normal for 48 h under 110 degrees C temperature condition. Then the amino acids analyzed by using A-200 Amino Nova analyzer. The results of this study indicated that the ratio of essential amino acids to total amino acids was 65.6%. The concentration of essnyial amino acids were: Lysine = 9.5, histidine = 19.8, threonine = 0.6, valine = 6.6, methionine = 2.1, isoleucine = 7.3, leucine = 6.8, phenylalanine = 4.3 and arginine = 8.3 g/100 g of extracted protein that indicated the obtained microbial protein can be a good or suitable substitute in the food program of animal feed.

  13. Microbial community in the soil determines the forest recovery post-exposure to gamma irradiation.

    PubMed

    Shah, Vishal; Shah, Shreya; Mackey, Herman; Kambhampati, Murty; Collins, Daniel; Dowd, Scot E; Colichio, Robert; McDonnell, Kevin T; Green, Timothy

    2013-10-15

    Exposure of an ecosystem to ionizing radiation remains a possibility either due to accidents involving nuclear fuel rods or contamination with high-level radioactive wastes. While the short and long-term effect of ionizing radiation on higher eukaryotes has been well documented, we do not have an understanding on the recovery of the microbial community post radiation. Here we report that at a site within Brookhaven National Laboratory that was radiated from 1961 to 1978 with γ rays (Gamma Forest), the ecosystem has not yet fully recovered from the effects of radiation. The current vegetation type in the Gamma Forest varies as one goes away from the source of ionizing radiation, with the region closest to the source having no vegetation. The microbial tag-encoded FLX amplicon pyrosequencing analysis of the soil from different regions suggests that the current microbial community structure is identical in all the Zones. When soil samples from each vegetation zone of the Gamma Forest were radiated with 1.8 kGy γ radiation and survival microbial community analyzed, clear difference in the microbial communities were observed. It is evident based on the experimental data that the colonization of soil with Nitrosomonadaceae is critical for the higher plants in pine barrens to reestablish and grow after the area had been exposed to ionizing radiation.

  14. Effect of dietary protein content on ileal amino acid digestibility, growth performance, and formation of microbial metabolites in ileal and cecal digesta of early-weaned pigs.

    PubMed

    Htoo, J K; Araiza, B A; Sauer, W C; Rademacher, M; Zhang, Y; Cervantes, M; Zijlstra, R T

    2007-12-01

    Diarrhea incidence in weaned pigs may be associated with the concentration of intestinal microbial metabolites (ammonia, amines, and VFA) that are influenced by dietary CP content. Three experiments were conducted to determine effects of a low-protein, AA-supplemented diet on ileal AA digestibility, growth performance, diarrhea incidence, and concentration of microbial metabolites in ileal and cecal digesta of pigs weaned at 14 d of age. In Exp. 1, 8 pigs fitted with a simple T-cannula at the distal ileum were assigned in a crossover design to 2 diets containing 24 or 20% CP using wheat, corn, full-fat soybeans, whey powder, fish meal, and blood plasma as the main ingredients. Supplemental AA were added to the diets to meet the AA standards according to the 1998 NRC recommendations. Chromic oxide was used as an indigestible marker. Diets were fed at 2.5 times the ME requirement for maintenance. The reduction of dietary CP decreased (P < 0.05) the apparent ileal digestibility of most AA, except Lys, Met, Thr, Val, and Pro. Dietary CP content did not affect the pH of ileal digesta or ileal concentrations of ammonia N, cadaverine, putrescine, or VFA. In Exp. 2, 8 pigs fitted with a simple T-cannula in the cecum were assigned to 2 diets, similar to Exp. 1. Dietary CP content did not affect the pH of cecal digesta. The reduction in CP content decreased (P < 0.05) cecal ammonia N, acetic acid, isobutyric acid, isovaleric acid, total VFA, and putrescine concentrations by 28 to 39%. In Exp. 3, 32 pigs were assigned to 2 diets, similar to Exp. 1, according to a randomized complete block design. Pigs had free access to feed and water. Dietary CP content did not affect growth performance or fecal consistency scores during the 3-wk study, and diarrhea was not observed. The results of these experiments indicate that lowering the dietary CP content combined with supplementation of AA markedly reduced the production of potentially harmful microbial metabolites in cecal digesta of

  15. Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

    SciTech Connect

    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.

  16. Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

    SciTech Connect

    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...

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

    PubMed

    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.

  18. A new mechanistic growth model for simultaneous determination of lag phase duration and exponential growth rate and a new Bĕlehdrádek-type model for evaluating the effect of temperature on growth rate.

    PubMed

    Huang, Lihan

    2011-06-01

    A new mechanistic growth model was developed to describe microbial growth under isothermal conditions. The new mathematical model was derived from the basic observation of bacterial growth that may include lag, exponential, and stationary phases. With this model, the lag phase duration and exponential growth rate of a growth curve were simultaneously determined by nonlinear regression. The new model was validated using Listeria monocytogenes and Escherichia coli O157:H7 in broth or meat. Statistical results suggested that both bias factor (B(f)) and accuracy factor (A(f)) of the new model were very close to 1.0. A new Bĕlehdrádek-type rate model and the Ratkowsky square-root model were used to describe the temperature dependence of bacterial growth rate. It was observed that the maximum and minimum temperatures were more accurately estimated by a new Bĕlehdrádek-type rate model. Further, the inverse of square-roots of lag phases was found proportional to temperature, making it possible to estimate the lag phase duration from the growth temperature.

  19. Effect of a Bacillus-based direct-fed microbial feed supplement on growth performance and pen cleaning characteristics of growing-finishing pigs.

    PubMed

    Davis, M E; Parrott, T; Brown, D C; de Rodas, B Z; Johnson, Z B; Maxwell, C V; Rehberger, T

    2008-06-01

    A direct-fed microbial (DFM) based on a combination of Bacillus organisms specifically selected to increase the manure decomposition process was evaluated to determine its efficacy for improving growth performance and manure dissolution time. Three experiments involving 336 crossbred barrows and gilts were conducted to determine the effect of the Bacillus-based direct-fed microbial on growth performance and pen cleaning time. In each experiment, 2 dietary treatments (0 and 0.05% DFM) were fed during the growing-finishing period throughout the experiment, such that the DFM provided 1.47 x 10(8) cfu of Bacillus organisms per gram of supplement. Data from the 3 experiments were combined for analysis, such that there were 28 pens representing each of the 2 treatments. Pigs were weighed and feed intake was determined at the initiation and termination of each phase (starter, grower, and finisher). At the end of Exp. 1 and 3, pen cleaning time was determined by measuring the time required for each pen to be scraped and washed with a high-pressure sprayer. Additionally, 2 solid manure mat samples weighing approximately 4 g each were collected from solid manure buildup in each pen (16 pens/treatment), and the time required to completely disperse each manure mat sample was determined. Gain:feed improved (P < 0.05) in pigs fed Bacillus compared with the control diet during the finisher phase and throughout the combined growing-finishing period. The time required to dissolve the manure mat was reduced (P < 0.01) in samples collected from pens containing pigs fed Bacillus compared with samples from control pens. An additional evaluation was conducted in a commercial swine production facility using statistical process control analysis. Statistical process control analysis determined that supplementation with Bacillus increased the expected mean for ADG and decreased the expected mean for death loss percentage. Supplementation with a DFM composed of specifically selected Bacillus

  20. Metabolism of dinosaurs as determined from their growth

    NASA Astrophysics Data System (ADS)

    Lee, Scott A.

    2015-09-01

    A model based on cellular properties is used to analyze the mass growth curves of 20 dinosaurs. This analysis yields the first measurement of the average cellular metabolism of dinosaurs. The organismal metabolism is also determined. The cellular metabolism of dinosaurs is found to decrease with mass at a slower rate than is observed in extant animals. The organismal metabolism increases with the mass of the dinosaur. These results come from both the Saurischia and Ornithischia branches of Dinosauria, suggesting that the observed metabolic features were common to all dinosaurs. The results from dinosaurs are compared to data from extant placental and marsupial mammals, a monotreme, and altricial and precocial birds, reptiles, and fish. Dinosaurs had cellular and organismal metabolisms in the range observed in extant mesotherms.

  1. Metabolism of dinosaurs as determined from their growth.

    PubMed

    Lee, Scott A

    2015-09-01

    A model based on cellular properties is used to analyze the mass growth curves of 20 dinosaurs. This analysis yields the first measurement of the average cellular metabolism of dinosaurs. The organismal metabolism is also determined. The cellular metabolism of dinosaurs is found to decrease with mass at a slower rate than is observed in extant animals. The organismal metabolism increases with the mass of the dinosaur. These results come from both the Saurischia and Ornithischia branches of Dinosauria, suggesting that the observed metabolic features were common to all dinosaurs. The results from dinosaurs are compared to data from extant placental and marsupial mammals, a monotreme, and altricial and precocial birds, reptiles, and fish. Dinosaurs had cellular and organismal metabolisms in the range observed in extant mesotherms.

  2. Effects of heavy metals contained in soil irrigated with a mixture of sewage sludge and effluent for thirty years on soil microbial biomass and plant growth

    NASA Astrophysics Data System (ADS)

    Katanda, Y.; Mushonga, C.; Banganayi, F.; Nyamangara, J.

    The use of sewage effluent as a source of nutrients and water in peri-urban crop production is widespread in developing countries. A study was conducted in 2005 at Crowborough and Firle farms (near Harare) to assess effect of Cd on microbial biomass and activity, effect of sewage sludge and effluent on soybean (Glycine max L (Merr)) nodulation, and uptake of Zn and Cu by lettuce ( Lactuca sativa L.), mustard rape ( Brassica juncea L.), covo ( Brassica napus) and star grass ( Cynodon nlemfuensis). The soil that was used had been irrigated with sewage sludge and effluent for 30 years. Soil collected from Crowborough farm was enriched with Cd to different concentrations (0.4-5 mg Cd kg -1 soil) using Cd(NO 3) 2 and microbial biomass C and N (chloroform-incubation extraction) and respiration rates (CO 2 evolution) determined. A similar experiment to determine the effect of repeated addition of small amounts of Cd to soil over time on the same parameters was conducted. Three vegetables and star grass were grown in a pot experiment and harvested at six weeks after transplanting for the determination of above ground dry matter yield, and Zn and Cu, uptake. In another pot experiment, two soybean varieties, Magoye and Solitaire, were harvested after eight weeks and nodule number and effectiveness, and above ground dry matter yield were then determined. Cd significantly decreased biomass C (68%) and N (73%). Microbial respiration also significantly decreased. It was concluded that long-term application of sewage sludge and effluent to soil has negative effects on soil micro organisms, including Rhizobia. These micro organisms are essential for N-fixation. The damage to Rhizobia, caused diminished nodulation of soybean. Mustard rape and lettuce can accumulate Zn and Cu beyond toxic limits without apparent reduction in growth thereby posing a serious concern to the food chain. The consumption of mustard rape and lettuce grown on soil amended with sewage sludge and effluent at

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

    PubMed

    Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard R; Richter, Michael; Diez, María Suárez; Solano, Jennifer; Bargiela, Rafael; Golyshina, Olga V; Manteca, Ángel; Ramos, Juan Luis; Gallego, José R; Llorente, Irene; Martins dos Santos, Vitor A P; Jensen, Ole N; Peláez, Ana I; Sánchez, Jesús; Ferrer, Manuel

    2014-06-01

    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 ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including 'ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called 'ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.

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

    PubMed Central

    Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard R; Richter, Michael; Diez, María Suárez; Solano, Jennifer; Bargiela, Rafael; Golyshina, Olga V; Manteca, Ángel; Ramos, Juan Luis; Gallego, José R; Llorente, Irene; Martins dos Santos, Vitor AP; Jensen, Ole N; Peláez, Ana I; Sánchez, Jesús; Ferrer, Manuel

    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 ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths. PMID:24430486

  5. Determination of quantitative food consumption levels for use in microbial risk assessments: cheddar cheese as an example.

    PubMed

    Bahk, Gyung-Jin; Todd, Ewen C D

    2007-01-01

    Microbial risk assessment (MRA) is becoming increasingly used in the management of food safety because it can be used to quantify risks and help rank intervention strategies. The exposure assessment components of the assessments have become complex with many aspects of the contamination, survival, and growth of a pathogen in a food being taken into consideration. Insufficient consumption data constitutes an important data gap and consequently one of many sources of uncertainty in MRA even though the effects of uncertainty are smaller than those affecting bacterial concentration in foods. Therefore, food consumption data also play an important role in exposure assessment of MRA. In the United States, there are large-scale, nationwide sets of consumption data available for use in MRA, i.e., the National Health and Nutrition Examination Survey (NHANES). Newly released dietary interview data in the NHANES 2001 to 2002 survey show that it has been redesigned and that the data were sufficiently updated from previous versions to have more value for MRAs. We propose a model that can effectively use the new data sets and be incorporated into MRAs, using as an example consumption of Cheddar cheese/American-type cheese. This model included the prevalence of food eaten as well as the amount and frequency. We determined the amount of Cheddar/American cheese consumed per day with probability distribution (e.g., lognormal distribution). These could be further determined by gender, age, pregnancy, and combination food type, which we plan to do in the future. The frequency of the range of serving numbers for Cheddar/American cheese consumed per person per day and prevalence as the proportion of a population (e.g., survey respondents) eating a certain food in a day are also presented. Unlike traditional published mean values, the results of this model provide probability distribution intakes that can be compared with mean and median intakes. This allows values in the upper

  6. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids; Part I. Effects on growth performance, microbial populations and immune status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pigs (n=88) weaned at 19 ± 2 d of age were used in a 14 d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on immune status, Salmonella infection and shedding, and intestinal microbial populations following a Salmonella Typhimurium challenge. Pigs were ch...

  7. Biphasic toxicodynamic features of some antimicrobial agents on microbial growth: a dynamic mathematical model and its implications on hormesis

    PubMed Central

    2010-01-01

    Background In the present work, we describe a group of anomalous dose-response (DR) profiles and develop a dynamic model that is able to explain them. Responses were obtained from conventional assays of three antimicrobial agents (nisin, pediocin and phenol) against two microorganisms (Carnobacterium piscicola and Leuconostoc mesenteroides). Results Some of these anomalous profiles show biphasic trends which are usually attributed to hormetic responses. But they can also be explained as the result of the time-course of the response from a microbial population with a bimodal distribution of sensitivity to an effector, and there is evidence suggesting this last origin. In light of interest in the hormetic phenomenology and the possibility of confusing it with other phenomena, especially in the bioassay of complex materials we try to define some criteria which allow us to distinguish between sensu stricto hormesis and biphasic responses due to other causes. Finally, we discuss some problems concerning the metric of the dose in connection with the exposure time, and we make a cautionary suggestion about the use of bacteriocins as antimicrobial agents. Conclusions The mathematical model proposed, which combines the basis of DR theory with microbial growth kinetics, can generate and explain all types of anomalous experimental profiles. These profiles could also be described in a simpler way by means of bisigmoidal equations. Such equations could be successfully used in a microbiology and toxicology context to discriminate between hormesis and other biphasic phenomena. PMID:20723220

  8. Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost.

    PubMed

    García-Jaramillo, M; Redondo-Gómez, S; Barcia-Piedras, J M; Aguilar, M; Jurado, V; Hermosín, M C; Cox, L

    2016-04-15

    The presence of pesticides in surface and groundwater has grown considerably in the last decades as a consequence of the intensive farming activity. Several studies have shown the benefits of using organic amendments to prevent losses of pesticides from runoff or leaching. A particular soil from the Guadalquivir valley was placed in open air ponds and amended at 1 or 2% (w/w) with alperujo compost (AC), a byproduct from the olive oil industry. Tricyclazole dissipation, rice growth and microbial diversity were monitored along an entire rice growing season. An increase in the net photosynthetic rate of Oryza sativa plants grown in the ponds with AC was observed. These plants produced between 1100 and 1300kgha(-1) more rice than plants from the unamended ponds. No significant differences were observed in tricyclazole dissipation, monitored for a month in soil, surface and drainage water, between the amended and unamended ponds. The structure and diversity of bacteria and fungi communities were also studied by the use of the polymerase chain reaction denaturing gel electrophoresis (PCR-DGGE) from DNA extracted directly from soil samples. The banding pattern was similar for all treatments, although the density of bands varied throughout the time. Apparently, tricyclazole did not affect the structure and diversity of bacteria and fungi communities, and this was attributed to its low bioavailability. Rice cultivation under paddy field conditions may be more efficient under the effects of this compost, due to its positive effects on soil properties, rice yield, and soil microbial diversity.

  9. [The effect of soil inoculation with microbial pesticide destructors on plant growth and development].

    PubMed

    Lisina, T O; Garan'kina, N G; Kruglov, Iu V

    2001-01-01

    Soil inoculation with liquid cultures of Bacillus megaterium 501 and Exophiala nigrum A-29 capable of degrading several organophosphorus pesticides accelerated growth and development of experimental plants, formation of their generative organs, and improved their productivity. This was particularly observed under stress plant growth conditions on phytotoxic peach substrates. The microorganisms inoculated can probably degrade phytotoxins present in soils, thereby favoring the plant development.

  10. Effect of growth solution, membrane size and array connection on microbial fuel cell power supply for medical devices.

    PubMed

    Roxby, Daniel N; Nham Tran; Pak-Lam Yu; Nguyen, Hung T

    2016-08-01

    Implanted biomedical devices typically last a number of years before their batteries are depleted and a surgery is required to replace them. A Microbial Fuel Cell (MFC) is a device which by using bacteria, directly breaks down sugars to generate electricity. Conceptually there is potential to continually power implanted medical devices for the lifetime of a patient. To investigate the practical potential of this technology, H-Cell Dual Chamber MFCs were evaluated with two different growth solutions and measurements recorded for maximum power output both of individual MFCs and connected MFCs. Using Luria-Bertani media and connecting MFCs in a hybrid series and parallel arrangement with larger membrane sizes showed the highest power output and the greatest potential for replacing implanted batteries.

  11. Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

    SciTech Connect

    Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

    2016-08-15

    This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions in a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.

  12. Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

    DOE PAGES

    Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; ...

    2016-08-15

    This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions inmore » a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.« less

  13. Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

    NASA Astrophysics Data System (ADS)

    Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

    2016-10-01

    This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions in a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.

  14. Metal-Macrofauna Interactions Determine Microbial Community Structure and Function in Copper Contaminated Sediments

    PubMed Central

    Mayor, Daniel J.; Gray, Nia B.; Elver-Evans, Joanna; Midwood, Andrew J.; Thornton, Barry

    2013-01-01

    Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management. PMID:23741430

  15. Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

    PubMed

    Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

    2013-01-01

    Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

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

    PubMed

    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.

  17. Effect of high oxygen modified atmosphere packaging on microbial growth and sensorial qualities of fresh-cut produce.

    PubMed

    Jacxsens, L; Devlieghere, F; Van der Steen, C; Debevere, J

    2001-12-30

    The application of High Oxygen Atmospheres (HOA) (i.e. > 70% O2) for packaging ready-to-eat vegetables was evaluated as an alternative technique for low O2 Equilibrium Modified Atmosphere (EMA) packaging (3% O2-5% CO2-balance N2) for respiring products. Comparative experiments between both techniques were performed in-vitro and in-vivo. Typical spoilage causing microorganisms (Pseudomonas fluorescens, Candida lambica), the moulds Botrytis cinerea, Aspergillus flavus and the opportunistic psychrotrophic human pathogenic microorganism associated with refrigerated minimally processed vegetables. Aeromonas caviae (HG4), showed a retarded growth during the conducted in-vitro studies at 4 degrees C in 70%, 80% and 95% O2 as examples of HOA compared to the in-vitro experiments in 5% O2 (as example of EMA packaging) and the effect was more pronounced in 95% O2. The effect of the high O2-concentrations on the human pathogen Listeria monocytogenes resulted in an extended lag phase (95% O2). The plant pathogen Erwinia carotovora was increasingly stimulated by increasing high O2-concentrations. During a storage experiment of three types of ready-to-eat vegetables (mushroom slices, grated celeriac and shredded chicory endive), which are sensitive to enzymatic browning and microbial spoilage, the effect of EMA and HOA (95% O2-5% N2) on their quality and shelf life was compared. High O2 atmospheres were found to be particularly effective in inhibiting enzymatic browning of the tested vegetables. Also, the microbial quality was better as a reduction in yeast growth was observed. The HOA can be applied as an alternative for low O2 modified atmospheres for some specific types of ready-to-eat vegetables, sensitive to enzymatic browning and spoilage by yeasts.

  18. [Determination of sugars, organic acids and alcohols in microbial consortium fermentation broth from cellulose using high performance liquid chromatography].

    PubMed

    Jiang, Yan; Fan, Guifang; Du, Ran; Li, Peipei; Jiang, Li

    2015-08-01

    A high performance liquid chromatographic method was established for the determination of metabolites (sugars, organic acids and alcohols) in microbial consortium fermentation broth from cellulose. Sulfate was first added in the samples to precipitate calcium ions in microbial consortium culture medium and lower the pH of the solution to avoid the dissociation of organic acids, then the filtrates were effectively separated using high performance liquid chromatography. Cellobiose, glucose, ethanol, butanol, glycerol, acetic acid and butyric acid were quantitatively analyzed. The detection limits were in the range of 0.10-2.00 mg/L. The linear correlation coefficients were greater than 0.999 6 in the range of 0.020 to 1.000 g/L. The recoveries were in the range of 85.41%-115.60% with the relative standard deviations of 0.22% -4.62% (n = 6). This method is accurate for the quantitative analysis of the alcohols, organic acids and saccharides in microbial consortium fermentation broth from cellulose.

  19. Carbon source--a strong determinant of microbial community structure and performance of an anaerobic reactor.

    PubMed

    Kundu, K; Bergmann, I; Hahnke, S; Klocke, M; Sharma, S; Sreekrishnan, T R

    2013-12-01

    Industrial effluents differ in their organic composition thereby providing different carbon sources to the microbial communities involved in its treatment. This study aimed to investigate the correlation of microbial community structure with wastewater composition and reactor's performance. Self-immobilized granules were developed in simulated wastewater based on different carbon sources (glucose, sugarcane molasses, and milk) in three hybrid anaerobic reactors operated at 37°C. To study archaeal community structure, a polyphasic approach was used with both qualitative and quantitative analysis. While PCR-denaturing gradient gel electrophoresis of 16S rRNA gene did not reveal major shifts in diversity of archaea with change in substrate, quantification of different groups of methanogens and total bacteria by real-time PCR showed variations in relative abundances with the dominance of Methanosaetaceae and Methanobacteriales. These data were supported by differences in the ratio of total counts of archaea and bacteria analyzed by catalyzed reporter deposition - fluorescence in situ hybridization. During hydraulic and organic shocks, the molasses-based reactor showed the best performance followed by the milk- and the glucose-based reactor. The study indicates that carbon source shapes the microbial community structure more in terms of relative abundance with distinct metabolic capacities rather than its diversity itself.

  20. 'Everything is everywhere: but the environment selects': ubiquitous distribution and ecological determinism in microbial biogeography.

    PubMed

    O'Malley, Maureen A

    2008-09-01

    Recent discoveries of geographical patterns in microbial distribution are undermining microbiology's exclusively ecological explanations of biogeography and their fundamental assumption that 'everything is everywhere: but the environment selects'. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will trace the conceptual history of Beijerinck's claim that 'everything is everywhere' in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging 'everything is everywhere' reveals that philosophical issues from Beijerinck's era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography.

  1. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology.

    PubMed

    Gibson, Molly K; Forsberg, Kevin J; Dantas, Gautam

    2015-01-01

    Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.

  2. Active suppression of a leaf meristem orchestrates determinate leaf growth

    PubMed Central

    Alvarez, John Paul; Furumizu, Chihiro; Efroni, Idan; Eshed, Yuval; Bowman, John L

    2016-01-01

    Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly, shortly after leaf initiation, to gradually restrict the activity of a leaf meristem in Arabidopsis thaliana to marginal and basal domains, and that their absence confers persistent marginal growth to leaves, cotyledons and floral organs. Following primordia initiation, the restriction of the broadly acting leaf meristem to the margins is mediated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, whereas other marginal elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic of an ancestral shoot system from which seed plant leaves evolved. DOI: http://dx.doi.org/10.7554/eLife.15023.001 PMID:27710768

  3. Development of a predictive model for the growth kinetics of aerobic microbial population on pomegranate marinated chicken breast fillets under isothermal and dynamic temperature conditions.

    PubMed

    Lytou, Anastasia; Panagou, Efstathios Z; Nychas, George-John E

    2016-05-01

    The aim of this study was the development of a model to describe the growth kinetics of aerobic microbial population of chicken breast fillets marinated in pomegranate juice under isothermal and dynamic temperature conditions. Moreover, the effect of pomegranate juice on the extension of the shelf life of the product was investigated. Samples (10 g) of chicken breast fillets were immersed in marinades containing pomegranate juice for 3 h at 4 °C following storage under aerobic conditions at 4, 10, and 15 °C for 10 days. Total Viable Counts (TVC), Pseudomonas spp and lactic acid bacteria (LAB) were enumerated, in parallel with sensory assessment (odor and overall appearance) of marinated and non-marinated samples. The Baranyi model was fitted to the growth data of TVC to calculate the maximum specific growth rate (μmax) that was further modeled as a function of temperature using a square root-type model. The validation of the model was conducted under dynamic temperature conditions based on two fluctuating temperature scenarios with periodic changes from 6 to 13 °C. The shelf life was determined both mathematically and with sensory assessment and its temperature dependence was modeled by an Arrhenius type equation. Results showed that the μmax of TVC of marinated samples was significantly lower compared to control samples regardless temperature, while under dynamic temperature conditions the model satisfactorily predicted the growth of TVC in both control and marinated samples. The shelf-life of marinated samples was significantly extended compared to the control (5 days extension at 4 °C). The calculated activation energies (Ea), 82 and 52 kJ/mol for control and marinated samples, respectively, indicated higher temperature dependence of the shelf life of control samples compared to marinated ones. The present results indicated that pomegranate juice could be used as an alternative ingredient in marinades to prolong the shelf life of chicken.

  4. Foliar application of microbial and plant based biostimulants increases growth and potassium uptake in almond (Prunus dulcis [Mill.] D. A. Webb).

    PubMed

    Saa, Sebastian; Olivos-Del Rio, Andres; Castro, Sebastian; Brown, Patrick H

    2015-01-01

    The use of biostimulants has become a common practice in agriculture. However, there is little peer-reviewed research on this topic. In this study we tested, under controlled and replicated conditions, the effect of one biostimulant derived from seaweed extraction (Bio-1) and another biostimulant derived from microbial fermentation (Bio-2). This experiment utilized 2-years-old almond plants over two growing seasons in a randomized complete design with a full 2 × 4 factorial structure with two soil potassium treatments (125 μg g(-1) of K vs. 5 μg g(-1)) and four foliar treatments (No spray, Foliar-K, Bio-1, Bio-2). Rubidium was utilized as a surrogate for short-term potassium uptake and plant growth, nutrient concentration, and final plant biomass were evaluated. There was a substantial positive effect of both biostimulant treatments on total shoot leaf area, and significant increases in shoot length and biomass under adequate soil potassium supply with a positive effect of Bio-1 only under low K supply. Rubidium uptake was increased by Bio-1 application an effect that was greater under the low soil K treatment. Though significant beneficial effects of the biostimulants used on plant growth were observed, it is not possible to determine the mode of action of these materials. The results presented here illustrate the promise and complexity of research involving biostimulants.

  5. Foliar application of microbial and plant based biostimulants increases growth and potassium uptake in almond (Prunus dulcis [Mill.] D. A. Webb)

    PubMed Central

    Saa, Sebastian; Olivos-Del Rio, Andres; Castro, Sebastian; Brown, Patrick H.

    2015-01-01

    The use of biostimulants has become a common practice in agriculture. However, there is little peer-reviewed research on this topic. In this study we tested, under controlled and replicated conditions, the effect of one biostimulant derived from seaweed extraction (Bio-1) and another biostimulant derived from microbial fermentation (Bio-2). This experiment utilized 2-years-old almond plants over two growing seasons in a randomized complete design with a full 2 × 4 factorial structure with two soil potassium treatments (125 μg g-1 of K vs. 5 μg g-1) and four foliar treatments (No spray, Foliar-K, Bio-1, Bio-2). Rubidium was utilized as a surrogate for short-term potassium uptake and plant growth, nutrient concentration, and final plant biomass were evaluated. There was a substantial positive effect of both biostimulant treatments on total shoot leaf area, and significant increases in shoot length and biomass under adequate soil potassium supply with a positive effect of Bio-1 only under low K supply. Rubidium uptake was increased by Bio-1 application an effect that was greater under the low soil K treatment. Though significant beneficial effects of the biostimulants used on plant growth were observed, it is not possible to determine the mode of action of these materials. The results presented here illustrate the promise and complexity of research involving biostimulants. PMID:25755660

  6. A new mechanistic growth model for simultaneous determination of lag phase duration and exponential growth rate and a new Belehdradek-type model for evaluating the effect of temperature on growth rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new mechanistic growth model was developed to describe microbial growth under isothermal conditions. The new mathematical model was derived from the basic observation of bacterial growth that may include lag, exponential, and stationary phases. With this model, the lag phase duration and exponen...

  7. Microbial Growth Inferred from Nutrient Depletion in Deepwater Horizon Submerged Oil/Gas Plumes

    NASA Astrophysics Data System (ADS)

    Shiller, A. M.; Joung, D.

    2012-12-01

    The Deepwater Horizon accident resulted in a substantial uncontrolled hydrocarbon release to the northern Gulf of Mexico, much of which was entrained in deep submerged plumes. While bio-degradation of the hydrocarbons has been inferred from microbial biomass and genetics, the amount of conversion of oil and gas carbon to biomass remains uncertain. Here we examine correlated depletions of nitrate, phosphate, and oxygen in the submerged plumes during May 2010. Combining these correlations with published estimates of overall oxygen consumption, we estimate that the substantial portion of hydrocarbons in these plumes was initially converted to biomass. This contrasts with nutrient-limited surface waters where other work has suggested respiration to carbon dioxide to be the dominant fate of the hydrocarbons.

  8. Modeling of microbial substrate conversion, growth and product formation in a recycling fermentor.

    PubMed

    van Verseveld, H W; de Hollander, J A; Frankena, J; Braster, M; Leeuwerik, F J; Stouthamer, A H

    1986-01-01

    Paracoccus denitrificans and Bacillus licheniformis were grown in a carbon- and energy source-limited recycling fermentor with 100% biomass feedback. Experimental data for biomass accumulation and product formation as well as rates of carbon dioxide evolution and oxygen consumption were used in a parameter optimization procedure. This procedure was applied on a model which describes biomass growth as a linear function of the substrate consumption rate and the rate of product formation as a linear function of the biomass growth rate. The fitting procedure yielded two growth domains for P. denitrificans. In the first domain the values for the maximal growth yield and the maintenance coefficient were identical to those found in a series of chemostat experiments. The second domain could be described best with linear biomass increase, which is equal to a constant growth yield. Experimental data of a protease producing B. licheniformis also yielded two growth domains via the fitting procedure. Again, in the first domain, maximal growth yield and maintenance requirements were not significantly different from those derived from a series of chemostat experiments. Domain 2 behaviour was different from that observed with P. denitrificans. Product formation halts and more glucose becomes available for biomass formation, and consequently the specific growth rate increases in the shift from domain 1 to 2. It is concluded that for many industrial production processes, it is important to select organisms on the basis of a low maintenance coefficient and a high basic production of the desired product. It seems less important that the maximal production becomes optimized, which is the basis of most selection procedures.

  9. Triennial Growth Symposium: a review of science leading to host-targeted antibody strategies for preventing growth depression due to microbial colonization.

    PubMed

    Cook, M E

    2011-07-01

    In this review, the science used to develop host-targeted therapies for improving animal growth and feed efficiency is presented. In contrast to targeting the microbiota of the host, endogenous host proteins are targeted to regulate an overactive inflammatory response in the host. Activation of the immune/inflammatory systems of an animal is costly in terms of growth and feed efficiency. For example, reduced rates of BW gain and poorer feed efficiency in vaccinated animals compared with nonvaccinated animals have been well documented. Also, the growth rate and feed efficiency of animals colonized by microorganisms is only 80 to 90% of their germ-free counterparts. Further evidence of a cost associated with immune activation is that strategies that enhance the immune capability of an animal can reduce animal growth and feed efficiency. Research now indicates that the growth-promoting effects of antibiotics are indirect, and more likely the result of reduced immune activation due to decreased microbial exposure. Studies of mechanisms by which immune/inflammatory activation reduces animal growth and feed efficiency have shown that cytokines of the acute inflammatory response (i.e., IL-1 and tumor necrosis factor α) are key triggers for host muscle wasting. Cytokine-induced muscle wasting is linked to PG signaling pathways, and it has been proposed that regulation of the PG signaling pathways provide host targets for preventing an overreactive or unwarranted inflammatory event. Intestinal secretory phospholipase A(2) (sPLA(2)) has been found to be a useful and accessible (i.e., found in the intestinal lumen) host target for the regulation of an overreactive inflammatory response to conventional environments. This review presents the science and strategy for the regulation of intestinal sPLA(2) using orally administered egg yolk antibody against the enzyme. Clinically healthy animals fed egg antibodies to sPLA(2) had improved growth and feed efficiency. Literature

  10. Prediction of competitive microbial growth in mixed culture at dynamic temperature patterns.

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

    A novel competition model developed with the new logistic model and the Lotka-Volterra model successfully predicted the growth of bacteria in mixed culture using the mesophiles Staphylococcus aureus, Escherichia coli, and Salmonella at a constant temperature in our previous studies. In this study, we further studied the prediction of the growth of those bacteria in mixed culture at dynamic temperatures with various initial populations with the competition model. First, we studied the growth kinetics of the species in a monoculture at various constant temperatures ranging from 16℃ to 32℃. With the analyzed data in the monoculture, we then examined the prediction of bacterial growth in mixed culture with two and three species. The growth of the bacteria in the mixed culture at dynamic temperatures was successfully predicted with the model. The residuals between the observed and predicted populations at the data points were <0.5 log at most points, being 83.3% and 84.2% for the two-species mixture and the three-species mixture, respectively. The present study showed that the model could be applied to the competitive growth in mixed culture at dynamic temperature patterns.

  11. Growth of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, and Pseudomonas fluorescens 2-79

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence of human illness associated with the consumption of fresh sprouts has increased very sharply during the past decade. The objective of this study was to investigate the growth dynamics of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, an...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    PubMed

    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.

  14. Genetic determinants of prepubertal and pubertal growth and development.

    PubMed

    Thomis, Martine A; Towne, Bradford

    2006-12-01

    This article surveys the current general understanding of genetic influences on within- and between-population variation in growth and development in the context of establishing an International Growth Standard for Preadolescent and Adolescent Children. Traditional genetic epidemiologic analysis methods are reviewed, and evidence from family studies for genetic effects on different measures of growth and development is then presented. Findings from linkage and association studies seeking to identify specific genomic locations and allelic variants of genes influencing variation in growth and maturation are then summarized. Special mention is made of the need to study the interactions between genes and environments. At present, specific genes and polymorphisms contributing to variation in growth and maturation are only beginning to be identified. Larger genetic epidemiologic studies are needed in different parts of the world to better explore population differences in gene frequencies and gene-environment interactions. As advances continue to be made in molecular and statistical genetic methods, the genetic architecture of complex processes, including those of growth and development, will become better elucidated. For now, it can only be concluded that although the fundamental genetic underpinnings of the growth and development of children worldwide are likely to be essentially the same, there are also likely to be differences between populations in the frequencies of allelic gene variants that influence growth and maturation and in the nature of gene-environment interactions. This does not necessarily preclude an international growth reference, but it does have important implications for the form that such a reference might ultimately take.

  15. Determining the Molecular Growth Mechanisms of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Studies of the growth of tetragonal lysozyme crystals employing atomic force microscopy (AFM) have shown the advantages of this technique in investigating the growth mechanisms of protein crystals [1]. The resolution of these studies was in the micron range, which revealed surface features such as the occurrence of dislocations and 2D nucleation islands, similar to those found in inorganic systems. They clearly showed that the crystals grew by these surface growth mechanisms. However, the studies also revealed some surprising features, such as bimolecular growth step heights and pronounced growth anisotropies on the (110) face, which could not be explained. In previous studies we employed Periodic Bond Chain (PBC) theory to tetragonal lysozyme crystal growth and found that the crystals were constructed by strongly bonded molecular chains forming helices about the 43 axes [2,3]. The helices were connected to each other with weaker bonds. The growth process was shown to proceed by the formation of these 43 helices, resulting in bimolecular growth steps on the (110) face. It was also shown to explain many other observations on tetragonal lysozyme crystal growth. Although PBC analysis is not a new technique [4], it has not been widely used as the mechanisms predicted from it could not be experimentally verified. In this study the growth process of these crystals was investigated, particularly for the (110) face, employing some newly developed high resolution AFM techniques. These techniques allowed individual lysozyme molecules on the crystal faces to be resolved and predictions from PBC analyses to be tested. The analyses had shown that of the two possible packing arrangements on (110) faces, only one would actually occur. Employing the first of the newly developed techniques, these faces were scanned by high resolution AFM. The resulting images were then compared with the theoretically constructed images for the two possible packing arrangements on the (110) face

  16. Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination

    PubMed Central

    Wang, Guey-Horng; Cheng, Chiu-Yu; Liu, Man-Hai; Chen, Tzu-Yu; Hsieh, Min-Chi; Chung, Ying-Chien

    2016-01-01

    Fast hexavalent chromium (Cr(VI)) determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI)-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI) concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of the microbial fuel cell (MFC)-based biosensor indicated its potential as a reliable biosensor system. The MFC voltage decreased as the Cr(VI) concentration in the MFC increased. Two satisfactory linear relationships were observed between the Cr(VI) concentration and voltage output for various Cr(VI) concentration ranges (0.0125–0.3 mg/L and 0.3–5 mg/L). The MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in drinking water, groundwater, and electroplating wastewater in 45 min with low deviations (<10%). The use of the biosensor can help in preventing the violation of effluent regulations and the maximum allowable concentration of Cr(VI) in water. Thus, the developed MFC biosensor has potential as an early warning detection device for Cr(VI) determination even if O. anthropi YC152 is a possible opportunistic pathogen. PMID:27537887

  17. Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination.

    PubMed

    Wang, Guey-Horng; Cheng, Chiu-Yu; Liu, Man-Hai; Chen, Tzu-Yu; Hsieh, Min-Chi; Chung, Ying-Chien

    2016-08-16

    Fast hexavalent chromium (Cr(VI)) determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI)-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI) concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of the microbial fuel cell (MFC)-based biosensor indicated its potential as a reliable biosensor system. The MFC voltage decreased as the Cr(VI) concentration in the MFC increased. Two satisfactory linear relationships were observed between the Cr(VI) concentration and voltage output for various Cr(VI) concentration ranges (0.0125-0.3 mg/L and 0.3-5 mg/L). The MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in drinking water, groundwater, and electroplating wastewater in 45 min with low deviations (<10%). The use of the biosensor can help in preventing the violation of effluent regulations and the maximum allowable concentration of Cr(VI) in water. Thus, the developed MFC biosensor has potential as an early warning detection device for Cr(VI) determination even if O. anthropi YC152 is a possible opportunistic pathogen.

  18. Mapping high-growth phenotypes in the flux space of microbial metabolism

    PubMed Central

    Güell, Oriol; Massucci, Francesco Alessandro; Font-Clos, Francesc; Sagués, Francesc; Serrano, M. Ángeles

    2015-01-01

    Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to the study of a single optimal state, such as maximum biomass yield that is by far the most common assumption. Here, we confront optimal growth solutions to the whole set of feasible flux phenotypes (FFPs), which provides a benchmark to assess the likelihood of optimal and high-growth states and their agreement with experimental results. In addition, FFP maps are able to uncover metabolic behaviours, such as aerobic fermentation accompanying exponential growth on sugars at nutrient excess conditions, that are unreachable using standard models based on optimality principles. The information content of the full FFP space provides us with a map to explore and evaluate metabolic behaviour and capabilities, and so it opens new avenues for biotechnological and biomedical applications. PMID:26289659

  19. Determining the Kinetic Parameters Characteristic of Microalgal Growth.

    ERIC Educational Resources Information Center

    Martinez Sancho, Maria Eugenie; And Others

    1991-01-01

    An activity in which students obtain a growth curve for algae, identify the exponential and linear growth phases, and calculate the parameters which characterize both phases is described. The procedure, a list of required materials, experimental conditions, analytical technique, and a discussion of the interpretations of individual results are…

  20. Use of dissolved H2 concentrations to determine distribution of microbially catalyzed redox reactions in anoxic groundwater

    USGS Publications Warehouse

    Lovley, D.R.; Chapelle, F.H.; Woodward, J.C.

    1994-01-01

    The potential for using concentrations of dissolved H2 to determine the distribution of redox processes in anoxic groundwaters was evaluated. In pristine aquifers in which standard geochemical measurements indicated that Fe-(III) reduction, sulfate reduction, or methanogenesis was the terminal electron accepting process (TEAP), the H2 concentrations were similar to the H2 concentrations that have previously been reported for aquatic sediments with the same TEAPs. In two aquifers contaminated with petroleum products, it was impossible with standard geochemical analyses to determine which TEAPs predominated in specific locations. However, the TEAPs predicted from measurements of dissolved H2 were the same as those determined directly through measurements of microbial processes in incubated aquifer material. These results suggest that H2 concentrations may be a useful tool for analyzing the redox chemistry of nonequilibrium groundwaters.

  1. Effects of diets containing different concentrations of mannanoligosaccharide or antibiotics on growth performance, intestinal development, cecal and litter microbial populations, and carcass parameters of broilers.

    PubMed

    Baurhoo, B; Ferket, P R; Zhao, X

    2009-11-01

    The effects of 2 levels of mannanoligosaccharide (MOS) in feed were compared with antibiotic growth promoters on growth performance, intestinal morphology, cecal and litter microbial populations, and carcass parameters in broilers raised in a sanitary environment. Dietary treatments included: 1) antibiotic growth promoter-free diet (control), 2) VIRG (diet 1 + 16.5 mg/kg of virginiamycin), 3) BACT (diet 1 + 55 mg/kg of bacitracin), 4) LMOS (diet 1 + 0.2% MOS), and 5) HMOS (diet 1 + 0.5% MOS). Birds were randomly assigned to 3 replicate pens/treatment (n = 55/pen). Body weight and feed intake were recorded weekly throughout 38 d. At d 14, 24, and 34, a 1-cm segment of duodenum, jejunum, and ileum was used in morphological analysis (n = 9 birds/d per treatment). At the same bird ages, cecal contents were assayed for lactobacilli, bifidobacteria, Salmonella, Campylobacter, and Escherichia coli, whereas litter was analyzed for Salmonella, Campylobacter, and E. coli. Carcass yields (breast fillet and tenders, thigh, drumstick, and wing) were determined at d 38. Body weight, feed conversion, and carcass yields did not differ among treatments. In contrast to birds fed VIRG or BACT, LMOS and HMOS consistently increased (P < 0.05) villi height and goblet cell number per villus in all intestinal segments at d 24 and 34. Bifidobacteria concentrations were higher (P < 0.05) in LMOS- and HMOS-fed birds at all time points. Birds and litter from all treatments were free of Salmonella. At d 14 and 24, cecal E. coli and Campylobacter counts were not different among treatments. In comparison to birds fed control, at d 34, BACT, LMOS, and HMOS significantly reduced (P < 0.05) cecal E. coli concentrations, whereas Campylobacter counts were reduced (P < 0.05) by VIRG, BACT, and LMOS. Litter bacterial counts were not altered by dietary treatments. In conclusion, under conditions of this study, MOS conferred intestinal health benefits to chickens by improving its morphological

  2. Lead and cadmium-induced oxidative stress impacting mycelial growth of Oudemansiella radicata in liquid medium alleviated by microbial siderophores.

    PubMed

    Cao, Yan-Ru; Zhang, Xi-Yu; Deng, Jia-Yu; Zhao, Qi-Qi; Xu, Heng

    2012-04-01

    In this study, the effects of siderophores produced by six bacteria on mycelium growth, Cd and Pb accumulation, lipid peroxidation, protein content and antioxidant enzyme in Oudemansiella radicata were investigated in Cd and Pb-containing liquid medium. The results showed that inoculation with siderophore-containing filtrates (SCF) partly enhanced the growth of O. radicata after 15 days, with 0.8-32.4% biomass increase for Cd and 0.7-20.8% for Pb compared to control(s), which lacked siderophore. The maximum enhancement for accumulation were found to be confined to Bacillus sp. FFQ2(s) (26.5%) for Cd and Pseudomonas sp. CY63(s) (158.9%) for Pb. A significant decrease in MDA content indicated that lipid peroxidation in O. radicata was alleviated by siderophores. Besides, antioxidant enzyme SOD and POD activities also displayed obviously decrease in SCF-treated mycelium compared to control(s) treatment, while CAT activity did not present significant change. Protein level in O. radicata treated by SCF increased from 0.3 to 138.0% for Cd and from 10.9 to 107.1% for Pb compared to control(s). Therefore, the present work suggests that microbial siderophores can reduce the toxicity of metals to mycelium and then alleviate heavy metals-inducing oxidative stress in O. radicata.

  3. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

    PubMed Central

    McElfresh, Cameron; Wong, Lily R.

    2015-01-01

    Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. PMID:26070672

  4. Statistical support for the ATL program. [microbial growth in zero gravity

    NASA Technical Reports Server (NTRS)

    Hinkelmann, K.; Myers, R. H.

    1976-01-01

    Statistical experimental designs are presented for various numbers of organisms and agar solutions pertinent to the experiment, ""colony growth in zero gravity''. Missions lasting 7 and 30 days are considered. For the designs listed, the statistical analysis of the observations obtained on the space shuttle are outlined.

  5. The mechanism of ethanol treatment on inhibiting lettuce enzymatic browning and microbial growth

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tissue browning of fresh-cut lettuce greatly affects its quality and consumers’ appreciation. This study investigated the effects of ethanol treatment on enzymatic browning and natural microflora growth of lettuce stem discs. After treated with 20% ethanol for 2 min and then drained by a spinner, le...

  6. Use of poisons in determination of microbial manganese binding rates in seawater

    SciTech Connect

    Rosson, R.A.; Tebo, B.M.; Nealson, K.H.

    1984-04-01

    A method was developed to determine whether microorganisms mediate the precipitation of manganese(II) in the marine environment. Radioactive /sup 54/Mn(II) was used as a tracer to measure the precipitation (binding and oxidation) of Mn(II) (i.e., the /sup 54/Mn(II) trapped on 0.2-..mu..m membrane filters) in the presence and absence of biological poisons. A variety of antibiotics, fixatives, and metabolic inhibitors were tested in laboratory control experiments to select poisons that did not interfere in the chemistry of manganese. The poisons were deemed suitable if (i) they did not complex Mn(II) more strongly than the ion-exchange resin Chelex 100, (ii) they did not interfere in the adsorption of /sup 54/Mn(II) onto synthetic deltaMnO/sub 2/ (manganate), (iii) they did not cause desorption of /sup 54/Mn(II) which had been preadsorbed onto synthetic manganate, and (iv) they did not solubilize synthetic /sup 54/manganate. In addition, several known chelators, reducing agents, and buffers normally added to microbiological growth media or used in biochemical assays were tested. Most additions interfered to some extent with manganese chemistry. However, at least one inhibitor, sodium azide, or a mixture of sodium azide, penicillin, and tetracycline was shown to be appropriate for use in field studies of /sup 54/Mn(II) binding. Formaldehyde could also be used in short incubations (1 to 3 h) but was not suitable for longer time course studies. The method was applied to studies of Mn(II) precipitation in Saanich Inlet, British Columbia, Canada. Bacteria were shown to significantly enhance the rate of Mn(II) removal from solution in the manganese-rich particulate layer which occurs just above the oxygen-hydrogen sulfide interface in the water column. 23 references.

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

    SciTech Connect

    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.

  8. Effects of Polyurethane Foams on Microbial Growth in Fuel-Water Systems

    PubMed Central

    Cooney, J. J.

    1969-01-01

    Four, open-cell, ester-base polyurethane foams were examined for their effect on growth of fuel-utilizing organisms in jet fuel-water systems. Three foams contained a potential biocide, tetraethylthiuram E (0.66%), sodium omadine (0.07%), or zinc omadine (0.07%), all w/v. These were compared with a control foam which did not contain an additive. Each foam was examined in fuel-water systems containing JP-4 fuel, JP-4 fuel plus 0.1% anti-icing additive (AIA), or JP-5 fuel. Pure cultures of a fuel-grown bacterium, Pseudomonas aeruginosa, and of a fuel-grown fungus, Hormodendrum (Cladosporium) sp., served as test organisms. In control cultures without foam and in cultures containing control foam, P. aeruginosa achieved maximum stationary-phase populations of approximately 108 viable cells per ml, and Hormodendrum sp. produced an extensive mycelial mat. In the three fuel systems examined, tetraethylthiuram E- and sodium omadine-containing foams had little effect on growth of the bacterium; foam with zinc omadine decreased the rate of bacterial growth but had little effect on total populations. Tetraethylthiuram E decreased the rate of fungal growth and showed its greatest effect in JP-4 plus AIA. Foam with sodium omadine or zinc omadine markedly decreased fungal growth in all three fuel systems. The data suggest that either sodium omadine or zinc omadine in polyurethane foam may be a useful antifungal agent; and that tetraethylthiuram E and AIA could exert a synergistic effect, particularly at AIA concentrations which have been reported to occur in some field situations. Images PMID:16349836

  9. Inhibition of vitamin B12-dependent microbial growth by nitrous oxide

    SciTech Connect

    Alston, T.A. )

    1991-01-01

    In methionine-free media, nitrous oxide inhibits the growth of an auxotrophic strain of Escherichia coli lacking a cobalamin-independent pathway for the de novo synthesis of methionine. Prototrophic E. coli is similarly inhibited by nitrous oxide if the cobalamin-independent pathway is selectively depressed by sulfanilamide. Nitrous oxide thus effectively inactivates cobalamin-dependent 5-methyltetrahydrofolate-homocysteine methyltransferase in intact bacteria.

  10. Microbial cooperation in the rhizosphere improves liquorice growth under salt stress.

    PubMed

    Egamberdieva, Dilfuza; Wirth, Stephan; Li, Li; Abd Allah, Elsayed Fathi; Lindström, Kristina

    2016-10-26

    Liquorice (Glycyrrhiza uralensis Fisch.) is one of the most widely used plants in food production, and it can also be used as an herbal medicine or for reclamation of salt-affected soils. Under salt stress, inhibition of plant growth, nutrient acquisition and symbiotic interactions between the medicinal legume liquorice and rhizobia have been observed. We recently evaluated the interactions between rhizobia and root-colonizing Pseudomonas in liquorice grown in potting soil and observed increased plant biomass, nodule numbers and nitrogen content after combined inoculation compared to plants inoculated with Mesorhizobium alone. Several beneficial effects of microbes on plants have been reported; studies examining the interactions between symbiotic bacteria and root-colonizing Pseudomonas strains under natural saline soil conditions are important, especially in areas where a hindrance of nutrients and niches in the rhizosphere are high. Here, we summarize our recent observations regarding the combined application of rhizobia and Pseudomonas on the growth and nutrient uptake of liquorice as well as the salt stress tolerance mechanisms of liquorice by a mutualistic interaction with microbes. Our observations indicate that microbes living in the rhizosphere of liquorice can form a mutualistic association and coordinate their involvement in plant adaptations to stress tolerance. These results support the development of combined inoculants for improving plant growth and the symbiotic performance of legumes under hostile conditions.

  11. A Method for Bioinformatic Analysis of Transposon Insertion Sequencing (INSeq) Results for Identification of Microbial Fitness Determinants.

    PubMed

    Wang, Nengding; Ozer, Egon A

    2017-01-01

    Transposon insertion sequencing is a process whereby microbial fitness determinants can be identified on a genome-wide scale. This process uses high-throughput next generation sequencing to screen for changes in the composition of a pool of transposon mutants after exposure to selective conditions. One commonly used process for generating transposon insertion sequencing libraries is called INSeq that works with mutant pools produced using a modified Mariner transposon. Libraries produced using the INSeq process are sequenced on the Illumina platform. In this chapter, we describe our method for processing the raw Illumina sequencing reads, aligning the reads to a reference sequence to determine read counts, and using the online transposon insertion sequencing data analysis server, ESSENTIALS, to interpret the results.

  12. Impact of flue gas desulfurization-calcium sulfite and gypsum on soil microbial activity and wheat growth

    SciTech Connect

    Lee, Y.B.; Bigham, J.M.; Dick, W.A.; Kim, P.J.

    2008-08-15

    We conducted greenhouse tests to evaluate the effects of FGD-CaSO{sub 3} applied at rates of 0, 2.2, 4.4, and 8.8 Mg ha(-1) on wheat growth, soil enzyme activities, and the chemical properties of two soils with differing pH (4.0 vs. 6.2). A gypsum treatment applied at the rate of 2.2 Mg ha{sup -1} was used as a positive control. Exchangeable Ca{sup 2+} and water-extractable Ca{sup 2+} and SO{sub 4}{sup 2-} increased significantly with increasing FGD-CaSO{sub 3} application. SO{sub 4}{sup 2-} increased in both soils, indicating rapid oxidation of SO{sub 3}{sup 2-} to SO{sub 4}{sup 2-} when neither water nor oxygen was limiting. No changes in soil pH were measured. Applications of 2.2, 4.4, or 8.8 Mg CaSO{sub 3} ha{sup -1} to the pH 6.2 soil produced no effect on wheat growth or the uptake of N, P, Ca{sup 2+}, and Mg{sup 2+}. The uptake of SO{sub 4}{sup 2-} -S increased, whereas K uptake decreased. No significant differences in the activities of urease, {beta}-glucosidase, alkaline phosphatase, or arylsulfatase were observed relative to a control. In the acid soil, an application of 2.2 Mg ha{sup -1} FGD-CaSO{sub 3} increased wheat root growth and dry matter yield compared with an untreated control. The uptake of N, P, Ca{sup 2+}, and K{sup +} also increased presumably because of enhanced root development resulting from decreases in exchangeable Al{sup 3+} and increases in soluble Ca{sup 2+}. Wheat growth and alkaline phosphatase and arylsulfatase activities were significantly inhibited by addition of 8.8 Mg ha{sup -1} of FGD-CaSO{sub 3} compared with the untreated control or the same soil receiving 2.2 Mg ha{sup -1} gypsum. We conclude that surface applications of FGD-CaSO{sub 3} may be as effective as gypsum for inhibiting soil crusting, improving water infiltration, and promoting the movement of Ca{sup 2+} into acid subsoils. Moreover, application rates of equal to or less than 4.4 Mg ha-1 should have no negative impact on soil microbial activities or plant growth.

  13. Nutrient competition as a determinant for cancer growth

    NASA Astrophysics Data System (ADS)

    Scalerandi, M.; Romano, A.; Pescarmona, G. P.; Delsanto, P. P.; Condat, C. A.

    1999-02-01

    Competition for available nutrients is known to be crucial for cancer development. Based on this fact, a model is proposed that can describe the manifold of morphologies and growth rates characteristic of tumoral growth. The formulation of a consistent set of rules governing the microscopic interactions leads to a system of coupled nonlinear iteration equations. These equations contain both deterministic and stochastic terms and are amenable to direct numerical simulation. They allow us to test the effects of such parameters as the availability, diffusivity, and binding rate of nutrients and the mobility, death, and multiplication rates of cancer cells on tumor morphology and development. Detailed numerical solutions are presented.

  14. Inhibition of microbial growth by ajoene, a sulfur-containing compound derived from garlic.

    PubMed Central

    Naganawa, R; Iwata, N; Ishikawa, K; Fukuda, H; Fujino, T; Suzuki, A

    1996-01-01

    Ajoene, a garlic-derived sulfur-containing compound that prevents platelet aggregation, exhibited broad-spectrum antimicrobial activity. Growth of gram-positive bacteria, such as Bacillus cereus, Bacillus subtilis, Mycobacterium smegmatis, and Streptomyces griseus, was inhibited at 5 micrograms of ajoene per ml. Staphylococcus aureus and Lactobacillus plantarum also were inhibited below 20 micrograms of ajoene per ml. For gram-negative bacteria, such as Escherichia coli, Klebsiella pneumoniae, and Xanthomonas maltophilia, MICs were between 100 and 160 micrograms/ml. Ajoene also inhibited yeast growth at concentrations below 20 micrograms/ml. The microbicidal effect of ajoene on growing cells was observed at slightly higher concentrations than the corresponding MICs. B. cereus and Saccharomyces cerevisiae were killed at 30 micrograms of ajoene per ml after 24 h of cultivation when cultivation was started at 10(5) cells per ml. However, the minimal microbicidal concentrations for resting cells were at 10 to 100 times higher concentrations than the corresponding MICs. The disulfide bond in ajoene appears to be necessary for the antimicrobial activity of ajoene, since reduction by cysteine, which reacts with disulfide bonds, abolished its antimicrobial activity. PMID:8900018

  15. Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities

    PubMed Central

    Lara, Lidia Susana; Rodriguez, Alia; Uribe-Vélez, Daniel; Sanders, Ian R.

    2016-01-01

    Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities. PMID:27253975

  16. Fighting fish (Betta splendens) bubble nests do not inhibit microbial growth.

    PubMed

    Brown, Alexandria C; Clotfelter, Ethan D

    2012-12-01

    Some organisms produce antimicrobial substances in nesting foam to favorably manipulate the environment to which their developing offspring are exposed. We tested if fighting fish Betta splendens foamy nest material, which is comprised of bubbles produced in the oral cavity of nesting males, has antimicrobial properties against a pathogenic bacteria (Edwardsiella tarda), a nonpathogenic bacteria (Escherichia coli), or a pathogenic oomycete (Saprolegnia parasitica). We also tested if exposure to nest material increases larval survival by performing in vitro fertilizations and individually incubating eggs in bubble nest extract or tank water (control). Our results show no evidence of antimicrobial properties of bubble nests. On the contrary, bubble nests provided favorable microenvironments for the growth of Saprolegnia parasitica. Our results confirm earlier work citing the importance of male nest attendance, and suggest that the mechanism responsible for decreased survival in the absence of attending males is pathogenic microbes.

  17. Interventions for control of Salmonella: Clearance of Microbial growth from rubber picker fingers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted to determine if a surface material with antimicrobial properties combined with an effective disinfectant could achieve total clearance of bacterial contamination. Prior to beginning the project, new rubber picker fingers collected from three processing facilities were tested fo...

  18. 75 FR 40774 - Determination Under the African Growth and Opportunity Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-14

    ... IMPLEMENTATION OF TEXTILE AGREEMENTS Determination Under the African Growth and Opportunity Act AGENCY: Committee...'' and ``ethnic printed fabrics'' and qualify for preferential treatment under the African Growth and... Growth and Opportunity Act (Title I of the Trade and Development Act of 2000, Pub. L. No....

  19. 78 FR 36749 - Determination Under the African Growth and Opportunity Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-19

    ... IMPLEMENTATION OF TEXTILE AGREEMENTS Determination Under the African Growth and Opportunity Act AGENCY: Committee... ``ethnic printed fabrics'' and qualify for preferential treatment under the African Growth and Opportunity.... SUPPLEMENTARY INFORMATION: Authority: Sections 112(a) and 112(b)(6) of the African Growth and Opportunity...

  20. 76 FR 6840 - Determinations Under the African Growth and Opportunity Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-08

    ... TRADE REPRESENTATIVE Determinations Under the African Growth and Opportunity Act AGENCY: Office of the... toward implementing and following, the customs procedures required by the African Growth and Opportunity... applicable visa requirements. See Visa Requirements Under the African Growth and Opportunity Act, 66 FR...

  1. 78 FR 16908 - Determinations Under the African Growth and Opportunity Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-19

    ... Determinations Under the African Growth and Opportunity Act AGENCY: Office of the United States Trade... following, the customs procedures required by the African Growth and Opportunity Act (AGOA). Therefore, as... the applicable visa requirements. See Visa Requirements Under the African Growth and Opportunity...

  2. Measurement of Microbial DNA Polymerase Activity Enables Detection and Growth Monitoring of Microbes from Clinical Blood Cultures

    PubMed Central

    Zweitzig, Daniel R.; Riccardello, Nichol M.; Morrison, John; Rubino, Jason; Axelband, Jennifer; Jeanmonod, Rebecca; Sodowich, Bruce I.; Kopnitsky, Mark J.; O’Hara, S. Mark

    2013-01-01

    Surveillance of bloodstream infections (BSI) is a high priority within the hospital setting. Broth-based blood cultures are the current gold standard for detecting BSI, however they can require lengthy incubation periods prior to detection of positive samples. We set out to demonstrate the feasibility of using enzymatic template generation and amplification (ETGA)-mediated measurement of DNA polymerase activity to detect microbes from clinical blood cultures. In addition to routine-collected hospital blood cultures, one parallel aerobic blood culture was collected and immediately refrigerated until being transported for ETGA analysis. After refrigeration holding and transport, parallel-collected cultures were placed into a BACTEC incubator and ETGA time-course analysis was performed. Of the 308 clinical blood cultures received, 22 were BACTEC positive, and thus were initially selected for ETGA time course analysis. The ETGA assay detected microbial growth in all 22 parallel-positive blood cultures in less time than a BACTEC incubator and also yielded genomic DNA for qPCR-based organism identification. In summary, feasibility of detecting microbes from clinical blood culture samples using the ETGA blood culture assay was demonstrated. Additional studies are being considered towards development of clinically beneficial versions of this methodology. PMID:24155986

  3. Automated inference procedure for the determination of cell growth parameters

    NASA Astrophysics Data System (ADS)

    Harris, Edouard A.; Koh, Eun Jee; Moffat, Jason; McMillen, David R.

    2016-01-01

    The growth rate and carrying capacity of a cell population are key to the characterization of the population's viability and to the quantification of its responses to perturbations such as drug treatments. Accurate estimation of these parameters necessitates careful analysis. Here, we present a rigorous mathematical approach for the robust analysis of cell count data, in which all the experimental stages of the cell counting process are investigated in detail with the machinery of Bayesian probability theory. We advance a flexible theoretical framework that permits accurate estimates of the growth parameters of cell populations and of the logical correlations between them. Moreover, our approach naturally produces an objective metric of avoidable experimental error, which may be tracked over time in a laboratory to detect instrumentation failures or lapses in protocol. We apply our method to the analysis of cell count data in the context of a logistic growth model by means of a user-friendly computer program that automates this analysis, and present some samples of its output. Finally, we note that a traditional least squares fit can provide misleading estimates of parameter values, because it ignores available information with regard to the way in which the data have actually been collected.

  4. Growth of (101) Faces of Tetragonal Lysozyme Crystals: Determination of the Growth Mechanism

    NASA Technical Reports Server (NTRS)

    Li, Meirong; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    Measurements of the macroscopic growth rates of the (101) face of tetragonal lysozyme crystals indicate an unusual dependence on the supersaturation (Forsythe, Nadarajah & Pusey, 1998), similar to that observed for the (110) face. As done before for the (110) face, in this study the surface packing arrangement for the (101) face was constructed, based on earlier microscopic observations and theoretical analysis of the internal molecular packing. This allowed the minimum growth unit for this face to be identified as a tetramer corresponding to a single turn of helices centered about the 4(sub 3) axes, and the minimum growth step to be of unimolecular height. A macroscopic mathematical model for the growth of the (101) face was developed, based on the formation of aggregate growth units in solution and the addition of a unit to the crystal face by dislocation and two-dimensional nucleation mechanisms. The calculations showed that the best fits were obtained for tetramer or octamer growth units in this model, indicating that average size of the growth unit participating in the growth process was between these two sizes.

  5. Oligonucleotide microarrays for identification of microbial pathogens and detection of their virulence-associated or drug-resistance determinants.

    PubMed

    Volokhov, Dmitriy V; Kong, Hyesuk; Herold, Keith; Chizhikov, Vladimir E; Rasooly, Avraham

    2011-01-01

    Microarrays are spatially ordered arrays with ligands chemically immobilized in discrete spots on a solid matrix, usually a microscope slide. Microarrays are a high-throughput large-scale screening system enabling simultaneous identification of a large number of labeled target molecules (up to several hundred thousand) that bind specifically to the immobilized ligands of the array. DNA microarrays represent a promising tool for clinical, environmental, and industrial microbiology since the technology allows relatively rapid identification of large number of genetic determinants simultaneously, providing detailed genomic level information regarding the pathogen species, including identification of their virulence-associated factors and the presence of antibiotic resistance genes. In this chapter, we describe key aspects and methodologies important for the development and use of DNA microarrays for microbial diagnostics.

  6. One-pot enzymatic conversion of carbon dioxide and utilization for improved microbial growth.

    PubMed

    Hong, Sung-Gil; Jeon, Hancheol; Kim, Han Sol; Jun, Seung-Hyun; Jin, EonSeon; Kim, Jungbae

    2015-04-07

    We developed a process for one-pot CO2 conversion and utilization based on simple conversion of CO2 to bicarbonate at ambient temperature with no energy input, by using the cross-linking-based composites of carboxylated polyaniline nanofibers (cPANFs) and carbonic anhydrase. Carbonic anhydrase was immobilized on cPANFs via the approach of magnetically separable enzyme precipitate coatings (Mag-EPC), which consists of covalent enzyme attachment, enzyme precipitation, and cross-linking with amine-functionalized magnetic nanoparticles. Mag-EPC showed a half-life of 236 days under shaking, even resistance to 70% ethanol sterilization, and recyclability via facile magnetic separation. For one-pot CO2 conversion and utilization, Mag-EPC was used to accelerate the growth of microalga by supplying bicarbonate from CO2, representing 1.8-fold increase of cell concentration when compared to the control sample. After two repeated uses via simple magnetic separation, the cell concentration with Mag-EPC was maintained as high as the first cycle. This one-pot CO2 conversion and utilization is an alternative as well as complementary process to adsorption-based CO2 capture and storage as an environmentally friendly approach, demanding no energy input based on the effective action of the stabilized enzyme system.

  7. The gompertz function can coherently describe microbial mineralization of growth-sustaining pesticides.

    PubMed

    Johnsen, Anders R; Binning, Philip J; Aamand, Jens; Badawi, Nora; Rosenbom, Annette E

    2013-08-06

    Mineralization of (14)C-labeled tracers is a common way of studying the environmental fate of xenobiotics, but it can be difficult to extract relevant kinetic parameters from such experiments since complex kinetic functions or several kinetic functions may be needed to adequately describe large data sets. In this study, we suggest using a two-parameter, sigmoid Gompertz function for parametrizing mineralization curves. The function was applied to a data set of 252 normalized mineralization curves that represented the potential for degradation of the herbicide MCPA in three horizons of an agricultural soil. The Gompertz function fitted most of the normalized curves, and trends in the data set could be visualized by a scatter plot of the two Gompertz parameters (rate constant and time delay). For agricultural topsoil, we also tested the effect of the MCPA concentration on the mineralization kinetics. Reduced initial concentrations lead to shortened lag-phases, probably due to reduced need for bacterial growth. The effect of substrate concentration could be predicted by simply changing the time delay of the Gompertz curves. This delay could to some extent also simulate concentration effects for 2,4-D mineralization in agricultural soil and aquifer sediment and 2,6-dichlorobenzamide mineralization in single-species, mineral medium.

  8. Antimicrobial activity of transition metal acid MoO(3) prevents microbial growth on material surfaces.

    PubMed

    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.

  9. Microbial growth at hyperaccelerations up to 403,627 x g.

    PubMed

    Deguchi, Shigeru; Shimoshige, Hirokazu; Tsudome, Mikiko; Mukai, Sada-atsu; Corkery, Robert W; Ito, Susumu; Horikoshi, Koki

    2011-05-10

    It is well known that prokaryotic life can withstand extremes of temperature, pH, pressure, and radiation. Little is known about the proliferation of prokaryotic life under conditions of hyperacceleration attributable to extreme gravity, however. We found that living organisms can be surprisingly proliferative during hyperacceleration. In tests reported here, a variety of microorganisms, including Gram-negative Escherichia coli, Paracoccus denitrificans, and Shewanella amazonensis; Gram-positive Lactobacillus delbrueckii; and eukaryotic Saccharomyces cerevisiae, were cultured while being subjected to hyperaccelerative conditions. We observed and quantified robust cellular growth in these cultures across a wide range of hyperacceleration values. Most notably, the organisms P. denitrificans and E. coli were able to proliferate even at 403,627 × g. Analysis shows that the small size of prokaryotic cells is essential for their proliferation under conditions of hyperacceleration. Our results indicate that microorganisms cannot only survive during hyperacceleration but can display such robust proliferative behavior that the habitability of extraterrestrial environments must not be limited by gravity.

  10. Microbial growth at hyperaccelerations up to 403,627 × g

    PubMed Central

    Deguchi, Shigeru; Shimoshige, Hirokazu; Tsudome, Mikiko; Mukai, Sada-atsu; Corkery, Robert W.; Ito, Susumu; Horikoshi, Koki

    2011-01-01

    It is well known that prokaryotic life can withstand extremes of temperature, pH, pressure, and radiation. Little is known about the proliferation of prokaryotic life under conditions of hyperacceleration attributable to extreme gravity, however. We found that living organisms can be surprisingly proliferative during hyperacceleration. In tests reported here, a variety of microorganisms, including Gram-negative Escherichia coli, Paracoccus denitrificans, and Shewanella amazonensis; Gram-positive Lactobacillus delbrueckii; and eukaryotic Saccharomyces cerevisiae, were cultured while being subjected to hyperaccelerative conditions. We observed and quantified robust cellular growth in these cultures across a wide range of hyperacceleration values. Most notably, the organisms P. denitrificans and E. coli were able to proliferate even at 403,627 × g. Analysis shows that the small size of prokaryotic cells is essential for their proliferation under conditions of hyperacceleration. Our results indicate that microorganisms cannot only survive during hyperacceleration but can display such robust proliferative behavior that the habitability of extraterrestrial environments must not be limited by gravity. PMID:21518884

  11. Parenting Styles: A Key Factor to Self Determination and Personal Growth of Adults

    ERIC Educational Resources Information Center

    Aslam, Manika Arbab; Sultan, Sarwat

    2014-01-01

    The study was conducted to explore the impact of parenting styles of adolescents on their self-determination and personal growth. The data was collected from 300 adults evenly divided by gender, aged 23-38 years. To measure the parenting styles, level of self-determination and personal growth, the Caregivers Practices Report, Self Determination…

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

    PubMed

    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 < 0.001) nutrient digestibility except for ADF. However, CP digestibility increased (P < 0.001) only for the high-concentrate diets including grass hay. Likewise, N retention, ruminal NH(3)-N concentration, and urinary excretion of purine derivatives increased (P < 0.05) with increasing concentrate in animals fed diets based on grass hay (0.23 vs. 0.13 g of retained N/g of digested N, 30.1 vs. 12.9 mg of NH(3)-N/100 mL, and 11.5 vs. 8.40 mmol/d, respectively), but not (P > 0.05) when diets included alfalfa hay. Total protozoa numbers and holotricha proportion were greater and less (P < 0.001), respectively, in high- than in low-concentrate diets. The F:C affected (P < 0.001) ruminal pH but not total VFA concentration (P = 0.12). Ammonia-N concentration was similar (P = 0.13) over time, whereas pH, VFA concentration, and protozoa numbers differed (P < 0.001) among diets. Estimated MNF was strongly influenced by using either the purine bases:N ratio obtained in our experimental conditions or values reported in the literature for small ruminants. There was a F:C effect (P = 0.006) on MNF estimated from LAB but not from SAB. The effect of F:C shifting from 70:30 to 30:70 in goat diets depends on the type of forage used. The MNF measured in goats fed different diets was influenced by the bacterial pellet (LAB or SAB). In addition

  13. Growth of ectomycorrhizal mycelia and composition of soil microbial communities in oak forest soils along a nitrogen deposition gradient.

    PubMed

    Nilsson, Lars Ola; Bååth, Erland; Falkengren-Grerup, Ursula; Wallander, Håkan

    2007-08-01

    Deciduous forests may respond differently from coniferous forests to the anthropogenic deposition of nitrogen (N). Since fungi, especially ectomycorrhizal (EM) fungi, are known to be negatively affected by N deposition, the effects of N deposition on the soil microbial community, total fungal biomass and mycelial growth of EM fungi were studied in oak-dominated deciduous forests along a nitrogen deposition gradient in southern Sweden. In-growth mesh bags were used to estimate the production of mycelia by EM fungi in 19 oak stands in the N deposition gradient, and the results were compared with nitrate leaching data obtained previously. Soil samples from 154 oak forest sites were analysed regarding the content of phospholipid fatty acids (PLFAs). Thirty PLFAs associated with microbes were analysed and the PLFA 18:2omega6,9 was used as an indicator to estimate the total fungal biomass. Higher N deposition (20 kg N ha(-1)y(-1) compared with 10 kg N ha(-1)y(-1)) tended to reduce EM mycelial growth. The total soil fungal biomass was not affected by N deposition or soil pH, while the PLFA 16:1omega5, a biomarker for arbuscular mycorrhizal (AM) fungi, was negatively affected by N deposition, but also positively correlated to soil pH. Other PLFAs positively affected by soil pH were, e.g., i14:0, a15:0, 16:1omega9, a17:0 and 18:1omega7, while some were negatively affected by pH, such as i15:0, 16:1omega7t, 10Me17:0 and cy19:0. In addition, N deposition had an effect on the PLFAs 16:1omega7c and 16:1omega9 (negatively) and cy19:0 (positively). The production of EM mycelia is probably more sensitive to N deposition than total fungal biomass according to the fungal biomarker PLFA 18:2omega6,9. Low amounts of EM mycelia covaried with increased nitrate leaching, suggesting that EM mycelia possibly play an important role in forest soil N retention at increased N input.

  14. Inhibition of bacterial growth in sweet cheese whey by carbon dioxide as determined by culture-independent community profiling.

    PubMed

    Lo, Raquel; Xue, Tian; Weeks, Mike; Turner, Mark S; Bansal, Nidhi

    2016-01-18

    Whey is a valuable co-product from cheese making that serves as a raw material for a wide range of products. Its rich nutritional content lends itself to rapid spoilage, thus it typically needs to be pasteurised and refrigerated promptly. Despite the extensive literature on milk spoilage bacteria, little is known about the spoilage bacteria of whey. The utility of carbon dioxide (CO2) to extend the shelf-life of raw milk and cottage cheese has been well established, but its application in whey preservation has not yet been explored. This study aims to characterise the microbial populations of fresh and spoiled sweet whey by culture-independent community profiling using 454 pyrosequencing of 16S rRNA gene amplicons and to determine whether carbonation is effective in inhibiting bacterial growth in sweet whey. The microbiota of raw Cheddar and Mozzarella whey was dominated by cheese starter bacteria. After pasteurisation, two out of the three samples studied became dominated by diverse environmental bacteria from various phyla, with Proteobacteria being the most dominant. Diverse microbial profiles were maintained until spoilage occurred, when the entire population was dominated by just one or two genera. Whey spoilage bacteria were found to be similar to those of milk. Pasteurised Cheddar and Mozzarella whey was spoiled by Bacillus sp. or Pseudomonas sp., and raw Mozzarella whey was spoiled by Pseudomonas sp., Serratia sp., and other members of the Enterobacteriaceae family. CO2 was effective in inhibiting bacterial growth of pasteurised Cheddar and Mozzarella whey stored at 15°C and raw Mozzarella whey stored at 4°C. The spoilage bacteria of the carbonated samples were similar to those of the non-carbonated controls.

  15. Inhibitory effects of Lactobacillus fermentum on microbial growth and biofilm formation.

    PubMed

    Rybalchenko, Oxana V; Bondarenko, Viktor M; Orlova, Olga G; Markov, Alexander G; Amasheh, S

    2015-10-01

    Beneficial effects of Lactobacilli have been reported, and lactic bacteria are employed for conservation of foods. Therefore, the effects of a Lactobacillus fermentum strain were analyzed regarding inhibitory effects on staphylococci, Candida albicans and enterotoxigenic enterobacteria by transmission electron microscopy (TEM). TEM of bacterial biofilms was performed using cocultures of bacteriocin-producing L. fermentum 97 with different enterotoxigenic strains: Staphylococcus epidermidis expressing the ica gene responsible for biofilm formation, Staphylococcus aureus producing enterotoxin type A, Citrobacter freundii, Enterobacter cloaceae, Klebsiella oxytoca, Proteus mirabilis producing thermolabile and thermostable enterotoxins determined by elt or est genes, and Candida albicans. L. fermentum 97 changed morphological features and suppressed biofilm formation of staphylococci, enterotoxigenic enterobacteria and Candida albicans; a marked transition to resting states, a degradation of the cell walls and cytoplasm, and a disruption of mature bacterial biofilms were observed, the latter indicating efficiency even in the phase of higher cell density.

  16. Growth determinations for unattached bacteria in a contaminated aquifer.

    USGS Publications Warehouse

    Harvey, R.W.; George, L.H.

    1987-01-01

    Growth rates of unattached bacteria in groundwater contaminated with treated sewage and collected at various distances from the source of contamination were estimated by using frequency of dividing cells and tritiated-thymidine uptake and compared with growth rates obtained with unsupplemented, closed-bottle incubations. Estimates of bacterial generation times [(In 2)/mu] along a 3-km-long transect in oxygen-depleted (0.1 to 0.7 mg of dissolved oxygen liter-1) groundwater ranged from 16 h at 0.26 km downgradient from an on-land, treated-sewage outfall to 139 h at 1.6 km and correlated with bacterial abundance (r2 = 0.88 at P less than 0.001). Partitioning of assimilated thymidine into nucleic acid generally decreased with distance from the contaminant source, and one population in heavily contaminated groundwater assimilated little thymidine during a 20-h incubation. Several assumptions commonly made when frequency of dividing cells and tritiated-thymidine uptake are used were not applicable to the groundwater samples.

  17. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    SciTech Connect

    Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Fang, Yilin; Mahadevan, Radhakrishnan; Lovley, Derek R.

    2013-09-07

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under

  18. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

    2012-12-01

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model

  19. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    NASA Astrophysics Data System (ADS)

    Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

    2013-09-01

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model

  20. Statistical Optimization of Medium Components for Mass Production of Plant Growth-Promoting Microbial Inoculant Pseudomonas trivialis BIHB 745 (MTCC5336).

    PubMed

    Vyas, Pratibha; Rahi, Praveen; Chadha, B S; Gulati, Arvind

    2014-06-01

    Optimizing nutritional requirements for mass production of microbial inoculants in shortened time has relevance for their economical field application. Therefore, the present study aimed at selecting suitable growth medium, optimizing its components, and up-scaling inoculum production for plant growth-promoting Pseudomonas trivialis BIHB 745. Of the different media tested, the culture exhibited maximal viable colony count in trypticase soya broth with 17.6 % increased biomass on optimizing levels of carbon source, nitrogen source, and NaCl using response surface methodology. A twofold higher biomass with 9 h shorter incubation period was obtained in optimized medium in a bioreactor in comparison to shake flasks.

  1. Population Dynamics within a Microbial Consortium during Growth on Diesel Fuel in Saline Environments†

    PubMed Central

    Kleinsteuber, Sabine; Riis, Volker; Fetzer, Ingo; Harms, Hauke; Müller, Susann

    2006-01-01

    The diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near Comodoro Rivadavia in Patagonia (Argentina) were investigated. Community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% NaCl were monitored by single-strand conformation polymorphism community fingerprinting of the PCR-amplified V4-V5 region of the 16S rRNA genes. Information obtained by this qualitative approach was extended by flow cytometric analysis to follow quantitatively the dynamics of community structures at different salinities. Dominant and newly developing clusters of individuals visualized via their DNA patterns versus cell sizes were used to identify the subcommunities primarily involved in the degradation process. To determine the most active species, subcommunities were separated physically by high-resolution cell sorting and subsequent phylogenetic identification by 16S rRNA gene sequencing. Reduced salinity favored the dominance of Sphingomonas spp., whereas at elevated salinities, Ralstonia spp. and a number of halophilic genera, including Halomonas, Dietzia, and Alcanivorax, were identified. The combination of cytometric sorting with molecular characterization allowed us to monitor community adaptation and to identify active and proliferating subcommunities. PMID:16672500

  2. [Determination of E. coli with MUG (Fluorocult)-lauryl sulfate broth for the testing of microbial contamination in drugs].

    PubMed

    Huang, H; Oberkötter, E; Blume, H

    1994-06-01

    A test method for the determination of Escherichia coli in plant materials with the MUG (Fluorocult)-lauryl sulfate broth is described. It was found that more than 75% of the commonly used vegetable drugs exhibit fluorescence quench effects to different degrees when determining E. coli with the MUG-lauryl sulfate broth. Therefore a simple combination of two procedures was evaluated in order to avoid the matrix interferences: in a first step the drug sample was diluted eight times in a proportion of 1:10 with MUG-lauryl sulfate broth in eight separate tubes from 1 g down to 10(-7) g/tube (1st test series) and the resulting samples were incubated for 40 h at 36 degrees C. Subsequently, the tubes were tested for fluorescence. If the first tube of this series was found without fluorescence, in a second step a subsequent series of MUG-lauryl sulfate broth (2nd test series) was inoculated with 0.5 ml of the incubated culture from each of the first three tubes of series 1 and incubated again for 24 h at 36 degrees C. The results were evaluated from gas production, fluorescence as well as indole formation. Thus, the method allowed a simple and reproducible enumeration of E. coli for the test on microbial contamination in medicinal plant materials. The method was successfully applied to samples of 38 vegetable drugs for quantitative determination of E. coli (8 samples were found being contaminated with E. coli).

  3. Use of 13C-Labeled Substrates to Determine Relative Methane Production Rates in Hypersaline Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kelley, C. A.; Bebout, B.; Chanton, J.

    2015-12-01

    Rates and pathways of methane production were determined from photosynthetic soft microbial mats and gypsum-encrusted endoevaporites collected in hypersaline environments from California, Mexico and Chile, as well as an organic-rich mud from a pond in the El Tatio volcanic fields, Chile. Samples (mud, homogenized soft mats and endoevaporites) were incubated anaerobically with deoxygenated site water, and the increase in methane concentration through time in the headspaces of the incubation vials was used to determine methane production rates. To ascertain the substrates used by the methanogens, 13C-labeled methylamines, methanol, dimethylsulfide, acetate or bicarbonate were added to the incubations (one substrate per vial) and the stable isotopic composition of the resulting methane was measured. The vials amended with 13C-labeled methylamines produced the most 13C-enriched methane, generally followed by the 13C-labeled methanol-amended vials. The stable isotope data and the methane production rates were used to determine first order rate constants for each of the substrates at each of the sites. Estimates of individual substrate use revealed that the methylamines produced 55 to 92% of the methane generated, while methanol was responsible for another 8 to 40%.

  4. The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth.

    PubMed

    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 pHKCl 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.

  5. [Effects of bio-mulching on rhizosphere soil microbial population, enzyme activity and tree growth in poplar plantation].

    PubMed

    Liu, Jiu-Jun; Fang, Sheng-Zuo; Xie, Bao-Dong; Hao, Juan-Juan

    2008-06-01

    Coriaria nepalensis, Pteridium aquilinum var. latiuscukum, Imperata cylindrical var. major, and Quercus fabric were used as mulching materials to study their effects on the rhizosphere soil microbial population and enzyme activity and the tree growth in poplar plantation. The results showed that after mulching with test materials, the populations of both bacteria and fungi in rhizosphere soil were more than those of the control. Of the mulching materials, I. cylindrical and Q. fabric had the best effect, with the numbers of bacteria and fungi being 23.56 and 1.43 times higher than the control, respectively. The bacterial and fungal populations in rhizosphere soil increased with increasing mulching amount. When the mulching amount was 7.5 kg m(-2), the numbers of bacteria and fungi in rhizosphere soil were 0.5 and 5.14 times higher than the control, respectively. Under bio-mulching, the bacterial and fungal populations in rhizosphere soil had a similar annual variation trend, which was accorded with the annual fluctuation of soil temperature and got to the maximum in July and the minimum in December. The urease and phosphatase activities in rhizosphere soil also increased with increasing mulching amount. As for the effects of different mulching materials on the enzyme activities, they were in the order of C. nepalensis > P. aquilinum > I. cylindrical > Q. fabric. The annual variation of urease and phosphatase activities in rhizosphere soil was similar to that of bacterial and fungal populations, being the highest in July and the lowest in December. Bio-mulching promoted the tree height, DBH, and biomass of poplar trees significantly.

  6. Aggregate Size and Architecture Determine Microbial Activity Balance for One-Stage Partial Nitritation and Anammox ▿

    PubMed Central

    Vlaeminck, Siegfried E.; Terada, Akihiko; Smets, Barth F.; De Clippeleir, Haydée; Schaubroeck, Thomas; Bolca, Selin; Demeestere, Lien; Mast, Jan; Boon, Nico; Carballa, Marta; Verstraete, Willy

    2010-01-01

    Aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB) cooperate in partial nitritation/anammox systems to remove ammonium from wastewater. In this process, large granular microbial aggregates enhance the performance, but little is known about granulation so far. In this study, three suspended-growth oxygen-limited autotrophic nitrification-denitrification (OLAND) reactors with different inoculation and operation (mixing and aeration) conditions, designated reactors A, B, and C, were used. The test objectives were (i) to quantify the AerAOB and AnAOB abundance and the activity balance for the different aggregate sizes and (ii) to relate aggregate morphology, size distribution, and architecture putatively to the inoculation and operation of the three reactors. A nitrite accumulation rate ratio (NARR) was defined as the net aerobic nitrite production rate divided by the anoxic nitrite consumption rate. The smallest reactor A, B, and C aggregates were nitrite sources (NARR, >1.7). Large reactor A and C aggregates were granules capable of autonomous nitrogen removal (NARR, 0.6 to 1.1) with internal AnAOB zones surrounded by an AerAOB rim. Around 50% of the autotrophic space in these granules consisted of AerAOB- and AnAOB-specific extracellular polymeric substances. Large reactor B aggregates were thin film-like nitrite sinks (NARR, <0.5) in which AnAOB were not shielded by an AerAOB layer. Voids and channels occupied 13 to 17% of the anoxic zone of AnAOB-rich aggregates (reactors B and C). The hypothesized granulation pathways include granule replication by division and budding and are driven by growth and/or decay based on species-specific physiology and by hydrodynamic shear and mixing. PMID:19948857

  7. Growth performance and gastrointestinal microbial ecology responses of piglets receiving Saccharomyces cerevisiae fermentation products after an oral challenge with Escherichia coli (K88).

    PubMed

    Kiarie, E; Bhandari, S; Scott, M; Krause, D O; Nyachoti, C M

    2011-04-01

    The effects of Saccharomyces cerevisiae fermentation products (YFP) on growth performance and gastrointestinal (GIT) microbial ecology in 90 weanling pigs orally challenged with Escherichia coli K88(+) (ETEC) were investigated. The YFP were an original YFP product (XPC) and a water-suspendable yeast fermentation prototype (WSYFP) from a commercial company. Treatments consisted of a negative control (NC, no in-feed or in-water additive), carbadox (AB, 55 mg of carbadox/kg of feed), XPC (in feed, 0.2%), and WSYFP (in water, 0.5, 1, or 2 g/pig per day), and each was allotted to 5 pens (3 pigs/pen). The diets met the 1998 NRC specifications. Pigs were acclimated to treatments for a 7-d period before an ETEC challenge. On d 8, blood was collected from pigs to determine the baseline packed cell volume (PCV) measurement, and pigs were orally challenged with ETEC. At various time points postchallenge, blood samples were taken, performance measures and fecal consistency scores were recorded, and gut digesta and tissue samples were taken to evaluate GIT morphology, microbial ecology, and metabolites. Preplanned contrasts were used for comparison. Pigs receiving YFP had greater ADFI than NC pigs on d 3 (424 vs. 378 g/d; P = 0.01) and d 7 (506 vs. 458 g/d; P = 0.03) postchallenge. This effect of YFP on ADFI was similar to that of AB on d 3, but pigs receiving AB ate more (576 vs. 506 g/d; P = 0.03) at d 7 than pigs receiving YFP. Pigs exhibited reduced (P < 0.001) PCV upon ETEC challenge; however, pigs receiving additives sustained a greater (P < 0.05) PCV at 72 h compared with the NC group. Compared with the NC pigs, pigs receiving YFP showed a smaller (P < 0.05) number of ileal mucosa adherent ETEC and prevalence of the order Enterobacteriales in the ileal digesta, which corresponded to less (5.09 vs. 6.97 mg/dL; P = 0.03) colonic ammonia on d 7 postchallenge. Most of the indices for ileal digesta bacterial richness and diversity were greater (P < 0.01) for YFP pigs compared

  8. Influence of superdoses of a novel microbial phytase on growth performance, tibia ash, and gizzard phytate and inositol in young broilers.

    PubMed

    Walk, C L; Santos, T T; Bedford, M R

    2014-05-01

    An experiment was conducted to evaluate the influence of a novel microbial phytase on performance, tibia ash, and the content of phytate, phytate esters, and inositol in the gizzard of young broilers. Male Cobb 500 broilers (n = 1,680) were fed 1 of 7 experimental diets: positive control (PC) formulated to meet or exceed nutrient recommendations; PC plus dicalcium phosphate (PC+DCP) formulated to provide Ca and P at 0.10% above the PC; PC plus 500 U/kg of microbial phytase (PC+500); negative control (NC) with Ca and P reduced from the PC by 0.16% and 0.15%, respectively; and the NC plus phytase at 500 (NC+500), 1,000 (NC+1,000), or 1,500 (NC+1,500) U/kg. Diets were fed in crumbled form to 20 birds/pen and 12 replicate pens/diet from d 0 to 21. On d 21, 4 birds/pen were euthanized for collection of right tibias and gizzard digesta for determination of tibia ash and gizzard phytate. In general, broilers fed the NC diet had reduced (P ≤ 0.05) feed intake and BW gain compared with broilers fed diets supplemented with phytase, but not different than the PC or PC+DCP. Phytase supplementation in the NC diet improved (P ≤ 0.05) BW gain comparable with or above that of the PC. Feed conversion ratio was improved in broilers fed the NC+1,000 or NC+1,500 compared with broilers fed all other diets. Tibia ash was reduced (P ≤ 0.05) in broilers fed the NC compared with broilers fed all other diets, and phytase supplementation improved tibia ash comparable with the PC. Phytase supplementation reduced (P ≤ 0.05) phytate (inositol hexa-phosphate) concentration in the gizzard. Inositol concentration in the gizzard was higher (P ≤ 0.05) in birds fed NC+1,000 or NC+1,500 compared with all other diets and this was correlated with growth performance (P ≤ 0.05) rather than tibia ash (P > 0.05). Improvements in feed conversion ratio associated with superdoses of phytase may be attributed to phytate destruction and the provision of inositol.

  9. Effectiveness of hydrothermal-calcium chloride treatment and chitosan on quality retention and microbial growth during storage of fresh-cut papaya.

    PubMed

    Ayón-Reyna, Lidia E; Tamayo-Limón, Ransés; Cárdenas-Torres, Feliznando; López-López, Martha E; López-Angulo, Gabriela; López-Moreno, Héctor S; López-Cervántes, Jaime; López-Valenzuela, José A; Vega-García, Misael O

    2015-03-01

    Rapid degradation of fresh-cut papaya limits its marketability. Hydrothermal treatments in combination with a calcium dip, applied to whole fruit before slicing, and also the application of chitosan as a coating film, have been found to have very good results in maintaining the quality of fresh-cut fruits. Based on these considerations, the aim of this study was to evaluate the effect of hydrothermal treatment (HT; 49 °C, 25 min) containing calcium chloride (Ca; 1%, w/v) followed by dipping in chitosan (Chit; 1%, w/v, 3 min) on the physical, chemical, and microbial qualities of papaya slices stored at 5 °C for 10 d. Pulp color, firmness, ascorbic acid, total phenolics, β-carotene, and lycopene were evaluated every 2 d while the microbial quality (mesophilics, psychrophilics, molds, and yeasts) was evaluated every 5 d. Fruit treated with HT-Ca and HT-Ca + Chit showed better color and firmness retention than Control and Chit. Papaya slices treated with HT-Ca + Chit had higher nutritional content and lower microbial growth at the end of storage. The application of the HT-Ca + Chit could be used to reduce deterioration processes, maintaining physical, chemical, and microbial qualities and increasing the shelf life of fresh-cut papaya stored at 5 °C.

  10. Growth conditions determine different melatonin levels in Lupinus albus L.

    PubMed

    Arnao, Marino B; Hernández-Ruiz, Josefa

    2013-09-01

    Melatonin, an indoleamine, which has recently been assigned several roles in plant physiology as a growth promoter, as rooting agent, and as antioxidant in senescence delay and cytoprotection, seems to have a relevant function in plant stress situations. The presence of melatonin increases the resistance of lupin plant tissues (Lupinus albus L.) against natural or artificially induced adverse situations. In this work, we studied the response of lupin plants in controlled stress situations (drought-, anaerobic-, pH-, and cold stress and using ZnSO4 , NaCl, and H2 O2 as chemical stressors) and measured the changes in endogenous melatonin levels in lupin plants. Also, the effect of abscisic acid, ethylene, and natural environmental conditions were evaluated. In general, nearly all stressful factors caused an increase in melatonin in the investigated organs. The chemical stress provoked by ZnSO4 or NaCl caused the most pronounced changes in the endogenous level of melatonin, followed by cold and drought stressors. In some cases, the level of melatonin increased 12-fold with respect to the levels in control plants, indicating that melatonin biosynthesis is upregulated in common stress situations, in which it may serve as a signal molecule and/or as a direct antistress agent due to its well-known antioxidative properties.

  11. Isolate-specific effects of ultraviolet radiation on photosynthesis, growth and mycosporine-like amino acids in the microbial mat-forming cyanobacterium Microcoleus chthonoplastes.

    PubMed

    Pattanaik, Bagmi; Roleda, Michael Y; Schumann, Rhena; Karsten, Ulf

    2008-03-01

    Microcoleus chthonoplastes constitutes one of the dominant microorganisms in intertidal microbial mat communities. In the laboratory, the effects of repeated daily exposure to ultraviolet radiation (16:8 light:dark cycle) was investigated in unicyanobacterial cultures isolated from three different localities (Baltic Sea = WW6; North Sea = STO and Brittany = BRE). Photosynthesis and growth were measured in time series (12-15 days) while UV-absorbing mycosporine-like amino acids (MAAs) and cellular integrity were determined after 12 and 3 days exposure to three radiation treatments [PAR (22 mumol photon m(-2) s(-1)) = P; PAR + UV-A (8 W m(-2)) = PA; PAR + UV-A + UV-B (0.4 W m(-2)) = PAB]. Isolate-specific responses to UVR were observed. The proximate response to radiation stress after 1-day treatment showed that isolate WW6 was the most sensitive to UVR. However, repeated exposure to radiation stress indicated that photosynthetic efficiency (F (v)/F (m)) of WW6 acclimated to UVR. Conversely, although photosynthesis in STO exhibited lower reduction in F (v)/F (m) during the first day, the values declined over time. The BRE isolate was the most tolerant to radiation stress with the lowest reduction in F (v)/F (m )sustained over time. While photosynthetic efficiencies of different isolates were able to acclimate to UVR, growth did not. The discrepancy seems to be due to the higher cell density used for photosynthesis compared to the growth measurement. Apparently, the cell density used for photosynthesis was not high enough to offer self-shading protection because cellular damage was also observed in those filaments under UVR. Most likely, the UVR acclimation of photosynthesis reflects predominantly the performance of the surviving cells within the filaments. Different strategies were observed in MAAs synthesis. Total MAAs content in WW6 was not significantly different between all the radiation treatments. In contrast, the additional fluence of UV-A and UV

  12. Effects of dietary supplementation of modified zinc oxide on growth performance, nutrient digestibility, blood profiles, fecal microbial shedding and fecal score in weanling pigs.

    PubMed

    Cho, Jin Ho; Upadhaya, Santi Devi; Kim, In Ho

    2015-06-01

    One hundred and forty piglets ((Landrace × Yorkshire) × Duroc, 21 day of age) with an initial weight of 6.50 ± 0.71 kg, were randomly allotted into four treatments to determine the effects of a modified form of zinc oxide (ZnO) on growth performance, nutrient digestibility, blood profiles, fecal microbial shedding and fecal score in weanling pigs. Dietary treatments were: (i) NC, negative control, basal diet containing zinc (Zn) from the premix; (ii) PC, positive control, basal diet containing Zn-free premix + 3000 ppm ZnO; (iii) H1, basal diet containing Zn-free premix + 3000 ppm ZnO (phase 1, days 1 to 14)/200 ppm modified ZnO (phase 2, days 15 to 42); (iv) H2, basal diet containing Zn-free premix + 300 ppm modified ZnO (phase 1)/200 ppm modified ZnO (phase 2). During days 1 to 14, average daily gains (ADG) were higher (P = 0.04) in PC, H1 and H2 groups than that in NC group. Overall, H1 treatment increased the ADG compared with NC (P = 0.05). On day 14, the alkaline phosphatase and plasma Zn concentration were increased (P = 0.01 and 0.04, respectively) in PC, H1 and H2 treatments compared with NC treatment. On days 14 and 42, the fecal Lactobacillus counts in NC group were lowest (P = 0.01, P = 0.04 respectively) among treatments. All supplemented groups showed lower (P = 0.03) fecal score than NC treatment on days 21 and 28. In conclusion, dietary supplementation with modified ZnO increased growth rates and reduced fecal scores in weanling pig. Modified ZnO could be used as a substitute to ZnO as a growth promoter and reduce Zn excretion to the environment because of the lower dosage. [Correction added on 3 February 2015, after first online publication: the initial weight of '6.50 ± 1.11 kg' has been replaced with '6.50 ± 0.71 kg' in the abstract.].

  13. Determination of charge transfer resistance and capacitance of microbial fuel cell through a transient response analysis of cell voltage.

    PubMed

    Ha, Phuc Thi; Moon, Hyunsoo; Kim, Byung Hong; Ng, How Yong; Chang, In Seop

    2010-03-15

    An alternative method for determining the charge transfer resistance and double-layer capacitance of microbial fuel cells (MFCs), easily implemented without a potentiostat, was developed. A dynamic model with two parameters, the charge transfer resistance and double-layer capacitance of electrodes, was derived from a linear differential equation to depict the current generation with respect to activation overvoltage. This model was then used to fit the transient cell voltage response to the current step change during the continuous operation of a flat-plate type MFC fed with acetate. Variations of the charge transfer resistance and the capacitance value with respect to the MFC design conditions (biocatalyst existence and electrode area) and operating parameters (acetate concentration and buffer strength in the catholyte) were then determined to elucidate the validity of the proposed method. This model was able to describe the dynamic behavior of the MFC during current change in the activation loss region; having an R(2) value of over 0.99 in most tests. Variations of the charge transfer resistance value (thousands of Omega) according to the change of the design factors and operational factors were well-correlated with the corresponding MFC performances. However, though the capacitance values (approximately 0.02 F) reflected the expected trend according to the electrode area change and catalyst property, they did not show significant variation with changes in either the acetate concentration or buffer strength.

  14. Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China

    NASA Astrophysics Data System (ADS)

    Ma, L.; Guo, C.; Lü, X.; Yuan, S.; Wang, R.

    2015-04-01

    Global environmental factors impact soil microbial communities and further affect organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about the relative contributions of climate factors, soil properties, vegetation types, land management practices and spatial structure (which serves as a proxy for underlying effects of temperature and precipitation for spatial variation) on soil microbial community composition and biomass at large spatial scales. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations at a regional scale in northeastern China (850 × 50 km). The results showed that soil moisture and land use changes were most closely related to microbial community composition and biomass at the regional scale, while soil total C content and climate effects were weaker but still significant. Factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Higher contributions of gram-positive bacteria were found in wetter soils, whereas higher contributions of gram-negative bacteria and fungi were observed in drier soils. The contributions of gram-negative bacteria and fungi were lower in heavily disturbed soils than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate and soil properties were not the most important drivers governing microbial community composition and biomass because of inclusion of irrigated and managed practices, and thus soil moisture and land use appear to be primary determinants of microbial community composition and biomass at the regional scale in northeastern China.

  15. Microbial growth under humic-free conditions in a supraglacial stream system on the Cotton Glacier, Antarctica

    NASA Astrophysics Data System (ADS)

    Foreman, Christine M.; Cory, Rose M.; Morris, Cindy E.; SanClements, Michael D.; Smith, Heidi J.; Lisle, John T.; Miller, Penney L.; Chin, Yu-Ping; McKnight, Diane M.

    2013-09-01

    During the austral summers of 2004 and 2009, we sampled a supraglacial stream on the Cotton Glacier, Antarctica. The stream dissolved organic matter (DOM) was low (44-48 μM C) and lacked detectable humic fluorescence signatures. Analysis of the excitation emissions matrices (EEMs) indicated that amino-acid fluorophores dominated, consistent with DOM of microbial origin, with little humic-like fluorescence. In most aquatic ecosystems, humic DOM attenuates harmful UV radiation and its absence may represent an additional stressor influencing the microbial community. Nonetheless, the stream contained an active microbial assemblage with bacterial cell abundances from 2.94 × 104 to 4.97 × 105 cells ml-1, and bacterial production ranging from 58.8 to 293.2 ng C l-1 d-1. Chlorophyll-a concentrations ranged from 0.3 to 0.53 μg l-1 indicating that algal phototrophs were the probable source of the DOM. Microbial isolates produced a rainbow of pigment colors, suggesting adaptation to stress, and were similar to those from other cryogenic systems (Proteobacteria and Bacteroidetes lineages). Supraglacial streams provide an example of contemporary microbial processes on the glacier surface and a natural laboratory for studying microbial adaptation to the absence of humics.

  16. Introducing a novel interaction model structure for the combined effect of temperature and pH on the microbial growth rate.

    PubMed

    Akkermans, Simen; Noriega Fernandez, Estefanía; Logist, Filip; Van Impe, Jan F

    2017-01-02

    Efficient modelling of the microbial growth rate can be performed by combining the effects of individual conditions in a multiplicative way, known as the gamma concept. However, several studies have illustrated that interactions between different effects should be taken into account at stressing environmental conditions to achieve a more accurate description of the growth rate. In this research, a novel approach for modeling the interactions between the effects of environmental conditions on the microbial growth rate is introduced. As a case study, the effect of temperature and pH on the growth rate of Escherichia coli K12 is modeled, based on a set of computer controlled bioreactor experiments performed under static environmental conditions. The models compared in this case study are the gamma model, the model of Augustin and Carlier (2000), the model of Le Marc et al. (2002) and the novel multiplicative interaction model, developed in this paper. This novel model enables the separate identification of interactions between the effects of two (or more) environmental conditions. The comparison of these models focuses on the accuracy, interpretability and compatibility with efficient modeling approaches. Moreover, for the separate effects of temperature and pH, new cardinal parameter model structures are proposed. The novel interaction model contributes to a generic modeling approach, resulting in predictive models that are (i) accurate, (ii) easily identifiable with a limited work load, (iii) modular, and (iv) biologically interpretable.

  17. Experimental determination of magnesium isotope fractionation during higher plant growth

    NASA Astrophysics Data System (ADS)

    Bolou-Bi, Emile B.; Poszwa, Anne; Leyval, Corinne; Vigier, Nathalie

    2010-05-01

    Two higher plant species (rye grass and clover) were cultivated under laboratory conditions on two substrates (solution, phlogopite) in order to constrain the corresponding Mg isotope fractionations during plant growth and Mg uptake. We show that bulk plants are systematically enriched in heavy isotopes relative to their nutrient source. The Δ 26Mg plant-source range from 0.72‰ to 0.26‰ for rye grass and from 1.05‰ to 0.41‰ for clover. Plants grown on phlogopite display Mg isotope signatures (relative to the Mg source) ˜0.3‰ lower than hydroponic plants. For a given substrate, rye grass display lower δ 26Mg (by ˜0.3‰) relative to clover. Magnesium desorbed from rye grass roots display a δ 26Mg greater than the nutrient solution. Adsorption experiments on dead and living rye grass roots also indicate a significant enrichment in heavy isotopes of the Mg adsorbed on the root surface. Our results indicate that the key processes responsible for heavy isotope enrichment in plants are located at the root level. Both species also exhibit an enrichment in light isotopes from roots to shoots (Δ 26Mg leaf-root = -0.65‰ and -0.34‰ for rye grass and clover grown on phlogopite respectively, and Δ 26Mg leaf-root of -0.06‰ and -0.22‰ for the same species grown hydroponically). This heavy isotope depletion in leaves can be explained by biological processes that affect leaves and roots differently: (1) organo-Mg complex (including chlorophyll) formation, and (2) Mg transport within plant. For both species, a positive correlation between δ 26Mg and K/Mg was observed among the various organs. This correlation is consistent with the link between K and Mg internal cycles, as well as with formation of organo-magnesium compounds associated with enrichment in heavy isotopes. Considering our results together with the published range for δ 26Mg of natural plants and rivers, we estimate that a significant change in continental vegetation would induce a change of

  18. In vitro study on the effect of doxycycline on the microbial activity of soil determined by redox-potential measuring system.

    PubMed

    Szakmár, Katalin; Reichart, Olivér; Szatmári, István; Erdősi, Orsolya; Szili, Zsuzsanna; László, Noémi; Székely Körmöczy, Péter; Laczay, Péter

    2014-09-01

    The potential effect of doxycycline on the microbial activity was investigated in three types of soil. Soil samples were spiked with doxycycline, incubated at 25°C and tested at 0, 2, 4 and 6 days after treatment. The microbiological activity of the soil was characterized by the viable count determined by plate pouring and by the time necessary to reach a defined rate of the redox-potential decrease termed as time to detection (TTD).The viable count of the samples was not changed during the storage. The TTD values, however exhibited a significant increase in the 0.2-1.6 mg/kg doxycycline concentration range compared to the untreated samples indicating concentration-dependent inhibitory effect on microbial activity. The potency of the effect was different in the 3 soil types. To describe the combined effect of the doxycycline concentration and time on the biological activity of one type of soil a mathematical model was constructed and applied.The change of microbial metabolic rate could be measured also without (detectable) change of microbial count when the traditional microbiological methods are not applicable. The applied new redox potential measurement-based method is a simple and useful procedure for the examination of microbial activity of soil and its potential inhibition by antibiotics.

  19. Carbon and hydrogen isotope fractionation by microbial methane oxidation: Improved determination

    SciTech Connect

    Mahieu, Koenraad . E-mail: Koenraad.Mahieu@Ugent.be; Visscher, Alex De; Vanrolleghem, Peter A.; Cleemput, Oswald Van

    2006-07-01

    Isotope fractionation is a promising tool for quantifying methane oxidation in landfill cover soils. For good quantification an accurate determination of the isotope fractionation factor ({alpha}) of methane oxidation based on independent batch experiments with soil samples from the landfill cover is required. Most studies so far used data analysis methods based on approximations of the Rayleigh model to determine {alpha}. In this study, the two most common approximations were tested, the simplified Rayleigh approach and the Coleman method. To do this, the original model of Rayleigh was described in measurable variables, methane concentration and isotopic abundances, and fitted to batch oxidation data by means of a weighted non-linear errors-in-variables regression technique. The results of this technique were used as a benchmark to which the results of the two conventional approximations were compared. Three types of batch data were used: simulated data, data obtained from the literature, and data obtained from new batch experiments conducted in our laboratory. The Coleman approximation was shown to be acceptable but not recommended for carbon fractionation (error on {alpha} - 1 up to 5%) and unacceptable for hydrogen fractionation (error up to 20%). The difference between the simplified Rayleigh approach and the exact Rayleigh model is much smaller for both carbon and hydrogen fractionation (error on {alpha} - 1 < 0.05%). There is also a small difference when errors in both variables (methane concentration and isotope abundance) are accounted for instead of assuming an error-free independent variable. By means of theoretical calculations general criteria, not limited to methane, {sup 13}C, or D, were developed for the validity of the simplified Rayleigh approach when using labelled compounds.

  20. Microbial field pilot study

    SciTech Connect

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Coates, J.D.; Chisholm, J.L.

    1993-05-01

    A multi-well microbially enhanced oil recovery field pilot has been performed in the Southeast Vassar Vertz Sand Unit in Payne County, Oklahoma. The primary emphasis of the experiment was preferential plugging of high permeability zones for the purpose of improving waterflood sweep efficiency. Studies were performed to determine reservoir chemistry, ecology, and indigenous bacteria populations. Growth experiments were used to select a nutrient system compatible with the reservoir that encouraged growth of a group of indigenous nitrate-using bacteria and inhibit growth of sulfate-reducing bacteria. A specific field pilot area behind an active line drive waterflood was selected. Surface facilities were designed and installed. Injection protocols of bulk nutrient materials were prepared to facilitate uniform distribution of nutrients within the pilot area. By the end of December, 1991, 82.5 tons (75.0 tonnes) of nutrients had been injected in the field. A tracer test identified significant heterogeneity in the SEVVSU and made it necessary to monitor additional production wells in the field. The tracer tests and changes in production behavior indicate the additional production wells monitored during the field trial were also affected. Eighty two and one half barrels (13.1 m[sup 3]) of tertiary oil have been recovered. Microbial activity has increased CO[sub 2] content as indicated by increased alkalinity. A temporary rise in sulfide concentration was experienced. These indicate an active microbial community was generated in the field by the nutrient injection. Pilot area interwell pressure interference test results showed that significant permeability reduction occurred. The interwell permeabilities in the pilot area between the injector and the three pilot production wells were made more uniform which indicates a successful preferential plugging enhanced oil recovery project.

  1. Correlations between arsenic in Maine groundwater and microbial populations as determined by fluorescence in situ hybridization.

    PubMed

    Weldon, Jennifer M; MacRae, Jean D

    2006-04-01

    Arsenic is known to cause serious health effects when consumed in drinking water. In the state of Maine, approximately half of the population relies on private groundwater wells for their drinking water. Of those wells, as many as 13% may contain arsenic levels above the current EPA maximum contaminant level of 10 microgl(-1). Microorganisms can potentially contribute to arsenic release into groundwater through several mechanisms. Some can reduce arsenate to arsenite, which is more toxic and may be more mobile. Sulfurospirillum species NP4, which was isolated from well water, respires arsenate and could act in this way. Microorganisms can also act indirectly by reducing bedrock surface coatings, such as iron oxyhydroxides, that adsorb arsenic in the groundwater environment. The genus Geobacter contains many species that are capable of iron reduction that could play a role in the indirect release of arsenic into groundwater. Water samples from Northport, ME and the Branch Lake region of Ellsworth, ME, which both have elevated groundwater arsenic levels, have been probed using fluorescence in situ hybridization (FISH), to determine the percentage of the population that is NP4 and the percentage that are Geobacter species. Geobacter abundance correlates well with the total arsenic concentration indicating that indirect mechanisms could be important in releasing arsenic. NP4 appears to be reducing arsenate since its prevalence correlates well with arsenite, the end product of arsenate respiration.

  2. Microbial diversity and dynamics of microbial communities during back-slop soaking of soybeans as determined by PCR-DGGE and molecular cloning.

    PubMed

    Yan, Yinzhuo; Wolkers-Rooijackers, Judith; Nout, M J Robert; Han, Beizhong

    2013-10-01

    Tempe is a traditional fermented food in Indonesia. The manufacture process is quite complex, which comprises two stages, preparatory soaking of soybeans and fungal solid state fermentation. Daily addition of previous soak water (back-slopping) during the soybean soaking step is considered to be crucial in the manufacture of high quality tempe. The microbial diversity and dynamics of the microbial communities evolving during back-slop soaking of soybeans for tempe making was investigated by culture-independent PCR-DGGE and molecular cloning. Both DNA and total RNA were isolated and included in this study, to obtain a view on the succession of total and viable bacteria in the complex microbiota. DGGE profiles indicated that Enterobacter sp., Enterococcus sp., Pseudomonas putida, Leuconostoc fallax, Pediococcus pentosaceus, and Weissella cibaria, were the predominant bacteria. Their occurrence shifted dramatically during the back-slop soaking procedure. This study combined with previous culture-dependent studies could gain a better understanding of the complex microbiota of traditional fermented food and give useful information for its quality control.

  3. Temperature dependence of protein solubility-determination, application to crystallization, and growth kinetics studies

    NASA Technical Reports Server (NTRS)

    Rosenberger, Franz

    1993-01-01

    A scintillation method was developed for determinations of the temperature dependence of the solubility, and of nucleation induction times of proteins, in 50-100 mu(l) volumes of solution. Solubility data for lysozyme and horse serum albumin were obtained for various combinations of pH and precipitant concentrations. These data and the nucleation induction information were used for dynamic crystallization control, that is, for the controlled separation of nucleation and growth stages. Individual lysozyme and horse serum albumin crystals were grown in 15-20 mu(l) solution volumes contained in x-ray capillaries. The morphology and kinetics of the growth and dissolution of lysozyme in aqueous solutions with 2.5 percent NaCl and at pH = 4.5 was studied in situ with a depth resolution of 300 A (4 unit cells) by high resolution optical microscopy and digital image processing. The bulk super- or under saturation, sigma, of the solution inside a closed growth cell was controlled by temperature. The growth habit was bound by (110) and (101) faces that grew through layer spreading, although with different growth rate dependencies on supersaturation/temperature. At sigma less than 10 (obtained at higher temperatures) growth was purely kinetic ally controlled, with impurity effects (macrostep formation and kinetic hindrance) becoming significant for sigma less than 2. At sigma greater than 10 (lower temperatures), anisotropies in the interfacial kinetics were more pronounced, with interfacial kinetics and bulk transport becoming equally important to the growth morphology. Growth rates were growth history dependent. The formation of striations (layers of irregularly incorporated solution) was unambiguously correlated with growth temperature variations. Etching exposed dislocations and various high-index faces whose growth morphologies were studied during return to the steady state growth form. Growth steps were observed to originate from two-dimensional nuclei or from outcrops

  4. Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

    SciTech Connect

    Wang, Gangsheng; Mayes, Melanie; Gu, Lianhong; Schadt, Christopher Warren

    2014-01-01

    Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in notable model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and the major parameters are the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-driven processes and to provide improved estimates of microbial activities.

  5. Use of a spectrophotometric bioassay for determination of microbial sensitivity to manuka honey.

    PubMed

    Patton, Thomas; Barrett, John; Brennan, James; Moran, Noel

    2006-01-01

    The antimicrobial activity of manuka honey has been well documented (Molan, 1992a,b,c, 1997) [Molan, P.C., 1992. The antibacterial activity of honey. 1: the nature of the antibacterial activity. Bee World 73 (1) 5-28; Molan, P.C., 1992. The antibacterial activity of honey. 2: variation in the potency of the antibacterial activity. Bee World 73 (2) 59-76; Molan, P.C., 1992. Medicinal uses for honey. Beekeepers Quarterly 26; Molan, P.C., 1997. Finding New Zealand honeys with outstanding antibacterial and antifungal activity. New Zealand Beekeeper 4 (10) 20-26]. The current bioassays for determining this antimicrobial effect employ a well diffusion (Ahn and Stiles, 1990) [Ahn, C., Stiles, M.E., 1990. Antibacterial activity of lactic acid bacteria isolated from vacuum-packed meats. Journal of Applied Bacteriology 69, 302-310], (Weston et al., 1999) [Weston, R.J., Mitchell, K.R., Allen, K.L., 1999. Antibacterial phenolic components of New Zealand manuka honey. J. Food Chem. 64, 295-301] or disc diffusion (Taormina et al., 2001) [Taormina, Peter J., Niemira, Brendan A., Beuchat, Larry R., 2001. Inhibitory activity of honey against food borne pathogens as influenced by the presence of hydrogen peroxide and level of antioxidant power. Int. J. Food Microbiol. 69, 217-225] assay using zones of inhibition as indicators of bacterial susceptibility. The development of a 24-h spectrophotometric assay employing 96-well microtiter plates, that is more sensitive and more amenable to statistical analysis than the assays currently employed, was undertaken. This simple and rapid assay permits extensive kinetic studies even in the presence of low honey concentrations, and is capable of detecting inhibitory levels below those recorded for well or disc diffusion assays. In this paper, we compare the assay to both well and disc diffusion assays. The results we obtained for the spectrophotometric method MIC values show that this method has greater sensitivity than the standard well and

  6. A new insight into potential regulation on growth and power generation of Geobacter sulfurreducens in microbial fuel cells based on energy viewpoint.

    PubMed

    Wei, Jincheng; Liang, Peng; Cao, Xiaoxin; Huang, Xia

    2010-04-15

    The anode potential in microbial fuel cells (MFCs) defines the possible metabolic energy gain (PMEG) for the bacteria growth. This study focused on the mechanism behind anode potential controlling microbial growth and power generation in MFCs from an energy perspective. Four sets of MFCs were operated with varied conditions: three with different applied anode potential (-160, 0, and 400 mV vs standard hydrogen electrode (SHE)) and one with an external resistor (500 Omega). A model strain Geobacter sulfurreducens was used here. The evolution of biomass was measured and its quantitative relationship with PMEG was analyzed. Linear voltammetry and cyclic voltammetry were also carried out. Results indicated a notable gain in biomass and power density when anode potential increased from -160 to 0 mV. However, no gain in biomass and power generation was detected when anode potential further increased to 400 mV. At anode potential of 0 mV and below, G. sulfurreducens extracted a significant portion of PMEG for growth, while utilization of PMEG significantly decreased at 400 mV. Furthermore, the anode potential has a minor influence on individual G. sulfurreducens cell activity, and the maximum power density of MFC proportionate to biomass.

  7. Comparison effects of dietary iron dextran and bacterial-iron supplementation on growth performance, fecal microbial flora, and blood profiles in sows and their litters.

    PubMed

    Zhao, Pinyao; Upadhaya, Santi Devi; Li, Jian; Kim, Inho

    2015-11-01

    This study was conducted to compare effects of dietary administration of iron dextran and bacterial-iron on growth performance, fecal microbial flora, and blood profiles in sows and their litters. A total of 20 multiparous sows (Landrace × Yorkshire) were randomly allotted into two treatments: (i) ID (basal diet, piglets were injected with iron dextran); (ii) BR (basal diet + bacterial-iron; bacterial-iron was given to sows, piglets were not injected with iron dextran). There were five replicates per treatment with two sows per replicate. No differences were observed on sow and piglet growth performance, fecal microbial flora as well as sow blood profiles between ID and BR treatments. In piglets, blood iron, red blood cell and hemoglobin concentrations in ID treatment were higher (P < 0.05) on days 12 and 24. Furthermore, concentration of white blood cells in BR treatment was lower (P < 0.05) on day 12. However, the percentage of lymphocytes on day 12 was increased (P < 0.05) in BR treatment. In conclusion, effect of iron dextran and bacterial-iron has no difference on growth performance in lactating sows and piglets, but iron dextran injection has higher blood iron, white blood cell, red blood cell and hemoglobin concentrations in piglets.

  8. Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

    SciTech Connect

    Li, Zhou; Wang, Yingfeng; Yao, Qiuming; Justice, Nicholas B.; Ahn, Tae-Hyuk; Xu, Dong; Hettich, Robert {Bob} L; Banfield, Jillian F.; Pan, Chongle

    2014-01-01

    Detailed characterization of posttranslational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.

  9. Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth

    PubMed Central

    Oikonomou, Georgios; Teixeira, Andre Gustavo Vieira; Foditsch, Carla; Bicalho, Marcela Lucas; Machado, Vinicius Silva; Bicalho, Rodrigo Carvalho

    2013-01-01

    In this study, we use barcoded pyrosequencing of the 16S rRNA gene to characterize the fecal microbiota of neonatal calves and identify possible relationships of certain microbiota profiles with health and weight gain. Fecal samples were obtained weekly from 61 calves from birth until weaning (seventh week of the calves' life). Firmicutes was the most prevalent phylum, with a prevalence ranging from 63.84% to 81.90%, followed by Bacteroidetes (8.36% to 23.93%), Proteobacteria (3.72% to 9.75%), Fusobacteria (0.76% to 5.67%), and Actinobacteria (1.02% to 2.35%). Chao1 index gradually increased from the first to the seventh postnatal week. Chao1 index was lower during the third, fourth, and fifth week of life in calves that suffered from pneumonia and were treated with antibiotics. Diarrhea incidence during the first four weeks of the calves' life was also associated with a reduction of microbial diversity during the third week of life. Increased fecal microbial diversity after the second week of life was associated with higher weight gain. Using discriminant analysis we were able to show differences in the microbiota profiles between different weeks of life, between high and low weight gain groups of calves, and between calves affected and not affected with diarrhea during the first four weeks life. The prevalence of Faecalibacterium spp. in the first week of life was associated with weight gain and the incidence of diarrhea, with higher prevalence being associated with higher weight gain and less diarrhea. Representative sequences from Faecalibacterium spp. were closely affiliated to Faecalibacterium prausnitzii. Results presented here provide new information regarding the intestinal microbiota of neonatal calves and its association with health and growth. Fecal microbial diversity was associated with calf age, disease status and growth rates. Results suggesting a possible beneficial effect of Faecalibacterium spp. on health and growth are promising. PMID:23646192

  10. Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

    PubMed

    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.

  11. Indirect microbial detection

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R. (Inventor)

    1981-01-01

    The growth of microorganisms in a sample is detected and monitored by culturing microorganisms in a growth medium and detecting a change in potential between two electrodes, separated from the microbial growth by a barrier which is permeable to charged paticles but microorganism impermeable.

  12. Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis.

    PubMed

    Bizzarro, S; Laine, M L; Buijs, M J; Brandt, B W; Crielaard, W; Loos, B G; Zaura, E

    2016-02-01

    Antibiotics are often used in the treatment of chronic periodontitis, which is a major cause of tooth loss. However, evidence in favour of a microbial indication for the prescription of antibiotics is lacking, which may increase the risk of the possible indiscriminate use of antibiotics, and consequent, microbial resistance. Here, using an open-ended technique, we report the changes in the subgingival microbiome up to one year post-treatment of patients treated with basic periodontal therapy with or without antibiotics. Antibiotics resulted in a greater influence on the microbiome 3 months after therapy, but this difference disappeared at 6 months. Greater microbial diversity, specific taxa and certain microbial co-occurrences at baseline and not the use of antibiotics predicted better clinical treatment outcomes. Our results demonstrate the predictive value of specific subgingival bacterial profiles for the decision to prescribe antibiotics in the treatment of periodontitis, but they also indicate the need for alternative therapies based on ecological approaches.

  13. Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis

    PubMed Central

    Bizzarro, S.; Laine, M. L.; Buijs, M. J.; Brandt, B. W.; Crielaard, W.; Loos, B. G.; Zaura, E.

    2016-01-01

    Antibiotics are often used in the treatment of chronic periodontitis, which is a major cause of tooth loss. However, evidence in favour of a microbial indication for the prescription of antibiotics is lacking, which may increase the risk of the possible indiscriminate use of antibiotics, and consequent, microbial resistance. Here, using an open-ended technique, we report the changes in the subgingival microbiome up to one year post-treatment of patients treated with basic periodontal therapy with or without antibiotics. Antibiotics resulted in a greater influence on the microbiome 3 months after therapy, but this difference disappeared at 6 months. Greater microbial diversity, specific taxa and certain microbial co-occurrences at baseline and not the use of antibiotics predicted better clinical treatment outcomes. Our results demonstrate the predictive value of specific subgingival bacterial profiles for the decision to prescribe antibiotics in the treatment of periodontitis, but they also indicate the need for alternative therapies based on ecological approaches. PMID:26830979

  14. Effects of dilution rate and retention time of concentrate on efficiency of microbial growth, methane production, and ruminal fermentation in Rusitec fermenters.

    PubMed

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

    2009-08-01

    The objective of this study was to investigate the effects of 2 dilution rates (DL) and 2 concentrate retention times (RT) on microbial growth, methane production, and fermentation of a 30:70 alfalfa hay:concentrate diet in Rusitec fermenters maintained at similar pH. The DL were 3.78 (low DL, LDL) and 5.42%/h (high DL, HDL), and concentrate RT was either 24 h (T24) or 48 h (T48). Forage RT was 48 h in all fermenters. Apparent disappearance of diet DM and NDF was greater in HDL fermenters compared with LDL fermenters, but there was a significant DL x concentrate RT interaction, showing that the effect of DL was more pronounced in T48 compared with T24 fermenters. Methane production was not affected by DL, but was greater in T48 compared with T24 fermenters, which was consistent with the increased fiber degradation in T48 fermenters. Increasing DL augmented volatile fatty acid production and molar proportions of propionate, isovalerate, and valerate, and reduced those of caproate, but no effects were observed on acetate, butyrate, and isobutyrate proportions. Increasing concentrate RT resulted in greater volatile fatty acid production and proportions of acetate, butyrate, and caproate, but reduced those of propionate, valerate, and isovalerate. Ammonia-N production was not affected by concentrate RT, but was greater at HDL compared with LDL. Microbial growth was not affected by DL, but microbial growth efficiency was lower in HDL compared with LDL fermenters. Concentrate RT affected microbial growth and its efficiency, with both being greater in T48 compared with T24 fermenters. Carboxymetylcellulase and xylanase activities in ruminal fluid were greater in HDL compared with LDL fermenters, but were not affected by concentrate RT. There were DL x concentrate RT interactions for diet apparent disappearance, molar proportions of propionate, butyrate, isovalerate, and caproate, and acetate:propionate ratio, indicating that effects of DL on these variables were

  15. Direct in Situ Determination of the Mechanisms Controlling Nanoparticle Nucleation and Growth

    SciTech Connect

    Woehl, Taylor J.; Evans, James E.; Arslan, Ilke; Ristenpart, William D.; Browning, Nigel D.

    2012-10-23

    Although nanocrystal morphology is controllable using conventional colloidal synthesis, multiple characterization techniques are typically needed to determine key properties like the nucleation rate, induction time, growth rate, and the resulting morphology. Recently, researchers have demonstrated growth of nanocrystals by in situ electron beam reduction, offering direct observations of single nanocrystals and eliminating the need for multiple characterization techniques; however, they found nanocrystal morphologies consistent with two different growth mechanisms for the same electron beam parameters. Here we show that the electron beam current plays a role analogous to the concentration of reducing agent in conventional synthesis, by controlling the growth mechanism and final morphology of silver nanocrystals grown via in situ electron beam reduction. We demonstrate that low beam currents encourage reaction limited growth that yield nanocrystals with faceted structures, while higher beam currents encourage diffusion limited growth that yield spherical nanocrystals. By isolating these two growth regimes, we demonstrate a new level of control over nanocrystal morphology, regulated by the fundamental growth mechanism. We find that the induction threshold dose for nucleation is independent of the beam current used for imaging, but is a function of the interaction volume size. Our results indicate that in situ electron microscopy data can be interpreted by classical models, by allowing simultaneous measurement of nucleation induction times, growth rates, and evolution of nanocrystal morphology. The results suggest that systematic dose experiments should be performed for all future in situ liquid studies to confirm the exact mechanisms underlying observations of nucleation and growth.

  16. Comparison of signaling interactions determining annual and perennial plant growth in response to low temperature

    PubMed Central

    Wingler, Astrid

    2015-01-01

    Low temperature inhibits plant growth despite the fact that considerable rates of photosynthetic activity can be maintained. Instead of lower rates of photosynthesis, active inhibition of cell division and expansion is primarily responsible for reduced growth. This results in sink limitation and enables plants to accumulate carbohydrates that act as compatible solutes or are stored throughout the winter to enable re-growth in spring. Regulation of growth in response to temperature therefore requires coordination with carbon metabolism, e.g., via the signaling metabolite trehalose-6-phosphate. The phytohormones gibberellin (GA) and jasmonate (JA) play an important role in regulating growth in response to temperature. Growth restriction at low temperature is mainly mediated by DELLA proteins, whose degradation is promoted by GA. For annual plants, it has been shown that the GA/DELLA pathway interacts with JA signaling and C-repeat binding factor dependent cold acclimation, but these interactions have not been explored in detail for perennials. Growth regulation in response to seasonal factors is, however, particularly important in perennials, especially at high latitudes. In autumn, growth cessation in trees is caused by shortening of the daylength in interaction with phytohormone signaling. In perennial grasses seasonal differences in the sensitivity to GA may enable enhanced growth in spring. This review provides an overview of the signaling interactions that determine plant growth at low temperature and highlights gaps in our knowledge, especially concerning the seasonality of signaling responses in perennial plants. PMID:25628637

  17. Direct In Situ Determination of the Mechanisms Controlling Nanoparticle Nucleation and Growth

    PubMed Central

    Woehl, Taylor J.; Evans, James E.; Arslan, Ilke; Ristenpart, William D.; Browning, Nigel D.

    2012-01-01

    Although nanocrystal morphology is controllable using conventional colloidal synthesis, multiple characterization techniques are typically needed to determine key properties like the nucleation rate, induction time, growth rate, and the resulting morphology. Recently, researchers have demonstrated growth of nanocrystals by in situ electron beam reduction, offering direct observations of single nanocrystals and eliminating the need for multiple characterization techniques; however, they found nanocrystal morphologies consistent with two different growth mechanisms for the same electron beam parameters. Here we show that the electron beam current plays a role analogous to the concentration of reducing agent in conventional synthesis, by controlling the growth mechanism and final morphology of silver nanocrystals grown via in situ electron beam reduction. We demonstrate that low beam currents encourage reaction limited growth that yield nanocrystals with faceted structures, while higher beam currents encourage diffusion limited growth that yield spherical nanocrystals. By isolating these two growth regimes, we demonstrate a new level of control over nanocrystal morphology, regulated by the fundamental growth mechanism. We find that the induction threshold dose for nucleation is independent of the beam current, pixel dwell time, and magnification being used. Our results indicate that in situ electron microscopy data can be interpreted by classical models, by allowing simultaneous measurement of nucleation induction times, growth rates, and evolution of nanocrystal morphology. The results suggest that systematic dose experiments should be performed for all future in situ liquid studies to confirm the exact mechanisms underlying observations of nucleation and growth. PMID:22957797

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate rate of passage and nutrient digestibility. Yet nothing is known relative to their potential impact on fecal microbial ecology and subsequent VFA generation. Two experiments utilizing a total o...

  19. Linking microbial carbon utilization with microbially-derived soil organic matter

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

    Soil microbial communities are fundamental to plant C turnover, as all C inputs eventually pass through the microbial biomass. In turn, there is increasing evidence that this biomass accumulates as a significant portion of stable soil organic matter (SOM) via physiochemical interactions with the soil matrix. However, when exploring SOM dynamics, these two processes are often regarded as discrete from one another, despite potentially important linkages between microbial C utilization and the fate of that biomass C as SOM. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil C inputs that influence microbial biomass production and microbial C allocation. Microbial physiology, such as microbial growth efficiency (MGE), growth rate and turnover have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM accumulation may not necessarily be a function of resistance to decay but the degree to which it optimizes microbial biomass production. To examine the relationship between microbial C utilization and microbial contributions to SOM, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine 1) if, in absence of plant-derived C, chemically complex SOM similar to natural soils can accumulate through the production of microbial residues and 2) how differences in C utilization of simple substrates, varying in energy yields, influence the quantity and chemistry of newly formed SOM. Over the course of the incubation, MGE

  20. Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures†

    PubMed Central

    Kucharzyk, Katarzyna H.; Deshusses, Marc A.; Porter, Kaitlyn A.; Hsu-Kim, Heileen

    2016-01-01

    Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHg using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production. PMID:26211614

  1. Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures.

    PubMed

    Kucharzyk, Katarzyna H; Deshusses, Marc A; Porter, Kaitlyn A; Hsu-Kim, Heileen

    2015-09-01

    Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHg using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production.

  2. Highly sensitive and selective amperometric microbial biosensor for direct determination of p-nitrophenyl-substituted organophosphate nerve agents.

    PubMed

    Lei, Yu; Mulchandani, Priti; Wang, Joseph; Chen, Wilfred; Mulchandani, Ashok

    2005-11-15

    We report herein a whole cell-based amperometric biosensor for highly selective, highly sensitive, direct, single-step, rapid, and cost-effective determination of organophosphate pesticides with a p-nitrophenyl substituent. The biosensor was comprised of a p-nitrophenol degrader, Pseudomonas putida JS444, genetically engineered to express organophosphorus hydrolase (OPH) on the cell surface immobilized on the carbon paste electrode. Surface-expressed OPH catalyzed hydrolysis of the p-nitrophenyl substituent organophosphorus pesticides such as paraoxon, parathion, and methyl parathion to release p-nitrophenol, which was subsequently degraded by the enzymatic machinery of P. putida JS444. The electrooxidization current of the intermediates was measured and correlated to the concentration of organophosphates. The best sensitivity and response time were obtained using a sensor constructed with 0.086 mg dry weight of cells operating at 600 mV applied potential (vs Ag/AgCl reference) in 50 mM citrate--phosphate pH 7.5 buffer with 50 microM CoCl2 at room temperature. Under optimum operating conditions the biosensor measured as low as 0.28 ppb of paraoxon, 0.26 ppb of methyl parathion, and 0.29 ppb parathion. These detection limits are comparable to cholinesterase inhibition-based biosensors. Unlike the inhibition-based format, this biosensor manifests a selective response to organophosphate pesticides with a p-nitrophenyl substituent only, has a simplified single-step protocol with short response time, and can be used for repetitive/multiple and on-line analysis. The service life of the microbial amperometric biosensor was 5 days when stored in the operating buffer at 4 degrees C. The new biosensor offers great promise for rapid environmental monitoring of OP pesticides with nitrophenyl substituent.

  3. Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

    SciTech Connect

    Brockman, Fred; Selker, John

    2003-09-14

    activities are low. Specific objectives were to: (1) Conduct laboratory studies of how physical and hydrologic features of the vadose zone control the spatial distribution of microbial growth and the ability of microorganisms to colonize microbially sparse or ''empty'' regions of the vadose zone. (2) Characterize microbiological properties of a carbon tetrachloride-contaminated deep vadose zone site at the DOE Hanford Site. (3) Evaluate the potential for gas phase feeding of carbon, nitrogen, and phosphorus to deep vadose zone microbial communities. (4) Use field and laboratory data generated from the project to parameterize an unsaturated zone transport model with microbial growth, colonization, and biotransformation kinetics and conduct reactive transport simulations.Pacific Northwest National Lab (PNNL) and Oregon State University (OSU) jointly addressed objectives 1, 3, and 4. PNNL addressed objective 2. For objective 4, laboratory data was simulated during the project; field data was not used in modeling and simulation due to the late initiation of the field study and the small number (n=24) of samples studied.

  4. A test procedure for determining the influence of stress ratio on fatigue crack growth

    NASA Technical Reports Server (NTRS)

    Fitzgerald, J. H.; Wei, R. P.

    1974-01-01

    A test procedure is outlined by which the rate of fatigue crack growth over a range of stress ratios and stress intensities can be determined expeditiously using a small number of specimens. This procedure was developed to avoid or circumvent the effects of load interactions on fatigue crack growth, and was used to develop data on a mill annealed Ti-6Al-4V alloy plate. Experimental data suggest that the rates of fatigue crack growth among the various stress ratios may be correlated in terms of an effective stress intensity range at given values of K max. This procedure is not to be used, however, for determining the corrosion fatigue crack growth characteristics of alloys when nonsteady-state effects are significant.

  5. Phosphorus status and microbial community of paddy soil with the growth of annual ryegrass (Lolium multiflorum Lam.) under different phosphorus fertilizer treatments*

    PubMed Central

    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

  6. Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface

    SciTech Connect

    Wang, Cong; Zhang, Ping; Li, Zi; Li, DaFang

    2015-10-15

    Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.

  7. Fluorometric Determination of Adenosine Nucleotide Derivatives as Measures of the Microfouling, Detrital, and Sedimentary Microbial Biomass and Physiological Status

    PubMed Central

    Davis, William M.; White, David C.

    1980-01-01

    Adenosine, adenine, cyclic adenosine monophosphate (AMP), AMP, nicotinamide adenine dinucleotide, adenosine diphosphate, and adenosine triphosphate (ATP) were recovered quantitatively from aqueous portions of lipid extracts of microfouling, detrital, and sedimentary microbial communities. These could be detected quantitatively in the picomolar range by forming their 1-N6-etheno derivatives and analyzing by high-pressure liquid chromatography with fluorescence detection. Lipid extraction and subsequent analysis allowed the simultaneous measurement of the m