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Sample records for bacterial population dynamics

  1. Population dynamics on heterogeneous bacterial substrates

    Science.gov (United States)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  2. Dynamics of genome rearrangement in bacterial populations.

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    Aaron E Darling

    2008-07-01

    represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes.

  3. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment

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    Leilei Qu

    2016-01-01

    Full Text Available During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1 have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.

  4. Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.

    Science.gov (United States)

    McGarvey, J A; Franco, R B; Palumbo, J D; Hnasko, R; Stanker, L; Mitloehner, F M

    2013-06-01

    To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes. © 2013 The Society for Applied Microbiology No claim to US Government works.

  5. The population and evolutionary dynamics of homologous gene recombination in bacterial populations.

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    Bruce R Levin

    2009-08-01

    Full Text Available In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination -- broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT -- plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1 the contribution of HGR to the rate of adaptive evolution in these populations and (2 the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1 HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2 once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent

  6. Short-term wavelike dynamics of bacterial populations in response to nutrient input from fresh plant residues

    NARCIS (Netherlands)

    Zelenev, V.V.; Bruggen, van A.H.C.; Semenov, A.M.

    2005-01-01

    The objectives of the research were to investigate short-term dynamics of bacterial populations in soil after a disturbance in the form of fresh organic matter incorporation and to investigate how these dynamics are linked to those of some environmental parameters. To reach these objectives, soil

  7. The type VI secretion system impacts bacterial invasion and population dynamics in a model intestinal microbiota

    Science.gov (United States)

    Logan, Savannah L.; Shields, Drew S.; Hammer, Brian K.; Xavier, Joao B.; Parthasarathy, Raghuveer

    Animal gastrointestinal tracts are home to a diverse community of microbes. The mechanisms by which microbial species interact and compete in this dense, physically dynamic space are poorly understood, limiting our understanding of how natural communities are assembled and how different communities could be engineered. Here, we focus on a physical mechanism for competition: the type VI secretion system (T6SS). The T6SS is a syringe-like organelle used by certain bacteria to translocate effector proteins across the cell membranes of target bacterial cells, killing them. Here, we use T6SS+ and T6SS- strains of V. cholerae, the pathogen that causes cholera in humans, and light sheet fluorescence microscopy for in vivo imaging to show that the T6SS provides an advantage to strains colonizing the larval zebrafish gut. Furthermore, we show that T6SS+ bacteria can invade and alter an existing population of a different species in the zebrafish gut, reducing its abundance and changing the form of its population dynamics. This work both demonstrates a mechanism for altering the gut microbiota with an invasive species and explores the processes controlling the stability and dynamics of the gut ecosystem. Research Corporation, Gordon and Betty Moore Foundation, and the Simons Foundation.

  8. BACTERIAL POPULATION DYNAMICS IN WASTE OILY EMULSIONS FROM THE METAL-PROCESSING INDUSTRY

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    Paweł Kaszycki

    2014-07-01

    Full Text Available Oil-containing wastewaters are regarded as main industrial pollutants of soil and water environments. They can occur as free-floating oil, unstable or stable oil-in-water (O/W emulsions, and in the case of extreme organic load, as water-in-oil (W/O emulsions. In this study two types of oily effluents, a typical O/W emulsion marked as E1 and a W/O emulsion E2, both discharged by local metal processing plants were examined to test their toxicity to microbial communities and the ability to serve as nutrient sources for bacterial growth. The organic contaminant load of the samples was evaluated on the basis of chemical oxygen demand (COD parameter values and was equal to 48 200 mg O2·dm-3 and >300 000 mg O2·dm-3 for E1 and E2, respectively.Both emulsions proved to be non toxic to bacterial communities and were shown to contain biodiverse autochthonous microflora consisting of several bacterial strains adapted to the presence of xenobiotics (the total of 1.36 · 106 CFU·cm-3 and 1.72 · 105 CFU·cm-3 was determined for E1 and E2, respectively. These indigenous bacteria as well as exogenously inoculated specialized allochthonous microorganisms were biostimulated so as to proliferate within the wastewater environment whose organic content served as the only source of carbon. The most favorable cultivation conditions were determined as fully aerobic growth at the temperature of 25 ºC. In 9 to 18 day-tests, autochthonous as well as bioaugmented allochthonous bacterial population dynamics were monitored. For both emulsions tested there was a dramatic increase (up to three orders of magnitude in bacterial frequency, as compared to the respective initial values. The resultant high biomass densities suggest that the effluents are susceptible to bioremediation. A preliminary xenobiotic biodegradation test confirmed that mixed auto- and allochthonous bacterial consortia obtained upon inoculation of the samples with microbiocenoses preselected for efficient

  9. Red Sea Acropora hemprichii Bacterial Population Dynamics under Adverse Anthropogenic Conditions

    KAUST Repository

    Lizcano, Javier

    2012-08-01

    Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

  10. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

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    Lijuan Zhou

    Full Text Available Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB, a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and

  11. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

    Science.gov (United States)

    Zhou, Lijuan; Powell, Charles A; Li, Wenbin; Irey, Mike; Duan, Yongping

    2013-01-01

    Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.

  12. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    Science.gov (United States)

    Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

    2014-03-01

    A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

  13. Modeling physiological processes that relate toxicant exposure and bacterial population dynamics.

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    Tin Klanjscek

    Full Text Available Quantifying effects of toxicant exposure on metabolic processes is crucial to predicting microbial growth patterns in different environments. Mechanistic models, such as those based on Dynamic Energy Budget (DEB theory, can link physiological processes to microbial growth.Here we expand the DEB framework to include explicit consideration of the role of reactive oxygen species (ROS. Extensions considered are: (i additional terms in the equation for the "hazard rate" that quantifies mortality risk; (ii a variable representing environmental degradation; (iii a mechanistic description of toxic effects linked to increase in ROS production and aging acceleration, and to non-competitive inhibition of transport channels; (iv a new representation of the "lag time" based on energy required for acclimation. We estimate model parameters using calibrated Pseudomonas aeruginosa optical density growth data for seven levels of cadmium exposure. The model reproduces growth patterns for all treatments with a single common parameter set, and bacterial growth for treatments of up to 150 mg(Cd/L can be predicted reasonably well using parameters estimated from cadmium treatments of 20 mg(Cd/L and lower. Our approach is an important step towards connecting levels of biological organization in ecotoxicology. The presented model reveals possible connections between processes that are not obvious from purely empirical considerations, enables validation and hypothesis testing by creating testable predictions, and identifies research required to further develop the theory.

  14. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil.

    Science.gov (United States)

    Zrafi-Nouira, Ines; Guermazi, Sonda; Chouari, Rakia; Safi, Nimer M D; Pelletier, Eric; Bakhrouf, Amina; Saidane-Mosbahi, Dalila; Sghir, Abdelghani

    2009-07-01

    The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

  15. Dynamic Changes in Bacterial Population and Corresponding Exoenzyme Activity in Response to a Tropical Phytoplankton Bloom Chattonella marina

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    Anit M. Thomas

    2014-01-01

    Full Text Available The raphidophyte Chattonella marina (Subrahmanyan Hara & Chihara bloom which causes lethal effects on marine ecosystem has been reported intermittently from Indian waters. In the present study, periodic samplings were made in a Chattonella marina bloom area, off Mahe, on 27 and 29 October and 1 November 2011 (in different phases of the bloom to assess the associated bacterial population and their exoenzyme activity. Microbial community composition of Chattonella marina bloom revealed a twentyfold increase in bacterial load over the nonbloom area. The bacterial genera, Micrococcus, Flavobacterium, Vibrio, and Pseudomonas, increased significantly during the declining phase of the bloom. An assessment of the extracellular enzyme production also showed a marked increase in percentage of bacterial strains, potent in protease production, suggesting the possible role of proteolytic bacteria in bloom crash. This study reveals the bacterial community succession during the bloom and indicates that bacteria play an important role in bloom regulation.

  16. Population dynamics

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    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  17. Bacterial computing with engineered populations.

    Science.gov (United States)

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  18. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    Science.gov (United States)

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  19. Effect of autochthonous bacteriocin-producing Lactococcus lactis on bacterial population dynamics and growth of halotolerant bacteria in Brazilian charqui.

    Science.gov (United States)

    Biscola, Vanessa; Abriouel, Hikmate; Todorov, Svetoslav Dimitrov; Capuano, Verena Sant'Anna Cabral; Gálvez, Antonio; Franco, Bernadette Dora Gombossy de Melo

    2014-12-01

    Charqui is a fermented, salted and sun-dried meat product, widely consumed in Brazil and exported to several countries. Growth of microorganisms in this product is unlikely due to reduced Aw, but halophilic and halotolerant bacteria may grow and cause spoilage. Charqui is a good source of lactic acid bacteria able to produce antimicrobial bacteriocins. In this study, an autochthonous bacteriocinogenic strain (Lactococcus lactis subsp. lactis 69), isolated from charqui, was added to the meat used for charqui manufacture and evaluated for its capability to prevent the growth of spoilage bacteria during storage up to 45 days. The influence of L. lactis 69 on the bacterial diversity during the manufacturing of the product was also studied, using denaturing gradient gel electrophoresis (DGGE). L. lactis 69 did not affect the counts and diversity of lactic acid bacteria during manufacturing and storage, but influenced negatively the populations of halotolerant microorganisms, reducing the spoilage potential. The majority of tested virulence genes was absent, evidencing the safety and potential technological application of this strain as an additional hurdle to inhibit undesirable microbial growth in this and similar fermented meat products. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Heterotrophic bacterial populations in tropical sandy beaches

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.; LokaBharathi, P.A.

    Distribution pattern of heterotrophic bacterial flora of three sandy beaches of the west coast of India was studied. The population in these beaches was microbiologically different. Population peaks of halotolerant and limnotolerant forms were...

  1. Oscillating dynamics of bacterial populations and their predators in response to fresh organic matter added to soil: The simulation model 'BACWAVE-WEB'

    NARCIS (Netherlands)

    Zelenev, V.V.; Bruggen, van A.H.C.; Leffelaar, P.A.; Bloem, J.; Semenov, A.M.

    2006-01-01

    Recently, regular oscillations in bacterial populations and growth rates of bacterial feeding nematodes (BFN) were shown to occur after addition of fresh organic matter to soil. This paper presents a model developed to investigate potential mechanisms of those oscillations, and whether they were

  2. Population dynamics of toxic phytoplankton and bacterial flora in the waters of the low Adriatic sea; Dinamica di popolazione di fitoplancton tossico e flora batterica nel basso Adriatico

    Energy Technology Data Exchange (ETDEWEB)

    Caroppo, C.; Stabili, L.; Cavallo, R.A.; Pastore, M. [CNR, Ist. Sperimentale Talassografico Attlio Cerruti, Taranto (Italy); Marchiori, E. [Rome Univ., Rome (Italy). Dipt. di Chimica Organica; Bruno, M. [Istituto Superiore di Sanita' , Laboratorio di Igiene Ambientale, Rome (Italy)

    2000-07-01

    The coastal areas of the Southern Adriatic Sea, in particular the Apulian ones, may be considered an example of intact ecosystem and represent an ideal term of comparison to other marine ecosystems having higher levels of pollution (Northern Adriatic Sea). In order to evaluate the sanitary levels of this environment, four transect were investigated during two years monitoring (April 1995-March 1997) along the Otranto Channel coasts, by joint research groups of the Environmental Hygiene Laboratory of the Istituto Superiore di Sanita' and the Istituto Sperimentale Talassografico A. Cerruti of CNR in Taranto. The study underlines the phytoplanktic and bacterial population dynamics, and the detection of the microbiological water quality along the coast tract Brindisi-Lecce-Otranto-S. Maria di Leuca. The results acquired pointed out population dynamics of some potantially toxic species of Dinophysis genus and Pseudo-nitzschia delicatissima. These depended on the winter nutrient loads due to the ASW (Adriatic Superficial Waters) and to the LIW (Levantine Intermediate Waters). The bacterial community was mainly constituted by genera Aeromonas, Photobacterium, Cytophaga and Pseudomonas. Also the presence of Enterobacteriaceae family was relevant. Among the pathogenic vibrios the most frequently isolated species were Vibrio alginolyticus and Vibrio vulnificus. [Italian] Considerando che le zone del basso Adriatico, in particolare quelle pugliesi, costituiscono un biotopo ancora relativamente inalterato, esse sono state oggetto di un'indagine sperimentale condotta in 24 mesi di attivita' (aprile 1995-marzo 1997) lungo le coste del Canale di Otranto, ad opera di un gruppo congiunto del Laboratorio di Igiene Ambientale dell'Istituto Superiore di Sanita' e dei laboratori dell'Istituto Sperimentale Talassografico A. Cerruti del CNR di Taranto, ai fini di valutare lo stato di salute di questo ambiente, che fornisce, con buona probabilita', un

  3. Market Squid Population Dynamics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains population dynamics data on paralarvae, juvenile and adult market squid collected off California and the US Pacific Northwest. These data were...

  4. Fish population dynamics

    National Research Council Canada - National Science Library

    Gulland, J. A

    1977-01-01

    This book describes how the dynamics of fish populations can be analysed in terms of the factors affecting their rates of growth, mortality and reproduction, with particular emphasis on the effects of fishing...

  5. Dinâmica das populações bacterianas em solos de Cerrados Dynamic of bacterial populations from Cerrado soils

    Directory of Open Access Journals (Sweden)

    João Carlos Pereira

    1999-05-01

    Full Text Available Nos ambientes tropicais, os Cerrados destacam-se pelo seu potencial agrícola. Apesar das funções dos microrganismos no crescimento das plantas e na produtividade das culturas, existem poucas informações dos efeitos resultantes do manejo do solo, na ecologia microbiana. Neste estudo, foram avaliados os efeitos das condições ambientais e das práticas agrícolas sobre as populações bacterianas. As densidades das populações em solos com vegetação nativa foram variáveis e diferenciadas. Em Sete Lagoas, MG, as populações de actinomicetos variaram de 1,7 a 50 X 10(4 UFC/g de solo seco, enquanto em Planaltina as densidades das populações bacterianas em solo com primeiro e segundo ano de cultivo de soja foram semelhantes, mas superiores ao solo com vegetação nativa. A utilização agrícola deste solo não resultou em desequilíbrios acentuados das populações de actinomicetos provenientes de esporos e hifas. As relações esporos/hifas variaram de 1,1 a 5,8. Na rizosfera da soja, os coeficientes de correlação entre as populações de actinomicetos com as demais populações bacterianas foram significativos. Os resultados evidenciam que as práticas agrícolas utilizadas na introdução da cultura da soja em solos de Cerrados pode influenciar o equilíbrio das populações na comunidade bacteriana.Among tropical environments, Cerrados stand out because of its agriculture potencial. Although microorganisms play an important role on soil sustainability and crop production, few information is available on the effects of soil management systems on Cerrado's microbial ecology. In this study the effects of environmental conditions and soil management practices on bacterial populations were evaluated. Bacterial population densities in soil under native vegetation were variable and diferentiated. Actinomycetes densities varied from 1.7 to 50 X 10(4 CFU/g dry soil in Sete Lagoas region, Brazil, whereas bacterial populations in both the

  6. Synchronization and survival of connected bacterial populations

    Science.gov (United States)

    Gokhale, Shreyas; Conwill, Arolyn; Ranjan, Tanvi; Gore, Jeff

    Migration plays a vital role in controlling population dynamics of species occupying distinct habitat patches. While local populations are vulnerable to extinction due to demographic or environmental stochasticity, migration from neighboring habitat patches can rescue these populations through colonization of uninhabited regions. However, a large migratory flux can synchronize the population dynamics in connected patches, thereby enhancing the risk of global extinction during periods of depression in population size. Here, we investigate this trade-off between local rescue and global extinction experimentally using laboratory populations of E. coli bacteria. Our model system consists of co-cultures of ampicillin resistant and chloramphenicol resistant strains that form a cross-protection mutualism and exhibit period-3 oscillations in the relative population density in the presence of both antibiotics. We quantify the onset of synchronization of oscillations in a pair of co-cultures connected by migration and demonstrate that period-3 oscillations can be disturbed for moderate rates of migration. These features are consistent with simulations of a mechanistic model of antibiotic deactivation in our system. The simulations further predict that the probability of survival of connected populations in high concentrations of antibiotics is maximized at intermediate migration rates. We verify this prediction experimentally and show that survival is enhanced through a combination of disturbance of period-3 oscillations and stochastic re-colonization events.

  7. Bacterial Populations Associated with Smokeless Tobacco Products

    Science.gov (United States)

    Han, Jing; Sanad, Yasser M.; Deck, Joanna; Sutherland, John B.; Li, Zhong; Walters, Matthew J.; Duran, Norma; Holman, Matthew R.

    2016-01-01

    ABSTRACT There are an estimated 8 million users of smokeless tobacco products (STPs) in the United States, and yet limited data on microbial populations within these products exist. To better understand the potential microbiological risks associated with STP use, a study was conducted to provide a baseline microbiological profile of STPs. A total of 90 samples, representing 15 common STPs, were purchased in metropolitan areas in Little Rock, AR, and Washington, DC, in November 2012, March 2013, and July 2013. Bacterial populations were evaluated using culture, pyrosequencing, and denaturing gradient gel electrophoresis (DGGE). Moist-snuff products exhibited higher levels of bacteria (average of 1.05 × 106 CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 101 CFU/g STP) and some chewing tobacco products (average of 2.54 × 105 CFU/g STP). The most common species identified by culturing were Bacillus pumilus, B. licheniformis, B. safensis, and B. subtilis, followed by members of the genera Oceanobacillus, Staphylococcus, and Tetragenococcus. Pyrosequencing analyses of the 16S rRNA genes identified the genera Tetragenococcus, Carnobacterium, Lactobacillus, Geobacillus, Bacillus, and Staphylococcus as the predominant taxa. Several species identified are of possible concern due to their potential to cause opportunistic infections and reported abilities to reduce nitrates to nitrites, which may be an important step in the formation of carcinogenic tobacco-specific N′-nitrosamines. This report provides a microbiological baseline to help fill knowledge gaps associated with microbiological risks of STPs and to inform potential regulations regarding manufacture and testing of STPs. IMPORTANCE It is estimated that there 8 million users of smokeless tobacco products (STPs) in the United States; however, there are limited data on microbial populations that exist within these products. The current study was undertaken to better understand the

  8. Efeito do cultivo da soja na dinâmica da população bacteriana, em solos de cerrado Effects of soybean cultivation on the bacterial population dynamics in cerrado soils

    Directory of Open Access Journals (Sweden)

    JOÃO CARLOS PEREIRA

    2000-06-01

    Full Text Available Este trabalho teve por objetivo avaliar a influência do cultivo da soja sobre a dinâmica da população bacteriana, em dois solos de Cerrado do Estado de São Paulo, originalmente cobertos com Paspalum notatum (em Barretos e Brachiaria decumbens (em S��o Carlos. Nesses solos, a densidade da população de bactérias em geral variou de 398,1 x 10³ a 467,7 x 10³ e de 123 x 10³ a 218,8 x 10³ ufc (unidades formadoras de colônias/g de solo seco, respectivamente. O cultivo da soja, em ambos os solos, resultou em incrementos variados nos números de ufc/g de solo seco da população de bactérias em geral, das resistentes aos antibióticos estreptomicina e cloranfenicol, e de actinomicetos. A população de actinomicetos ocorreu no solo principalmente como esporos, e as variações das relações esporos/hifas entre os solos não-rizosférico e rizosférico não foram significativas. Os resultados evidenciam que o cultivo da soja influenciou de forma diferenciada a população desses solos.The effect of soybean cultivation on the population dynamics of the bacterial community was evaluated in two "Cerrado" soils of São Paulo State, Brazil. The experimental areas, in the vicinities of the cities of São Carlos and Barretos, were previously cultivated, respectively, with Paspalum notatum and Brachiaria decumbens. The bacterial population densities in these soils varied from 398.1 x 10³ to 467.7 x 10³ cfu (colony forming units and from 123 x 10³ to 218.8 x 10³ cfu/g of dried soil, respectively, in São Carlos and Barretos soils. Soybean cultivation in both soils resulted in increments in the total bacterial population density, in the actinomycetes population, and in the bacterial population resistant to the antibiotics streptomycin and chloramphenicol. Actinomycetes were present in these soils mainly as spores. Soybean cultivation did not alter the actinomycetes spores/hyphae ratio when comparing rhizospheric and non-rhizospheric soils

  9. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations

  10. Bacterial Pneumonia in Elderly Japanese Populations

    Directory of Open Access Journals (Sweden)

    Naoya Miyashita

    2018-01-01

    Full Text Available Bacterial pneumonia is one of the most important infectious diseases in terms of incidence, effect on quality of life, mortality, and impact on society. Pneumonia was the third leading cause of death in Japan in 2011. In 2016, 119 650 Japanese people died of pneumonia, 96% of whom were aged 65 years and above. The symptoms of pneumonia in elderly people are often atypical. Aspiration pneumonia is seen more frequently than in young people because of swallowing dysfunction in the elderly. The mortality rate is also higher in the elderly than in young people. In Japan, the population is aging at an unprecedented rate, and pneumonia in the elderly will be increasingly important in medicine and medical economics in the future. To manage pneumonia in the elderly, it is important to accurately evaluate its severity, administer appropriate antibiotic treatment, and implement effective preventive measures.

  11. Modelling within-host spatiotemporal dynamics of invasive bacterial disease.

    Directory of Open Access Journals (Sweden)

    Andrew J Grant

    2008-04-01

    Full Text Available Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS] in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host-pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host-pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics.

  12. Bacterial charity work leads to population-wide resistance.

    Science.gov (United States)

    Lee, Henry H; Molla, Michael N; Cantor, Charles R; Collins, James J

    2010-09-02

    Bacteria show remarkable adaptability in the face of antibiotic therapeutics. Resistance alleles in drug target-specific sites and general stress responses have been identified in individual end-point isolates. Less is known, however, about the population dynamics during the development of antibiotic-resistant strains. Here we follow a continuous culture of Escherichia coli facing increasing levels of antibiotic and show that the vast majority of isolates are less resistant than the population as a whole. We find that the few highly resistant mutants improve the survival of the population's less resistant constituents, in part by producing indole, a signalling molecule generated by actively growing, unstressed cells. We show, through transcriptional profiling, that indole serves to turn on drug efflux pumps and oxidative-stress protective mechanisms. The indole production comes at a fitness cost to the highly resistant isolates, and whole-genome sequencing reveals that this bacterial altruism is made possible by drug-resistance mutations unrelated to indole production. This work establishes a population-based resistance mechanism constituting a form of kin selection whereby a small number of resistant mutants can, at some cost to themselves, provide protection to other, more vulnerable, cells, enhancing the survival capacity of the overall population in stressful environments.

  13. The impact of natural transformation on adaptation in spatially structured bacterial populations.

    Science.gov (United States)

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-06-20

    Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

  14. Environmental impact of mining activity in Bor area as indicated by the distribution of heavy metals and bacterial population dynamics in sediment

    Directory of Open Access Journals (Sweden)

    Filimon M. N.

    2016-01-01

    Full Text Available The environmental impact of inorganic pollution is pronounced in water adjacent to Bor Copper Smelter Complex (RTB Bor, Serbia, with Cu, Zn, Pb, and As being the main determinants of aquatic pollution pattern. Communities of microorganisms present in the sediments are mainly affected by heavy metal pollution. Some groups of bacteria can be considered pollution bio-indicators, due to their sensibility and ability to bioaccumulate heavy metals, thus contributing to reducing pollution. This study investigates the relationships between trace element accumulation and heterogeneity in sediment bacteria community structure found in water streams adjacent to the Bor Copper Smelter Complex (RTB Bor, Serbia. Our results showed no contamination with copper, zinc, nickel, iron, and chromium, but did show a low to moderate contamination with lead and a moderate to high contamination with arsenic in aquatic sediments within the area of interest. Spatial heterogeneity in sediment-associated bacterial communities did not relate significantly to location of sampling sites, except for iron reducing bacteria. Iron reducing bacteria and nitrifying bacteria were the best distinguishing groups of bacteria. However, only iron reducing bacteria were significantly influenced by sampling locations. The iron reducing bacteria has correlated negatively with the degree of sediment contamination with lead, and therefore, we suggest that this group of bacteria could serve as potential bio-indicators of inorganic water contamination in Bor RTB area.

  15. Measurement of Behavioral Evolution in Bacterial Populations

    Science.gov (United States)

    Austin, Robert

    2013-03-01

    A curious aspect of bacterial behavior under stress is the induction of filamentation: the anomalous growth of certain bacteria in which cells continue to elongate but do not divide into progeny. We show that E.coli under the influence of the genotoxic antibiotic ciprofloxacin have robust filamentous growth, which provides individual bacteria a mesoscopic niche for evolution until resistant progeny can bud off and propagate. Hence, filamentation is a form of genomic amplification where even a single, isolated bacteria can have access to multiple genomes. We propose a model that predicts that the first arrival time of the normal sized progeny should follow a Gompertz distribution with the mean first arrival time proportional to the elongation rate of filament. These predictions agree with our experimental measurements. Finally, we suggest bacterial filament growth and budding has many similarities to tumor growth and metastasis and can serve as a simpler model to study those complicated processes. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

  16. Africa population dynamics

    OpenAIRE

    Akinyoade, A.; Damen, J.C.M.; Dietz, A.J.; Kilama, B.B.; Omme, van, G.

    2014-01-01

    Africa's population has grown extremely rapidly over the last fifty years from 289 million inhabitants in 1961 to more than 1 billion today. This is a growth rate of 350% in just half a century and the number of urban residents has increased even more quickly: from 65 million in 1960 to 460 million today, or from 20% to 46% of the population as a whole. Demographers predict that soon more than 50% of all Africans will be living in cities. The average life expectancy, literacy rates and primar...

  17. Africa population dynamics

    NARCIS (Netherlands)

    Akinyoade, A.; Damen, J.C.M.; Dietz, A.J.; Kilama, B.B.; Omme, van G.

    2014-01-01

    Africa's population has grown extremely rapidly over the last fifty years from 289 million inhabitants in 1961 to more than 1 billion today. This is a growth rate of 350% in just half a century and the number of urban residents has increased even more quickly: from 65 million in 1960 to 460 million

  18. Mathematical Modelling of Bacterial Meningitis Transmission Dynamics with Control Measures

    Directory of Open Access Journals (Sweden)

    Joshua Kiddy K. Asamoah

    2018-01-01

    Full Text Available Vaccination and treatment are the most effective ways of controlling the transmission of most infectious diseases. While vaccination helps susceptible individuals to build either a long-term immunity or short-term immunity, treatment reduces the number of disease-induced deaths and the number of infectious individuals in a community/nation. In this paper, a nonlinear deterministic model with time-dependent controls has been proposed to describe the dynamics of bacterial meningitis in a population. The model is shown to exhibit a unique globally asymptotically stable disease-free equilibrium E0, when the effective reproduction number RVT≤1, and a globally asymptotically stable endemic equilibrium E1, when RVT>1; and it exhibits a transcritical bifurcation at RVT=1. Carriers have been shown (by Tornado plot to have a higher chance of spreading the infection than those with clinical symptoms who will sometimes be bound to bed during the acute phase of the infection. In order to find the best strategy for minimizing the number of carriers and ill individuals and the cost of control implementation, an optimal control problem is set up by defining a Lagrangian function L to be minimized subject to the proposed model. Numerical simulation of the optimal problem demonstrates that the best strategy to control bacterial meningitis is to combine vaccination with other interventions (such as treatment and public health education. Additionally, this research suggests that stakeholders should press hard for the production of existing/new vaccines and antibiotics and their disbursement to areas that are most affected by bacterial meningitis, especially Sub-Saharan Africa; furthermore, individuals who live in communities where the environment is relatively warm (hot/moisture are advised to go for vaccination against bacterial meningitis.

  19. Multi-fractal characterization of bacterial swimming dynamics: a case study on real and simulated Serratia marcescens

    OpenAIRE

    Koorehdavoudi, Hana; Bogdan, Paul; Wei, Guopeng; Marculescu, Radu; Zhuang, Jiang; Carlsen, Rika Wright; Sitti, Metin

    2017-01-01

    To add to the current state of knowledge about bacterial swimming dynamics, in this paper, we study the fractal swimming dynamics of populations of Serratia marcescens bacteria both in vitro and in silico, while accounting for realistic conditions like volume exclusion, chemical interactions, obstacles and distribution of chemoattractant in the environment. While previous research has shown that bacterial motion is non-ergodic, we demonstrate that, besides the non-ergodicity, the bacterial sw...

  20. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  1. Dynamic metabolic exchange governs a marine algal-bacterial interaction.

    Science.gov (United States)

    Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

    2016-11-18

    Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens , a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale.

  2. Nonlinear Relaxation in Population Dynamics

    Science.gov (United States)

    Cirone, Markus A.; de Pasquale, Ferdinando; Spagnolo, Bernardo

    We analyze the nonlinear relaxation of a complex ecosystem composed of many interacting species. The ecological system is described by generalized Lotka-Volterra equations with a multiplicative noise. The transient dynamics is studied in the framework of the mean field theory and with random interaction between the species. We focus on the statistical properties of the asymptotic behaviour of the time integral of the ith population and on the distribution of the population and of the local field.

  3. Bacterial interaction forces in adhesion dynamics

    NARCIS (Netherlands)

    Boks, Niels Peter

    2009-01-01

    Wanneer interactiekrachten tussen bacteriën en oppervlakken bepaald worden, hangen deze erg af van de gebruikte meettechniek. De mechanismen die verantwoordelijk zijn voor deze verschillen zijn echter nog niet duidelijk. Om hier meer inzicht in te krijgen, zijn in dit onderzoek interactiekrachten

  4. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  5. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO 2 could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

  6. Population dynamics of rural Ethiopia.

    Science.gov (United States)

    Bariabagar, H

    1978-01-01

    2 rounds of the national sample surveys, conducted by the central statistical office of Ethiopia during 1964-1967 and 1969-1971, provide the only comprehensive demographic data for the country and are the basis for this discussion of rural Ethiopia's population dynamics. The population of Ethiopia is predominantly rural. Agglomerations of 2000 and over inhabitants constitute about 14% of the population, and this indicates that Ethiopia has a low level of urbanization. In rural Ethiopia, international migration was negligent in the 1970's and the age structure can be assumed to be the results of past trends of fertility and mortality conditions. The reported crude birthrate (38.2), crude death rate (12.3) and infant mortality rate (90) of rural Ethiopia fall short of the averages for African countries. Prospects of population growth of rural Ethiopia would be immense. At the rate of natural increase of between 2.4 and 3.0% per annum, the population would double in 24-29 years. Regarding population issues, the programs of the National Democratic Revolution of Ethiopia faces the following main challenging problems: 1) carrying out national population censuses in order to obtain basic information for socialist planning; 2) minimizing or curtailing the existing high urban growth rates; 3) reducing rapidly growing population; and 5) mobilizing Ethiopian women to participate in the social, economic and political life of the country in order to create favorable conditions for future fertility reduction.

  7. Population dynamics in variable environments

    CERN Document Server

    Tuljapurkar, Shripad

    1990-01-01

    Demography relates observable facts about individuals to the dynamics of populations. If the dynamics are linear and do not change over time, the classical theory of Lotka (1907) and Leslie (1945) is the central tool of demography. This book addresses the situation when the assumption of constancy is dropped. In many practical situations, a population will display unpredictable variation over time in its vital rates, which must then be described in statistical terms. Most of this book is concerned with the theory of populations which are subject to random temporal changes in their vital rates, although other kinds of variation (e. g. , cyclical) are also dealt with. The central questions are: how does temporal variation work its way into a population's future, and how does it affect our interpretation of a population's past. The results here are directed at demographers of humans and at popula­ tion biologists. The uneven mathematical level is dictated by the material, but the book should be accessible to re...

  8. Mucin dynamics in intestinal bacterial infection.

    Directory of Open Access Journals (Sweden)

    Sara K Lindén

    Full Text Available Bacterial gastroenteritis causes morbidity and mortality in humans worldwide. Murine Citrobacter rodentium infection is a model for gastroenteritis caused by the human pathogens enteropathogenic Escherichia coli and enterohaemorrhagic E. coli. Mucin glycoproteins are the main component of the first barrier that bacteria encounter in the intestinal tract.Using Immunohistochemistry, we investigated intestinal expression of mucins (Alcian blue/PAS, Muc1, Muc2, Muc4, Muc5AC, Muc13 and Muc3/17 in healthy and C. rodentium infected mice. The majority of the C. rodentium infected mice developed systemic infection and colitis in the mid and distal colon by day 12. C. rodentium bound to the major secreted mucin, Muc2, in vitro, and high numbers of bacteria were found in secreted MUC2 in infected animals in vivo, indicating that mucins may limit bacterial access to the epithelial surface. In the small intestine, caecum and proximal colon, the mucin expression was similar in infected and non-infected animals. In the distal colonic epithelium, all secreted and cell surface mucins decreased with the exception of the Muc1 cell surface mucin which increased after infection (p<0.05. Similarly, during human infection Salmonella St Paul, Campylobacter jejuni and Clostridium difficile induced MUC1 in the colon.Major changes in both the cell-surface and secreted mucins occur in response to intestinal infection.

  9. Nonlinear dynamics of interacting populations

    CERN Document Server

    Bazykin, Alexander D

    1998-01-01

    This book contains a systematic study of ecological communities of two or three interacting populations. Starting from the Lotka-Volterra system, various regulating factors are considered, such as rates of birth and death, predation and competition. The different factors can have a stabilizing or a destabilizing effect on the community, and their interplay leads to increasingly complicated behavior. Studying and understanding this path to greater dynamical complexity of ecological systems constitutes the backbone of this book. On the mathematical side, the tool of choice is the qualitative the

  10. Bacterial dynamics in a microphytobenthic biofilm: A tidal mesocosm approach

    Science.gov (United States)

    Agogué, Hélène; Mallet, Clarisse; Orvain, Francis; De Crignis, Margot; Mornet, Françoise; Dupuy, Christine

    2014-09-01

    In intertidal mudflats, during low tide exposure, microphytobenthos (MPB) migrate vertically through the surface sediment and form, with the heterotrophic bacteria, a transient biofilm. Inside this biofilm, multiple interactions exist between MPB and bacteria. These micro-organisms secrete a wide range of extracellular polymeric substances (EPS), which are major components of the biofilm matrix. In this study, we used a tidal mesocosm experiment in order to decipher the interactions of the MPB-EPS-bacteria complex within the biofilm. We tried to determine if the EPS could control bacterial activities and/or production and/or richness according to the age of the biofilm and to the immersion/emersion period. The dynamics of biomasses of MPB and prokaryotes, the bacterial production, the hydrolysis of predominating organic constituents in the dissolved organic carbon (DOC) pool (i.e., carbohydrates and polypeptides), and the bacterial structure were studied in relation to the different EPS fractions (carbohydrates and proteins: colloidal and bound) dynamics during 8 days. Our experiment had emphasized the influence of the environmental conditions (light, immersion/emersion) on the interactions within the biofilm and also on the effects on biofilm aging. Bacterial production was always inhibited by the bound EPS-carbohydrate, especially during low tide. Our results suggest that the concentration and composition of EPS had a major role in the bacterial/MPB interactions: these interactions can be either positive or negative in order to regulate the productive phases of MPB and bacteria.

  11. Species and Scale Dependence of Bacterial Motion Dynamics

    Science.gov (United States)

    Sund, N. L.; Yang, X.; Parashar, R.; Plymale, A.; Hu, D.; Kelly, R.; Scheibe, T. D.

    2017-12-01

    Many metal reducing bacteria are motile with their motion characteristics described by run-and-tumble behavior exhibiting series of flights (jumps) and waiting (residence) time spanning a wide range of values. Accurate models of motility allow for improved design and evaluation of in-situ bioremediation in the subsurface. While many bioremediation models neglect the motion of the bacteria, others treat motility using an advection dispersion equation, which assumes that the motion of the bacteria is Brownian.The assumption of Brownian motion to describe motility has enormous implications on predictive capabilities of bioremediation models, yet experimental evidence of this assumption is mixed [1][2][3]. We hypothesize that this is due to the species and scale dependence of the motion dynamics. We test our hypothesis by analyzing videos of motile bacteria of five different species in open domains. Trajectories of individual cells ranging from several seconds to few minutes in duration are extracted in neutral conditions (in the absence of any chemical gradient). The density of the bacteria is kept low so that the interaction between the bacteria is minimal. Preliminary results show a transition from Fickian (Brownian) to non-Fickian behavior for one species of bacteria (Pelosinus) and persistent Fickian behavior of another species (Geobacter).Figure: Video frames of motile bacteria with the last 10 seconds of their trajectories drawn in red. (left) Pelosinus and (right) Geobacter.[1] Ariel, Gil, et al. "Swarming bacteria migrate by Lévy Walk." Nature Communications 6 (2015).[2] Saragosti, Jonathan, Pascal Silberzan, and Axel Buguin. "Modeling E. coli tumbles by rotational diffusion. Implications for chemotaxis." PloS one 7.4 (2012): e35412.[3] Wu, Mingming, et al. "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique." Applied and Environmental Microbiology 72.7 (2006): 4987-4994.

  12. Bacterial subversion of host actin dynamics at the plasma membrane.

    Science.gov (United States)

    Carabeo, Rey

    2011-10-01

    Invasion of non-phagocytic cells by a number of bacterial pathogens involves the subversion of the actin cytoskeletal remodelling machinery to produce actin-rich cell surface projections designed to engulf the bacteria. The signalling that occurs to induce these actin-rich structures has considerable overlap among a diverse group of bacteria. The molecular organization within these structures act in concert to internalize the invading pathogen. This dynamic process could be subdivided into three acts - actin recruitment, engulfment, and finally, actin disassembly/internalization. This review will present the current state of knowledge of the molecular processes involved in each stage of bacterial invasion, and provide a perspective that highlights the temporal and spatial control of actin remodelling that occurs during bacterial invasion. © 2011 Blackwell Publishing Ltd.

  13. Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces.

    Science.gov (United States)

    McDonald, Bradon R; Currie, Cameron R

    2017-06-06

    Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces , with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new

  14. Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

    Directory of Open Access Journals (Sweden)

    Bradon R. McDonald

    2017-06-01

    Full Text Available Lateral gene transfer (LGT profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces. Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.

  15. Plasmids foster diversification and adaptation of bacterial populations in soil.

    Science.gov (United States)

    Heuer, Holger; Smalla, Kornelia

    2012-11-01

    It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  16. Bacterial Associates Modify Growth Dynamics of the Dinoflagellate Gymnodinium catenatum.

    Science.gov (United States)

    Bolch, Christopher J S; Bejoy, Thaila A; Green, David H

    2017-01-01

    Marine phytoplankton cells grow in close association with a complex microbial associate community known to affect the growth, behavior, and physiology of the algal host. The relative scale and importance these effects compared to other major factors governing algal cell growth remain unclear. Using algal-bacteria co-culture models based on the toxic dinoflagellate Gymnodinium catenatum , we tested the hypothesis that associate bacteria exert an independent effect on host algal cell growth. Batch co-cultures of G. catenatum were grown under identical environmental conditions with simplified bacterial communities composed of one-, two-, or three-bacterial associates. Modification of the associate community membership and complexity induced up to four-fold changes in dinoflagellate growth rate, equivalent to the effect of a 5°C change in temperature or an almost six-fold change in light intensity (20-115 moles photons PAR m -2 s -1 ). Almost three-fold changes in both stationary phase cell concentration and death rate were also observed. Co-culture with Roseobacter sp. DG874 reduced dinoflagellate exponential growth rate and led to a more rapid death rate compared with mixed associate community controls or co-culture with either Marinobacter sp. DG879, Alcanivorax sp. DG881. In contrast, associate bacteria concentration was positively correlated with dinoflagellate cell concentration during the exponential growth phase, indicating growth was limited by supply of dinoflagellate-derived carbon. Bacterial growth increased rapidly at the onset of declining and stationary phases due to either increasing availability of algal-derived carbon induced by nutrient stress and autolysis, or at mid-log phase in Roseobacter co-cultures potentially due to the onset of bacterial-mediated cell lysis. Co-cultures with the three bacterial associates resulted in dinoflagellate and bacterial growth dynamics very similar to more complex mixed bacterial community controls, suggesting that

  17. Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L..

    Directory of Open Access Journals (Sweden)

    Mingna Chen

    Full Text Available Plant health and soil fertility are affected by plant-microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including

  18. Analysis of Population Dynamics in World Economy

    OpenAIRE

    Martin, Gress

    2011-01-01

    Population dynamics is an important topic in current world economy. The size and growth of population have an impact on economic growth and development of individual countries and vice versa, economic development influences demographic variables in a country. The aim of the article is to analyze historical development of world population, population stock change and relations between population stock change and economic development.

  19. Allee effects on population dynamics with delay

    International Nuclear Information System (INIS)

    Celik, C.; Merdan, H.; Duman, O.; Akin, O.

    2008-01-01

    In this paper, we study the stability analysis of equilibrium points of population dynamics with delay when the Allee effect occurs at low population density. Mainly, our mathematical results and numerical simulations point to the stabilizing effect of the Allee effects on population dynamics with delay

  20. Role of antimicrobial peptides in controlling symbiotic bacterial populations.

    Science.gov (United States)

    Mergaert, P

    2018-04-25

    Covering: up to 2018 Antimicrobial peptides (AMPs) have been known for well over three decades as crucial mediators of the innate immune response in animals and plants, where they are involved in the killing of infecting microbes. However, AMPs have now also been found to be produced by eukaryotic hosts during symbiotic interactions with bacteria. These symbiotic AMPs target the symbionts and therefore have a more subtle biological role: not eliminating the microbial symbiont population but rather keeping it in check. The arsenal of AMPs and the symbionts' adaptations to resist them are in a careful balance, which contributes to the establishment of the host-microbe homeostasis. Although in many cases the biological roles of symbiotic AMPs remain elusive, for a number of symbiotic interactions, precise functions have been assigned or proposed to the AMPs, which are discussed here. The microbiota living on epithelia in animals, from the most primitive ones to the mammals, are challenged by a cocktail of AMPs that determine the specific composition of the bacterial community as well as its spatial organization. In the symbiosis of legume plants with nitrogen-fixing rhizobium bacteria, the host deploys an extremely large panel of AMPs - called nodule-specific cysteine-rich (NCR) peptides - that drive the bacteria into a terminally differentiated state and manipulate the symbiont physiology to maximize the benefit for the host. The NCR peptides are used as tools to enslave the bacterial symbionts, limiting their reproduction but keeping them metabolically active for nitrogen fixation. In the nutritional symbiotic interactions of insects and protists that have vertically transmitted bacterial symbionts with reduced genomes, symbiotic AMPs could facilitate the integration of the endosymbiont and host metabolism by favouring the flow of metabolites across the symbiont membrane through membrane permeabilization.

  1. Bacterial population solitary waves can defeat rings of funnels

    International Nuclear Information System (INIS)

    Morris, Ryan J; Phan, Trung V; Austin, Robert H; Black, Matthew; Bos, Julia A; Lin, Ke-Chih; Kevrekidis, Ioannis G

    2017-01-01

    We have constructed a microfabricated circular corral for bacteria made of rings of concentric funnels which channel motile bacteria outwards via non-hydrodynamic interactions with the funnel walls. Initially bacteria do move rapidly outwards to the periphery of the corral. At the edge, nano-slits allow for the transport of nutrients into the device while keeping the bacteria from escaping. After a period of time in which the bacteria increase their cell density in this perimeter region, they are then able to defeat the physical constrains of the funnels by launching back-propagating collective waves. We present the basic data and some nonlinear modeling which can explain how bacterial population waves propagate through a physical funnel, and discuss possible biological implications. (paper)

  2. Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes.

    Science.gov (United States)

    Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J

    2007-10-01

    To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.

  3. Population dynamics at high Reynolds number

    NARCIS (Netherlands)

    Perlekar, P.; Benzi, R.; Nelson, D.R.; Toschi, F.

    2010-01-01

    We study the statistical properties of population dynamics evolving in a realistic two-dimensional compressible turbulent velocity field. We show that the interplay between turbulent dynamics and population growth and saturation leads to quasi-localization and a remarkable reduction in the carrying

  4. Flow and active mixing have a strong impact on bacterial growth dynamics in the proximal large intestine

    Science.gov (United States)

    Cremer, Jonas; Segota, Igor; Yang, Chih-Yu; Arnoldini, Markus; Groisman, Alex; Hwa, Terence

    2016-11-01

    More than half of fecal dry weight is bacterial mass with bacterial densities reaching up to 1012 cells per gram. Mostly, these bacteria grow in the proximal large intestine where lateral flow along the intestine is strong: flow can in principal lead to a washout of bacteria from the proximal large intestine. Active mixing by contractions of the intestinal wall together with bacterial growth might counteract such a washout and allow high bacterial densities to occur. As a step towards understanding bacterial growth in the presence of mixing and flow, we constructed an in-vitro setup where controlled wall-deformations of a channel emulate contractions. We investigate growth along the channel under a steady nutrient inflow. Depending on mixing and flow, we observe varying spatial gradients in bacterial density along the channel. Active mixing by deformations of the channel wall is shown to be crucial in maintaining a steady-state bacterial population in the presence of flow. The growth-dynamics is quantitatively captured by a simple mathematical model, with the effect of mixing described by an effective diffusion term. Based on this model, we discuss bacterial growth dynamics in the human large intestine using flow- and mixing-behavior having been observed for humans.

  5. Bistable responses in bacterial genetic networks: Designs and dynamical consequences

    Science.gov (United States)

    Tiwari, Abhinav; Ray, J. Christian J.; Narula, Jatin; Igoshin, Oleg A.

    2011-01-01

    A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles for networks with bistable responses. PMID:21385588

  6. Compositional Stability of a Salivary Bacterial Population against Supragingival Microbiota Shift following Periodontal Therapy

    OpenAIRE

    山中, 渉

    2013-01-01

    Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.862.6 months), and their bacterial composition was inves...

  7. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

  8. Population dynamics and population control of Galium aparine L.

    NARCIS (Netherlands)

    Weide, van der R.Y.

    1993-01-01

    The population biology of Galium aparine L. needs to be better understood, in order to be able to rationalize decisions about the short- and long-term control of this weed species for different cropping practices.

    A population dynamics model was developed to

  9. provisional analysis of population dynamics

    Indian Academy of Sciences (India)

    Nicholas Mitchison

    2018-01-11

    Jan 11, 2018 ... Western populations covered by OMIM, or are so mediated to a lesser extent. This we attribute ... tlenecks affected southern Asia: a coalescence analysis of ... included comprehensive survey of previous work (Atkin- son et al.

  10. Population dynamics and rural poverty.

    Science.gov (United States)

    Fong, M S

    1985-01-01

    An overview of the relationship between demographic factors and rural poverty in developing countries is presented. The author examines both the micro- and macro-level perspectives of this relationship and the determinants and consequences of population growth. The author notes the prospects for a rapid increase in the rural labor force and considers its implications for the agricultural production structure and the need for institutional change. Consideration is also given to the continuing demand for high fertility at the family level and the role of infant and child mortality in the poverty cycle. "The paper concludes by drawing attention to the need for developing the mechanism for reconciliation of social and individual optima with respect to family size and population growth." The need for rural development projects that take demographic factors into account is stressed as is the need for effective population programs. (summary in FRE, ITA) excerpt

  11. POPULATION DYNAMICS OF PSEUDO-NITZSCHIA SPECIES ...

    African Journals Online (AJOL)

    nb

    current study aimed at assessing the population dynamics of Pseudo-nitzschia ... and to the developing aquaculture industry ... B. Hotel. Pangani Island. Bongoyo Island. Mbudya Island. Msasani Bay ... Salinity values did not show clear trends.

  12. Relationships between greenhouse gas emissions and cultivable bacterial populations in conventional, organic and long-term grass plots as affected by environmental variables and disturbances

    NARCIS (Netherlands)

    Bruggen, van A.H.C.; He, M.; Zelenev, V.V.; Semenov, V.M.; Semenov, A.M.; Kuznetsova, T.V.; Khodzaeva, Anna K.; Kuznetsov, A.M.; Semenov, M.V.

    2017-01-01

    Daily dynamics of greenhouse gas (GHG) emissions and cultivable bacterial populations have rarely been examined. The objectives were: (1) to investigate if dynamics of GHG emissions can be described by harmonics and are related to those of cultivable bacteria after soil disturbances in three

  13. Dynamics of bacterial community in the gut of Cornu aspersum

    Directory of Open Access Journals (Sweden)

    ZDRAVKA KOLEVA

    2015-12-01

    Full Text Available The dynamics of the bacterial community in the intestinal tract of Cornu aspersum was investigated during different states of its life cycle. Two approaches were applied – culture and non-culture. The non-culture approach was performed by ARDRA of 16S rDNA using two of the six tested endonucleases. Data were analyzed by hierarchical cluster analysis. The restriction of 16S rDNA samples from the snail of different physiological states with endonucleases HinfI and Csp6I resulted in generation of different profiles depending on the snail states. By the culture approach we found that the total number of cultivable bacteria, representatives of Enterobacteriaceae, lactic acid bacteria, amylolitic and cellulolytic bacteria were the most abundant in active state of the snails. Cellulolytic bacteria were not detected in juveniles of C. aspersum. Escherichia coli, Clostridium perfringens as well as bacteria from the genus Salmonella, Shigella and Pseudomonas were not detected. Bacteria of the genus Aeromonas were found in juveniles of C. aspersum, after that their number decrease and were not found in hibernating snails. On the base of the two applied approaches this study shows that the bacterial flora in the intestinal tract of C. aspersum is affected by the seasonal and environmental variations and undergoes quantitative and qualitative changes during the different states of the life cycle. The snails harbor in their gut intestinal bacteria, which possess biochemical potentiality to degrade the plant components.

  14. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans.

    Science.gov (United States)

    Wietz, Matthias; Wemheuer, Bernd; Simon, Heike; Giebel, Helge-Ansgar; Seibt, Maren A; Daniel, Rolf; Brinkhoff, Thorsten; Simon, Meinhard

    2015-10-01

    The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy.

    Directory of Open Access Journals (Sweden)

    Wataru Yamanaka

    Full Text Available Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.8 ± 2.6 months, and their bacterial composition was investigated using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis using the UniFrac distance metric revealed that the overall bacterial community composition of saliva is distinct from that of supragingival plaque, both pre- and post-therapy. Temporal variation following therapy in the salivary bacterial population was significantly smaller than in the plaque microbiota, and the post-therapy saliva sample was significantly more similar to that pre-therapy from the same individual than to those from other subjects. Following periodontal therapy, microbial richness and biodiversity were significantly decreased in the plaque microbiota, but not in the salivary bacterial population. The operational taxonomic units whose relative abundances changed significantly after therapy were not common to the two microbiotae. These results reveal the compositional stability of salivary bacterial populations against shifts in the supragingival microbiota, suggesting that the effect of the supragingival plaque microbiota on salivary bacterial population composition is limited.

  16. Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

    Science.gov (United States)

    Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

    2011-09-01

    An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

  17. Bioconvection as a Consequence of Bio-Stratification in Bacterial Populations

    Science.gov (United States)

    Shoup, Daniel; Strickland, Benjamin; Hoeger, Kentaro; Ursell, Tristan

    The collective motion of bacterial populations in solution can generate convective currents that significantly alter fluid motion and material transport. Known as bioconvection, this process is highly influenced by stimuli such as nutrients and toxins that can attract or repel bacteria via chemotaxis. Despite its prevalence in natural environments, ranging from the ocean floor to fluid in the human gut, this dynamic process and the physical and biological factors that influence it remain largely unexplored. To close this gap, we measure and analyze spontaneous bioconvection arising from the collective movement of dense populations of bacteria, such as Escherichia coli and Bacillus subtilis. By combining microscopy and image analysis, we find that modulations of the fluid volume geometry, erasure of the air-liquid interface, chemical perturbations like nutrients or antibiotics all alter the development of these dense bacterial masses and in turn the bio-convective currents and corresponding transport phenomena they generate. Our work suggests biophysical principles of material and organismal transport that apply to a broad range of systems where organisms can sense gradients and move within their environments.

  18. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations.

    Science.gov (United States)

    Logsdon, Michelle M; Aldridge, Bree B

    2018-01-01

    Model bacteria, such as E. coli and B. subtilis , tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.

  19. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations

    Directory of Open Access Journals (Sweden)

    Michelle M. Logsdon

    2018-03-01

    Full Text Available Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.

  20. Population dynamics of Borrelia burgdorferi in Lyme disease

    Directory of Open Access Journals (Sweden)

    Sebastian Christoph Binder

    2012-03-01

    Full Text Available Many chronic inflammatory diseases are known to be caused by persistent bacterial or viral infections. A well-studied example is the tick-borne infection by the gram-negative Spirochaetes of the genus Borrelia in humans and other mammals, causing severe symptoms of chronic inflammation and subsequent tissue damage (Lyme Disease, particularly in large joints and the central nervous system, but also in the heart and other tissues of untreated patients. Although killed efficiently by human phagocytic cells in vitro, Borrelia exhibits a remarkably high infectivity in mice and men. In experimentally infected mice, the first immune response almost clears the infection. However, approximately one week post infection, the bacterial population recovers and reaches an even larger size before entering the chronic phase. We developed a mathematical model describing the bacterial growth and the immune response against Borrelia burgdorferi in the C3H mouse strain that has been established as an experimental model for Lyme disease. The peculiar dynamics of the infection exclude two possible mechanistic explanations for the regrowth of the almost cleared bacteria. Neither the hypothesis of bacterial dissemination to different tissue nor a limitation of phagocytic capacity were compatible with experiment. The mathematical model predicts that Borrelia recovers from the strong initial immune response by the regrowth of an immune-resistant sub-population of the bacteria. The chronic phase appears as an equilibration of bacterial growth and adaptive immunity. This result has major implications for the development of the chronic phase of Borrelia infections as well as on potential protective clinical interventions.

  1. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

    Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

  2. Stochastic population dynamic models as probability networks

    Science.gov (United States)

    M.E. and D.C. Lee. Borsuk

    2009-01-01

    The dynamics of a population and its response to environmental change depend on the balance of birth, death and age-at-maturity, and there have been many attempts to mathematically model populations based on these characteristics. Historically, most of these models were deterministic, meaning that the results were strictly determined by the equations of the model and...

  3. Modeling the population dynamics of Pacific yew.

    Science.gov (United States)

    Richard T. Busing; Thomas A. Spies

    1995-01-01

    A study of Pacific yew (Taxus brevifolia Nutt.) population dynamics in the mountains of western Oregon and Washington was based on a combination of long-term population data and computer modeling. Rates of growth and mortality were low in mature and old-growth forest stands. Diameter growth at breast height ranged from 0 to 3 centimeters per decade...

  4. Population dynamical responses to climate change

    DEFF Research Database (Denmark)

    Forchhammer, Mads; Schmidt, Niels Martin; Høye, Toke Thomas

    2008-01-01

    approaches, we analyse concurrently the influence of climatic variability and trophic interactions on the temporal population dynamics of species in the terrestrial vertebrate community at Zackenberg. We describe and contrast the population dynamics of three predator species (arctic fox Alopex lagopus, stoat...... of arctic fox were not significantly related to changes in lemming abundance, both the stoat and the breeding of long-tailed skua were mainly related to lemming dynamics. The predator-prey system at Zackenberg differentiates from previously described systems in high-arctic Greenland, which, we suggest...

  5. How Resource Phenology Affects Consumer Population Dynamics.

    Science.gov (United States)

    Bewick, Sharon; Cantrell, R Stephen; Cosner, Chris; Fagan, William F

    2016-02-01

    Climate change drives uneven phenology shifts across taxa, and this can result in changes to the phenological match between interacting species. Shifts in the relative phenology of partner species are well documented, but few studies have addressed the effects of such changes on population dynamics. To explore this, we develop a phenologically explicit model describing consumer-resource interactions. Focusing on scenarios for univoltine insects, we show how changes in resource phenology can be reinterpreted as transformations in the year-to-year recursion relationships defining consumer population dynamics. This perspective provides a straightforward path for interpreting the long-term population consequences of phenology change. Specifically, by relating the outcome of phenological shifts to species traits governing recursion relationships (e.g., consumer fecundity or competitive scenario), we demonstrate how changes in relative phenology can force systems into different dynamical regimes, with major implications for resource management, conservation, and other areas of applied dynamics.

  6. Population Dynamics and Air Pollution

    DEFF Research Database (Denmark)

    Flachs, Esben Meulengracht; Sørensen, Jan; Bønløkke, Jacob

    2013-01-01

    Objective. To explore how three different assumptions on demographics affect the health impact of Danish emitted air pollution in Denmark from 2005 to 2030, with health impact modeled from 2005 to 2050. Methods. Modeled air pollution from Danish sources was used as exposure in a newly developed......) a static year 2005 population, (2) morbidity and mortality fixed at the year 2005 level, or (3) an expected development. Results. The health impact of air pollution was estimated at 672,000, 290,000, and 280,000 lost life years depending on demographic assumptions and the corresponding social costs at 430.......4 M€, 317.5 M€, and 261.6 M€ through the modeled years 2005–2050. Conclusion. The modeled health impact of air pollution differed widely with the demographic assumptions, and thus demographics and assumptions on demographics played a key role in making health impact assessments on air pollution....

  7. Population dynamics in vasopressin cells.

    Science.gov (United States)

    Leng, Gareth; Brown, Colin; Sabatier, Nancy; Scott, Victoria

    2008-01-01

    Most neurons sense and code change, and when presented with a constant stimulus they adapt, so as to be able to detect a fresh change. However, for some things it is important to know their absolute level; to encode such information, neurons must sustain their response to an unchanging stimulus while remaining able to respond to a change in that stimulus. One system that encodes the absolute level of a stimulus is the vasopressin system, which generates a hormonal signal that is proportional to plasma osmolality. Vasopressin cells sense plasma osmolality and secrete appropriate levels of vasopressin from the neurohypophysis as needed to control water excretion; this requires sustained secretion under basal conditions and the ability to increase (or decrease) secretion should plasma osmolality change. Here we explore the mechanisms that enable vasopressin cells to fulfill this function, and consider how coordination between the cells might distribute the secretory load across the population of vasopressin cells. 2008 S. Karger AG, Basel.

  8. Structural stability of nonlinear population dynamics.

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  9. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  10. Petroleum-hydrocarbon utilization by native bacterial population ...

    African Journals Online (AJOL)

    Two Nigerian crude oils (Bonny light and Escravos blend) were exposed to the wastewater canal via oil impregnated membrane filters (0.45 μm diameter) for 21 days in a microcosm experiment. Bacterial petroleum-hydrocarbon utilizers were later harvested from both the millipore membrane filters and laboratory ...

  11. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

    Science.gov (United States)

    Kamath, Pauline L.; Foster, Jeffrey T.; Drees, Kevin P.; Luikart, Gordon; Quance, Christine; Anderson, Neil J.; Clarke, P. Ryan; Cole, Eric K.; Drew, Mark L.; Edwards, William H.; Rhyan, Jack C.; Treanor, John J.; Wallen, Rick L.; White, Patrick J.; Robbe-Austerman, Suelee; Cross, Paul C.

    2016-01-01

    Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (B3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.

  12. Microbiological studies in schirmacher oasis, Antarctica: Effect of temperature on bacterial populations

    Digital Repository Service at National Institute of Oceanography (India)

    Matondkar, S.G.P.

    Seasonal and site wise variation in size and diversity of bacterial population was observed in Schirmacher Oasis, Antarctica. Prevailing soil temperature limited the distribution and abundance of groups of bacteria like psychrophiles, psychrotrophs...

  13. Bacterial incorporation of tritiated thymidine and populations of bacteriophagous fauna in the rhizosphere of wheat

    DEFF Research Database (Denmark)

    Christensen, Henrik; Griffiths, Bryan; Christensen, Søren

    1992-01-01

    Bacterial and microfaunal populations, and bacterial productivity measured by tritiated thymidine (3HTdr) incorporation, in the rhizosphere of wheat seedlings were measured. Soil from planted pots was fractionated into rhizosphere and non-rhizosphere (bulk) soil, while unplanted soil was taken from...... pots without plants. Total bacterial counts and biovolume did not differ between fractions but viable (plate) counts were 8 times higher in the rhizosphere compared to bulk and unplanted soil. 3HTdr was incorporated at a constant rate with low variability in bulk or unplanted soil. In rhizosphere soil...... 3HTdr incorporation was lower than in bulk or unplanted soils and showed high variability. The populations of bacterial-feeding protozoa and nematodes indicated that rhizosphere bacterial activity was actually 3–4 times greater in rhizosphere than bulk soil in accordance with the results...

  14. Particle algorithms for population dynamics in flows

    International Nuclear Information System (INIS)

    Perlekar, Prasad; Toschi, Federico; Benzi, Roberto; Pigolotti, Simone

    2011-01-01

    We present and discuss particle based algorithms to numerically study the dynamics of population subjected to an advecting flow condition. We discuss few possible variants of the algorithms and compare them in a model compressible flow. A comparison against appropriate versions of the continuum stochastic Fisher equation (sFKPP) is also presented and discussed. The algorithms can be used to study populations genetics in fluid environments.

  15. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Energy Technology Data Exchange (ETDEWEB)

    Bai, F; Lo, C; Berry, R; Xing, J

    2009-03-19

    The Bacterial Flagellar Motor is a rotary molecular machine that rotates the helical filaments which propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation and switching mechanism of the motor. In our previous paper, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here we further analyze this model. In this paper we show (1) the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with the latest experiment by Lo et al.; (2) with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, recently observed by Yuan and Berg; (3) the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwelling time distribution. Predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental verification.

  16. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Science.gov (United States)

    Bai, Fan; Lo, Chien-Jung; Berry, Richard M.; Xing, Jianhua

    2009-01-01

    Abstract The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here, we further analyze that model, showing that 1), the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with latest experiments; 2), with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, as recently observed; and 3), the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwell-time distribution. The predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental procedures for verification. PMID:19383460

  17. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  18. Population dynamics of Pseudo-nitzschia species ...

    African Journals Online (AJOL)

    The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

  19. Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation.

    Science.gov (United States)

    Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E

    2012-03-01

    Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The

  20. Of the Phrensy: an update on the epidemiology and pathogenesis of bacterial meningitis in the pediatric population [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Andrew Janowski

    2017-01-01

    Full Text Available In the past century, advances in antibiotics and vaccination have dramatically altered the incidence and clinical outcomes of bacterial meningitis. We review the shifting epidemiology of meningitis in children, including after the implementation of vaccines that target common meningitic pathogens and the introduction of intrapartum antibiotic prophylaxis offered to mothers colonized with Streptococcus agalactiae. We also discuss what is currently known about the pathogenesis of meningitis. Recent studies of the human microbiome have illustrated dynamic relationships of bacterial and viral populations with the host, which may potentiate the risk of bacterial meningitis.

  1. Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property

    OpenAIRE

    Side, Domenico Delle; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Di Salvo, Marco; Talà, Adelfia; Chechkin, Aleksei; Seno, Flavio; Trovato, Antonio

    2017-01-01

    We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distri...

  2. Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure.

    Science.gov (United States)

    Rungrassamee, Wanilada; Klanchui, Amornpan; Maibunkaew, Sawarot; Karoonuthaisiri, Nitsara

    2016-01-01

    The intestinal microbiota play important roles in health of their host, contributing to maintaining the balance and resilience against pathogen. To investigate effects of pathogen to intestinal microbiota, the bacterial dynamics upon a shrimp pathogen, Vibrio harveyi, exposures were determined in two economically important shrimp species; the black tiger shrimp (BT) and the Pacific white shrimp (PW). Both shrimp species were reared under the same diet and environmental conditions. Shrimp survival rates after the V. harveyi exposure revealed that the PW shrimp had a higher resistance to the pathogen than the BT shrimp. The intestinal bacterial profiles were determined by denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing of the 16S rRNA sequences under no pathogen challenge control and under pathogenic V. harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control in BT and PW intestines. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. The barcoded pyrosequencing analysis showed the similar bacterial community structures in intestines of BT and PW shrimp under a normal condition. However, during the time course exposure to V. harveyi, the relative abundance of bacteria belong to Vibrio genus was higher in the BT intestines at 12h after the exposure, whereas relative abundance of vibrios was more stable in PW intestines. The principle coordinates analysis based on weighted-UniFrac analysis showed that intestinal bacterial population in the BT shrimp lost their ability to restore their bacterial balance during the 72-h period of exposure to the pathogen, while the PW shrimp were able to reestablish their bacterial population to resemble those seen in the unexposed control group. This observation of bacterial disruption might correlate to different mortality rates observed between the two shrimp species

  3. Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

    Science.gov (United States)

    Domin, Hanna; Zurita-Gutiérrez, Yazmín H.; Scotti, Marco; Buttlar, Jann; Hentschel Humeida, Ute; Fraune, Sebastian

    2018-01-01

    The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. PMID:29740401

  4. Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

    Directory of Open Access Journals (Sweden)

    Hanna Domin

    2018-04-01

    Full Text Available The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.

  5. The failure rate dynamics in heterogeneous populations

    International Nuclear Information System (INIS)

    Cha, Ji Hwan; Finkelstein, Maxim

    2013-01-01

    Most populations encountered in real world are heterogeneous. In reliability applications, the mixture (observed) failure rate, obviously, can be considered as a measure of ‘average’ quality in these populations. However, in addition to this average measure, some variability characteristics for failure rates can be very helpful in describing the time-dependent changes in quality of heterogeneous populations. In this paper, we discuss variance and the coefficient of variation of the corresponding random failure rate as variability measures for items in heterogeneous populations. Furthermore, there is often a risk that items of poor quality are selected for important missions. Therefore, along with the ‘average quality’ of a population, more ‘conservative’ quality measures should be also defined and studied. For this purpose, we propose the percentile and the tail-mixture of the failure rates as the corresponding conservative measures. Some illustrative examples are given. -- Highlights: ► This paper provides the insight on the variability measures in heterogeneous populations. ► The conservative quality measures in heterogeneous populations are defined. ► The utility of these measures is illustrated by meaningful examples. ► This paper provides a better understanding of the dynamics in heterogeneous populations

  6. Characterization by culture-dependent and culture-1 independent methods of the 2 bacterial population of suckling-lamb packaged in different atmospheres

    NARCIS (Netherlands)

    Oses, S.M.; Diez, A.M.; Melero, B.; Luning, P.A.; Jaime, I.; Rovira, J.

    2013-01-01

    This study offers insight into the dynamics of bacterial populations in fresh cuts of suckling lamb under four different atmospheric conditions: air (A), and three Modified Atmosphere Packaging (MAP) environments, 15%O2/30%CO2/55%N2 (C, commercial), 70%O2/30%CO2 (O), and 15%O2/85%CO2 (H) for 18

  7. Dominance of a clonal green sulfur bacterial population in a stratified lake

    DEFF Research Database (Denmark)

    Gregersen, Lea H; Habicht, Kirsten S; Peduzzi, Sandro

    2009-01-01

    surveys using FISH cell counting and population multilocus sequence typing [clone library sequence analysis of the small subunit (SSU) rRNA locus and two loci involved in photosynthesis in GSB: fmoA and csmCA]. All bacterial populations clearly stratified according to water column chemistry. The GSB...

  8. Bacterial communities differ among Drosophila melanogaster populations and affect host resistance against parasitoids

    NARCIS (Netherlands)

    Chaplinska, Mariia; Gerritsma, Sylvia; Dini-Andreote, Francisco; Falcao Salles, Joana; Wertheim, Bregje

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population

  9. Changes in bacterial populations along roots of wheat (Tricticum aestivum L.) seedlings

    NARCIS (Netherlands)

    Liljeroth, E.; Burgers, S.L.G.E.; Veen, van J.A.

    1991-01-01

    In this study the bacterial populations on root tips (1–2 days old) of wheat (Triticum aestivum L.) were compared with the populations on root segments about 1 week older (root base). The isolates were characterized with a set of physiological tests and the test results were used to group the

  10. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network

    KAUST Repository

    El Chakhtoura, Joline; Prest, Emmanuelle I E C; Saikaly, Pascal; van Loosdrecht, Mark C.M.; Hammes, Frederik A.; Vrouwenvelder, Johannes S.

    2015-01-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during

  11. PCR-DGGE Analysis of Bacterial Population Attached to the Bovine Rumen Wall

    OpenAIRE

    Lukáš, F. (Filip); Šimůnek, J. (Jiří); Mrázek, J. (Jakub); Kopečný, J. (Jan)

    2010-01-01

    We isolated and amplified by PCR 16S rDNA from bacteria attached to the bovine rumen wall and analyzed it by denaturing gradient gel electrophoresis (DGGE) with subsequent sequence analysis. The attached bacterial community differed from the bacteria of rumen content; however, no differences were observed among the five epithelial sampling sites taken from each animal. The DGGE profile of the bacterial population attached to the rumen wall represented a high inter-animal variation.

  12. Microbial Ecophysiology of Whey Biomethanation: Characterization of Bacterial Trophic Populations and Prevalent Species in Continuous Culture

    OpenAIRE

    Chartrain, M.; Zeikus, J. G.

    1986-01-01

    The organization and species composition of bacterial trophic groups associated with lactose biomethanation were investigated in a whey-processing chemostat by enumeration, isolation, and general characterization studies. The bacteria were spatially organized as free-living forms and as self-immobilized forms appearing in flocs. Three dominant bacterial trophic group populations were present (in most probable number per milliliter) whose species numbers varied with the substrate consumed: hyd...

  13. Effect of exogenous inoculants on enhancing oil recovery and indigenous bacterial community dynamics in long-term field pilot of low permeability reservoir.

    Science.gov (United States)

    Li, Jing; Xue, Shuwen; He, Chunqiu; Qi, Huixia; Chen, Fulin; Ma, Yanling

    2018-03-20

    Pseudomonas aeruginosa DN1 strain and Bacillus subtilis QHQ110 strain were chosen as rhamnolipid and lipopeptide producer respectively, to evaluate the efficiency of exogenous inoculants on enhancing oil recovery (EOR) and to explore the relationship between injected bacteria and indigenous bacterial community dynamics in long-term filed pilot of Hujianshan low permeability water-flooded reservoir for 26 months. Core-flooding tests showed that the oil displacement efficiency increased by 18.46% with addition of exogenous consortia. Bacterial community dynamics using quantitative PCR and high-throughput sequencing revealed that the exogenous inoculants survived and could live together with indigenous bacterial populations. They gradually became the dominant community after the initial activation, while their comparative advantage weakened continually after 3 months of the first injection. The bacterial populations did not exert an observable change in the process of the second injection of exogenous inoculants. On account of facilitating oil emulsification and accelerating bacterial growth with oil as the carbon source by the injection of exogenous consortia, γ-proteobacteria was finally the prominent bacterial community at class level varying from 25.55 to 32.67%, and the dominant bacterial populations were increased by 2-3 orders of magnitude during the whole processes. The content of organic acids and rhamnolipids in reservoir were promoted with the change of bacterial community diversity, respectively. Cumulative oil increments reached 26,190 barrels for 13 months after the first injection, and 55,947 barrels of oil had been accumulated in all of A20 wells block through two rounds of bacterial consortia injection. The performance of EOR has a cumulative improvement by the injection of exogenous inoculants without observable inhibitory effect on the indigenous bacterial populations, demonstrating the application potential in low permeability water

  14. Evolutionary Dynamics and Diversity in Microbial Populations

    Science.gov (United States)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  15. Nonlinear Stochastic Modelling of Antimicrobial resistance in Bacterial Populations

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber

    -mutator population. The growth rates of the two populations were initially compared by a maximum likelihood approach and the growth rates were found to be equal. Thereafter a model for the competing growth was developed. The models showthat mutatorswill obtain a higher fitness by adapting faster to an environment...... an important role for the evolution of resistance. When growing under stressed conditions, such as in the presence of antibiotics, mutators are considered to have an advantages in comparison to non-mutators. This has been supported by a mathematical model for competing growth between a mutator and a non...

  16. Delay differential systems for tick population dynamics.

    Science.gov (United States)

    Fan, Guihong; Thieme, Horst R; Zhu, Huaiping

    2015-11-01

    Ticks play a critical role as vectors in the transmission and spread of Lyme disease, an emerging infectious disease which can cause severe illness in humans or animals. To understand the transmission dynamics of Lyme disease and other tick-borne diseases, it is necessary to investigate the population dynamics of ticks. Here, we formulate a system of delay differential equations which models the stage structure of the tick population. Temperature can alter the length of time delays in each developmental stage, and so the time delays can vary geographically (and seasonally which we do not consider). We define the basic reproduction number [Formula: see text] of stage structured tick populations. The tick population is uniformly persistent if [Formula: see text] and dies out if [Formula: see text]. We present sufficient conditions under which the unique positive equilibrium point is globally asymptotically stable. In general, the positive equilibrium can be unstable and the system show oscillatory behavior. These oscillations are primarily due to negative feedback within the tick system, but can be enhanced by the time delays of the different developmental stages.

  17. Bacterial population in traditional sourdough evaluated by molecular methods

    NARCIS (Netherlands)

    Randazzo, C.L.; Heilig, G.H.J.; Restuccia, C.; Giudici, P.; Caggia, C.

    2005-01-01

    Aims: To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Methods and Results: Forty-five LAB isolates were

  18. Influence of Immigration on Epiphytic Bacterial Populations on Navel Orange Leaves

    OpenAIRE

    Lindow, S. E.; Andersen, G. L.

    1996-01-01

    Factors that influenced the increase in epiphytic bacterial population size on navel orange leaves during winter months were investigated to test the assumption that such populations were the result of multiplication on orange leaves. The population sizes of bacteria of different kinds, including ice nucleation-active (Ice(sup+)) bacteria, were from 6- to 30-fold larger on leaves of navel orange trees adjacent to other plant species than on trees growing near other citrus species. Total and I...

  19. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  20. Critical dynamics in population vaccinating behavior.

    Science.gov (United States)

    Pananos, A Demetri; Bury, Thomas M; Wang, Clara; Schonfeld, Justin; Mohanty, Sharada P; Nyhan, Brendan; Salathé, Marcel; Bauch, Chris T

    2017-12-26

    Vaccine refusal can lead to renewed outbreaks of previously eliminated diseases and even delay global eradication. Vaccinating decisions exemplify a complex, coupled system where vaccinating behavior and disease dynamics influence one another. Such systems often exhibit critical phenomena-special dynamics close to a tipping point leading to a new dynamical regime. For instance, critical slowing down (declining rate of recovery from small perturbations) may emerge as a tipping point is approached. Here, we collected and geocoded tweets about measles-mumps-rubella vaccine and classified their sentiment using machine-learning algorithms. We also extracted data on measles-related Google searches. We find critical slowing down in the data at the level of California and the United States in the years before and after the 2014-2015 Disneyland, California measles outbreak. Critical slowing down starts growing appreciably several years before the Disneyland outbreak as vaccine uptake declines and the population approaches the tipping point. However, due to the adaptive nature of coupled behavior-disease systems, the population responds to the outbreak by moving away from the tipping point, causing "critical speeding up" whereby resilience to perturbations increases. A mathematical model of measles transmission and vaccine sentiment predicts the same qualitative patterns in the neighborhood of a tipping point to greatly reduced vaccine uptake and large epidemics. These results support the hypothesis that population vaccinating behavior near the disease elimination threshold is a critical phenomenon. Developing new analytical tools to detect these patterns in digital social data might help us identify populations at heightened risk of widespread vaccine refusal. Copyright © 2017 the Author(s). Published by PNAS.

  1. Dynamic Computational Model of Symptomatic Bacteremia to Inform Bacterial Separation Treatment Requirements.

    Directory of Open Access Journals (Sweden)

    Sinead E Miller

    Full Text Available The rise of multi-drug resistance has decreased the effectiveness of antibiotics, which has led to increased mortality rates associated with symptomatic bacteremia, or bacterial sepsis. To combat decreasing antibiotic effectiveness, extracorporeal bacterial separation approaches have been proposed to capture and separate bacteria from blood. However, bacteremia is dynamic and involves host-pathogen interactions across various anatomical sites. We developed a mathematical model that quantitatively describes the kinetics of pathogenesis and progression of symptomatic bacteremia under various conditions, including bacterial separation therapy, to better understand disease mechanisms and quantitatively assess the biological impact of bacterial separation therapy. Model validity was tested against experimental data from published studies. This is the first multi-compartment model of symptomatic bacteremia in mammals that includes extracorporeal bacterial separation and antibiotic treatment, separately and in combination. The addition of an extracorporeal bacterial separation circuit reduced the predicted time of total bacteria clearance from the blood of an immunocompromised rodent by 49%, compared to antibiotic treatment alone. Implementation of bacterial separation therapy resulted in predicted multi-drug resistant bacterial clearance from the blood of a human in 97% less time than antibiotic treatment alone. The model also proposes a quantitative correlation between time-dependent bacterial load among tissues and bacteremia severity, analogous to the well-known 'area under the curve' for characterization of drug efficacy. The engineering-based mathematical model developed may be useful for informing the design of extracorporeal bacterial separation devices. This work enables the quantitative identification of the characteristics required of an extracorporeal bacteria separation device to provide biological benefit. These devices will potentially

  2. Phase resetting reveals network dynamics underlying a bacterial cell cycle.

    Science.gov (United States)

    Lin, Yihan; Li, Ying; Crosson, Sean; Dinner, Aaron R; Scherer, Norbert F

    2012-01-01

    Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS).

  3. Dynamics of germs responsible for acute bacterial meningitis in ...

    African Journals Online (AJOL)

    The aim of this study was to analyze ten (10) years of epidemiological surveillance data of meningitis in Burkina Faso for high risk germs patterns identification in order to contribute to the strengthening of prevention strategies. A retrospective study of the past decade (2005- 2014) of cases of acute bacterial meningitis ...

  4. 10 original article dynamics of germs responsible for acute bacterial ...

    African Journals Online (AJOL)

    boaz

    The aim of this study was to analyze ten (10) years of epidemiological surveillance data of meningitis in Burkina Faso for high risk germs patterns identification in order to contribute to the strengthening of prevention strategies. A retrospective study of the past decade (2005- 2014) of cases of acute bacterial meningitis ...

  5. Dynamics of Vaginal Bacterial Communities in Women Developing Bacterial Vaginosis, Candidiasis, or No Infection, Analyzed by PCR-Denaturing Gradient Gel Electrophoresis and Real-Time PCR▿

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G. G.; Brigidi, Patrizia

    2007-01-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA. PMID:17644631

  6. Dynamics of vaginal bacterial communities in women developing bacterial vaginosis, candidiasis, or no infection, analyzed by PCR-denaturing gradient gel electrophoresis and real-time PCR.

    Science.gov (United States)

    Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia

    2007-09-01

    The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

  7. Influence of copper on Euplotes sp. and associated bacterial population

    Directory of Open Access Journals (Sweden)

    Guilherme Oliveira Andrade da Silva

    2014-05-01

    Full Text Available The influence of copper on the ciliate Euplotes sp. and associated bacteria isolated from sediment samples of Guanabara Bay were investigated in bioassays. This region is highly affected by heavy metals such as copper, from solid waste constantly dumped in the bay and other sources such as industrial effluents, antifouling paints, atmospheric deposition and urban drainage, and even today there are few data on the metal toxicity to the ecosystem of the Bay of Guanabara. Bioassays were conducted to estimate the LC50-24 h of copper, in order to determine the concentration of metal bearing 50% of the population mortality. The results indicated that the concentrations of 0.05 and 0.009 mg L-1 presented no toxicity to Euplotes sp. The associated bacteria are tolerant to copper concentrations used in bioassays, and suggest that they could be used as a potential agent in the bioremediation of areas affected by copper.

  8. Population Model with a Dynamic Food Supply

    Science.gov (United States)

    Dickman, Ronald; da Silva Nascimento, Jonas

    2009-09-01

    We propose a simple population model including the food supply as a dynamic variable. In the model, survival of an organism depends on a certain minimum rate of food consumption; a higher rate of consumption is required for reproduction. We investigate the stationary behavior under steady food input, and the transient behavior of growth and decay when food is present initially but is not replenished. Under a periodic food supply, the system exhibits period-doubling bifurcations and chaos in certain ranges of the reproduction rate. Bifurcations and chaos are favored by a slow reproduction rate and a long period of food-supply oscillation.

  9. Noise-induced effects in population dynamics

    Science.gov (United States)

    Spagnolo, Bernardo; Cirone, Markus; La Barbera, Antonino; de Pasquale, Ferdinando

    2002-03-01

    We investigate the role of noise in the nonlinear relaxation of two ecosystems described by generalized Lotka-Volterra equations in the presence of multiplicative noise. Specifically we study two cases: (i) an ecosystem with two interacting species in the presence of periodic driving; (ii) an ecosystem with a great number of interacting species with random interaction matrix. We analyse the interplay between noise and periodic modulation for case (i) and the role of the noise in the transient dynamics of the ecosystem in the presence of an absorbing barrier in case (ii). We find that the presence of noise is responsible for the generation of temporal oscillations and for the appearance of spatial patterns in the first case. In the other case we obtain the asymptotic behaviour of the time average of the ith population and discuss the effect of the noise on the probability distributions of the population and of the local field.

  10. Characteristics of phylogenetic diversity in airborne bacterial populations in China

    Science.gov (United States)

    Chaudhry, Zahra; Santarpia, Joshua L.; Martins, J. V.

    2011-05-01

    Considering their potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known about the composition or dynamics of the atmosphere's biological aerosols. The few studies that have examined phylogenetic diversity in China focused on a single sampling period, whereas this study spans 3 months and includes over 300 samples. The 300+ samples were categorized by month and direction of their back-trajectory. DNA extraction was carried out on the pooled samples in a quantitative manner to allow for comparison between the amount of extracted material and the amount of initial total aerosol mass. Within an individual month, samples originating from similar land types and approximately equidistant to the sampling location exhibited similar diversity, whereas samples originating from much greater distances and from different land types included phyla unique to that location. Phyla from the same origin also varied from one month to the next. The biological diversity found from the Phylochips reinforces the hypothesis that air samples carry a biological record of their history.

  11. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Directory of Open Access Journals (Sweden)

    Amy Apprill

    Full Text Available Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae, and examine the potential for a core bacterial community and its variability with host (endogenous or geographic/environmental (exogenous specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding, suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp., as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could

  12. Bacterial population in traditional sourdough evaluated by molecular methods.

    Science.gov (United States)

    Randazzo, C L; Heilig, H; Restuccia, C; Giudici, P; Caggia, C

    2005-01-01

    To study the microbial communities in artisanal sourdoughs, manufactured by traditional procedure in different areas of Sicily, and to evaluate the lactic acid bacteria (LAB) population by classical and culture-independent approaches. Forty-five LAB isolates were identified both by phenotypic and molecular methods. The restriction fragment length polymorphism and 16S ribosomal DNA gene sequencing gave evidence of a variety of species with the dominance of Lactobacillus sanfranciscensis and Lactobacillus pentosus, in all sourdoughs tested. Culture-independent method, such as denaturing gradient gel electrophoresis (DGGE) of the V6-V8 regions of the 16S rDNA, was applied for microbial community fingerprint. The DGGE profiles revealed the dominance of L. sanfranciscensis species. In addition, Lactobacillus-specific primers were used to amplify the V1-V3 regions of the 16S rDNA. DGGE profiles flourished the dominance of L. sanfranciscensis and Lactobacillus fermentum in the traditional sourdoughs, and revealed that the closely related species Lactobacillus kimchii and Lactobacillus alimentarius were not discriminated. Lactobacillus-specific PCR-DGGE analysis is a rapid tool for rapid detection of Lactobacillus species in artisanal sourdough. This study reports a characterization of Lactobacillus isolates from artisanal sourdoughs and highlights the value of DGGE approach to detect uncultivable Lactobacillus species.

  13. Defined bacterial populations in the rumens of gnotobiotic lambs.

    Science.gov (United States)

    Lysons, R J; Alexander, T J; Wellstead, P D; Hobson, P N; Mann, S O; Stewart, C S

    1976-06-01

    Five gnotobiotic lambs were fed on sterile diets until they were killed at 13 to 21 weeks of age. They were dosed orally with different combinations of 11 species of rumen bacteria. The biochemical reactions of each of the bacteria inoculated had been determined in pure culture in vitro, and they were chosen to perform the main reactions known to be associated with digestion in the normal mature rumen. Two of the bacteria could not be reisolated, but the remainder had established readily in the rumen, forming stable, mixed, defined populations. The total numbers of bacteria in the rumen, and the viable counts of most of the individual species were comparable to those of normal sheep. The concentration of volatile fatty acids was lower, however, and in four of the lambs there was a higher proportion of butyric acid and a lower proportion of propionic acid than in normal sheep. Cellulolytic, ureolytic, and methanogenic activities appeared to be taking place and lactate-utilizing bacteria appeared to reverse the accumulation of lactate which resulted from the activity of lactate-producing bacteria. Some of the bacteria also established at high levels in the caecum.

  14. Bacterial population of piggery-waste anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

    Hobson, P N; Shaw, B G

    1974-08-01

    A survey was made of the anaerobic and facultatively anaerobic bacteria present in piggery waste, digesting piggery waste and domestic anaerobic sludge used to start a piggery waste digester. An influence of the input waste was shown in that streptococci, the predominant facultatively anaerobic bacteria in the piggery waste, were the predominant bacteria in the digesting waste, and they replaced Entrobacter, predominant in the domestic sludge, when a piggery waste digestion had been established from this latter material. Cellulolytic or methanogenic bacteria could not be detected in the piggery waste but populations of these, and other hydrolytic bacteria, became established at different times during the build-up of digestion by gradual addition of piggery waste to water. The bacteria concerned in degradation of the waste constituents were all anaerobes. Production of methane from H/sub 2//CO/sub 2/, formate and butyrate could be detected in mixed cultures from dilutions of digester contents, but the only methanogenic bacterium that could be isolated in pure culture was Methanobacterium formicicum, which uses H/sub 2//CO/sub 2/ or formate only.

  15. Bayesian modeling of recombination events in bacterial populations

    Directory of Open Access Journals (Sweden)

    Dowson Chris

    2008-10-01

    Full Text Available Abstract Background We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html.

  16. Population Dynamic of Dendronephthya sp.-Associated Bacteria in Natural and Artificial Habitats

    Directory of Open Access Journals (Sweden)

    SUSAN SOKA

    2011-06-01

    Full Text Available Dendronephthya sp. is a soft coral that has huge distribution starting from Indopacific, Tonga, Solomon Islands to Great Barrier Reef in Australia. However, this soft corals survive only in short period after cultivation in artificial habitat (aquarium. Recent study showed that the soft coral Dendronephtya sp. has an association or symbiotic relationship with several bacteria, commonly known as coral associated bacteria (CAB. In this study, we compared the population dynamic of Dendronephthya sp.-associated bacteria in natural and artificial habitat, resulting different bacterial community profiles using terminal restriction fragment length polymorphism (T-RFLP analysis of bacterial community DNA. There were 15 main classes of bacterial population identified along with uncultured microorganism, uncultured organism, uncultured bacteria and unidentified organism. Members of Actinobacteria, Arthrobacteria, Chlorobia, Caldilineae, -proteobacteria and Proteobacteria were predicted to give contributions in the survival ability of both Dendronephthya sp. The cultivation of soft corals after 2 weeks in artificial habitat increases bacterial population similarity on 2 different samples by 10%. Bacterial population similarity in artificial habitat would increase along with the longer cultivation time of soft corals.

  17. Population Dynamic of Dendronephthya sp.-Associated Bacteria in Natural and Artificial Habitats

    Directory of Open Access Journals (Sweden)

    SUSAN SOKA

    2011-06-01

    Full Text Available Dendronephthya sp. is a soft coral that has huge distribution starting from Indopacific, Tonga, Solomon Islands to Great Barrier Reef in Australia. However, this soft corals survive only in short period after cultivation in artificial habitat (aquarium. Recent study showed that the soft coral Dendronephtya sp. has an association or symbiotic relationship with several bacteria, commonly known as coral associated bacteria (CAB. In this study, we compared the population dynamic of Dendronephthya sp.-associated bacteria in natural and artificial habitat, resulting different bacterial community profiles using terminal restriction fragment length polymorphism (T-RFLP analysis of bacterial community DNA. There were 15 main classes of bacterial population identified along with uncultured microorganism, uncultured organism, uncultured bacteria and unidentified organism. Members of Actinobacteria, Arthrobacteria, Chlorobia, Caldilineae, Δ-proteobacteria and Proteobacteria were predicted to give contributions in the survival ability of both Dendronephthya sp. The cultivation of soft corals after 2 weeks in artificial habitat increases bacterial population similarity on 2 different samples by 10%. Bacterial population similarity in artificial habitat would increase along with the longer cultivation time of soft corals.

  18. Effect of dietary monensin on the bacterial population structure of dairy cattle colonic contents.

    Science.gov (United States)

    McGarvey, Jeffery A; Hamilton, Scott W; DePeters, Edward J; Mitloehner, Frank M

    2010-02-01

    To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the bacterial population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day(-1)) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their bacterial population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the bacterial population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the bacterial population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.

  19. Growth strategy of heterotrophic bacterial population along successional sequence on spoil of brown coal colliery substrate

    Czech Academy of Sciences Publication Activity Database

    Krištůfek, Václav; Elhottová, Dana; Chroňáková, Alica; Dostálková, I.; Picek, T.; Kalčík, Jiří

    2005-01-01

    Roč. 50, č. 5 (2005), s. 427-435 ISSN 0015-5632 R&D Projects: GA ČR(CZ) GA526/03/1259 Institutional research plan: CEZ:AV0Z60660521 Keywords : growth strategy * heterotrophic bacterial population * brown coal colliery spoil Subject RIV: EH - Ecology, Behaviour Impact factor: 0.918, year: 2005

  20. Dynamic analysis of a parasite population model

    Science.gov (United States)

    Sibona, G. J.; Condat, C. A.

    2002-03-01

    We study the dynamics of a model that describes the competitive interaction between an invading species (a parasite) and its antibodies in an living being. This model was recently used to examine the dynamical competition between Tripanosoma cruzi and its antibodies during the acute phase of Chagas' disease. Depending on the antibody properties, the model yields three types of outcomes, corresponding, respectively, to healing, chronic disease, and host death. Here, we study the dynamics of the parasite-antibody interaction with the help of simulations, obtaining phase trajectories and phase diagrams for the system. We show that, under certain conditions, the size of the parasite inoculation can be crucial for the infection outcome and that a retardation in the stimulated production of an antibody species may result in the parasite gaining a definitive advantage. We also find a criterion for the relative sizes of the parameters that are required if parasite-generated decoys are indeed to help the invasion. Decoys may also induce a qualitatively different outcome: a limit cycle for the antibody-parasite population phase trajectories.

  1. [Population dynamics and development in the Caribbean].

    Science.gov (United States)

    Boland, B

    1995-12-01

    The impact is examined of socioeconomic factors on Caribbean population dynamics. This work begins by describing the socioeconomic context of the late 1980s and early 1990s, under the influence of the economic changes and crises of the 1980s. The small size, openness, dependency, and lack of diversification of the Caribbean economies have made them vulnerable to external pressures. The Bahamas and Belize had economic growth rates exceeding 5% annually during 1981-90, but most of the countries had low or negative growth. Unemployment, poverty, the structural adjustment measures adopted in the mid-1980s, and declines in social spending exacerbated general economic conditions. In broad terms, the population situation of the Caribbean is marked by diversity of sizes and growth rates. A few countries oriented toward services and tourism had demographic growth rates exceeding 3%, while at least 7 had almost no growth or negative growth. Population growth rates reflected different combinations of natural increase and migration. Crude death rates ranged from around 5/1000 to 11/1000, except in Haiti, and all countries of the region except Haiti had life expectancies of 70 years or higher. Despite fertility decline, the average crude birth rate was still relatively high at 26/1000, and the rate of natural increase was 1.8% annually for the region. Nearly half of the regional population was under 15 or over 65 years old. The body of this work provides greater detail on mortality patterns, variations by sex, infant mortality, causes of death, and implications for policy. The discussion of fertility includes general patterns and trends, age specific fertility rates, contraceptive prevalence, levels of adolescent fertility and age factors in adolescent sexual behavior, characteristics of adolescent unions, contraceptive usage, health and social consequences of adolescent childbearing, and the search for solutions. The final section describes the magnitude and causes of

  2. Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

    Directory of Open Access Journals (Sweden)

    Jason Karslake

    2016-10-01

    Full Text Available The inoculum effect (IE is an increase in the minimum inhibitory concentration (MIC of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

  3. Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population.

    Science.gov (United States)

    Qi, Z; Cao, H; Jiang, H; Zhao, J; Tang, Z

    2016-01-01

    To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population. DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02. Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P endodontalis, T. forsythia and P. gingivalis may contribute to abscesses or sinus tracts of endodontic origin with bacterial synergism in a Chinese population. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  4. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

    Science.gov (United States)

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin; Lamendella, Regina

    2016-06-15

    Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial

  5. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Science.gov (United States)

    Müller, Maren Stella; Scheu, Stefan; Jousset, Alexandre

    2013-01-01

    Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  6. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Maren Stella Müller

    Full Text Available Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG, pyrrolnitrin (PRN and hydrogen cyanide (HCN in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks, as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  7. Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

    Science.gov (United States)

    Kühn, I; Allestam, G; Stenström, T A; Möllby, R

    1991-01-01

    A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution. PMID:1781680

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

    Science.gov (United States)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

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

  9. Population dynamics of Vibrio fischeri during infection of Euprymna scolopes.

    Science.gov (United States)

    McCann, Jessica; Stabb, Eric V; Millikan, Deborah S; Ruby, Edward G

    2003-10-01

    The luminous bacterium Vibrio fischeri colonizes a specialized light-emitting organ within its squid host, Euprymna scolopes. Newly hatched juvenile squid must acquire their symbiont from ambient seawater, where the bacteria are present at low concentrations. To understand the population dynamics of V. fischeri during colonization more fully, we used mini-Tn7 transposons to mark bacteria with antibiotic resistance so that the growth of their progeny could be monitored. When grown in culture, there was no detectable metabolic burden on V. fischeri cells carrying the transposon, which inserts in single copy in a specific intergenic region of the V. fischeri genome. Strains marked with mini-Tn7 also appeared to be equivalent to the wild type in their ability to infect and multiply within the host during coinoculation experiments. Studies of the early stages of colonization suggested that only a few bacteria became associated with symbiotic tissue when animals were exposed for a discrete period (3 h) to an inoculum of V. fischeri cells equivalent to natural population levels; nevertheless, all these hosts became infected. When three differentially marked strains of V. fischeri were coincubated with juvenile squid, the number of strains recovered from an individual symbiotic organ was directly dependent on the size of the inoculum. Further, these results indicated that, when exposed to low numbers of V. fischeri, the host may become colonized by only one or a few bacterial cells, suggesting that symbiotic infection is highly efficient.

  10. Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

    Science.gov (United States)

    Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

    2017-12-01

    Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

  11. Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.

    Science.gov (United States)

    Stoffels, M; Amann, R; Ludwig, W; Hekmat, D; Schleifer, K H

    1998-03-01

    This study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (Solvesso100). The starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and Solvesso100 as the sole carbon source. The bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotides. Two significant shifts in the bacterial community structure could be demonstrated. The original inoculum from the wastewater of the car factory was rich in proteobacteria of the alpha and beta subclasses, while the final fermentor enrichment was dominated by bacteria closely related to Pseudomonas putida or Pseudomonas mendocina, which both belong to the gamma subclass of the class Proteobacteria. A second significant shift was observed when the fermentor culture was transferred as inoculum to the trickle-bed bioreactor. The community structure in the bioreactor gradually returned to a higher complexity, with the dominance of beta and alpha subclass proteobacteria, whereas the gamma subclass proteobacteria sharply declined. Obviously, the preceded pollutant adaptant did not lead to a significant enrichment of bacteria that finally dominated in the trickle-bed bioreactor. In the course of experiments, three new 16S as well as 23S rRNA-targeted probes for beta subclass proteobacteria were designed, probe SUBU1237 for the genera Burkholderia and Sutterella, probe ALBO34a for the genera Alcaligenes and Bordetella, and probe Bcv13b for Burkholderia cepacia and Burkholderia vietnamiensis. Bacteria hybridizing with the probe Bcv13b represented the main Solvesso100-degrading population in the reactor.

  12. Bacterial populations associated with the dirty area of a South African poultry abattoir.

    Science.gov (United States)

    Geornaras, I; de Jesus, A E; von Holy, A

    1998-06-01

    Bacterial populations associated with three sample types from the neck region of poultry carcasses in the dirty area of an abattoir were characterized. Sample types before and after scalding were skin only, feathers only, and a skin and feather combination. The neck skin of carcasses after the defeathering processing stage was also sampled. Bacterial populations associated with water from the scald tank, rubber fingers at the exit of the defeathering machine, and air in the dirty area were also characterized. Bacterial colonies (751) were randomly isolated from yeast extract-supplemented tryptone soya agar plates exhibiting 30 to 300 colonies. Micrococcus spp. were isolated in the highest proportion from pre-and postscalded carcass samples (63.5 to 86.1% of isolates), regardless of the sample type. Conversely, Enterobacteriaceae (40.3%), Acinetobacter (19.4%), and Aeromonas/Vibrio (12.5%) species predominated on neck skin samples taken from mechanically defeathered carcasses. Isolates from the rubber fingers were, however, predominantly Micrococcus spp. (94.4%). Bacterial groups isolated in the highest proportion from scald tank water samples were Micrococcus spp. (38.3%), species of Enterobacteriaceae (29.1%), and lactic acid bacteria (17.0%). Corynebacterium spp., species of Enterobacteriaceae, and Micrococcus spp. were dominant on air settle plates.

  13. Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

    OpenAIRE

    Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

    2006-01-01

    Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populat...

  14. Distribution and life strategies of two bacterial populations in a eutrophic lake

    Science.gov (United States)

    Weinbauer; Hofle

    1998-10-01

    Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plusssee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i. e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h-1) were higher than those of the entire bacterial community (0.04 to 0.08 h-1) but lower than those of PU7718 (0.26 to 0.31 h-1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically

  15. Allee effects on population dynamics in continuous (overlapping) case

    International Nuclear Information System (INIS)

    Merdan, H.; Duman, O.; Akin, O.; Celik, C.

    2009-01-01

    This paper presents the stability analysis of equilibrium points of a continuous population dynamics with delay under the Allee effect which occurs at low population density. The mathematical results and numerical simulations show the stabilizing role of the Allee effects on the stability of the equilibrium point of this population dynamics.

  16. Growth-rate-dependent dynamics of a bacterial genetic oscillator

    Science.gov (United States)

    Osella, Matteo; Lagomarsino, Marco Cosentino

    2013-01-01

    Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular “chassis” in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

  17. Dynamical consequences of bandpass feedback loops in a bacterial phosphorelay.

    Directory of Open Access Journals (Sweden)

    Shaunak Sen

    Full Text Available Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit consisting of a phosphorelay embedded in multiple transcriptional feedback loops, which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are "bandpass"-like, in the sense that activation occurs within a limited band of Spo0A∼P concentrations. Additionally, recent results show that the phosphorelay activation occurs in pulses, in a cell-cycle dependent fashion. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation remains unclear. In order to address this question, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation.

  18. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    NARCIS (Netherlands)

    Prest, E.I.E.D.; Weissbrodt, D.G.; Hammes, F; van Loosdrecht, Mark C.M.; Vrouwenvelder, J.S.

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year

  19. Supplemental Dietary Inulin of Variable Chain Lengths Alters Intestinal Bacterial Populations in Young Pigs123

    Science.gov (United States)

    Patterson, Jannine K.; Yasuda, Koji; Welch, Ross M.; Miller, Dennis D.; Lei, Xin Gen

    2010-01-01

    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits. PMID:20980641

  20. Perturbation analysis of transient population dynamics using matrix projection models

    DEFF Research Database (Denmark)

    Stott, Iain

    2016-01-01

    Non-stable populations exhibit short-term transient dynamics: size, growth and structure that are unlike predicted long-term asymptotic stable, stationary or equilibrium dynamics. Understanding transient dynamics of non-stable populations is important for designing effective population management...... these methods to know exactly what is being measured. Despite a wealth of existing methods, I identify some areas that would benefit from further development....

  1. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed; Shamma, Jeff S.

    2017-01-01

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population

  2. DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED ...

    African Journals Online (AJOL)

    ACSS

    DYNAMICS OFCercospora zeina POPULATIONS IN MAIZE-BASED AGRO- ..... Population differentiation of Cercospora zeina in three districts of Uganda based on analysis of molecular variance ..... interactions: The example of the Erysiphe.

  3. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    Science.gov (United States)

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  4. Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

    2017-08-16

    Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

  5. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

    Science.gov (United States)

    Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

    2017-01-01

    Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

  6. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    Science.gov (United States)

    Mathis, Roland; Ackermann, Martin

    2016-01-01

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  7. Dynamics of highly polydisperse colloidal suspensions as a model system for bacterial cytoplasm.

    Science.gov (United States)

    Hwang, Jiye; Kim, Jeongmin; Sung, Bong June

    2016-08-01

    There are various kinds of macromolecules in bacterial cell cytoplasm. The size polydispersity of the macromolecules is so significant that the crystallization and the phase separation could be suppressed, thus stabilizing the liquid state of bacterial cytoplasm. On the other hand, recent experiments suggested that the macromolecules in bacterial cytoplasm should exhibit glassy dynamics, which should be also affected significantly by the size polydispersity of the macromolecules. In this work, we investigate the anomalous and slow dynamics of highly polydisperse colloidal suspensions, of which size distribution is chosen to mimic Escherichia coli cytoplasm. We find from our Langevin dynamics simulations that the diffusion coefficient (D_{tot}) and the displacement distribution functions (P(r,t)) averaged over all colloids of different sizes do not show anomalous and glassy dynamic behaviors until the system volume fraction ϕ is increased up to 0.82. This indicates that the intrinsic polydispersity of bacterial cytoplasm should suppress the glass transition and help maintain the liquid state of the cytoplasm. On the other hand, colloids of each kind show totally different dynamic behaviors depending on their size. The dynamics of colloids of different size becomes non-Gaussian at a different range of ϕ, which suggests that a multistep glass transition should occur. The largest colloids undergo the glass transition at ϕ=0.65, while the glass transition does not occur for smaller colloids in our simulations even at the highest value of ϕ. We also investigate the distribution (P(θ,t)) of the relative angles of displacement for macromolecules and find that macromolecules undergo directionally correlated motions in a sufficiently dense system.

  8. Biodegradation of polycyclic aromatic hydrocarbons, selection and dynamics of bacterial populations in the rhizosphere in relation with the distance to roots; Biodegradation des Hydrocarbures Aromatiques Polycycliques, selection et dynamique des populations bacteriennes dans la rhizosphere en fonction de la distance aux racines

    Energy Technology Data Exchange (ETDEWEB)

    Corgie, St.

    2004-03-01

    The biodegradation of Polycyclic Aromatic Hydrocarbons (PAH) is mainly performed by microorganisms that can use these compounds as sole source of carbon and energy. Such capacity has been amply studied to use and optimise microbial activity for remediation of contaminated soils. The use of plants has been suggested to increase and accelerate biodegradation rate by improving microbial activity. However, biodegradation mechanisms still remain poorly described as the interactions between plant, pollutant and rhizosphere microflora are often complex. A simplified compartmented device was developed to study rhizospheric processes, especially biodegradation of PAH, as a function of distance to roots, where root exudates and/or PAH were the only carbon sources for microbial growth. The development and use of bio-molecular techniques (nucleic acid isolation, PCR, RT-PCR, TGGE, hybridization with a degradation gene specific probe) permitted to follow the structure of bacterial communities. Gradients of phenanthrene biodegradation were observed as a function of distance to roots, in parallel to spatial and temporal variations in bacterial community structure. These bacterial communities, as well as PAH biodegradation rate, also depended on the aromaticity of PAH and were modified by the symbiosis between plant and an arbuscular mycorrhizal fungus. (author)

  9. Bacterial population in intestines of the black tiger shrimp (Penaeus monodon under different growth stages.

    Directory of Open Access Journals (Sweden)

    Wanilada Rungrassamee

    Full Text Available Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon, bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15, 1- (J1, 2- (J2, and 3-month-old (J3 juveniles using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases were obtained, which were categorized by barcode for PL15 (7,045 sequences, J1 (3,055 sequences, J2 (13,130 sequences and J3 (1,890 sequences. Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.

  10. Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages.

    Science.gov (United States)

    Rungrassamee, Wanilada; Klanchui, Amornpan; Chaiyapechara, Sage; Maibunkaew, Sawarot; Tangphatsornruang, Sithichoke; Jiravanichpaisal, Pikul; Karoonuthaisiri, Nitsara

    2013-01-01

    Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.

  11. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  12. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  13. BIGSdb: Scalable analysis of bacterial genome variation at the population level

    Directory of Open Access Journals (Sweden)

    Maiden Martin CJ

    2010-12-01

    Full Text Available Abstract Background The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner. Results The Bacterial Isolate Genome Sequence Database (BIGSDB is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole genome data, to be efficiently linked for a limitless number of bacterial specimens. The system builds on the widely used mlstdbNet software, developed for the storage and distribution of multilocus sequence typing (MLST data, and incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into 'schemes' for isolate characterisation or for evolutionary or functional analyses. Isolates and loci can be indexed by multiple names and any number of alternative schemes can be accommodated, enabling cross-referencing of different studies and approaches. LIMS functionality of the software enables linkage to and organisation of laboratory samples. The data are easily linked to external databases and fine-grained authentication of access permits multiple users to participate in community annotation by setting up or contributing to different schemes within the database. Some of the applications of BIGSDB are illustrated with the genera Neisseria and Streptococcus. The BIGSDB source code and documentation are available at http://pubmlst.org/software/database/bigsdb/. Conclusions Genomic data can be used to characterise bacterial isolates in many different ways but it can also be efficiently exploited for evolutionary or functional studies. BIGSDB

  14. Effects of an invasive plant on population dynamics in toads.

    Science.gov (United States)

    Greenberg, Daniel A; Green, David M

    2013-10-01

    When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989-2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads' marshland breeding areas. Our results showed density-dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long-term time series to identify shifts in population dynamics coincident with the advent of population decline. © 2013 Society for Conservation Biology.

  15. The habits of highly effective phages: population dynamics as a framework for identifying therapeutic phages

    Directory of Open Access Journals (Sweden)

    James J Bull

    2014-11-01

    Full Text Available The use of bacteriophages as antibacterial agents is being actively researched on a global scale. Typically, the phages used are isolated from the wild by plating on the bacteria of interest, and a far larger set of candidate phages is often available than can be used in any application. When an excess of phages is available, how should the best phages be identified? Here we consider phage-bacterial population dynamics as a basis for evaluating and predicting phage success. A central question is whether the innate dynamical properties of phages are the determinants of success, or instead, whether extrinsic, indirect effects can be responsible. We address the dynamical perspective, motivated in part by the absence of dynamics in previously suggested principles of phage therapy. Current mathematical models of bacterial-phage dynamics do not capture the realities of in vivo dynamics, nor is this likely to change, but they do give insight to qualitative properties that may be generalizable. In particular, phage adsorption rate may be critical to treatment success, so understanding the effects of the in vivo environment on host availability may allow prediction of useful phages prior to in vivo experimentation. Principles for predicting efficacy may be derived by developing a greater understanding of the in vivo system, or such principles could be determined empirically by comparing phages with known differences in their dynamic properties. The comparative approach promises to be a powerful method of discovering the key to phage success. We offer five recommendations for future study: (i compare phages differing in treatment efficacy to identify the phage properties associated with success, (ii assay dynamics in vivo, (iii understand mechanisms of bacterial escape from phages, (iv test phages in model infections that are relevant to the intended clinical applications, and (v develop new classes of models for phage growth in spatially heterogeneous

  16. Temporal dynamics of bacterial and fungal communities in a genetically modified (GM) rice ecosystem.

    Science.gov (United States)

    Lee, Seung-Hoon; Kim, Chang-Gi; Kang, Hojeong

    2011-04-01

    We assessed the temporal dynamics of bacterial and fungal communities in a soil ecosystem supporting genetically modified (GM) rice (Oryza sativa L., ABC-TPSP; fusion of trehalose-6-phosphate synthase and phosphatase). Using terminal restriction fragment length polymorphism analysis and real-time quantitative PCR, we compared bacterial and fungal communities in the soils underlying GM rice (ABC-TPSP), and its host cultivar (Nakdong) during growing seasons and non-growing seasons. Overall, the soils supporting GM and non-GM rice did not differ significantly in diversity indices, including ribotype numbers, for either bacteria or fungi. The diversity index (H) in both the bacterial and fungal communities was correlated with water content, dissolved organic carbon (DOC), and ammonium nitrogen, and the correlation was stronger in fungi than in bacteria. Multivariate analysis showed no differences in microbial community structures between the two crop genotypes, but such differences did appear in time, with significant changes observed after harvest. Gene copy number was estimated as 10(8)~10(11) and 10(5)~10(7) per gram of soil for bacteria and fungi, respectively. As observed for community structure, the rice genotypes did not differ significantly in either bacterial- or fungal-specific gene copy numbers, although we observed a seasonal change in number. We summarize the results of this study as follows. (1) GM rice did not influence soil bacterial and fungal community structures as compared to non-GM rice in our system, (2) both bacterial and fungal communities changed with the growth stage of either rice genotype, (3) fungal communities were less variable than bacterial communities, and (4) although several environmental factors, including ammonium nitrogen and DOC correlated with shifts in microbial community structure, no single factor stood out.

  17. Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

    Science.gov (United States)

    Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Letícia Piton; Vieira, Armando Augusto Henriques

    2014-01-01

    Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways. PMID:24465807

  18. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  19. Evolutionary dynamics with fluctuating population sizes and strong mutualism.

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  20. The dynamic nature and territory of transcriptional machinery in the bacterial chromosome

    Directory of Open Access Journals (Sweden)

    Ding Jun Jin

    2015-05-01

    Full Text Available Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

  1. Population dynamics model for plasmid bearing and plasmid lacking ...

    African Journals Online (AJOL)

    Streptokinase production in bioreactor is well associated to cell population dynamics. It is an established fact that two types of cell populations are found to emerge from the initial pool of recombinant cell population. This phenomenon leads to an undesired loss in yield of the product. Primary metabolites, like acetic acid etc ...

  2. Dynamic laser speckle to detect motile bacterial response of Pseudomonas aeruginosa

    International Nuclear Information System (INIS)

    Sendra, H; Murialdo, S; Passoni, L

    2007-01-01

    This proposal deals with the technique for detection of motile response of Pseudomonas aeruginosa using dynamic laser speckle or biospeckle as an alternative method. The study of bacterial displacement plays an essential role in biocatalysts processes and biodegradation. Hence, some biodegrading enzymes are benign catalytic that could be used for the production of industrially useful compounds as well as in wastewater treatments. This work presents an experimental set up and a computational process using frame sequences of dynamic laser speckle as a novel application. The objective was the detection of different levels of motility in bacteria. The encouraging results were achieved through a direct and non invasive observation method of the phenomenon

  3. Stochastic population dynamics under resource constraints

    Energy Technology Data Exchange (ETDEWEB)

    Gavane, Ajinkya S., E-mail: ajinkyagavane@gmail.com; Nigam, Rahul, E-mail: rahul.nigam@hyderabad.bits-pilani.ac.in [BITS Pilani Hyderabad Campus, Shameerpet, Hyd - 500078 (India)

    2016-06-02

    This paper investigates the population growth of a certain species in which every generation reproduces thrice over a period of predefined time, under certain constraints of resources needed for survival of population. We study the survival period of a species by randomizing the reproduction probabilities within a window at same predefined ages and the resources are being produced by the working force of the population at a variable rate. This randomness in the reproduction rate makes the population growth stochastic in nature and one cannot predict the exact form of evolution. Hence we study the growth by running simulations for such a population and taking an ensemble averaged over 500 to 5000 such simulations as per the need. While the population reproduces in a stochastic manner, we have implemented a constraint on the amount of resources available for the population. This is important to make the simulations more realistic. The rate of resource production then is tuned to find the rate which suits the survival of the species. We also compute the mean life time of the species corresponding to different resource production rate. Study for these outcomes in the parameter space defined by the reproduction probabilities and rate of resource production is carried out.

  4. Dynamic instability in the hook-flagellum system that triggers bacterial flicks

    Science.gov (United States)

    Jabbarzadeh, Mehdi; Fu, Henry Chien

    2018-01-01

    Dynamical bending, buckling, and polymorphic transformations of the flagellum are known to affect bacterial motility, but run-reverse-flick motility of monotrichous bacteria also involves the even more flexible hook connecting the flagellum to its rotary motor. Although flick initiation has been hypothesized to involve either static Euler buckling or dynamic bending of the hook, the precise mechanism of flick initiation remains unknown. Here, we find that flicks initiate via a dynamic instability requiring flexibility in both the hook and flagellum. We obtain accurate estimates of forces and torques on the hook that suggest that flicks occur for stresses below the (static) Euler buckling criterion, then provide a mechanistic model for flick initiation that requires combined bending of the hook and flagellum. We calculate the triggering torque-stiffness ratio and find that our predicted onset of dynamic instability corresponds well with experimental observations.

  5. EFFECT OF REFINED PETROLEUM PRODUCTS CONTAMINATION ON BACTERIAL POPULATION AND PHYSICOCHEMICAL CHARACTERISTICS OF CULTIVATED AGRICULTURAL SOIL

    Directory of Open Access Journals (Sweden)

    Adewale Sogo Olalemi

    2012-10-01

    Full Text Available An investigation into the effect of refined petroleum products contamination on bacterial population and physicochemical characteristics of cultivated agricultural soil was carried out. The soil samples obtained from the Teaching and Research Farm, Obakekere, Federal University of Technology, Akure, Ondo State were contaminated with varying volumes of petrol, diesel and kerosene. The results revealed higher bacterial populations in uncontaminated soils than contaminated soils. The counts of bacteria ranged from 3.0 × 105 to 5.0 × 105 cfu/g in uncontaminated soils and 1.0 × 105 to 3.0 × 105 cfu/g in contaminated soils. The isolated bacteria were identified as Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, Corynebacterium variabilis, Pseudomonas fluorescens. The contamination had no significant effect on pH, potassium, sodium, organic carbon and nitrogen content of the soils, while the moisture, calcium, phosphorus and magnesium content of the contaminated soils were significantly different (P < 0.05 compared with the uncontaminated soils. The ability of Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, and Pseudomonas fluorescens to utilize the refined petroleum products suggest that these bacteria had potential to bioremediate petroleum contaminated soils.

  6. Impact of bioremediation treatments on the biodegradation of buried oil and predominant bacterial populations

    International Nuclear Information System (INIS)

    Swannell, R.P.J.; Mitchell, D.J.; Waterhouse, J.C.; Miskin, I.P.; Head, I.M.; Petch, S.; Jones, D.M.; Willis, A.; Lee, K.; Lepo, J.E.

    2000-01-01

    The feasibility of using mineral fertilizers as a bioremediation treatment for oil buried in fine sediments was tested in field trials at a site in the south-west of England. The plots were divided into three blocks of four treatments including untreated, fertilized, oiled unfertilized and oiled fertilized plots. The changes in residual hydrocarbons were monitored to study the biodegradation of Arabian Light Crude Oil which is known to have a high portion of biodegradable components. Samples were extracted at random points at intervals of 0, 42 and 101 days. The analysis process identified a range of aliphatic and aromatic hydrocarbons, as well as a range of geochemical biomarkers. The final results suggested that the oil in the fertilized plots was more degraded than in the oiled, unfertilized control plots. Three way, factorial analysis of variance was used to analyse the data from the oiled fertilized and oiled unfertilized plots. No significant effect of treatment on the degradation of aromatic hydrocarbons was observed. The results also showed that oil treatment and treatment with oil and fertilizer increased the abundance of hydrocarbon-degrading bacterial population. One significant observation was that different bacterial populations were stimulated in response to oil alone and a bioremediation treatment. It was concluded that the addition of inorganic fertilizers to the oiled oxic fine sediment substantially enhanced the level of biodegradation compared to untreated oiled sediment. Bioremediation is a feasible treatment for oil spills where the oil is buried in fine sediment. 14 refs., 1 tab., 4 figs

  7. Stochastic dynamics and logistic population growth

    Science.gov (United States)

    Méndez, Vicenç; Assaf, Michael; Campos, Daniel; Horsthemke, Werner

    2015-06-01

    The Verhulst model is probably the best known macroscopic rate equation in population ecology. It depends on two parameters, the intrinsic growth rate and the carrying capacity. These parameters can be estimated for different populations and are related to the reproductive fitness and the competition for limited resources, respectively. We investigate analytically and numerically the simplest possible microscopic scenarios that give rise to the logistic equation in the deterministic mean-field limit. We provide a definition of the two parameters of the Verhulst equation in terms of microscopic parameters. In addition, we derive the conditions for extinction or persistence of the population by employing either the momentum-space spectral theory or the real-space Wentzel-Kramers-Brillouin approximation to determine the probability distribution function and the mean time to extinction of the population. Our analytical results agree well with numerical simulations.

  8. Seasonal population dynamics and energy consumption by ...

    African Journals Online (AJOL)

    Dynamiques saisonnières de population et consommation énergétique par les oiseaux aquatiques d'un petit estuaire tempéré De simples mesures des dynamiques de population et de consommation énergétique peuvent fournir des informations de base sur le rôle des consommateurs au sein des réseaux trophiques, ...

  9. Statistical dynamics of regional populations and economies

    Science.gov (United States)

    Huo, Jie; Wang, Xu-Ming; Hao, Rui; Wang, Peng

    Quantitative analysis of human behavior and social development is becoming a hot spot of some interdisciplinary studies. A statistical analysis on the population and GDP of 150 cities in China from 1990 to 2013 is conducted. The result indicates the cumulative probability distribution of the populations and that of the GDPs obeying the shifted power law, respectively. In order to understand these characteristics, a generalized Langevin equation describing variation of population is proposed, which is based on the correlations between population and GDP as well as the random fluctuations of the related factors. The equation is transformed into the Fokker-Plank equation to express the evolution of population distribution. The general solution demonstrates a transition of the distribution from the normal Gaussian distribution to a shifted power law, which suggests a critical point of time at which the transition takes place. The shifted power law distribution in the supercritical situation is qualitatively in accordance with the practical result. The distribution of the GDPs is derived from the well-known Cobb-Douglas production function. The result presents a change, in supercritical situation, from a shifted power law to the Gaussian distribution. This is a surprising result-the regional GDP distribution of our world will be the Gaussian distribution one day in the future. The discussions based on the changing trend of economic growth suggest it will be true. Therefore, these theoretical attempts may draw a historical picture of our society in the aspects of population and economy.

  10. Missing cycles: Effect of climate change on population dynamics

    Indian Academy of Sciences (India)

    population dynamics of the larch budmoth – an insect pest which causes massive defoliation of entire larch forests ... hypothesized that global warming has led to the collapse of the cycles ... When temperatures increase after winter, and the.

  11. A linear model of population dynamics

    Science.gov (United States)

    Lushnikov, A. A.; Kagan, A. I.

    2016-08-01

    The Malthus process of population growth is reformulated in terms of the probability w(n,t) to find exactly n individuals at time t assuming that both the birth and the death rates are linear functions of the population size. The master equation for w(n,t) is solved exactly. It is shown that w(n,t) strongly deviates from the Poisson distribution and is expressed in terms either of Laguerre’s polynomials or a modified Bessel function. The latter expression allows for considerable simplifications of the asymptotic analysis of w(n,t).

  12. Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar.

    Science.gov (United States)

    Li, Sha; Li, Pan; Liu, Xiong; Luo, Lixin; Lin, Weifeng

    2016-05-01

    Solid-state acetic acid fermentation (AAF), a natural or semi-controlled fermentation process driven by reproducible microbial communities, is an important technique to produce traditional Chinese cereal vinegars. Highly complex microbial communities and metabolites are involved in traditional Chinese solid-state AAF, but the association between microbiota and metabolites during this process are still poorly understood. In this study, we performed amplicon 16S rRNA gene sequencing on the Illumina MiSeq platform, PCR-denaturing gradient gel electrophoresis, and metabolite analysis to trace the bacterial dynamics and metabolite changes under AAF process. A succession of bacterial assemblages was observed during the AAF process. Lactobacillales dominated all the stages. However, Acetobacter species in Rhodospirillales were considerably accelerated during AAF until the end of fermentation. Quantitative PCR results indicated that the biomass of total bacteria showed a "system microbe self-domestication" process in the first 3 days, and then peaked at the seventh day before gradually decreasing until the end of AAF. Moreover, a total of 88 metabolites, including 8 organic acids, 16 free amino acids, and 66 aroma compounds were detected during AAF. Principal component analysis and cluster analyses revealed the high correlation between the dynamics of bacterial community and metabolites.

  13. Dynamics of a structured neuron population

    International Nuclear Information System (INIS)

    Pakdaman, Khashayar; Salort, Delphine; Perthame, Benoît

    2010-01-01

    We study the dynamics of assemblies of interacting neurons. For large fully connected networks, the dynamics of the system can be described by a partial differential equation reminiscent of age-structure models used in mathematical ecology, where the 'age' of a neuron represents the time elapsed since its last discharge. The nonlinearity arises from the connectivity J of the network. We prove some mathematical properties of the model that are directly related to qualitative properties. On the one hand, we prove that it is well-posed and that it admits stationary states which, depending upon the connectivity, can be unique or not. On the other hand, we study the long time behaviour of solutions; both for small and large J, we prove the relaxation to the steady state describing asynchronous firing of the neurons. In the middle range, numerical experiments show that periodic solutions appear expressing re-synchronization of the network and asynchronous firing

  14. POPULATION DYNAMICS OF THE WANDERING ALBATROSS ...

    African Journals Online (AJOL)

    Changes in several demographic parameters that appear to be influenced by both environmental and anthropogenic effects are described. From 1994–2001, the proportion of first-time breeders in the population was positively correlated with the maximum ENSO (Niño 3) index, whereas from 1984–2000 the annual survival ...

  15. Stochastic population dynamics of a montane ground-dwelling squirrel.

    Science.gov (United States)

    Hostetler, Jeffrey A; Kneip, Eva; Van Vuren, Dirk H; Oli, Madan K

    2012-01-01

    Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λbounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

  16. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

    Directory of Open Access Journals (Sweden)

    Justin Wright

    2017-11-01

    ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.

  17. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed

    2017-01-05

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population games, namely so-called “stable games”. In particular, it was shown that a combination of stable games and (an analogue of) passive evolutionary dynamics results in stable convergence to Nash equilibrium. This paper considers the converse question of necessary conditions for evolutionary dynamics to exhibit stable behaviors for all generalized stable games. Using methods from robust control analysis, we show that if an evolutionary dynamic does not satisfy a passivity property, then it is possible to construct a generalized stable game that results in instability. The results are illustrated on selected evolutionary dynamics with particular attention to replicator dynamics, which are also shown to be lossless, a special class of passive systems.

  18. Bacterial community dynamics in surface flow constructed wetlands for the treatment of swine waste.

    Science.gov (United States)

    Ibekwe, A M; Ma, J; Murinda, Shelton; Reddy, G B

    2016-02-15

    Constructed wetlands are generally used for the removal of waste from contaminated water. In the swine production system, wastes are traditionally flushed into an anaerobic lagoon which is then sprayed on agricultural fields. However, continuous spraying of lagoon wastewater on fields can lead to high N and P accumulations in soil or lead to runoff which may contaminate surface or ground water with pathogens and nutrients. In this study, continuous marsh constructed wetland was used for the removal of contaminants from swine waste. Using pyrosequencing, we assessed bacterial composition within the wetland using principal coordinate analysis (PCoA) which showed that bacterial composition from manure influent and lagoon water were significantly different (P=0.001) from the storage pond to the final effluent. Canonical correspondence analysis (CCA) showed that different bacterial populations were significantly impacted by ammonium--NH4 (P=0.035), phosphate--PO4(3-) (P=0.010), chemical oxygen demand--COD (P=0.0165), total solids--TS (P=0.030), and dissolved solids--DS (P=0.030) removal, with 54% of the removal rate explained by NH4+PO4(3-) according to a partial CCA. Our results showed that different bacterial groups were responsible for the composition of different wetland nutrients and decomposition process. This may be the major reason why most wetlands are very efficient in waste decomposition. Published by Elsevier B.V.

  19. The dynamic instability in the hook/flagellum system that triggers bacterial flicks

    Science.gov (United States)

    Jabbarzadeh, Mehdi; Fu, Henry

    2017-11-01

    Dynamical bending, buckling, and polymorphic transformations of the flagellum are known to affect bacterial motility, but run-reverse-flick motility of monotrichous bacteria also involves the even more flexible hook, which connects the flagellum to the cell body. Here, we identify the dynamic buckling mechanism that produces flicks in Vibrio alginolyticus. Estimates of forces and torques on the hook from experimental observations suggest that flicks are triggered at stresses below the hook's static Euler buckling criterion. Using an accurate linearization of the Kirchoff rod model for the hook in a model of a swimming bacterium with rigid flagellum, we show that as hook stiffness decreases there is a transition from on-axis flagellar rotation with small hook deflections to flagellar precession with large deflections. When flagellum flexibility is incorporated, the precession is disrupted by significant flagellar bending - i.e., incipient flicks. The predicted onset of dynamic instabilities corresponds well with experimentally observed flick events.

  20. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms.

    Science.gov (United States)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-02-19

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a 'last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections.

  1. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    Science.gov (United States)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S.; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. PMID:26892159

  2. Population dynamics and distribution of the coffee berry borer ...

    African Journals Online (AJOL)

    Population dynamics and distribution of coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae) were studied on Coffea arabica L. in southwestern region of Ethiopia. Thirty coffee trees were sampled at weekly intervals from 2000 to 2001. Findings of this study showed that coffee berry borer population ...

  3. Ruffed grouse population dynamics in the central and southern Appalachians

    Science.gov (United States)

    John M. Giuliano Tirpak; C. Allan Miller; Thomas J. Allen; Steve Bittner; David A. Buehler; John W. Edwards; Craig A. Harper; William K. Igo; Gary W. Norman; M. Seamster; Dean F. Stauffer

    2006-01-01

    Ruffed grouse (Bonasa urnbellus; hereafter grouse) populations in the central and southern Appalachians are in decline. However, limited information on the dynamics of these populations prevents the development of effective management strategies to reverse these trends. We used radiotelemetry data collected on grouse to parameterize 6 models of...

  4. Stage-Structured Population Dynamics of AEDES AEGYPTI

    Science.gov (United States)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  5. [The dynamics of heath indicators of population of industrial town].

    Science.gov (United States)

    Kalinkin, D E; Karpov, A B; Takhauov, R M; Samoĭlova, Iu A

    2013-01-01

    The article presents the results of analysis of dynamics of health indicators of population of industrial town (medical demographic indicators, disability, morbidity of social hygienically important diseases) during 1970-2010. The classified administrative territorial municipality of Seversk constructed near the Siberian chemical industrial center, the internationally first-rate complex of nuclear industry enterprises was used as a research base. It is demonstrated that dynamics of health indicators of studied population had such negative tendencies as rapid population ageing, population loss due to decrease of natality and increase of mortality (population of able-bodied age included), prevalence of cardio-vascular diseases, malignant neoplasms and external causes, chronization of diseases. The established tendencies are to be considered in management decision making targeted to support and promote population health in industrial towns.

  6. Effect of antibiotics on bacterial populations: a multi-hierachical selection process.

    Science.gov (United States)

    Martínez, José Luis

    2017-01-01

    Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

  7. Dynamics of Population on the Verge of Extinction

    OpenAIRE

    Oborny, B.; Meszena, G.; Szabo, G.

    2005-01-01

    Theoretical considerations suggest that extinction in dispersal-limited populations is necessarily a threshold-like process that is analogous to a critical phase transition in physics. We use this analogy to find robust, common features in the dynamics of extinctions, and suggest early warning signals which may indicate that a population is endangered. As the critical threshold of extinction is approached, the population spontaneously fragments into discrete subpopulations and, consequently, ...

  8. Geography, European colonization, and past population dynamics in Africa

    OpenAIRE

    Vaz Silva, Luis

    2005-01-01

    Past population dynamics in Africa have remained largely elusive due to the lack of demographic data. Researchers are understandably deterred from trying to explain what is not known and African historical population estimates suffer from this lack of interest. In this paper I explain present day African population densities using mostly ecological factors as explanatory variables. I find evidence supporting the view that ecological factors deeply affected precolonial patterns of human settle...

  9. Effect of buctril super (Bromoxynil herbicide on soil microbial biomass and bacterial population

    Directory of Open Access Journals (Sweden)

    Zafar Abbas

    2014-02-01

    Full Text Available The present study aimed to evaluate the effect of bromoxynil herbicide on soil microorganisms, with the hypothesis that this herbicide caused suppression in microbial activity and biomass by exerting toxic effect on them. Nine sites of Punjab province (Pakistan those had been exposed to bromoxynil herbicide for about last ten years designated as soil 'A' were surveyed in 2011 and samples were collected and analyzed for Microbial Biomass Carbon (MBC, Biomass Nitrogen (MBN, Biomass Phosphorus (MBP and bacterial population. Simultaneously, soil samples from the same areas those were not exposed to herbicide designated as soil 'B' were taken. At all the sites MBC, MBN and MBP ranged from 131 to 457, 1.22 to 13.1 and 0.59 to 3.70 µg g-1 in the contaminated soils (Soil A, which was 187 to 573, 1.70 to 14.4 and 0.72 to 4.12 µg g-1 in the soils without contamination (soil B. Bacterial population ranged from 0.67 to 1.84x10(8 and 0.87 to 2.37x10(8 cfu g-1 soil in the soils A and B, respectively. Bromoxynil residues ranged from 0.09 to 0.24 mg kg-1 at all the sites in soil A. But no residues were detected in the soil B. Due to lethal effect of bromoxynil residues on the above parameters, considerable decline in these parameters was observed in the contaminated soils. Results depicted that the herbicide had left toxic effects on soil microbial parameters, thus confirmed that continuous use of this herbicide affected the quality of soil and sustainable crop production.

  10. Modelling the Dynamics of an Aedes albopictus Population

    Directory of Open Access Journals (Sweden)

    Thomas Anung Basuki

    2010-08-01

    Full Text Available We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.

  11. Enhanced Microgrid Dynamic Performance Using a Modulated Power Filter Based on Enhanced Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Ahmed M. Othman

    2017-06-01

    Full Text Available This paper presents a design of microgrid (MG with enhanced dynamic performance. Distributed energy resources (DER are widely used in MGs to match the various load types and profiles. DERs include solar PV cells, wind energy sources, fuel cells, batteries, micro gas-engines and storage elements. MG will include AC/DC circuits, developed power electronics devices, inverters and power electronic controllers. A novel modulated power filters (MPF device will be applied in MG design. Enhanced bacterial foraging optimization (EBFO will be proposed to optimize and set the MPF parameters to enhance and tune the MG dynamic response. Recent dynamic control is applied to minimize the harmonic reference content. EBFO will adapt the gains of MPF dynamic control. The present research achieves an enhancement of MG dynamic performance, in addition to ensuring improvements in the power factor, bus voltage profile and power quality. MG operation will be evaluated by the dynamic response to be fine-tuned by MPF based on EBFO. Digital simulations have validated the results to show the effectiveness and efficient improvement by the proposed strategy.

  12. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network.

    Science.gov (United States)

    El-Chakhtoura, Joline; Prest, Emmanuelle; Saikaly, Pascal; van Loosdrecht, Mark; Hammes, Frederik; Vrouwenvelder, Hans

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network

    KAUST Repository

    El Chakhtoura, Joline

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic.

  14. Coupling population dynamics with earth system models: the POPEM model.

    Science.gov (United States)

    Navarro, Andrés; Moreno, Raúl; Jiménez-Alcázar, Alfonso; Tapiador, Francisco J

    2017-09-16

    Precise modeling of CO 2 emissions is important for environmental research. This paper presents a new model of human population dynamics that can be embedded into ESMs (Earth System Models) to improve climate modeling. Through a system dynamics approach, we develop a cohort-component model that successfully simulates historical population dynamics with fine spatial resolution (about 1°×1°). The population projections are used to improve the estimates of CO 2 emissions, thus transcending the bulk approach of existing models and allowing more realistic non-linear effects to feature in the simulations. The module, dubbed POPEM (from Population Parameterization for Earth Models), is compared with current emission inventories and validated against UN aggregated data. Finally, it is shown that the module can be used to advance toward fully coupling the social and natural components of the Earth system, an emerging research path for environmental science and pollution research.

  15. Dynamical community structure of populations evolving on genotype networks

    International Nuclear Information System (INIS)

    Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

    2015-01-01

    Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

  16. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype and bacterial diversity (16S rDNA metabarcoding were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.

  17. Bacterial community dynamics in a rumen fluid bioreactor during in-vitro cultivation.

    Science.gov (United States)

    Zapletalová, Martina; Kašparovská, Jitka; Křížová, Ludmila; Kašparovský, Tomáš; Šerý, Omar; Lochman, Jan

    2016-09-20

    To study the various processes in the rumen the in vitro techniques are widely used to realize more controlled and reproducible conditions compared to in vivo experiments. Mostly, only the parameters like pH changes, volatile fatty acids content or metabolite production are monitored. In this study we examine the bacterial community dynamics of rumen fluid in course of ten day cultivation realize under standard conditions described in the literature. Whereas the pH values, total VFA content and A/P ratio in bioreactor were consistent with natural conditions in the rumen, the mean redox-potential values of -251 and -243mV were much more negative. For culture-independent assessment of bacterial community composition, the Illumina MiSeq results indicated that the community contained 292 bacterial genera. In course of ten days cultivation a significant changes in the microbial community were measured when Bacteroidetes to Firmicutes ratio changed from 3.2 to 1.2 and phyla Proteobacteria and Actinobacteria represented by genus Bifidobacterium and Olsenella significantly increased. The main responsible factor of these changes seems to be very low redox potential in bioreactor together with accumulation of simple carbohydrates in milieu as a result of limited excretion of fermented feed and absence of nutrient absorbing mechanisms. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization

    Science.gov (United States)

    Igoshin, Oleg

    2011-03-01

    Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. This work is supported by National Institutes of Health grant 1R01GM096189-01.

  19. Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics

    Science.gov (United States)

    Greulich, Philip; Doležal, Jakub; Scott, Matthew; Evans, Martin R.; Allen, Rosalind J.

    2017-12-01

    Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance—yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment regimen. In particular, in the clinic, antibiotic treatment is time-dependent. Here, we use a theoretical model, previously applied to steady-state bacterial growth, to predict the dynamical response of a bacterial cell to a time-dependent dose of ribosome-targeting antibiotic. Our results depend strongly on whether the antibiotic shows reversible transport and/or low-affinity ribosome binding (‘low-affinity antibiotic’) or, in contrast, irreversible transport and/or high affinity ribosome binding (‘high-affinity antibiotic’). For low-affinity antibiotics, our model predicts that growth inhibition depends on the duration of the antibiotic pulse, and can show a transient period of very fast growth following removal of the antibiotic. For high-affinity antibiotics, growth inhibition depends on peak dosage rather than dose duration, and the model predicts a pronounced post-antibiotic effect, due to hysteresis, in which growth can be suppressed for long times after the antibiotic dose has ended. These predictions are experimentally testable and may be of clinical significance.

  20. Dynamics of epidemics outbreaks in heterogeneous populations

    Science.gov (United States)

    Brockmann, Dirk; Morales-Gallardo, Alejandro; Geisel, Theo

    2007-03-01

    The dynamics of epidemic outbreaks have been investigated in recent years within two alternative theoretical paradigms. The key parameter of mean field type of models such as the SIR model is the basic reproduction number R0, the average number of secondary infections caused by one infected individual. Recently, scale free network models have received much attention as they account for the high variability in the number of social contacts involved. These models predict an infinite basic reproduction number in some cases. We investigate the impact of heterogeneities of contact rates in a generic model for epidemic outbreaks. We present a system in which both the time periods of being infectious and the time periods between transmissions are Poissonian processes. The heterogeneities are introduced by means of strongly variable contact rates. In contrast to scale free network models we observe a finite basic reproduction number and, counterintuitively a smaller overall epidemic outbreak as compared to the homogeneous system. Our study thus reveals that heterogeneities in contact rates do not necessarily facilitate the spread to infectious disease but may well attenuate it.

  1. Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil.

    Science.gov (United States)

    Reed-Jones, Neiunna L; Marine, Sasha Cahn; Everts, Kathryne L; Micallef, Shirley A

    2016-01-04

    Cover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated with Escherichia coli and Listeria innocua in the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (P cover crop was a factor for E. coli in year 1 (P = 0.004) and for L. innocua in year 2 (P = 0.011). In year 1, E. coli levels were highest in the rye and hairy vetch-rye plots. In year 2, L. innocua levels were higher in hairy vetch-rye (P = 0.01) and hairy vetch (P = 0.03) plots than in the rye plot. Bacterial populations grew (P cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  2. Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp.

    Directory of Open Access Journals (Sweden)

    Cécile Clavaud

    Full Text Available The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject's were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05. These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface.

  3. Molecular analysis of bacterial populations in water samples from two Uranium mill tailings by using RISA retrieval

    International Nuclear Information System (INIS)

    Selenska-Pobell, S.; Radeva, G.

    2004-01-01

    Ribosomal intergenic spacer amplification (RISA) retrieval was applied to analyse the natural bacterial communities in drain waters of two uranium mill tailings - Gittersee/Coschuetz in Germany and Shiprock in the USA. About 35% of the clones from RISA library constructed for the samples of the German tailings represented a microdiverse population of Planctomycetales. The rest of the clones were affiliated with rather diverse bacterial groups including γ- and δ-Proteobacteria, Cytophaga/Flavobacterium/Bacteroides (CFB), Nitrospira, Verrucomicrobia and Actinobacteria. 8% of the cloned sequences represented a novel bacterial lineage from the recently described division NC3. Bacterial diversity in the Shiprock mill tailings was found to be significantly lower. RISA library constructed for those samples contained only two larger groups of clones representing β-proteobacterial species and one small group which was affiliated with δ-Proteobacteria. (authors)

  4. Molecular analysis of bacterial populations in water samples from two Uranium mill tailings by using RISA retrieval

    Energy Technology Data Exchange (ETDEWEB)

    Selenska-Pobell, S [Forschungszentrum Rossendorf, Institute of Radiochemistry, Dresden (Germany); Radeva, G [Bulgarian Academy of Sciences, Institute of Molecular Biology, Sofia (Bulgaria)

    2004-07-01

    Ribosomal intergenic spacer amplification (RISA) retrieval was applied to analyse the natural bacterial communities in drain waters of two uranium mill tailings - Gittersee/Coschuetz in Germany and Shiprock in the USA. About 35% of the clones from RISA library constructed for the samples of the German tailings represented a microdiverse population of Planctomycetales. The rest of the clones were affiliated with rather diverse bacterial groups including {gamma}- and {delta}-Proteobacteria, Cytophaga/Flavobacterium/Bacteroides (CFB), Nitrospira, Verrucomicrobia and Actinobacteria. 8% of the cloned sequences represented a novel bacterial lineage from the recently described division NC3. Bacterial diversity in the Shiprock mill tailings was found to be significantly lower. RISA library constructed for those samples contained only two larger groups of clones representing {beta}-proteobacterial species and one small group which was affiliated with {delta}-Proteobacteria. (authors)

  5. Computer simulation of population dynamics inside the urban environment

    Science.gov (United States)

    Andreev, A. S.; Inovenkov, I. N.; Echkina, E. Yu.; Nefedov, V. V.; Ponomarenko, L. S.; Tikhomirov, V. V.

    2017-12-01

    In this paper using a mathematical model of the so-called “space-dynamic” approach we investigate the problem of development and temporal dynamics of different urban population groups. For simplicity we consider an interaction of only two population groups inside a single urban area with axial symmetry. This problem can be described qualitatively by a system of two non-stationary nonlinear differential equations of the diffusion type with boundary conditions of the third type. The results of numerical simulations show that with a suitable choice of the diffusion coefficients and interaction functions between different population groups we can receive different scenarios of population dynamics: from complete displacement of one population group by another (originally more “aggressive”) to the “peaceful” situation of co-existence of them together.

  6. Bounds on the dynamics of sink populations with noisy immigration.

    Science.gov (United States)

    Eager, Eric Alan; Guiver, Chris; Hodgson, Dave; Rebarber, Richard; Stott, Iain; Townley, Stuart

    2014-03-01

    Sink populations are doomed to decline to extinction in the absence of immigration. The dynamics of sink populations are not easily modelled using the standard framework of per capita rates of immigration, because numbers of immigrants are determined by extrinsic sources (for example, source populations, or population managers). Here we appeal to a systems and control framework to place upper and lower bounds on both the transient and future dynamics of sink populations that are subject to noisy immigration. Immigration has a number of interpretations and can fit a wide variety of models found in the literature. We apply the results to case studies derived from published models for Chinook salmon (Oncorhynchus tshawytscha) and blowout penstemon (Penstemon haydenii). Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    Directory of Open Access Journals (Sweden)

    Zak Frentz

    2015-10-01

    Full Text Available Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

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

    Science.gov (United States)

    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. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

    Directory of Open Access Journals (Sweden)

    Alvaro Sanchez

    Full Text Available 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

  10. Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations.

    Science.gov (United States)

    Goitom, Eyerusalem; Kilsdonk, Laurens J; Brans, Kristien; Jansen, Mieke; Lemmens, Pieter; De Meester, Luc

    2018-01-01

    There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top-down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S-map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top-down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

  11. Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments.

    Science.gov (United States)

    Almeida, C Marisa R; Oliveira, Tânia; Reis, Izabela; Gomes, Carlos R; Mucha, Ana P

    2017-12-01

    Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas

  12. Bacterial community dynamics during bioremediation of diesel oil-contaminated Antarctic soil.

    Science.gov (United States)

    Vázquez, S; Nogales, B; Ruberto, L; Hernández, E; Christie-Oleza, J; Lo Balbo, A; Bosch, R; Lalucat, J; Mac Cormack, W

    2009-05-01

    The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated

  13. Spatiotemporal dynamics of the bacterial microbiota on lacustrine Cladophora glomerata (Chlorophyta).

    Science.gov (United States)

    Braus, Michael J; Graham, Linda E; Whitman, Thea L

    2017-12-01

    The branched periphytic green alga Cladophora glomerata, often abundant in nearshore waters of lakes and rivers worldwide, plays important ecosystem roles, some mediated by epibiotic microbiota that benefit from host-provided surface, organic C, and O 2 . Previous microscopy and high-throughput sequencing studies have indicated surprising epibiont taxonomic and functional diversity, but have not included adequate consideration of sample replication or the potential for spatial and temporal variation. Here, we report the results of 16S rRNA amplicon-based phylum-to-genus taxonomic analysis of Cladophora-associated bacterial epibiota sampled in replicate from three microsites and at six times during the open-water season of 2014, from the same lake locale (Picnic Point, Lake Mendota, Dane Co., WI, USA) explored by high-throughput sequencing studies in two previous years. Statistical methods were used to test null hypotheses that the bacterial community: (i) is homogeneous across microsites tested, and (ii) does not change over the course of a growth season or among successive years. Results indicated a dynamic microbial community that is more strongly influenced by sampling day during the growth season than by microsite variation. A surprising diversity of bacterial genera known to be associated with the key function of methane-oxidation (methanotrophy), including relatively high-abundance of Crenothrix, Methylomonas, Methylovulum, and Methylocaldum-showed intraseasonal and interannual variability possibly related to temperature differences, and microsite preferences possibly related to variation in methane abundance. By contrast, a core assemblage of bacterial genera seems to persist over a growth season and from year to year, possibly transmitted by a persistent attached host resting stage. © 2017 Phycological Society of America.

  14. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System.

    Directory of Open Access Journals (Sweden)

    E I Prest

    Full Text Available Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP effluent and at one fixed location in the drinking water distribution network (NET. The samples were analysed for heterotrophic plate counts (HPC, Aeromonas plate counts, adenosine-tri-phosphate (ATP concentrations, and flow cytometric (FCM total and intact cell counts (TCC, ICC, water temperature, pH, conductivity, total organic carbon (TOC and assimilable organic carbon (AOC. Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time and in bacterial ATP concentrations (<1-3.6 ng L-1, which were congruent with water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson's correlation factor r = -0.35, and positively correlated with water temperature (r = 0.49. Collecting a large dataset at high frequency over a two year period enabled the characterization of previously

  15. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    KAUST Repository

    Prest, E. I.; Weissbrodt, D. G.; Hammes, F.; Van Loosdrecht, M. C M; Vrouwenvelder, Johannes S.

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (<1–3.6 ng L-1), which were congruent with water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson’s correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously

  16. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System.

    Science.gov (United States)

    Prest, E I; Weissbrodt, D G; Hammes, F; van Loosdrecht, M C M; Vrouwenvelder, J S

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson's correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously undocumented seasonal dynamics in the distribution

  17. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    KAUST Repository

    Prest, E. I.

    2016-10-28

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (<1–3.6 ng L-1), which were congruent with water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson’s correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously

  18. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

    Full Text Available The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1 the changes occurring within the communities along fixed time intervals, 2 the slow turnover of activated sludge communities and 3 the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

  19. Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts.

    Science.gov (United States)

    Cerveau, Nicolas; Leclercq, Sébastien; Leroy, Elodie; Bouchon, Didier; Cordaux, Richard

    2011-01-01

    Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52-171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes.

  20. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  1. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Title Structural and functi...onal analyses of bacterial lipopolysaccharides. Authors

  2. DMPD: The actions of bacterial DNA on murine macrophages. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 10534106 The actions of bacterial DNA on murine macrophages. Sester DP, Stacey KJ, ... Show The actions of bacterial DNA on murine macrophages. PubmedID 10534106 Title The actions of bacterial DNA on murine macrophage

  3. Shaping bacterial population behavior through computer-interfaced control of individual cells.

    Science.gov (United States)

    Chait, Remy; Ruess, Jakob; Bergmiller, Tobias; Tkačik, Gašper; Guet, Călin C

    2017-11-16

    Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.

  4. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

    OpenAIRE

    Haihan Zhang; Jingyu Jia; Shengnan Chen; Tinglin Huang; Yue Wang; Zhenfang Zhao; Ji Feng; Huiyan Hao; Sulin Li; Xinxin Ma

    2018-01-01

    The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal tr...

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

    Directory of Open Access Journals (Sweden)

    Duarte M.V.E.

    2003-01-01

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

  6. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  7. Network evolution induced by the dynamical rules of two populations

    International Nuclear Information System (INIS)

    Platini, Thierry; Zia, R K P

    2010-01-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (N a and N b ) and preferred degree (κ a and κ b a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees (k bb ) and (k ab ) presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal N a = N b , the ratio of the restricted degree θ 0 = (k ab )/(k bb ) appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t 1 = κ b ) the total number of links presents a linear evolution, where the two populations are indistinguishable and where θ 0 = 1. Interestingly, in the intermediate time regime (defined for t 1 2 ∝κ a and for which θ 0 = 5), the system reaches a transient stationary state, where the number of contacts among introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ 0 = 3

  8. Social Information Links Individual Behavior to Population and Community Dynamics.

    Science.gov (United States)

    Gil, Michael A; Hein, Andrew M; Spiegel, Orr; Baskett, Marissa L; Sih, Andrew

    2018-05-07

    When individual animals make decisions, they routinely use information produced intentionally or unintentionally by other individuals. Despite its prevalence and established fitness consequences, the effects of such social information on ecological dynamics remain poorly understood. Here, we synthesize results from ecology, evolutionary biology, and animal behavior to show how the use of social information can profoundly influence the dynamics of populations and communities. We combine recent theoretical and empirical results and introduce simple population models to illustrate how social information use can drive positive density-dependent growth of populations and communities (Allee effects). Furthermore, social information can shift the nature and strength of species interactions, change the outcome of competition, and potentially increase extinction risk in harvested populations and communities. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Population dynamics of active and total ciliate populations in arable soil amended with wheat

    DEFF Research Database (Denmark)

    Ekelund, F.; Frederiksen, Helle B.; Ronn, R.

    2002-01-01

    of the population may be encysted. The factors governing the dynamics of active and encysted cells in the soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in soil...... microcosms, the active and total populations of ciliates, their potential prey (bacteria and small protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable...

  10. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  11. Stochastic population dynamics of a montane ground-dwelling squirrel.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Hostetler

    Full Text Available Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008 study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1 for 9 out of 18 years. The stochastic population growth rate λ(s was 0.92, suggesting a declining population; however, the 95% CI on λ(s included 1.0 (0.52-1.60. Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

  12. SIR dynamics in structured populations with heterogeneous connectivity

    OpenAIRE

    Volz, Erik

    2005-01-01

    Most epidemic models assume equal mixing among members of a population. An alternative approach is to model a population as random network in which individuals may have heterogeneous connectivity. This paper builds on previous research by describing the exact dynamical behavior of epidemics as they occur in random networks. A system of nonlinear differential equations is presented which describes the behavior of epidemics spreading through random networks with arbitrary degree distributions. ...

  13. Detrimental effects of commercial zinc oxide and silver nanomaterials on bacterial populations and performance of wastewater systems

    Science.gov (United States)

    Mboyi, Anza-vhudziki; Kamika, Ilunga; Momba, MaggyN. B.

    2017-08-01

    The widespread use of commercial nanomaterials (NMs) in consumer products has raised environmental concerns as they can enter and affect the efficiency of the wastewater treatment plants. In this study the effect of various concentrations of zinc oxide NMs (nZnO) and silver NMs (nAg) on the selected wastewater bacterial species (Bacillus licheniformis, Brevibacillus laterosporus and Pseudomonas putida) was ascertained at different pH levels (pH 2, 7 and 10). Lethal concentrations (LC) of NMs and parameters such as chemical oxygen demand (COD) and dissolved oxygen (DO) were taken into consideration to assess the performance of a wastewater batch reactor. Bacterial isolates were susceptible to varying concentrations of both nZnO and nAg at pH 2, 7 and 10. It was found that a change in pH did not significantly affect the toxicity of test NMs towards target bacterial isolates. All bacterial species were significantly inhibited (p 0.05) in COD removal in the presence of increasing concentrations of NMs, which resulted in increasing releases of COD. Noticeably, there was no significant difference (p > 0.05) in the decrease in DO uptake in the presence of increasing NM concentrations for all bacterial isolates. The toxic effects of the target NMs on bacterial populations in wastewater may negatively impact the performance of biological treatment processes and may thus affect the efficiency of wastewater treatment plants in producing effluent of high quality.

  14. Estimating Traveler Populations at Airport and Cruise Terminals for Population Distribution and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jochem, Warren C [ORNL; Sims, Kelly M [ORNL; Bright, Eddie A [ORNL; Urban, Marie L [ORNL; Rose, Amy N [ORNL; Coleman, Phil R [ORNL; Bhaduri, Budhendra L [ORNL

    2013-01-01

    In recent years, uses of high-resolution population distribution databases are increasing steadily for environmental, socioeconomic, public health, and disaster-related research and operations. With the development of daytime population distribution, temporal resolution of such databases has been improved. However, the lack of incorporation of transitional population, namely business and leisure travelers, leaves a significant population unaccounted for within the critical infrastructure networks, such as at transportation hubs. This paper presents two general methodologies for estimating passenger populations in airport and cruise port terminals at a high temporal resolution which can be incorporated into existing population distribution models. The methodologies are geographically scalable and are based on, and demonstrate how, two different transportation hubs with disparate temporal population dynamics can be modeled utilizing publicly available databases including novel data sources of flight activity from the Internet which are updated in near-real time. The airport population estimation model shows great potential for rapid implementation for a large collection of airports on a national scale, and the results suggest reasonable accuracy in the estimated passenger traffic. By incorporating population dynamics at high temporal resolutions into population distribution models, we hope to improve the estimates of populations exposed to or at risk to disasters, thereby improving emergency planning and response, and leading to more informed policy decisions.

  15. Identification and dynamic modeling of biomarkers for bacterial uptake and effect of sulfonamide antimicrobials

    International Nuclear Information System (INIS)

    Richter, Merle K.; Focks, Andreas; Siegfried, Barbara; Rentsch, Daniel; Krauss, Martin; Schwarzenbach, René P.; Hollender, Juliane

    2013-01-01

    The effects of sulfathiazole (STA) on Escherichia coli with glucose as a growth substrate was investigated to elucidate the effect-based reaction of sulfonamides in bacteria and to identify biomarkers for bacterial uptake and effect. The predominant metabolite was identified as pterine-sulfathiazole by LC-high resolution mass spectrometry. The formation of pterine-sulfathiazole per cell was constant and independent of the extracellular STA concentrations, as they exceeded the modeled half-saturation concentration K M S of 0.011 μmol L −1 . The concentration of the dihydrofolic acid precursor para-aminobenzoic acid (pABA) increased with growth and with concentrations of the competitor STA. This increase was counteracted for higher STA concentrations by growth inhibition as verified by model simulation of pABA dynamics. The EC value for the inhibition of pABA increase was 6.9 ± 0.7 μmol L −1 STA, which is similar to that calculated from optical density dynamics indicating that pABA is a direct biomarker for the SA effect. - Highlights: ► Elucidation of the effect-based reaction of sulfonamides in bacteria. ► Identification of a biomarker for uptake and effect-based reaction of sulfonamides. ► Investigation of a biomarker for the bacterial growth inhibition by sulfonamides. ► Quantitative mechanistic modeling of biomarker dynamics using enzyme kinetics. ► Mechanistic quantitative linking of sulfonamide concentrations and effects. - Identification of specific biomarkers for the uptake and effect-based reaction of sulfonamides in bacteria and resulting growth inhibition.

  16. Stochastic population dynamics in populations of western terrestrial garter snakes with divergent life histories.

    Science.gov (United States)

    Miller, David A; Clark, William R; Arnold, Stevan J; Bronikowski, Anne M

    2011-08-01

    Comparative evaluations of population dynamics in species with temporal and spatial variation in life-history traits are rare because they require long-term demographic time series from multiple populations. We present such an analysis using demographic data collected during the interval 1978-1996 for six populations of western terrestrial garter snakes (Thamnophis elegans) from two evolutionarily divergent ecotypes. Three replicate populations from a slow-living ecotype, found in mountain meadows of northeastern California, were characterized by individuals that develop slowly, mature late, reproduce infrequently with small reproductive effort, and live longer than individuals of three populations of a fast-living ecotype found at lakeshore locales. We constructed matrix population models for each of the populations based on 8-13 years of data per population and analyzed both deterministic dynamics based on mean annual vital rates and stochastic dynamics incorporating annual variation in vital rates. (1) Contributions of highly variable vital rates to fitness (lambda(s)) were buffered against the negative effects of stochastic variation, and this relationship was consistent with differences between the meadow (M-slow) and lakeshore (L-fast) ecotypes. (2) Annual variation in the proportion of gravid females had the greatest negative effect among all vital rates on lambda(s). The magnitude of variation in the proportion of gravid females and its effect on lambda(s) was greater in M-slow than L-fast populations. (3) Variation in the proportion of gravid females, in turn, depended on annual variation in prey availability, and its effect on lambda(s) was 4 23 times greater in M-slow than L-fast populations. In addition to differences in stochastic dynamics between ecotypes, we also found higher mean mortality rates across all age classes in the L-fast populations. Our results suggest that both deterministic and stochastic selective forces have affected the evolution of

  17. Population dynamics of light-limited phytoplankton : Microcosm experiments

    NARCIS (Netherlands)

    Huisman, Jef

    This paper investigates the extent to which the predictions of an elementary model for light-limited growth are matched by laboratory experiments with light-limited phytoplankton. The model and experiments link the population dynamics of phytoplankton species with changes in the light gradient

  18. Distribution and population dynamics of Rhizobium sp. introduced into soil

    NARCIS (Netherlands)

    Postma, J.

    1989-01-01

    In this thesis the population dynamics of bacteria introduced into soil was studied. In the introduction, the existence of microhabitats favourable for the survival of indigenous bacteria is discussed. Knowledge about the distribution of introduced bacteria over

  19. seasonal population dynamics of rodents of mount chilalo, arsi ...

    African Journals Online (AJOL)

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    ABSTRACT: A study on seasonal population dynamics of rodents was carried out on Mount. Chilalo from .... vegetation growth, availability of food and water, and ... vegetation (3,300–4,200 masl) (Alemayehu. Mengistu, 1975; APEDO and ABRDP, 2004). The mountain is one of the Afrotropical biodiversity hotspots areas.

  20. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... Population dynamics of soil microbes and diversity of ... 25.78, 25.78, 86.26, 24.73, 68.0, 26.8 and 26.8 kDa proteins and equivalent to Cyt, Cry5 and Cry2 toxins ..... Molecular weight (kDa) of protein fractions of the BT isolates.

  1. Population dynamics of the invasive fish, Gambusia affinis , in ...

    African Journals Online (AJOL)

    Repeated-measures ANOVA analyses on the catch per unit effort (CPUE) of G. affinis between sampling events and dams revealed significant differences in population dynamics among dams, although an overall trend of rapid increase followed by plateau in summer, with a rapid decline in winter was seen in most dams.

  2. Individual based model of slug population and spatial dynamics

    NARCIS (Netherlands)

    Choi, Y.H.; Bohan, D.A.; Potting, R.P.J.; Semenov, M.A.; Glen, D.M.

    2006-01-01

    The slug, Deroceras reticulatum, is one of the most important pests of agricultural and horticultural crops in UK and Europe. In this paper, a spatially explicit individual based model (IbM) is developed to study the dynamics of a population of D. reticulatum. The IbM establishes a virtual field

  3. Network evolution induced by the dynamical rules of two populations

    Science.gov (United States)

    Platini, Thierry; Zia, R. K. P.

    2010-10-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (Na and Nb) and preferred degree (κa and \\kappa_b\\ll \\kappa_a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees langkbbrang and langkabrang presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal Na = Nb, the ratio of the restricted degree θ0 = langkabrang/langkbbrang appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ0 = 3.

  4. Dynamics of immune system gene expression upon bacterial challenge and wounding in a social insect (Bombus terrestris.

    Directory of Open Access Journals (Sweden)

    Silvio Erler

    2011-03-01

    Full Text Available The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT. There is a lack of immune genes in social insects (e.g. honeybees when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals. The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge.Antimicrobial peptides (AMP (abaecin, defensin 1, hymenoptaecin were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish and JNK pathway (basket. Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment.Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the

  5. An individual-based model of Zebrafish population dynamics accounting for energy dynamics

    DEFF Research Database (Denmark)

    Beaudouin, Remy; Goussen, Benoit; Piccini, Benjamin

    2015-01-01

    Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model...

  6. [Population dynamics and armed violence in Colombia, 1985-2010].

    Science.gov (United States)

    Salaya, Hernán Eduardo; Rodríguez, Jesús

    2014-09-01

    Describe changes in the population structure of Colombia's municipalities in relation to internal displacement in response to armed violence. A descriptive ecological study was carried out. Secondary sources were consulted, taken from the Consolidated Registry of Displaced Population and from the National Administrative Department of Statistics, to calculate expulsion and reception rates for population displaced by violence from 2002 to 2010. Based on these rates, four groups were created of municipalities in the extreme quartile for each rate during the entire period, which were classified as high expulsion, low expulsion, high reception, and low reception. Subsequently, population pyramids and structure indicators were constructed for each group of municipalities for two comparative reference years (1985 and 2010). Municipalities with high expulsion or reception rates experienced a slower epidemiological transition, with lower mean ages and aging indices. The high expulsion group had the least regression, based on the Sundbärg index. In the high reception group, the masculinity ratio decreased the most, especially among the economically active population, and it had the highest population growth. Population dynamics in Colombia have been affected by armed violence and changes in these dynamics are not uniform across the country, leading to important social, economic, and cultural consequences. This study is useful for decision-making and public policy making.

  7. Bridging the Timescales of Single-Cell and Population Dynamics

    Science.gov (United States)

    Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

    2018-04-01

    How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

  8. An EPA pilot study characterizing fungal and bacterial populations at homes after flooding events at the Martin Peña Channel community-Puerto Rico

    Science.gov (United States)

    The overall objective of this program is to characterize fungal and bacterial populations in the MPC residences in San Juan, Puerto Rico, following flooding events. These profiles will be generated by comparing the fungal and bacterial populations in two groups of residences: hom...

  9. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  10. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  11. Rethinking the logistic approach for population dynamics of mutualistic interactions.

    Science.gov (United States)

    García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

    2014-12-21

    Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.

    Science.gov (United States)

    Frenoy, Antoine; Bonhoeffer, Sebastian

    2018-05-01

    The stress-induced mutagenesis hypothesis postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to better withstand the stress. This has implications for antibiotic treatment: exposure to subinhibitory doses of antibiotics has been reported to increase bacterial mutation rates and thus probably the rate at which resistance mutations appear and lead to treatment failure. More generally, the hypothesis posits that stress increases evolvability (the ability of a population to generate adaptive genetic diversity) and thus accelerates evolution. Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet subinhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus providing more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress. We developed a system based on plasmid segregation that allows us to measure death and division rates simultaneously in bacterial populations. Using this system, we found that a substantial death rate occurs at the tested subinhibitory concentrations previously reported to increase mutation rate. Taking this death rate into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover, even when antibiotics increase mutation rate, we show that subinhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics. We conclude that antibiotic-induced mutagenesis is overestimated because of death and that understanding evolvability under stress requires accounting for the effects of stress on population dynamics as much as on mutation rate. Our goal here is dual: we show that population dynamics and, in particular, the

  13. Fed-Batch Production of Bacterial Ghosts Using Dielectric Spectroscopy for Dynamic Process Control

    Directory of Open Access Journals (Sweden)

    Andrea Meitz

    2016-03-01

    Full Text Available The Bacterial Ghost (BG platform technology evolved from a microbiological expression system incorporating the ϕX174 lysis gene E. E-lysis generates empty but structurally intact cell envelopes (BGs from Gram-negative bacteria which have been suggested as candidate vaccines, immunotherapeutic agents or drug delivery vehicles. E-lysis is a highly dynamic and complex biological process that puts exceptional demands towards process understanding and control. The development of a both economic and robust fed-batch production process for BGs required a toolset capable of dealing with rapidly changing concentrations of viable biomass during the E-lysis phase. This challenge was addressed using a transfer function combining dielectric spectroscopy and soft-sensor based biomass estimation for monitoring the rapid decline of viable biomass during the E-lysis phase. The transfer function was implemented to a feed-controller, which followed the permittivity signal closely and was capable of maintaining a constant specific substrate uptake rate during lysis phase. With the described toolset, we were able to increase the yield of BG production processes by a factor of 8–10 when compared to currently used batch procedures reaching lysis efficiencies >98%. This provides elevated potentials for commercial application of the Bacterial Ghost platform technology.

  14. Characterization of the rate and temperature sensitivities of bacterial remineralization of dissolved organic phosphorus by natural populations

    Directory of Open Access Journals (Sweden)

    Angelicque E. White

    2012-08-01

    Full Text Available Production, transformation, and degradation are the principal components of the cycling of dissolved organic matter (DOM in marine systems. Heterotrophic Bacteria (and Archaea play a large part in this cycling via enzymatic decomposition and intracellular transformations of organic material to inorganic carbon (C, nitrogen (N , and phosphorus (P. The rate and magnitude of inorganic nutrient regeneration from DOM is related to the elemental composition and lability of DOM substrates as well as the nutritional needs of the mediating organisms. While many previous efforts have focused on C and N cycling of DOM, less is known in regards to the controls of organic P utilization and remineralization by natural populations of bacteria. In order to constrain the relative time scales and degradation of select dissolved organic P (DOP compounds we have conducted a series of experiments focused on (1 assessment of the short-term lability of a range of DOP compounds, (2 characterization of labile DOP remineralization rates and (3 examination of temperature sensitivities of labile DOP remineralization for varying bacterial populations. Results reinforce previous findings of monoester and polyphosphate lability and the relative recalcitrance of a model phosphonate: 2-aminoethylphosphonate. High resolution time-series of P monoester remineralization indicates decay constants on the order of 0.67-7.04 d-1 for bacterial populations isolated from coastal and open ocean surface waters. The variability of these rates is predictably related to incubation temperature and initial concentrations of heterotrophic bacteria. Additional controls on DOP hydrolysis included seasonal shifts in bacterial populations and the physiological state of bacteria at the initiation of DOP addition experiments. Composite results indicate that bacterial hydrolysis of P-monoesters exceeds bacterial P demand and thus DOP remineralization efficiency may control P availability to autotrophs.

  15. Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Yongjin Qiu

    Full Text Available Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA using the Metagenomics RAST (MG-RAST metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus, 127 (I. persulcatus and 59 (H. flava. Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of

  16. Aspiration dynamics of multi-player games in finite populations.

    Science.gov (United States)

    Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

    2014-05-06

    On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

  17. Paths and patterns: the biology and physics of swimming bacterial populations

    Science.gov (United States)

    Kessler, J. O.; Strittmatter, R. P.; Swartz, D. L.; Wiseley, D. A.; Wojciechowski, M. F.

    1995-01-01

    The velocity distribution of swimming micro-organisms depends on directional cues supplied by the environment. Directional swimming within a bounded space results in the accumulation of organisms near one or more surfaces. Gravity, gradients of chemical concentration and illumination affect the motile behaviour of individual swimmers. Concentrated populations of organisms scatter and absorb light or consume molecules, such as oxygen. When supply is one-sided, consumption creates gradients; the presence of the population alters the intensity and the symmetry of the environmental cues. Patterns of cues interact dynamically with patterns of the consumer population. In suspensions, spatial variations in the concentration of organisms are equivalent to variations of mean mass density of the fluid. When organisms accumulate in one region whilst moving away from another region, the force of gravity causes convection that translocates both organisms and dissolved substances. The geometry of the resulting concentration-convection patterns has features that are remarkably reproducible. Of interest for biology are (1) the long-range organisation achieved by organisms that do not communicate, and (2) that the entire system, consisting of fluid, cells, directional supply of consumables, boundaries and gravity, generates a dynamic that improves the organisms' habitat by enhancing transport and mixing. Velocity distributions of the bacterium Bacillus subtilis have been measured within the milieu of the spatially and temporally varying oxygen concentration which they themselves create. These distributions of swimming speed and direction are the fundamental ingredients required for a quantitative mathematical treatment of the patterns. The quantitative measurement of swimming behaviour also contributes to our understanding of aerotaxis of individual cells.

  18. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    KAUST Repository

    Bargiela, Rafael

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  19. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    KAUST Repository

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Torné s, Jesú s; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V.; Cappello, Simone; Gertler, Christoph; Genovese, Marí a; Denaro, Renata; Martí nez-Martí nez, Mó nica; Fodelianakis, Stilianos; Amer, Ranya A.; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N.; Golyshina, Olga V.; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R.; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I.; Golyshin, Peter N.; Yakimov, Michail M.; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  20. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    Science.gov (United States)

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  1. Daily dynamics of bacterial numbers, CO2 emissions from soil and relationships between their wavelike fluctuations and succession of the microbial community

    Science.gov (United States)

    Semenov, A. M.; Bubnov, I. A.; Semenov, V. M.; Semenova, E. V.; Zelenev, V. V.; Semenova, N. A.

    2013-08-01

    The daily dynamics of the number of copiotrophic and oligotrophic bacteria (in colony-forming units) and CO2 emissions from cultivated soils after short- and long-term disturbances were studied for 25-27 days in a microfield experiment. The relationship of the wavelike fluctuations of the bacterial number and CO2 emission with the succession of the soil microbial community was determined by the polymerase chain reaction method—denaturing gradient gel electrophoresis (PCR-DGGE). Short-term disturbances involved the application of organic or mineral fertilizers, pesticides, and plant residues to the soils of different plots. The long-term effect was a result of using biological and intensive farming systems for three years. The short-term disturbances resulted in increased peaks of the bacterial number, the significance of which was confirmed by harmonics analysis. The daily dynamics of the structure of the soil microbial community, which was studied for 27 days by the DGGE method, also had an oscillatory pattern. Statistical processing of the data (principal components analysis, harmonics and cross-correlation analyses) has revealed significant fluctuations in the structure of microbial communities coinciding with those of the bacterial populations. The structure of the microbial community changed within each peak of the dynamics of the bacterial number (but not from peak to peak), pointing to the cyclical character of the short-term succession. The long-term effects resulted in a less intense response of the microbiota—a lower rate of CO2 emission from the soil cultivated according to the organic farming system.

  2. Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

    Science.gov (United States)

    De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

    2009-02-01

    Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to

  3. An age structured model for obesity prevalence dynamics in populations

    Directory of Open Access Journals (Sweden)

    Gilberto González Parra

    2010-08-01

    Full Text Available Objective. Modeling the correlation of the development of obesity in a population with age and time and predict the dynamics of the correlation of the development of obesity in a population with age and time under different scenarios in Valencia (Spain. Materials and methods. An age structured mathematical model is used to describe the future dynamics of obesity prevalence for different ages in human population with excess weight. Simulation of the model with parameters estimated using the Health Survey of the Region of Valencia 2000 (4.319 interviews and Health Survey of the Region of Valencia 2005 (4.012 interviews. The model considers only overweight and obese populations since these subpopulations are the most relevant on obesity health concern. Results. The model allows predicting and studying the prevalence of obesity for each age. Results showed an increasing trend of obesity in the following years in well accordance with the trend observed in several countries. Conclusions. Based on the numerical simulations it is possible to conclude that the age structured mathematical model is suitable to forecast the obesity epidemic in each age group in different countries. Additionally, this type of models may be applied to study other characteristics of other populations such animal populations.

  4. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  5. Differences in Bacterial Population in Rainbow Trout (Oncorhynchus mykiss Walbum Fry after Transfer from Incubator to Pools

    Directory of Open Access Journals (Sweden)

    Damir Kapetanović

    2005-01-01

    Full Text Available The microflora of rainbow trout (Oncorhynchus mykiss Walbaum fry from a commercial freshwater hatchery, along with important water quality parameters such as temperature, dissolved oxygen and pH, was analysed. Samples for bacteriological analysis were taken from gill, heart and kidney, from the third to the eighth week after hatching. Pure bacterial colonies were examined macroscopically, with Gram staining and biochemical tests. For final identification, the APILAB Plus programme (bioMérieux, France was used. The bacterial populations of rainbow trout fry changed depending on age. Most of the bacterial colonies were cultured from the gills (64.4 %, rather than the heart (21.8 % and kidney (13.8 %. The bacterial community of fry gills from an incubator was composed mostly of Gram-positive bacteria such as Renibacterium salmoninarum, Lactobacillus spp., Staphylococcus spp. and Corynebacterium aquaticum. After the transfer of fry from incubator into the pools the Gram-negative bacteria increased in number and became the dominant microflora of rainbow trout fry and comprised more than 95 % of its bacterial flora. Flavibacterium, Acinetobacter and Yersinia were the predominant Gram-negative genera in fry in the incubator, whereas Aeromonas and Pseudomonas were the main isolates from rainbow trout fry until the end of the experiment.

  6. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

    Science.gov (United States)

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-04-01

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ˜0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  7. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc1 complex

    International Nuclear Information System (INIS)

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-01-01

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc 1 bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins

  8. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Daniel R.; Matyushov, Dmitry V., E-mail: dmitrym@asu.edu [Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287 (United States)

    2015-04-28

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  9. Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase.

    Directory of Open Access Journals (Sweden)

    C F Reboul

    Full Text Available Dihydrodipicolinate synthase (DHDPS is an essential enzyme involved in the lysine biosynthesis pathway. DHDPS from E. coli is a homotetramer consisting of a 'dimer of dimers', with the catalytic residues found at the tight-dimer interface. Crystallographic and biophysical evidence suggest that the dimers associate to stabilise the active site configuration, and mutation of a central dimer-dimer interface residue destabilises the tetramer, thus increasing the flexibility and reducing catalytic efficiency and substrate specificity. This has led to the hypothesis that the tetramer evolved to optimise the dynamics within the tight-dimer. In order to gain insights into DHDPS flexibility and its relationship to quaternary structure and function, we performed comparative Molecular Dynamics simulation studies of native tetrameric and dimeric forms of DHDPS from E. coli and also the native dimeric form from methicillin-resistant Staphylococcus aureus (MRSA. These reveal a striking contrast between the dynamics of tetrameric and dimeric forms. Whereas the E. coli DHDPS tetramer is relatively rigid, both the E. coli and MRSA DHDPS dimers display high flexibility, resulting in monomer reorientation within the dimer and increased flexibility at the tight-dimer interface. The mutant E. coli DHDPS dimer exhibits disorder within its active site with deformation of critical catalytic residues and removal of key hydrogen bonds that render it inactive, whereas the similarly flexible MRSA DHDPS dimer maintains its catalytic geometry and is thus fully functional. Our data support the hypothesis that in both bacterial species optimal activity is achieved by fine tuning protein dynamics in different ways: E. coli DHDPS buttresses together two dimers, whereas MRSA dampens the motion using an extended tight-dimer interface.

  10. Efficient characterisation of large deviations using population dynamics

    Science.gov (United States)

    Brewer, Tobias; Clark, Stephen R.; Bradford, Russell; Jack, Robert L.

    2018-05-01

    We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. We use the simple symmetric exclusion process with periodic boundary conditions as a prototypical example and investigate the convergence of the results with respect to the algorithmic parameters, focussing on the dynamical phase transition between homogeneous and inhomogeneous states, where convergence is relatively difficult to achieve. We discuss how the performance of the algorithm can be optimised, and how it can be efficiently exploited on parallel computing platforms.

  11. Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses

    Directory of Open Access Journals (Sweden)

    Marilyn J. Roossinck

    2011-01-01

    Full Text Available Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., symbiogenesis have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics.

  12. Bacterial enteropathogens associated with diarrhea in a rural population of Haiti

    Directory of Open Access Journals (Sweden)

    Jackson JC

    2011-09-01

    Full Text Available John C Jackson, Anthony L Farone, Mary B Farone Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA Purpose: Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Patients and methods: Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBLTM Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBLTM CrystalTM Enteric/Nonferementing Identification system (Becton, Dickinson and Company. Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR. Results: Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. Conclusion: This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified. Keywords: Escherichia, Cronobacter, diarrheagenic, stool

  13. Effect of Soil Tillage Practices on Dynamic of Bacterial Communities in Soil

    OpenAIRE

    Mirna Mrkonjić Fuka; Mihaela Blažinkov; Viviane Radl; Danijel Jug; Nataša Hulak; Sulejman Redžepović; Michael Schloter

    2016-01-01

    Several studies have indicated that intensive tillage has notable effect on properties of the soil microbiota that may influence numerous important soils functions, e.g. mobilization of nutrients or change of the overall emission rates of greenhouse gases. Therefore, the aim of our study was to investigate dynamic of microbial communities in soil planted with soybean under different tillage systems. Moreover, abundance of populations harboring the nitrous- oxide reductase gene (nosZ) a...

  14. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

    KAUST Repository

    Bagchi, Samik; Garcia Tellez, Berenice; Rao, Hari Ananda; Lamendella, Regina; Saikaly, Pascal

    2014-01-01

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different

  15. Dynamics of a population of oscillatory and excitable elements.

    Science.gov (United States)

    O'Keeffe, Kevin P; Strogatz, Steven H

    2016-06-01

    We analyze a variant of a model proposed by Kuramoto, Shinomoto, and Sakaguchi for a large population of coupled oscillatory and excitable elements. Using the Ott-Antonsen ansatz, we reduce the behavior of the population to a two-dimensional dynamical system with three parameters. We present the stability diagram and calculate several of its bifurcation curves analytically, for both excitatory and inhibitory coupling. Our main result is that when the coupling function is broad, the system can display bistability between steady states of constant high and low activity, whereas when the coupling function is narrow and inhibitory, one of the states in the bistable regime can show persistent pulsations in activity.

  16. Structured population dynamics: continuous size and discontinuous stage structures.

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  17. Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico.

    Science.gov (United States)

    Liu, Jiqing; Bacosa, Hernando P; Liu, Zhanfei

    2016-01-01

    Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas , Sulfitobacter , and Reinekea , while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas , Oleibacter , and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus , while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas . Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water

  18. Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein.

    Directory of Open Access Journals (Sweden)

    Anthony J Brzoska

    Full Text Available Actin-like proteins (Alps are a diverse family of proteins whose genes are abundant in the chromosomes and mobile genetic elements of many bacteria. The low-copy-number staphylococcal multiresistance plasmid pSK41 encodes ParM, an Alp involved in efficient plasmid partitioning. pSK41 ParM has previously been shown to form filaments in vitro that are structurally dissimilar to those formed by other bacterial Alps. The mechanistic implications of these differences are not known. In order to gain insights into the properties and behavior of the pSK41 ParM Alp in vivo, we reconstituted the parMRC system in the ectopic rod-shaped host, E. coli, which is larger and more genetically amenable than the native host, Staphylococcus aureus. Fluorescence microscopy showed a functional fusion protein, ParM-YFP, formed straight filaments in vivo when expressed in isolation. Strikingly, however, in the presence of ParR and parC, ParM-YFP adopted a dramatically different structure, instead forming axial curved filaments. Time-lapse imaging and selective photobleaching experiments revealed that, in the presence of all components of the parMRC system, ParM-YFP filaments were dynamic in nature. Finally, molecular dissection of the parMRC operon revealed that all components of the system are essential for the generation of dynamic filaments.

  19. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants

    NARCIS (Netherlands)

    Araujo, W.L.; Marcon, J.; jr. Maccheroni, W.; Elsas, van J.D.; Vuurde, van J.W.L.; Azevedo, de J.L.

    2002-01-01

    Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as

  20. Biology as population dynamics: heuristics for transmission risk.

    Science.gov (United States)

    Keebler, Daniel; Walwyn, David; Welte, Alex

    2013-02-01

    Population-type models, accounting for phenomena such as population lifetimes, mixing patterns, recruitment patterns, genetic evolution and environmental conditions, can be usefully applied to the biology of HIV infection and viral replication. A simple dynamic model can explore the effect of a vaccine-like stimulus on the mortality and infectiousness, which formally looks like fertility, of invading virions; the mortality of freshly infected cells; and the availability of target cells, all of which impact on the probability of infection. Variations on this model could capture the importance of the timing and duration of different key events in viral transmission, and hence be applied to questions of mucosal immunology. The dynamical insights and assumptions of such models are compatible with the continuum of between- and within-individual risks in sexual violence and may be helpful in making sense of the sparse data available on the association between HIV transmission and sexual violence. © 2012 John Wiley & Sons A/S.

  1. Effect of temperature on the population dynamics of Aedes aegypti

    Science.gov (United States)

    Yusoff, Nuraini; Tokachil, Mohd Najir

    2015-10-01

    Aedes aegypti is one of the main vectors in the transmission of dengue fever. Its abundance may cause the spread of the disease to be more intense. In the study of its biological life cycle, temperature was found to increase the development rate of each stage of this species and thus, accelerate the process of the development from egg to adult. In this paper, a Lefkovitch matrix model will be used to study the stage-structured population dynamics of Aedes aegypti. In constructing the transition matrix, temperature will be taken into account. As a case study, temperature recorded at the Subang Meteorological Station for year 2006 until 2010 will be used. Population dynamics of Aedes aegypti at maximum, average and minimum temperature for each year will be simulated and compared. It is expected that the higher the temperature, the faster the mosquito will breed. The result will be compared to the number of dengue fever incidences to see their relationship.

  2. Interacting trophic forcing and the population dynamics of herring

    DEFF Research Database (Denmark)

    Lindegren, Martin; Ostman, Orjan; Gardmark, Anna

    2011-01-01

    -up nor top-down, but rather through multiple external and internal drivers. While in many studies single drivers have been identified, potential synergies of multiple factors, as well as their relative importance in regulating population dynamics of small pelagic fish, is a largely unresolved issue....... Using a statistical, age-structured modeling approach, we demonstrate the relative importance and influence of bottom-up (e.g., climate, zooplankton availability) and top-down (i.e., fishing and predation) factors on the population dynamics of Bothnian Sea herring (Clupea harengus) throughout its life...... cycle. Our results indicate significant bottom-up effects of zooplankton and interspecific competition from sprat (Sprattus sprattus), particularly on younger age classes of herring. Although top-down forcing through fishing and predation by grey seals (Halichoerus grypus) and Atlantic cod (Gadus morhua...

  3. Integrating population dynamics into mapping human exposure to seismic hazard

    Directory of Open Access Journals (Sweden)

    S. Freire

    2012-11-01

    Full Text Available Disaster risk is not fully characterized without taking into account vulnerability and population exposure. Assessment of earthquake risk in urban areas would benefit from considering the variation of population distribution at more detailed spatial and temporal scales, and from a more explicit integration of this improved demographic data with existing seismic hazard maps. In the present work, "intelligent" dasymetric mapping is used to model population dynamics at high spatial resolution in order to benefit the analysis of spatio-temporal exposure to earthquake hazard in a metropolitan area. These night- and daytime-specific population densities are then classified and combined with seismic intensity levels to derive new spatially-explicit four-class-composite maps of human exposure. The presented approach enables a more thorough assessment of population exposure to earthquake hazard. Results show that there are significantly more people potentially at risk in the daytime period, demonstrating the shifting nature of population exposure in the daily cycle and the need to move beyond conventional residence-based demographic data sources to improve risk analyses. The proposed fine-scale maps of human exposure to seismic intensity are mainly aimed at benefiting visualization and communication of earthquake risk, but can be valuable in all phases of the disaster management process where knowledge of population densities is relevant for decision-making.

  4. Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Anil, A.C.; Naik, S.D.; Gaonkar, C.C.

    and an assessment of the health of such an ecosystem benefits from high resolution observations. Virulent pathogenic Vibrio species are expected more frequently in tropical marine environments, since the virulence gene expression seems to increase at elevated... cells ml−1 (July 2009) to 5.9 x 107 cells ml−1 (February 2011) (Fig. 2b). Inter annual variations point out that the total bacterial abundance increased 5 from 2009 to 2011, while the viable bacterial numbers decreased. Complex physical, chemical...

  5. Structure and Origin of Xanthomonas arboricola pv. pruni Populations Causing Bacterial Spot of Stone Fruit Trees in Western Europe.

    Science.gov (United States)

    Boudon, Sylvain; Manceau, Charles; Nottéghem, Jean-Loup

    2005-09-01

    ABSTRACT Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, was found in 1995 in several orchards in southeastern France. We studied population genetics of this emerging pathogen in comparison with populations from the United States, where the disease was first described, and from Italy, where the disease has occurred since 1920. Four housekeeping genes (atpD, dnaK, efp, and glnA) and the intergenic transcribed spacer region were sequenced from a total of 3.9 kb of sequences, and fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed. A collection of 64 X. arboricola pv. pruni strains, including 23 strains from France, was analyzed. The X. arboricola pv. pruni population had a low diversity because no sequence polymorphisms were observed. Population diversity revealed by FAFLP was lower for the West European population than for the American population. The same bacterial genotype was detected from five countries on three continents, a geographic distribution that can be explained by human-aided migration of bacteria. Our data support the hypothesis that the pathogen originated in the United States and subsequently has been disseminated to other stone-fruit-growing regions of the world. In France, emergence of this disease was due to a recent introduction of the most prevalent genotype of the bacterium found worldwide.

  6. Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population.

    Science.gov (United States)

    Villette, P; Afonso, E; Couval, G; Levret, A; Galan, M; Tatard, C; Cosson, J F; Giraudoux, P

    2017-10-01

    High-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial richness for each organ ranged from 1·5 ± 0·4 (mean ± standard error) to 2·5 ± 0·4 bacteria/organ and did not differ significantly between organs. The average bacterial richness when organ assemblages were pooled within animals was 4·7 ± 0·6 bacteria/animal; Operational Taxonomic Unit accumulation analysis indicates that all five organs are required to obtain this. Organ type influences bacterial assemblage composition in a systematic way (PERMANOVA, 999 permutations, pseudo-F 4,51 = 1·37, P = 0·001). Our results demonstrate that the number of organs sampled influences the ability to detect bacterial pathogens, which can inform sampling decisions in public health and wildlife ecology.

  7. Bacterial meningitis in diabetes patients: a population-based prospective study

    Science.gov (United States)

    van Veen, Kiril E. B.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    Diabetes mellitus is associated with increased infection rates. We studied clinical features and outcome of community-acquired bacterial meningitis in diabetes patients. Patients were selected from a nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. A total of 183 of 1447 episodes (13%) occurred in diabetes patients. The incidence of bacterial meningitis in diabetes patients was 3.15 per 100,000 patients per year and the risk of acquiring bacterial meningitis was 2.2-fold higher for diabetes patients. S. pneumoniae was the causative organism in 139 of 183 episodes (76%) and L. monocytogenes in 11 of 183 episodes (6%). Outcome was unfavourable in 82 of 183 episodes (45%) and in 43 of 183 episodes (23%) the patient died. Diabetes was associated with death with an odds ratio of 1.63 (95% CI 1.12–2.37, P = 0.011), which remained after adjusting for known predictors of death in a multivariable analysis (OR 1.98 [95% CI 1.13–3.48], P = 0.017). In conclusion, diabetes is associated with a 2-fold higher risk of acquiring bacterial meningitis. Diabetes is a strong independent risk factor for death in community-acquired adult bacterial meningitis. PMID:27845429

  8. [Population dynamics of oligosporous actinomycetes in Chernozem soil].

    Science.gov (United States)

    Zenova, G M; Mikhaĭlova, N V; Zviagintsev, D G

    2000-01-01

    Investigation of the dynamics of an oligosporous actinomycete population in chernozem soil in the course of succession induced by soil wetting allowed us to reveal the time intervals and conditions optimal for the isolation of particular oligosporous actinomycetes. Saccharopolysporas and microbisporas proved to be best isolated in the early and late stages of succession, whereas actinomycetes of the subgroup Actinomadura and saccharomonosporas could be best isolated in the early and intermediate stages of succession.

  9. Scaling up population dynamic processes in a ladybird–aphid

    Czech Academy of Sciences Publication Activity Database

    Houdková, Kateřina; Kindlmann, Pavel

    2006-01-01

    Roč. 48, - (2006), s. 323-332 ISSN 1438-3896 R&D Projects: GA ČR(CZ) GEDIV/06/E013; GA MŠk(CZ) LC06073; GA AV ČR(CZ) IAA6087301; GA ČR(CZ) GD206/03/H034 Keywords : Aphids * Egg window * Ladybirds * Metapopulation * Model * Population dynamics Subject RIV: EH - Ecology, Behaviour Impact factor: 1.534, year: 2006

  10. Learning to Estimate Dynamical State with Probabilistic Population Codes.

    Directory of Open Access Journals (Sweden)

    Joseph G Makin

    2015-11-01

    Full Text Available Tracking moving objects, including one's own body, is a fundamental ability of higher organisms, playing a central role in many perceptual and motor tasks. While it is unknown how the brain learns to follow and predict the dynamics of objects, it is known that this process of state estimation can be learned purely from the statistics of noisy observations. When the dynamics are simply linear with additive Gaussian noise, the optimal solution is the well known Kalman filter (KF, the parameters of which can be learned via latent-variable density estimation (the EM algorithm. The brain does not, however, directly manipulate matrices and vectors, but instead appears to represent probability distributions with the firing rates of population of neurons, "probabilistic population codes." We show that a recurrent neural network-a modified form of an exponential family harmonium (EFH-that takes a linear probabilistic population code as input can learn, without supervision, to estimate the state of a linear dynamical system. After observing a series of population responses (spike counts to the position of a moving object, the network learns to represent the velocity of the object and forms nearly optimal predictions about the position at the next time-step. This result builds on our previous work showing that a similar network can learn to perform multisensory integration and coordinate transformations for static stimuli. The receptive fields of the trained network also make qualitative predictions about the developing and learning brain: tuning gradually emerges for higher-order dynamical states not explicitly present in the inputs, appearing as delayed tuning for the lower-order states.

  11. DMPD: Cellular reprogramming by gram-positive bacterial components: a review. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16885502 Cellular reprogramming by gram-positive bacterial components: a review. Bu...(.csml) Show Cellular reprogramming by gram-positive bacterial components: a review. PubmedID 16885502 Title... Cellular reprogramming by gram-positive bacterial components: a review. Authors

  12. DMPD: Role of Nods in bacterial infection. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17379560 Role of Nods in bacterial infection. Bourhis LL, Werts C. Microbes Infect.... 2007 Apr;9(5):629-36. Epub 2007 Jan 27. (.png) (.svg) (.html) (.csml) Show Role of Nods in bacterial infect...ion. PubmedID 17379560 Title Role of Nods in bacterial infection. Authors Bourhis LL, Werts C. Publication M

  13. Building the bridge between animal movement and population dynamics.

    Science.gov (United States)

    Morales, Juan M; Moorcroft, Paul R; Matthiopoulos, Jason; Frair, Jacqueline L; Kie, John G; Powell, Roger A; Merrill, Evelyn H; Haydon, Daniel T

    2010-07-27

    While the mechanistic links between animal movement and population dynamics are ecologically obvious, it is much less clear when knowledge of animal movement is a prerequisite for understanding and predicting population dynamics. GPS and other technologies enable detailed tracking of animal location concurrently with acquisition of landscape data and information on individual physiology. These tools can be used to refine our understanding of the mechanistic links between behaviour and individual condition through 'spatially informed' movement models where time allocation to different behaviours affects individual survival and reproduction. For some species, socially informed models that address the movements and average fitness of differently sized groups and how they are affected by fission-fusion processes at relevant temporal scales are required. Furthermore, as most animals revisit some places and avoid others based on their previous experiences, we foresee the incorporation of long-term memory and intention in movement models. The way animals move has important consequences for the degree of mixing that we expect to find both within a population and between individuals of different species. The mixing rate dictates the level of detail required by models to capture the influence of heterogeneity and the dynamics of intra- and interspecific interaction.

  14. Border Collision Bifurcations in a Generalized Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Lilia M. Ladino

    2016-01-01

    Full Text Available We analyze the dynamics of a generalized discrete time population model of a two-stage species with recruitment and capture. This generalization, which is inspired by other approaches and real data that one can find in literature, consists in considering no restriction for the value of the two key parameters appearing in the model, that is, the natural death rate and the mortality rate due to fishing activity. In the more general case the feasibility of the system has been preserved by posing opportune formulas for the piecewise map defining the model. The resulting two-dimensional nonlinear map is not smooth, though continuous, as its definition changes as any border is crossed in the phase plane. Hence, techniques from the mathematical theory of piecewise smooth dynamical systems must be applied to show that, due to the existence of borders, abrupt changes in the dynamic behavior of population sizes and multistability emerge. The main novelty of the present contribution with respect to the previous ones is that, while using real data, richer dynamics are produced, such as fluctuations and multistability. Such new evidences are of great interest in biology since new strategies to preserve the survival of the species can be suggested.

  15. Numerical modeling of the dynamic response of a bioluminescent bacterial biosensor.

    Science.gov (United States)

    Affi, Mahmoud; Solliec, Camille; Legentilhomme, Patrick; Comiti, Jacques; Legrand, Jack; Jouanneau, Sulivan; Thouand, Gérald

    2016-12-01

    Water quality and water management are worldwide issues. The analysis of pollutants and in particular, heavy metals, is generally conducted by sensitive but expensive physicochemical methods. Other alternative methods of analysis, such as microbial biosensors, have been developed for their potential simplicity and expected moderate cost. Using a biosensor for a long time generates many changes in the growth of the immobilized bacteria and consequently alters the robustness of the detection. This work simulated the operation of a biosensor for the long-term detection of cadmium and improved our understanding of the bioluminescence reaction dynamics of bioreporter bacteria inside an agarose matrix. The choice of the numerical tools is justified by the difficulty to measure experimentally in every condition the biosensor functioning during a long time (several days). The numerical simulation of a biomass profile is made by coupling the diffusion equation and the consumption/reaction of the nutrients by the bacteria. The numerical results show very good agreement with the experimental profiles. The growth model verified that the bacterial growth is conditioned by both the diffusion and the consumption of the nutrients. Thus, there is a high bacterial density in the first millimeter of the immobilization matrix. The growth model has been very useful for the development of the bioluminescence model inside the gel and shows that a concentration of oxygen greater than or equal to 22 % of saturation is required to maintain a significant level of bioluminescence. A continuous feeding of nutrients during the process of detection of cadmium leads to a biofilm which reduces the diffusion of nutrients and restricts the presence of oxygen from the first layer of the agarose (1 mm) and affects the intensity of the bioluminescent reaction. The main advantage of this work is to link experimental works with numerical models of growth and bioluminescence in order to provide a

  16. Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

    Science.gov (United States)

    Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

    2015-08-01

    Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

  17. A bacterial population analysis of granular sludge from an anaerobic digester treating a maize-processing waste

    Energy Technology Data Exchange (ETDEWEB)

    Howgrave-Graham, A.R.; Wallis, F.M. (Natal Univ., Pietermaritzburg (ZA). Dept. of Microbiology and Plant Pathology); Steyn, P.L. (Pretoria Univ. (South Africa))

    1991-01-01

    Microbial population studies were conducted on a dense granular sludge, with excellent settling, thickening and nutrient removal properties, from a South African clarigester treating effluent from a factory producing glucose and other carbohydrates from maize. The bacterial population comprised a heterogeneous group including acetogens, enterobacteria, sulphate-reducers, spirochaetes, heterofermentative lactobacilli and methanogens. The presence of these bacteria and lack of propionic acid and butyric acid bacteria suggests that the microbial activity of this anaerobic digester involved acetate and lactate metabolism rather than propionate or butyrate catabolism as a source of precursors for methane production. (author).

  18. Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

    Science.gov (United States)

    Yurk, Brian P; Cobbold, Christina A

    2018-12-01

    An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

  19. Drivers of waterfowl population dynamics: from teal to swans

    Science.gov (United States)

    Koons, David N.; Gunnarsson, Gunnar; Schmutz, Joel A.; Rotella, Jay J.

    2014-01-01

    Waterfowl are among the best studied and most extensively monitored species in the world. Given their global importance for sport and subsistence hunting, viewing and ecosystem functioning, great effort has been devoted since the middle part of the 20th century to understanding both the environmental and demographic mechanisms that influence waterfowl population and community dynamics. Here we use comparative approaches to summarise and contrast our understanding ofwaterfowl population dynamics across species as short-lived as the teal Anas discors and A.crecca to those such as the swans Cygnus sp. which have long life-spans. Specifically, we focus on population responses to vital rate perturbations across life history strategies, discuss bottom-up and top-down responses of waterfowlpopulations to global change, and summarise our current understanding of density dependence across waterfowl species. We close by identifying research needs and highlight ways to overcome the challenges of sustainably managing waterfowl populations in the 21st century.

  20. On the population dynamics of the malaria vector

    International Nuclear Information System (INIS)

    Ngwa, G.A.

    2005-10-01

    A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can establish itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing. (author)

  1. Linking animal population dynamics to alterations in foraging behaviour

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Sibly, Richard; Tougaard, Jakob

    Background/Question/Methods The survival of animal populations is strongly influenced by the individuals’ ability to forage efficiently, yet there are few studies of how populations respond when disturbances cause animals to deviate from their natural foraging behavior. Animals that respond...... that are increasingly exposed to noise from ships, wind turbines, etc. In the present study we investigate how the dynamics of the harbor porpoise population (Phocoena phocoena) in the inner Danish waters is influenced by disturbances using an agent- based simulation model. In the model animal movement, and hence...... the animals’ ability to forage efficiently and to sustain their energy intake, is influenced by noise emitted from wind turbines and ships. The energy levels in turn affect their survival. The fine-scale movements of the simulated animals was governed by a spatial memory, which allowed the model to produce...

  2. Studies on population dynamic of diamondback moth in the field

    International Nuclear Information System (INIS)

    Malakrong, A.; Limohpasmanee, W.; Keawchoung, P.; Kodcharint, P.

    1994-01-01

    The population dynamic of diamondback moth larva in the field was studied at Khao Khor High-land Agricultural Research Station during August-October 1993 and February-April 1994. The distribution patterns of diamondback moth larva was clumped when population was low and would change to be random when population was high. The maximun and minimum number of diamondback moth in the field were 71,203 and 2,732 larva/rai during March and September. Temperature, rainfall and age of cabbage were slightly relative with number of larva (r=-0.2891, p=0.30; r=-0.2816, p=0.31 and r=0.2931, p=0.29 respectively) but relative humidity has no effect on number of larva

  3. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

    KAUST Repository

    Bagchi, Samik

    2014-10-19

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different solids retention time (SRT). Rank-abundance curves showed few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2 vs. 10 days) on Shannon diversity index and OTU richness of both dominant and rare taxa. Nonmetric multidimensional scaling analysis showed that the total, dominant, and rare bacterial taxa were highly dynamic during the entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media.

  4. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities.

    Science.gov (United States)

    Martínez, M E; Ranilla, M J; Tejido, M L; Saro, C; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis

  5. Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory.

    Science.gov (United States)

    Medina, R F; Nachappa, P; Tamborindeguy, C

    2011-04-01

    Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  6. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    Science.gov (United States)

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

    2016-01-01

    Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down

  7. Population Dynamics of Early Human Migration in Britain.

    Directory of Open Access Journals (Sweden)

    Mayank N Vahia

    Full Text Available Early human migration is largely determined by geography and human needs. These are both deterministic parameters when small populations move into unoccupied areas where conflicts and large group dynamics are not important. The early period of human migration into the British Isles provides such a laboratory which, because of its relative geographical isolation, may allow some insights into the complex dynamics of early human migration and interaction.We developed a simulation code based on human affinity to habitable land, as defined by availability of water sources, altitude, and flatness of land, in choosing the path of migration. Movement of people on the British island over the prehistoric period from their initial entry points was simulated on the basis of data from the megalithic period. Topographical and hydro-shed data from satellite databases was used to define habitability, based on distance from water bodies, flatness of the terrain, and altitude above sea level. We simulated population movement based on assumptions of affinity for more habitable places, with the rate of movement tempered by existing populations. We compared results of our computer simulations with genetic data and show that our simulation can predict fairly accurately the points of contacts between different migratory paths. Such comparison also provides more detailed information about the path of peoples' movement over ~2000 years before the present era.We demonstrate an accurate method to simulate prehistoric movements of people based upon current topographical satellite data. Our findings are validated by recently-available genetic data. Our method may prove useful in determining early human population dynamics even when no genetic information is available.

  8. Environmental influence on population dynamics of the bivalve Anomalocardia brasiliana

    Science.gov (United States)

    Corte, Guilherme Nascimento; Coleman, Ross A.; Amaral, A. Cecília Z.

    2017-03-01

    Understanding how species respond to the environment in terms of population attributes (e.g. abundance, growth, mortality, fecundity, and productivity) is essential to protect ecologically and economically important species. Nevertheless, responses of macrobenthic populations to environmental features are overlooked due to the need of consecutive samplings and time-consuming measurements. We examined the population dynamics of the filter-feeding bivalve Anomalocardia brasiliana on a tidal flat over the course of one year to investigate the hypothesis that, as accepted for macrobenthic communities, populations inhabiting environments with low hydrodynamic conditions such as tidal flat should have higher attributes than populations inhabiting more energetic habitats (i.e. areas more influenced by wave energy such as reflective and intermediate beaches). This would be expected because the harsh conditions of more energetic habitats force organisms to divert more energy towards maintenance, resulting in lower population attributes. We found that A. brasiliana showed moderate growth and secondary production at the study area. Moreover the recruitment period was restricted to a few months. A comparison with previous studies showed that, contrary to expected, A. brasiliana populations from areas with low hydrodynamic conditions have lower abundance, growth, recruitment and turnover rate. It is likely that morphodynamic characteristics recorded in these environments, such as larger periods of air exposure and lower water circulation, may affect food conditions for filter-feeding species and increase competition. In addition, these characteristics may negatively affect macrobenthic species by enhancing eutrophication processes and anoxia. Overall, our results suggest that models accepted and applied at the macrobenthic community level might not be directly extended to A. brasiliana populations.

  9. An individual-based approach to explain plasmid invasion in bacterial populations

    DEFF Research Database (Denmark)

    Seoane, Jose Miguel; Yankelevich, Tatiana; Dechesne, Arnaud

    2011-01-01

    We present an individual-based experimental framework to identify and estimate the main parameters governing bacterial conjugation at the individual cell scale. From this analysis, we have established that transient periods of unregulated plasmid transfer within newly formed transconjugant cells...... of the growth cycle and that nongrowing cells, even when exposed to high nutrient concentrations, do not display conjugal activity. These results do not support previous hypotheses relating conjugation decay in the deeper cell layers of bacterial biofilms to nutrient depletion and low physiological activity. We...

  10. Alternating event processes during lifetimes: population dynamics and statistical inference.

    Science.gov (United States)

    Shinohara, Russell T; Sun, Yifei; Wang, Mei-Cheng

    2018-01-01

    In the literature studying recurrent event data, a large amount of work has been focused on univariate recurrent event processes where the occurrence of each event is treated as a single point in time. There are many applications, however, in which univariate recurrent events are insufficient to characterize the feature of the process because patients experience nontrivial durations associated with each event. This results in an alternating event process where the disease status of a patient alternates between exacerbations and remissions. In this paper, we consider the dynamics of a chronic disease and its associated exacerbation-remission process over two time scales: calendar time and time-since-onset. In particular, over calendar time, we explore population dynamics and the relationship between incidence, prevalence and duration for such alternating event processes. We provide nonparametric estimation techniques for characteristic quantities of the process. In some settings, exacerbation processes are observed from an onset time until death; to account for the relationship between the survival and alternating event processes, nonparametric approaches are developed for estimating exacerbation process over lifetime. By understanding the population dynamics and within-process structure, the paper provide a new and general way to study alternating event processes.

  11. Stochastic population dynamics in spatially extended predator-prey systems

    Science.gov (United States)

    Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

    2018-02-01

    Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex

  12. Population Dynamics of the Mediterranean Fruit Fly in Montenegro

    Directory of Open Access Journals (Sweden)

    Sanja Radonjić

    2013-01-01

    Full Text Available Population dynamics of the Mediterranean fruit fly was studied along Montenegro seacoast. Tephri traps baited with 3 component female-biased attractants were used in 11 different localities to monitor the fruit fly population in commercial citrus orchards, mixed-fruit orchards, and in backyards. From 2008–2010, the earliest captures were recorded no earlier than July. In 2011, the first adult fly was detected in mid-June. Low captures rates were recorded in July and August (below 0.5 flies per trap per day; FTD and peaked from mid-September to the end of October of each year. Our results indicate fluctuation of fly per trap per day depending on dates of inspection and locality, with significant differences in the adult population density. A maximum population was always reached in the area of Budva-Herceg Novi with an FTD of 66.5, 89.5, 71.63, and 24.64 (from 2008–2011 respectively. Fly activity lasts from mid-June/early-July to end December, with distinct seasonal variation in the population.

  13. Population dynamics of Ascaris suum in trickle-infected pigs.

    Science.gov (United States)

    Nejsum, Peter; Thamsborg, Stig M; Petersen, Heidi H; Kringel, Helene; Fredholm, Merete; Roepstorff, Allan

    2009-10-01

    The population dynamics of Ascaris suum was studied by long-term exposure of pigs to infective eggs. The pigs were experimentally inoculated with 25 A. suum eggs/kg/day, and 7, 8, and 8 pigs were necropsied at weeks 4, 8, and 14 postinoculation (PI), respectively. Despite the fact that the pigs were continuously reinfected, dramatic reductions in numbers of liver lesions (white spots) and migrating lung larvae were observed as a function of time. However, even at the end of the study, a few larvae were able to complete migration, but these larvae seemed unable to mature in the small intestine. Thus, the adult worm population seemed to consist of worms from the first part of the exposure period. The noticeable decrease in number of white spots suggests that the level of exposure is not reflected in the number of white spots in the late phase of a continuous infection. The serum levels of A. suum L3-specific IgG1 and IgA were significantly elevated by week 4 PI, after which the antibody levels declined. The population dynamics and parasite regulating mechanisms are discussed for A. suum in pigs as well as for the closely related species A. lumbricoides in humans.

  14. Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

    Science.gov (United States)

    Cushing, J M; Henson, Shandelle M

    2018-02-03

    For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

  15. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

    Science.gov (United States)

    Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

    2005-04-15

    The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

  16. Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations

    OpenAIRE

    Hirunsalee, Anan; Barker, K. R.; Beute, M. K.

    1995-01-01

    A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduc...

  17. Effect of DNA extraction and sample preservation method on rumen bacterial population.

    Science.gov (United States)

    Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopečný, Jan; Shingfield, Kevin J; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R John

    2014-10-01

    The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms

    OpenAIRE

    Lydon, Keri Ann; Glinski, Donna A.; Westrich, Jason R.; Henderson, W. Matthew; Lipp, Erin K.

    2017-01-01

    Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, 'Vibrio', a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrat...

  19. Exploiting Fast-Variables to Understand Population Dynamics and Evolution

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-11-01

    We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

  20. Cooperation guided by the coexistence of imitation dynamics and aspiration dynamics in structured populations

    Science.gov (United States)

    Xu, Kuangyi; Li, Kun; Cong, Rui; Wang, Long

    2017-02-01

    In the framework of the evolutionary game theory, two fundamentally different mechanisms, the imitation process and the aspiration-driven dynamics, can be adopted by players to update their strategies. In the former case, individuals imitate the strategy of a more successful peer, while in the latter case individuals change their strategies based on a comparison of payoffs they collect in the game to their own aspiration levels. Here we explore how cooperation evolves for the coexistence of these two dynamics. Intriguingly, cooperation reaches its lowest level when a certain moderate fraction of individuals pick aspiration-level-driven rule while the others choose pairwise comparison rule. Furthermore, when individuals can adjust their update rules besides their strategies, either imitation dynamics or aspiration-driven dynamics will finally take over the entire population, and the stationary cooperation level is determined by the outcome of competition between these two dynamics. We find that appropriate synergetic effects and moderate aspiration level boost the fixation probability of aspiration-driven dynamics most effectively. Our work may be helpful in understanding the cooperative behavior induced by the coexistence of imitation dynamics and aspiration dynamics in the society.

  1. Dynamic population gratings in rare-earth-doped optical fibres

    Energy Technology Data Exchange (ETDEWEB)

    Stepanov, Serguei [Optics Department, CICESE, km.107 carr. Tijuana-Ensenada, Ensenada, 22860, BC (Mexico)], E-mail: steps@cicese.mx

    2008-11-21

    Dynamic Bragg gratings can be recorded in rare-earth (e.g. Er, Yb) doped optical fibres by two counter-propagating mutually coherent laser waves via local saturation of the fibre optical absorption or gain (in optically pumped fibres). Typical recording cw light power needed for efficient grating formation is of sub-mW-mW scale which results in characteristic recording/erasure times of 10-0.1 ms. This review paper discusses fundamental aspects of the population grating formation, their basic properties, relating wave-mixing processes and also considers different applications of these dynamic gratings in single-frequency fibre lasers, tunable filters, optical fibre sensors and adaptive interferometry.

  2. Dynamic population gratings in rare-earth-doped optical fibres

    International Nuclear Information System (INIS)

    Stepanov, Serguei

    2008-01-01

    Dynamic Bragg gratings can be recorded in rare-earth (e.g. Er, Yb) doped optical fibres by two counter-propagating mutually coherent laser waves via local saturation of the fibre optical absorption or gain (in optically pumped fibres). Typical recording cw light power needed for efficient grating formation is of sub-mW-mW scale which results in characteristic recording/erasure times of 10-0.1 ms. This review paper discusses fundamental aspects of the population grating formation, their basic properties, relating wave-mixing processes and also considers different applications of these dynamic gratings in single-frequency fibre lasers, tunable filters, optical fibre sensors and adaptive interferometry.

  3. In vitro bacterial growth and in vivo ruminal microbiota populations associated with bloat in steers grazing wheat forage.

    Science.gov (United States)

    Min, B R; Pinchak, W E; Anderson, R C; Hume, M E

    2006-10-01

    The role of ruminal bacteria in the frothy bloat complex common to cattle grazing winter wheat has not been previously determined. Two experiments, one in vitro and another in vivo, were designed to elucidate the effects of fresh wheat forage on bacterial growth, biofilm complexes, rumen fermentation end products, rumen bacterial diversity, and bloat potential. In Exp. 1, 6 strains of ruminal bacteria (Streptococcus bovis strain 26, Prevotella ruminicola strain 23, Eubacterium ruminantium B1C23, Ruminococcus albus SY3, Fibrobacter succinogenes ssp. S85, and Ruminococcus flavefaciens C94) were used in vitro to determine the effect of soluble plant protein from winter wheat forage on specific bacterial growth rate, biofilm complexes, VFA, and ruminal H2 and CH4 in mono or coculture with Methanobrevibacter smithii. The specific growth rate in plant protein medium containing soluble plant protein (3.27% nitrogen) was measured during a 24-h incubation at 39 degrees C in Hungate tubes under a CO2 gas phase. A monoculture of M. smithii was grown similarly, except under H2:CO2 (1:1), in a basal methanogen growth medium supplemented likewise with soluble plant protein. In Exp. 2, 6 ruminally cannulated steers grazing wheat forage were used to evaluate the influence of bloat on the production of biofilm complexes, ruminal microbial biodiversity patterns, and ruminal fluid protein fractions. In Exp. 1, cultures of R. albus (P bloated than for nonbloated steers when grazing wheat forage. The molecular analysis of the 16S rDNA showed that 2 different ruminal microbiota populations developed between bloated and nonbloated animals grazing wheat forage. Bloat in cattle grazing wheat pastures may be caused by increased production of biofilm, resulting from a diet-influenced switch in the rumen bacterial population.

  4. Population dynamics of minimally cognitive individuals. Part 2: Dynamics of time-dependent knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Schmieder, R.W.

    1995-07-01

    The dynamical principle for a population of interacting individuals with mutual pairwise knowledge, presented by the author in a previous paper for the case of constant knowledge, is extended to include the possibility that the knowledge is time-dependent. Several mechanisms are presented by which the mutual knowledge, represented by a matrix K, can be altered, leading to dynamical equations for K(t). The author presents various examples of the transient and long time asymptotic behavior of K(t) for populations of relatively isolated individuals interacting infrequently in local binary collisions. Among the effects observed in the numerical experiments are knowledge diffusion, learning transients, and fluctuating equilibria. This approach will be most appropriate to small populations of complex individuals such as simple animals, robots, computer networks, agent-mediated traffic, simple ecosystems, and games. Evidence of metastable states and intermittent switching leads them to envision a spectroscopy associated with such transitions that is independent of the specific physical individuals and the population. Such spectra may serve as good lumped descriptors of the collective emergent behavior of large classes of populations in which mutual knowledge is an important part of the dynamics.

  5. Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals.

    Science.gov (United States)

    Stirling, J; Griffith, M; Blair, I; Cormican, M; Dooley, J S G; Goldsmith, C E; Glover, S G; Loughrey, A; Lowery, C J; Matsuda, M; McClurg, R; McCorry, K; McDowell, D; McMahon, A; Cherie Millar, B; Nagano, Y; Rao, J R; Rooney, P J; Smyth, M; Snelling, W J; Xu, J; Moore, J E

    2008-04-01

    Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July-September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.

  6. Isolation, Characterization and Application of Bacterial Population From Agricultural Soil at Sohag Province, Egypt

    Directory of Open Access Journals (Sweden)

    Bahig, A. E.

    2008-01-01

    Full Text Available Forty soil samples of agriculture soil were collected from two different sites in Sohag province, Egypt, during hot and cold seasons. Twenty samples were from soil irrigated with canal water (site A and twenty samples were from soil irrigated with wastewater (site B. This study aimed to compare the incidence of plasmids in bacteria isolated from soil and to investigate the occurrence of metal and antibiotic resistance bacteria, and consequently to select the potential application of these bacteria in bioremediation. The total bacterial count (CFU/gm in site (B was higher than that in site (A. Moreover, the CFU values in summer were higher than those values in winter at both sites. A total of 771 bacterial isolates were characterized as Bacillus, Micrococcus, Staphylococcus, Pseudomonas, Eschershia, Shigella, Xanthomonas, Acetobacter, Citrobacter, Enterobacter, Moraxella and Methylococcus. Minimum inhibitory concentrations (MICs of Pb+2, Cu+2, Zn+2, Hg+2, Co+2, Cd+2, Cr+3, Te+2, As+2 and Ni+2 for plasmid-possessed bacteria were determined and the highest MICs were 1200 µg/mL for lead, 800 µg/mL for both Cobalt and Arsenate, 1200 µg/mL for Nickel, 1000 µg/ml for Copper and less than 600 µg/mL for other metals. Bacterial isolates from both sites A and B showed multiple heavy metal resistance. A total of 337 bacterial isolates contained plasmids and the incidence of plasmids was approximately 25-50% higher in bacteria isolated from site (B than that from site (A. These isolates were resistance to different antibiotics. Approximately, 61% of the bacterial isolates were able to assimilate insecticide, carbaryl, as a sole source of carbon and energy. However, the Citrobacter AA101 showed the best growth on carbaryl.

  7. Self-organization of bacterial communities against environmental pH variation: Controlled chemotactic motility arranges cell population structures in biofilms.

    Science.gov (United States)

    Tasaki, Sohei; Nakayama, Madoka; Shoji, Wataru

    2017-01-01

    As with many living organisms, bacteria often live on the surface of solids, such as foods, organisms, buildings and soil. Compared with dispersive behavior in liquid, bacteria on surface environment exhibit significantly restricted mobility. They have access to only limited resources and cannot be liberated from the changing environment. Accordingly, appropriate collective strategies are necessarily required for long-term growth and survival. However, in spite of our deepening knowledge of the structure and characteristics of individual cells, strategic self-organizing dynamics of their community is poorly understood and therefore not yet predictable. Here, we report a morphological change in Bacillus subtilis biofilms due to environmental pH variations, and present a mathematical model for the macroscopic spatio-temporal dynamics. We show that an environmental pH shift transforms colony morphology on hard agar media from notched 'volcano-like' to round and front-elevated 'crater-like'. We discover that a pH-dependent dose-response relationship between nutritional resource level and quantitative bacterial motility at the population level plays a central role in the mechanism of the spatio-temporal cell population structure design in biofilms.

  8. Do farming practices influence population dynamics of rodents?

    DEFF Research Database (Denmark)

    Massawe, A W; Rwamugira, W; Leirs, Herwig

    2007-01-01

    A capture-mark-recapture study was conducted in crop fields in Morogoro, Tanzania, to investigate how the population dynamics of multimammate field rats, Mastomys natalensis, was influenced by the commonly practised land preparation methods and cropping systems. Two land preparation methods (trac...... practices. In maize fields in Tanzania, the crop is most susceptible to damage by M. natalensis in the first 2 weeks after planting, and therefore, lower densities of rodents will result into lower crop damage in tractor ploughed fields....

  9. Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning.

    Science.gov (United States)

    Michaels, Jonathan A; Dann, Benjamin; Scherberger, Hansjörg

    2016-11-01

    Recent models of movement generation in motor cortex have sought to explain neural activity not as a function of movement parameters, known as representational models, but as a dynamical system acting at the level of the population. Despite evidence supporting this framework, the evaluation of representational models and their integration with dynamical systems is incomplete in the literature. Using a representational velocity-tuning based simulation of center-out reaching, we show that incorporating variable latency offsets between neural activity and kinematics is sufficient to generate rotational dynamics at the level of neural populations, a phenomenon observed in motor cortex. However, we developed a covariance-matched permutation test (CMPT) that reassigns neural data between task conditions independently for each neuron while maintaining overall neuron-to-neuron relationships, revealing that rotations based on the representational model did not uniquely depend on the underlying condition structure. In contrast, rotations based on either a dynamical model or motor cortex data depend on this relationship, providing evidence that the dynamical model more readily explains motor cortex activity. Importantly, implementing a recurrent neural network we demonstrate that both representational tuning properties and rotational dynamics emerge, providing evidence that a dynamical system can reproduce previous findings of representational tuning. Finally, using motor cortex data in combination with the CMPT, we show that results based on small numbers of neurons or conditions should be interpreted cautiously, potentially informing future experimental design. Together, our findings reinforce the view that representational models lack the explanatory power to describe complex aspects of single neuron and population level activity.

  10. Optimal growth entails risky localization in population dynamics

    Science.gov (United States)

    Gueudré, Thomas; Martin, David G.

    2018-03-01

    Essential to each other, growth and exploration are jointly observed in alive and inanimate entities, such as animals, cells or goods. But how the environment's structural and temporal properties weights in this balance remains elusive. We analyze a model of stochastic growth with time correlations and diffusive dynamics that sheds light on the way populations grow and spread over general networks. This model suggests natural explanations of empirical facts in econo-physics or ecology, such as the risk-return trade-off and the Zipf law. We conclude that optimal growth leads to a localized population distribution, but such risky position can be mitigated through the space geometry. These results have broad applicability and are subsequently illustrated over an empirical study of financial data.

  11. Fast stochastic algorithm for simulating evolutionary population dynamics

    Science.gov (United States)

    Tsimring, Lev; Hasty, Jeff; Mather, William

    2012-02-01

    Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

  12. Outward migration may alter population dynamics and income inequality

    Science.gov (United States)

    Shayegh, Soheil

    2017-11-01

    Climate change impacts may drive affected populations to migrate. However, migration decisions in response to climate change could have broader effects on population dynamics in affected regions. Here, I model the effect of climate change on fertility rates, income inequality, and human capital accumulation in developing countries, focusing on the instrumental role of migration as a key adaptation mechanism. In particular, I investigate how climate-induced migration in developing countries will affect those who do not migrate. I find that holding all else constant, climate change raises the return on acquiring skills, because skilled individuals have greater migration opportunities than unskilled individuals. In response to this change in incentives, parents may choose to invest more in education and have fewer children. This may ultimately reduce local income inequality, partially offsetting some of the damages of climate change for low-income individuals who do not migrate.

  13. State-dependent neutral delay equations from population dynamics.

    Science.gov (United States)

    Barbarossa, M V; Hadeler, K P; Kuttler, C

    2014-10-01

    A novel class of state-dependent delay equations is derived from the balance laws of age-structured population dynamics, assuming that birth rates and death rates, as functions of age, are piece-wise constant and that the length of the juvenile phase depends on the total adult population size. The resulting class of equations includes also neutral delay equations. All these equations are very different from the standard delay equations with state-dependent delay since the balance laws require non-linear correction factors. These equations can be written as systems for two variables consisting of an ordinary differential equation (ODE) and a generalized shift, a form suitable for numerical calculations. It is shown that the neutral equation (and the corresponding ODE--shift system) is a limiting case of a system of two standard delay equations.

  14. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

    Science.gov (United States)

    Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

    2018-02-18

    The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

  15. Bacterial and Archaeal Community Dynamics at CO2-RICH Shallow-Sea Hydrothermal Vents (panarea, Italy)

    Science.gov (United States)

    Schubotz, F.; Huang, C.; Meyerdierks, A.; Amend, J.; Price, R. E.; Amann, R.; Hinrichs, K.; Summons, R. E.

    2013-12-01

    Shallow marine hydrothermal vents are highly dynamic systems with unique habitats that can support both chemosynthetic and photosynthetic communities at steep temperature and geochemical gradients. Here, we present a combined organic geochemical and microbiological approach to describe the microbial community composition and their metabolism at the CO2-rich shallow hydrothermal vents off Panarea Island, in Sicily. We investigated two contrasting hydrothermal environments: Hot Lake, a depression filled with hydrothermal fluids diffusing gradually out of the seafloor, with temperatures ranging from 40 to 70°C, and Blackpoint, a site with vigorous venting of hydrothermal gasses and fluids with temperatures as high as 135°C. At Hot Lake, Bacteria dominate the microbial community composition in the sediments. 16S rRNA clone libraries revealed Bacteriodetes-, Epsilonproteobacteria- and Deltaproteobacteria-related sequences as the most abundant members. Bacterial intact polar membrane lipids (IPLs) were dominated by the non-phosphorous containing ornithine lipids throughout all depths, indicating an important role of this aminolipid at elevated temperatures and/or low pH. At Hot Lake, archaeal IPLs were comprised mainly of glycosidic tetraethers and increased up to 20% of total IPLs with increasing temperature and depth. At the same site, archaeal 16S rRNA clone libraries were mainly comprised of Euryarchaea-affiliated sequences; crenarchaeotal sequences were only found in deeper sediment layers with temperatures of ca. 70°C. In contrast to Hot Lake, Archaea dominated sediments at the much hotter site at Blackpoint. Here, novel methylated H-shaped archaeal tetraethers, with multiple sugars as head groups, were the most abundant membrane lipids. Reports on these lipids in cultures are very limited, but their abundant occurrence at elevated temperatures suggests an important role in membrane homeostastis in thermophilic Archaea. Stable carbon isotope values of -35‰ to

  16. A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python.

    Science.gov (United States)

    Hoeflinger, Jennifer L; Hoeflinger, Daniel E; Miller, Michael J

    2017-01-01

    Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. DMPD: Targeting bacterial endotoxin: two sides of a coin. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available n M. Ann N Y Acad Sci. 2007 Jan;1096:1-17. (.png) (.svg) (.html) (.csml) Show Targeting bacterial endotoxin: two sides of a coin. Pub...medID 17405910 Title Targeting bacterial endotoxin: two sides of a coin. Authors Bo

  18. Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations.

    Science.gov (United States)

    Hirunsalee, A; Barker, K R; Beute, M K

    1995-06-01

    A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduction, and root-damage potentials on susceptible tobacco were similar for Ma1 and Ma2. In the mixed (1:1) population, Ma1 was dominant on peanut and Ma2 was dominant on both tobacco cultivars. Crop rotation affected the population dynamics of different nematode races. For years 2 and 3, the low numbers of Ma1 and Ma2 from a previous-year poor host increased rapidly on suitable hosts. Ma1 had greater reproduction factors ([RF] = population density at harvest/population density at preplandng) than did Ma2 and Ma1 + Ma2 in second-year peanut plots following first-year resistant tobacco, and in third-year peanut plots following second-year tobacco. In mixed infestations, Ma1 predominated over Ma2 in previous-year peanut plots, whereas Ma2 predominated over Ma1 in previous-year tobacco plots. Moderate damage on resistant tobacco was induced by Ma1 in the second year. In the third year, moderate damage on peanut was associated with 'Ma2' from previous-year peanut plots. The resistant tobacco supported sufficient reproduction of Ma1 over 2 years to effect moderate damage and yield suppression to peanut in year 3.

  19. Application of System Dynamics Methodology in Population Analysis

    Directory of Open Access Journals (Sweden)

    August Turina

    2009-09-01

    Full Text Available The goal of this work is to present the application of system dynamics and system thinking, as well as the advantages and possible defects of this analytic approach, in order to improve the analysis of complex systems such as population and, thereby, to monitor more effectively the underlying causes of migrations. This methodology has long been present in interdisciplinary scientific circles, but its scientific contribution has not been sufficiently applied in analysis practice in Croatia. Namely, the major part of system analysis is focused on detailed complexity rather than on dynamic complexity. Generally, the science of complexity deals with emergence, innovation, learning and adaptation. Complexity is viewed according to the number of system components, or through a number of combinations that must be continually analyzed in order to understand and consequently provide adequate decisions. Simulations containing thousands of variables and complex arrays of details distract overall attention from the basic cause patterns and key inter-relations emerging and prevailing within an analyzed population. Systems thinking offers a holistic and integral perspective for observation of the world.

  20. Representation of dynamical stimuli in populations of threshold neurons.

    Directory of Open Access Journals (Sweden)

    Tatjana Tchumatchenko

    2011-10-01

    Full Text Available Many sensory or cognitive events are associated with dynamic current modulations in cortical neurons. This raises an urgent demand for tractable model approaches addressing the merits and limits of potential encoding strategies. Yet, current theoretical approaches addressing the response to mean- and variance-encoded stimuli rarely provide complete response functions for both modes of encoding in the presence of correlated noise. Here, we investigate the neuronal population response to dynamical modifications of the mean or variance of the synaptic bombardment using an alternative threshold model framework. In the variance and mean channel, we provide explicit expressions for the linear and non-linear frequency response functions in the presence of correlated noise and use them to derive population rate response to step-like stimuli. For mean-encoded signals, we find that the complete response function depends only on the temporal width of the input correlation function, but not on other functional specifics. Furthermore, we show that both mean- and variance-encoded signals can relay high-frequency inputs, and in both schemes step-like changes can be detected instantaneously. Finally, we obtain the pairwise spike correlation function and the spike triggered average from the linear mean-evoked response function. These results provide a maximally tractable limiting case that complements and extends previous results obtained in the integrate and fire framework.

  1. Population dynamics of Trichuris suis in trickle-infected pigs.

    Science.gov (United States)

    Nejsum, P; Thamsborg, S M; Petersen, H H; Kringel, H; Fredholm, M; Roepstorff, A

    2009-05-01

    The population dynamics of Trichuris suis in pigs was studied during long-term experimental infections. Twenty-three 10-week-old pigs were inoculated with 5 T. suis eggs/kg/day. Seven, 8, and 8 pigs were necropsied at weeks 4, 8, and 14 post-start of infection (p.i.), respectively. The median numbers of worms in the colon were 538 (min-max: 277-618), 332 (14-1140) and 0 (0-4) at 4, 8, and 14 weeks p.i. respectively, suggesting an increased aggregation of the worms with time and acquisition of nearly sterile immunity. The serum levels of T. suis specific antibodies (IgG1, IgG2 and IgA) peaked at week 8 p.i. By week 14 p.i. the IgG2 and IgA antibody levels remained significantly elevated above the level of week 0. The population dynamics of T. suis trickle infections in pigs is discussed with focus on interpretation of diagnostic and epidemiological data of pigs, the use of pigs as a model for human Trichuris trichiura infections and the novel approach of using T. suis eggs in the treatment of patients with inflammatory bowel disease.

  2. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens.

    Science.gov (United States)

    Tako, Elad; Glahn, Raymond P; Knez, Marija; Stangoulis, James Cr

    2014-06-13

    Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. In this study we showed that prebiotics naturally found in wheat grains/bread products

  3. NMR relaxometric probing of ionic liquid dynamics and diffusion under mesoscopic confinement within bacterial cellulose ionogels

    Science.gov (United States)

    Smith, Chip J.; Gehrke, Sascha; Hollóczki, Oldamur; Wagle, Durgesh V.; Heitz, Mark P.; Baker, Gary A.

    2018-05-01

    Bacterial cellulose ionogels (BCIGs) represent a new class of material comprising a significant content of entrapped ionic liquid (IL) within a porous network formed from crystalline cellulose microfibrils. BCIGs suggest unique opportunities in separations, optically active materials, solid electrolytes, and drug delivery due to the fact that they can contain as much as 99% of an IL phase by weight, coupled with an inherent flexibility, high optical transparency, and the ability to control ionogel cross-sectional shape and size. To allow for the tailoring of BCIGs for a multitude of applications, it is necessary to better understand the underlying principles of the mesoscopic confinement within these ionogels. Toward this, we present a study of the structural, relaxation, and diffusional properties of the ILs, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]) and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([bmpy][Tf2N]), using 1H and 19F NMR T1 relaxation times, rotational correlation times, and diffusion ordered spectroscopy (DOSY) diffusion coefficients, accompanied by molecular dynamics (MD) simulations. We observed that the cation methyl groups in both ILs were primary points of interaction with the cellulose chains and, while the pore size in cellulose is rather large, [emim]+ diffusion was slowed by ˜2-fold, whereas [Tf2N]- diffusion was unencumbered by incorporation in the ionogel. While MD simulations of [bmpy][Tf2N] confinement at the interface showed a diffusion coefficient decrease roughly 3-fold compared to the bulk liquid, DOSY measurements did not reveal any significant changes in diffusion. This suggests that the [bmpy][Tf2N] alkyl chains dominate diffusion through formation of apolar domains. This is in contrast to [emim][Tf2N] where delocalized charge appears to preclude apolar domain formation, allowing interfacial effects to be manifested at a longer range in [emim][Tf2N].

  4. Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS Metabarcoding during Flax Dew-Retting

    Directory of Open Access Journals (Sweden)

    Christophe Djemiel

    2017-10-01

    Full Text Available Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples. Dominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes (bacteria and Ascomycota, Basidiomycota, and Zygomycota (fungi all of which have been previously associated with flax dew-retting except for Bacteroidetes and Basidiomycota that were identified for the first time. Rare phyla also identified for the first time in this process included Acidobacteria, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes, Nitrospirae and TM6 (bacteria, and Chytridiomycota (fungi. No differences in microbial communities and colonization dynamics were observed between early and standard flax harvests. In contrast, the common agricultural practice of swath turning affects both bacterial and fungal community membership and structure in straw samples and may contribute to a more uniform retting. Prediction of community function using PICRUSt indicated the presence of a large collection of potential bacterial enzymes capable of hydrolyzing backbones and side-chains of cell wall polysaccharides. Assignment of functional guild (functional group using FUNGuild software highlighted a change from parasitic to saprophytic trophic modes in fungi during retting. This work provides the first exhaustive description of the microbial communities involved in flax dew-retting and will provide a valuable benchmark in future studies aiming

  5. Modeling population dynamics of mitochondria in mammalian cells

    Science.gov (United States)

    Kornick, Kellianne; Das, Moumita

    Mitochondria are organelles located inside eukaryotic cells and are essential for several key cellular processes such as energy (ATP) production, cell signaling, differentiation, and apoptosis. All organisms are believed to have low levels of variation in mitochondrial DNA (mtDNA), and alterations in mtDNA are connected to a range of human health conditions, including epilepsy, heart failure, Parkinsons disease, diabetes, and multiple sclerosis. Therefore, understanding how changes in mtDNA accumulate over time and are correlated to changes in mitochondrial function and cell properties can have a profound impact on our understanding of cell physiology and the origins of some diseases. Motivated by this, we develop and study a mathematical model to determine which cellular parameters have the largest impact on mtDNA population dynamics. The model consists of coupled ODEs to describe subpopulations of healthy and dysfunctional mitochondria subject to mitochondrial fission, fusion, autophagy, and mutation. We study the time evolution and stability of each sub-population under specific selection biases and pressures by tuning specific terms in our model. Our results may provide insights into how sub-populations of mitochondria survive and evolve under different selection pressures. This work was supported by a Grant from the Moore Foundation.

  6. Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste.

    Science.gov (United States)

    Estrada-Bonilla, German A; Lopes, Cintia M; Durrer, Ademir; Alves, Paulo R L; Passaglia, Nicolle; Cardoso, Elke J B N

    2017-07-01

    Sugarcane processing generates a large quantity of residues, such as filter cake and ashes, which are sometimes composted prior to their amendment in soil. However, important issues still have to be addressed on this subject, such as the description of bacterial succession that occurs throughout the composting process and the possibilities of using phosphate-solubilizing bacteria (PSB) during the process to improve phosphorus (P) availability in the compost end product. Consequently, this study evaluated the bacterial diversity and P dynamics during the composting process when inoculated with Pseudomonas aeruginosa PSBR12 and Bacillus sp. BACBR01. To characterize the bacterial community structure during composting, and to compare PSB-inoculated compost with non-inoculated compost, partial sequencing of the bacterial 16S rRNA gene and sequential P fractionation were used. The data indicated that members of the order Lactobacillales prevailed in the early stages of composting for up to 30 days, mostly due to initial changes in pH and the C/N ratio. This dominant bacterial group was then slowly replaced by Bacillales during a composting process of up to 60 days. In addition, inoculation of PSB reduced the levels of Ca-bound P by 21% and increased the labile organic P fraction. In PSB-inoculated compost, Ca-P compound solubilization occurred concomitantly with an increase of the genus Bacillus. The bacterial succession and the final community is described in compost from sugarcane residues and the possible use of these inoculants to improve P availability in the final compost is validated. Copyright © 2017 Elsevier GmbH. All rights reserved.

  7. Plasmodium vivax Population Structure and Transmission Dynamics in Sabah Malaysia

    Science.gov (United States)

    Abdullah, Noor Rain; Barber, Bridget E.; William, Timothy; Norahmad, Nor Azrina; Satsu, Umi Rubiah; Muniandy, Prem Kumar; Ismail, Zakiah; Grigg, Matthew J.; Jelip, Jenarun; Piera, Kim; von Seidlein, Lorenz; Yeo, Tsin W.; Anstey, Nicholas M.; Price, Ric N.; Auburn, Sarah

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A S >0.5 [P<0.0001] in KK and KM) declined sharply when identical haplotypes were represented once (I A S  = 0.07 [P = 0.0076] in KM, and I A S = -0.003 [P = 0.606] in KK). All 8 recurrences, likely to be relapses, were homologous to the prior infection. These recurrences may promote the persistence of parasite lineages, sustaining local diversity. In summary, Sabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria

  8. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    DEFF Research Database (Denmark)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino...... acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a 'last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm...

  9. Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils

    DEFF Research Database (Denmark)

    Vargas-Bello-Pérez, E.; Cancino-Padilla, N.; Romero, J.

    2016-01-01

    Vegetable oils are used to increase energy density of dairy cow diets, although they can provoke changes in rumen bacteria populations and have repercussions on the biohydrogenation process. The aim of this study was to evaluate the effect of two sources of dietary lipids: soybean oil (SO......, an unsaturated source) and hydrogenated palm oil (HPO, a saturated source) on bacterial populations and the fatty acid profile of ruminal digesta. Three non-lactating Holstein cows fitted with ruminal cannulae were used in a 3×3 Latin square design with three periods consisting of 21 days. Dietary treatments...... parameters, whereas HPO can increase load of ruminal P. bryantii. Also, results observed in our targeted bacteria may have depended on the saturation degree of dietary oils....

  10. Sampling bacterial biodiversity from a highly contaminated stream flowing through a densely populated urban area in Karachi

    International Nuclear Information System (INIS)

    Enam, S.F.; Qureshi, H.; Qureshi, S.A.

    2011-01-01

    Few studies have attempted to understand the complexity of microbial populations in Pakistan where infectious diseases are prevalent. This study was undertaken to assess bacterial biodiversity in Nehr-e-Khayyam a heavily polluted stream connected to the Arabian Gulf, which runs through a densely populated urban area in Karachi, Pakistan. Methods: Employing a universal pair of oligonucleotides capable of amplifying species-specific segments of 16S rRNA gene from all Eubacteria, we generated a library of PCR products using total DNA purified from the collected sample, cloned the amplifers into pGEM-T-Easy and sequenced each recombinant clone. The obtained DNA sequences were subjected to bio-informatic analyses. Results: A total of 71 recombinant clones were obtained from the amplified 16S rDNA products and sequenced. Bioinformatics analyses revealed that 54 (out of 71) were unique sequences from which 42 shared >97% and 12 shared <97% homology to their database counterparts. One sequence originated from the plastid DNA of eukaryote Pyramimonas disomata. From the remaining 53 sequences, 45 were Proteo-bacteria and 8 Fermicute in origin. Among 71 sequences, Alpha-, Beta- and Gamma-proteobacteria species constituted 86% of Proteo-bacteria identified in the sample while only 13% were Fermicutes. Conclusions: The microbial niche in Nehr-e-Khayyam is occupied predominantly by heterotrophic Proteo-bacterial and Firmicute strains, some of which are known human pathogens. (author)

  11. Comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure

    OpenAIRE

    Song, Caihong; Li, Mingxiao; Jia, Xuan; Wei, Zimin; Zhao, Yue; Xi, Beidou; Zhu, Chaowei; Liu, Dongming

    2015-01-01

    This study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. To this end, pig manure (PM), chicken manure (CM), a mixture of PM and CM (PM + CM), and a mixture of PM, CM and anaerobic digestion residue (ADR) (PM + CM + ADR) were selected for thermophilic composting. The bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction–denaturing gra...

  12. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Science.gov (United States)

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  13. Effects of triclosan on bacterial community composition and 'Vibrio' populations in natural seawater microcosms

    Directory of Open Access Journals (Sweden)

    Keri Ann Lydon

    2017-05-01

    Full Text Available Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, 'Vibrio', a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm can induce a significant 'Vibrio' growth response (68–1,700 fold increases in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary, Doctors Arm Canal (Big Pine Key, FL, and Clam Bank Landing (North Inlet Estuary, Georgetown, SC. Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of 'Vibrio'naceae (17-fold, Pseudoalteromonadaceae (65-fold, Alteromonadaceae (108-fold, Colwelliaceae (430-fold, and Oceanospirillaceae (1,494-fold. While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to use triclosan as a carbon source. The results further suggest the potential for selection of 'Vibrio' in coastal environments, especially sediments, where triclosan may accumulate at high levels.

  14. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Directory of Open Access Journals (Sweden)

    Jordan Lee Harris

    Full Text Available Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  15. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Science.gov (United States)

    Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd Allah, Elsayed Fathi; Singh, Bhim Pratap

    2017-01-01

    The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  16. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Directory of Open Access Journals (Sweden)

    Dhaneshwaree Asem

    Full Text Available The gastrointestinal (GI habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk and a domesticated goat (Black Bengal were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF of D2 (alkaline pretreated pulpy biomass using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL and FPase (0.5 U/mL activities (55°C, pH 8. The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  17. Bacterial Population in Intestines of Litopenaeus vannamei Fed Different Probiotics or Probiotic Supernatant.

    Science.gov (United States)

    Sha, Yujie; Liu, Mei; Wang, Baojie; Jiang, Keyong; Qi, Cancan; Wang, Lei

    2016-10-28

    The interactions of microbiota in the gut play an important role in promoting or maintaining the health of hosts. In this study, in order to investigate and compare the effects of dietary supplementation with Lactobacillus pentosus HC-2 (HC-2), Enterococcus faecium NRW-2, or the bacteria-free supernatant of a HC-2 culture on the bacterial composition of Litopenaeus vannamei , Illumina sequencing of the V1-V2 region of the 16S rRNA gene was used. The results showed that unique species exclusively existed in specific dietary groups, and the abundance of Actinobacteria was significantly increased in the intestinal bacterial community of shrimp fed with the bacteria-free supernatant of an HC-2 culture compared with the control. In addition, the histology of intestines of the shrimp from the four dietary groups was also described, but no obvious improvements in the intestinal histology were observed. The findings in this work will help to promote the understanding of the roles of intestinal bacteria in shrimps when fed with probiotics or probiotic supernatant.

  18. Mean-field games with logistic population dynamics

    KAUST Repository

    Gomes, Diogo A.

    2013-12-01

    In its standard form, a mean-field game can be defined by coupled system of equations, a Hamilton-Jacobi equation for the value function of agents and a Fokker-Planck equation for the density of agents. Traditionally, the latter equation is adjoint to the linearization of the former. Since the Fokker-Planck equation models a population dynamic, we introduce natural features such as seeding and birth, and nonlinear death rates. In this paper we analyze a stationary meanfield game in one dimension, illustrating various techniques to obtain regularity of solutions in this class of systems. In particular we consider a logistic-type model for birth and death of the agents which is natural in problems where crowding affects the death rate of the agents. The introduction of these new terms requires a number of new ideas to obtain wellposedness. In a forthcoming publication we will address higher dimensional models. ©2013 IEEE.

  19. Mean-field games with logistic population dynamics

    KAUST Repository

    Gomes, Diogo A.; De Lima Ribeiro, Ricardo

    2013-01-01

    In its standard form, a mean-field game can be defined by coupled system of equations, a Hamilton-Jacobi equation for the value function of agents and a Fokker-Planck equation for the density of agents. Traditionally, the latter equation is adjoint to the linearization of the former. Since the Fokker-Planck equation models a population dynamic, we introduce natural features such as seeding and birth, and nonlinear death rates. In this paper we analyze a stationary meanfield game in one dimension, illustrating various techniques to obtain regularity of solutions in this class of systems. In particular we consider a logistic-type model for birth and death of the agents which is natural in problems where crowding affects the death rate of the agents. The introduction of these new terms requires a number of new ideas to obtain wellposedness. In a forthcoming publication we will address higher dimensional models. ©2013 IEEE.

  20. Richards-like two species population dynamics model.

    Science.gov (United States)

    Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

    2014-12-01

    The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished.

  1. Artificial bee colony algorithm with dynamic multi-population

    Science.gov (United States)

    Zhang, Ming; Ji, Zhicheng; Wang, Yan

    2017-07-01

    To improve the convergence rate and make a balance between the global search and local turning abilities, this paper proposes a decentralized form of artificial bee colony (ABC) algorithm with dynamic multi-populations by means of fuzzy C-means (FCM) clustering. Each subpopulation periodically enlarges with the same size during the search process, and the overlapping individuals among different subareas work for delivering information acting as exploring the search space with diffusion of solutions. Moreover, a Gaussian-based search equation with redefined local attractor is proposed to further accelerate the diffusion of the best solution and guide the search towards potential areas. Experimental results on a set of benchmarks demonstrate the competitive performance of our proposed approach.

  2. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    Science.gov (United States)

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  3. On the stochastic approach to marine population dynamics

    Directory of Open Access Journals (Sweden)

    Eduardo Ferrandis

    2007-03-01

    Full Text Available The purpose of this article is to deepen and structure the statistical basis of marine population dynamics. The starting point is the correspondence between the concepts of mortality, survival and lifetime distribution. This is the kernel of the possibilities that survival analysis techniques offer to marine population dynamics. A rigorous definition of survival and mortality based on their properties and their probabilistic versions is briefly presented. Some well established models for lifetime distribution, which generalise the usual simple exponential distribution, might be used with their corresponding survivals and mortalities. A critical review of some published models is also made, including original models proposed in the way opened by Caddy (1991 and Sparholt (1990, which allow for a continuously decreasing natural mortality. Considering these elements, the pure death process dealt with in the literature is used as a theoretical basis for the evolution of a marine cohort. The elaboration of this process is based on Chiang´s study of the probability distribution of the life table (Chiang, 1960 and provides specific structured models for stock evolution as a Markovian process. These models may introduce new ideas in the line of thinking developed by Gudmundsson (1987 and Sampson (1990 in order to model the evolution of a marine cohort by stochastic processes. The suitable approximation of these processes by means of Gaussian processes may allow theoretical and computational multivariate Gaussian analysis to be applied to the probabilistic treatment of fisheries issues. As a consequence, the necessary catch equation appears as a stochastic integral with respect to the mentioned Markovian process of the stock. The solution of this equation is available when the mortalities are proportional, hence the use of the proportional hazards model (Cox, 1959. The assumption of these proportional mortalities leads naturally to the construction of a

  4. Dynamical evolution of a fictitious population of binary Neptune Trojans

    Science.gov (United States)

    Brunini, Adrián

    2018-03-01

    We present numerical simulations of the evolution of a synthetic population of Binary Neptune Trojans, under the influence of the solar perturbations and tidal friction (the so-called Kozai cycles and tidal friction evolution). Our model includes the dynamical influence of the four giant planets on the heliocentric orbit of the binary centre of mass. In this paper, we explore the evolution of initially tight binaries around the Neptune L4 Lagrange point. We found that the variation of the heliocentric orbital elements due to the libration around the Lagrange point introduces significant changes in the orbital evolution of the binaries. Collisional processes would not play a significant role in the dynamical evolution of Neptune Trojans. After 4.5 × 109 yr of evolution, ˜50 per cent of the synthetic systems end up separated as single objects, most of them with slow diurnal rotation rate. The final orbital distribution of the surviving binary systems is statistically similar to the one found for Kuiper Belt Binaries when collisional evolution is not included in the model. Systems composed by a primary and a small satellite are more fragile than the ones composed by components of similar sizes.

  5. Evolutionary game dynamics in a growing structured population

    Energy Technology Data Exchange (ETDEWEB)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza (Spain); Traulsen, Arne [Emmy-Noether Group for Evolutionary Dynamics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen (Germany)], E-mail: traulsen@evolbio.mpg.de

    2009-08-15

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  6. Evolutionary game dynamics in a growing structured population

    International Nuclear Information System (INIS)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

    2009-01-01

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  7. Evolutionary Dynamics of Collective Action in Structured Populations

    Science.gov (United States)

    Santos, Marta Daniela de Almeida

    The pervasiveness of cooperation in Nature is not easily explained. If evolution is characterized by competition and survival of the fittest, why should selfish individuals cooperate with each other? Evolutionary Game Theory (EGT) provides a suitable mathematical framework to study this problem, central to many areas of science. Conventionally, interactions between individuals are modeled in terms of one-shot, symmetric 2-Person Dilemmas of Cooperation, but many real-life situations involve decisions within groups with more than 2 individuals, which are best-dealt in the framework of N-Person games. In this Thesis, we investigate the evolutionary dynamics of two paradigmatic collective social dilemmas - the N-Person Prisoner's Dilemma (NPD) and the N-Person Snowdrift Game (NSG) on structured populations, modeled by networks with diverse topological properties. Cooperative strategies are just one example of the many traits that can be transmitted on social networks. Several recent studies based on empirical evidence from a medical database have suggested the existence of a 3 degrees of influence rule, according to which not only our "friends", but also our friends' friends, and our friends' friends' friends, have a non-trivial influence on our decisions. We investigate the degree of peer influence that emerges from the spread of cooperative strategies, opinions and diseases on populations with distinct underlying networks of contacts. Our results show that networks naturally entangle individuals into interactions of many-body nature and that for each network class considered different processes lead to identical degrees of influence. None

  8. Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

    Science.gov (United States)

    Dey, Snigdhadip; Joshi, Amitabh

    2013-01-01

    Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

  9. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    Science.gov (United States)

    Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P biofertilizer in agroecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Population dynamics of caribou herds in southwestern Alaska

    Directory of Open Access Journals (Sweden)

    Patrick Valkenburg

    2003-04-01

    Full Text Available The five naturally occurring and one transplanted caribou (Rangifer tarandus granti herd in southwestern Alaska composed about 20% of Alaska's caribou population in 2001. All five of the naturally occurring herds fluctuated considerably in size between the late 1800s and 2001 and for some herds the data provide an indication of long-term periodic (40-50 year fluctuations. At the present time, the Unimak (UCH and Southern Alaska Peninsula (SAP are recovering from population declines, the Northern Alaska Peninsula Herd (NAP appears to be nearing the end of a protracted decline, and the Mulchatna Herd (MCH appears to now be declining after 20 years of rapid growth. The remaining naturally occurring herd (Kilbuck has virtually disappeared. Nutrition had a significant effect on the size of 4-month-old and 10-month-old calves in the NAP and the Nushagak Peninsula Herd (NPCH and probably also on population growth in at least 4 (SAP, NAP, NPCH, and MCH of the six caribou herds in southwestern Alaska. Predation does not appear to be sufficient to keep caribou herds in southwestern Alaska from expanding, probably because rabies is endemic in red foxes (Vulpes vulpes and is periodically transferred to wolves (Canis lupus and other canids. However, we found evidence that pneumonia and hoof rot may result in significant mortality of caribou in southwestern Alaska, whereas there is no evidence that disease is important in the dynamics of Interior herds. Cooperative conservation programs, such as the Kilbuck Caribou Management Plan, can be successful in restraining traditional harvest and promoting growth in caribou herds. In southwestern Alaska we also found evidence that small caribou herds can be swamped and assimilated by large herds, and fidelity to traditional calving areas can be lost.

  11. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Directory of Open Access Journals (Sweden)

    Luuk J G W van Wilderen

    2011-03-01

    Full Text Available Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio- physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox that describes the finite bleach (orientation effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective excitation (photoselection and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical

  12. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Science.gov (United States)

    van Wilderen, Luuk J G W; Lincoln, Craig N; van Thor, Jasper J

    2011-03-21

    Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is

  13. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

    Science.gov (United States)

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

    2015-01-01

    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

  14. Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target.

    Science.gov (United States)

    Frei, Priska; Pang, Lijuan; Silbermann, Marleen; Eriş, Deniz; Mühlethaler, Tobias; Schwardt, Oliver; Ernst, Beat

    2017-08-25

    Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

    Directory of Open Access Journals (Sweden)

    Haihan Zhang

    2018-02-01

    Full Text Available The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP from the outbreak to the decline period (p < 0.05 while Fe concentration increased sharply during the decline period (p < 0.05. The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02. Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of

  16. Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

    2014-02-01

    The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  17. Temporal Sampling of White Band Disease Infected Corals Reveals Complex and Dynamic Bacterial Communities

    Science.gov (United States)

    Gignoux-Wolfsohn, S.; Vollmer, S. V.; Aronson, F. M.

    2016-02-01

    White band disease (WBD) is a coral disease that is currently decimating populations of the endangered staghorn coral, Acropora cervicornis and elkhorn coral, A. palmata across the Caribbean. Since it was first reported in 1979, WBD has killed 95% of these critical reef-building Caribbean corals. WBD is infectious; it can be transmitted through the water column or by a corallivorous snail. While previous research shows that WBD is likely caused by bacteria, identification of a specific pathogen or pathogens has remained elusive. Much of the difficulty of understanding the etiology of the disease comes from a lack of information about how existing bacterial communities respond to disease and separating initial from secondary colonizers. In order to address this lack of information, we performed a fully-crossed tank infection experiment. We exposed healthy corals from two different sites to disease and healthy (control) homogenates from both sites, replicating genotype across tanks. We sampled every coral at three time points: before inoculation with the homogenate, after inoculation, and when the coral showed signs of disease. We then performed 16S rRNA gene sequencing on the Illumina HiSeq 2000. We saw significant differences between time points and disease state. Interestingly, at the first time point (time one) we observed differences between genotypes: every fragment from some genotypes was dominated by Endozoicomonas, while other genotypes were not dominated by one family. At time two we saw an increase in abundance of Alteromonadaceae and Flavobacteriaceae in all corals, and a larger increase in disease-exposed corals. At time three, we saw another increase in Flavobacteriaceae abundance in diseased corals, as well as an introduction of Francisella to diseased corals. While Flavobacteriaceae and Francisella were proposed as potential pathogens, their increase at time three suggests they may be secondary colonizers or opportunists. In genotypes that were

  18. Phase control of light amplification with dynamically irreversible pathways of population transfer in a Λ system

    International Nuclear Information System (INIS)

    Yuan Shi; Wu Jinhui; Gao Jinyue; Pan Chunliu

    2002-01-01

    We use the relative phase of two coherent fields for the control of light amplification with dynamically irreversible pathways of population transfer in a Λ system. The population inversion and gain with dynamically irreversible pathways of population transfer are shown as the relative phase is varied. We support our results by numerical calculation and analytical explanation

  19. Effect of Sucrose as Carbon Source and Probiotic Administrations on Bacterial Population Dinamic and Water Quality in White Shrimp, Litopenaeus vannamei Culture

    Directory of Open Access Journals (Sweden)

    . Sukenda

    2007-07-01

    Full Text Available Disinfection and nutrient enrichment prior stocking of  post larvae in the pond will be affected on the growth and composition of microbe.  Attention should be taken to some factors related to deterministic and stochastic factors of aquaculture environment  in order to develop microbe community.  This study was performed to determine effect of sucrose and probiotic supplementation to shrimp culture pond on water quality profile and population dynamic on shrimp culture media.  The treatments were supplementation of sucrose as carbon source, probiotic, and sucrose + probiotic into 25 L culture medium containing white shrimp, Litopenaeus vannamei.  Shrimp were fed commercial diet containing 30% protein by 5% body weight every day.  The result of study showed that bacterial population was increased by increasing time of shrimp rearing.  Increased of bacterial population was contrary to DO value.   Bacteria grew was heterotrop and vibrio that its intensity varied during experiment.  Supplementation of sucrose supported proliferation of bacteria including heterotrop, probiotik and vibrio groups.  Specifically, interaction between probiotic bacteria and vibrio was also found.  The presence of probiotic bacteria showed a negative impact on vibrio population.  Further, development of bacteria in general was also implicated to fluctuation of ammonia concentration in pond. Keywords: carbon, sucrose, probiotic, white shrimp, Litopenaeus vannamei   ABSTRAK Kegiatan disinfeksi dan pengkayaan nutrien sebelum penebaran PL akan mempengaruhi pola pertumbuhan dan komposisi mikroba di tambak. Hal-hal yang perlu diperhatikan dalam pengembangan komunitas mikroba adalah faktor-faktor deterministic dan sthocastic masing-masing lingkungan budidaya. Penelitian ini dilakukan untuk mengetahui pengaruh pemberian bahan berkarbon (sukrosa dan probiotik di tambak terhadap profil kualitas air serta dinamika populasi pada perairan budidaya. Pada penelitian ini

  20. Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

    International Nuclear Information System (INIS)

    Aguayo, S; Bozec, L; Donos, N; Spratt, D

    2015-01-01

    The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

  1. Particle-associated bacterial dynamics in a tropical tidal plain (Zuari estuary, India)

    Digital Repository Service at National Institute of Oceanography (India)

    DeSouza, M.J.B.D.; Nair, S.; LokaBharathi, P.A.; Chandramohan, D.

    that the estuarine bacterial community undergoes physiologi- cal stress leading to reduced bacterial production (del Giorgio & Bouvier 2002), which was not observed at this station. However, during the pre-monsoon season, when the salinity values are the highest... to be significant. As PAB abundance and production formed a signifi- cant portion of the microbial biomass in the Zuari waters, the BCD would be expected to be high. The reported BGE from marine system ranged from <10 to 50% (Azam et al. 1983, del Giorgio et al...

  2. Phenotypic resistance and the dynamics of bacterial escape from phage control

    DEFF Research Database (Denmark)

    Bull, James J.; Vegge, Christina Skovgaard; Schmerer, Matthew

    2014-01-01

    The canonical view of phage - bacterial interactions in dense, liquid cultures is that the phage will eliminate most of the sensitive cells; genetic resistance will then ascend to restore high bacterial densities. Yet there are various mechanisms by which bacteria may remain sensitive to phages...... mathematical models of these processes and suggest how different types of this 'phenotypic' resistance may be elucidated. We offer preliminary in vitro studies of a previously characterized E. coli model system and Campylobacter jejuni illustrating apparent phenotypic resistance. As phenotypic resistance may...

  3. Effects of gamma-irradiation before and after cooking on bacterial population and sensory quality of Dakgalbi

    International Nuclear Information System (INIS)

    Yoon, Young Min; Park, Jong-Heum; Lee, Ji-Hye; Park, Jae-Nam; Park, Jin-Kyu; Sung, Nak-Yun; Song, Beom-Seok; Kim, Jae-Hun; Yoon, Yohan; Gao, Meixu; Yook, Hong-Sun; Lee, Ju-Woon

    2012-01-01

    The purpose of this study was to compare the effect of gamma irradiation on the total bacterial population and the sensory quality of Dakgalbi irradiated before and after cooking. Fresh chicken meat was cut into small pieces and used to prepare Dakgalbi. For the preparation of Dakgalbi cooked with gamma-irradiated chicken meat and sauce (IBC), raw chicken meat and Dakgalbi sauce were irradiated and then stir-fried. For the preparation of Dakgalbi irradiated after cooking with raw chicken meat and sauce (IAC), raw chicken meat and Dakgalbi sauce were first cooked and subsequently irradiated. Under the accelerated storage condition of 35 °C for 7 days, bacteria in IBC were below the detection limit (1 log CFU/g) on day 1 but were detected on day 2 and gradually increased hereafter. In IAC, on the other hand, bacteria were not detected at all. Evaluation of sensory quality also decreased on both samples. However, IAC showed a better trend. Our results indicate that IAC protocol was a more effective method for reducing bacterial growth in Dakgalbi. - Highlights: ► We compared the microbial safety and sensory property of Dakgalbi irradiated before and after cooking. ► Dakgalbi irradiated after cooking can be more effective processing method on microbial safety. ► Sensory property decreased on both Dakgalbis by irradiation-induced off-flavor. ► Dakgalbi irradiated after cooking showed a better tendency on the sensory evaluation.

  4. Effects of gamma-irradiation before and after cooking on bacterial population and sensory quality of Dakgalbi

    Science.gov (United States)

    Yoon, Young Min; Park, Jong-Heum; Lee, Ji-Hye; Park, Jae-Nam; Park, Jin-Kyu; Sung, Nak-Yun; Song, Beom-Seok; Kim, Jae-Hun; Yoon, Yohan; Gao, Meixu; Yook, Hong-Sun; Lee, Ju-Woon

    2012-08-01

    The purpose of this study was to compare the effect of gamma irradiation on the total bacterial population and the sensory quality of Dakgalbi irradiated before and after cooking. Fresh chicken meat was cut into small pieces and used to prepare Dakgalbi. For the preparation of Dakgalbi cooked with gamma-irradiated chicken meat and sauce (IBC), raw chicken meat and Dakgalbi sauce were irradiated and then stir-fried. For the preparation of Dakgalbi irradiated after cooking with raw chicken meat and sauce (IAC), raw chicken meat and Dakgalbi sauce were first cooked and subsequently irradiated. Under the accelerated storage condition of 35 °C for 7 days, bacteria in IBC were below the detection limit (1 log CFU/g) on day 1 but were detected on day 2 and gradually increased hereafter. In IAC, on the other hand, bacteria were not detected at all. Evaluation of sensory quality also decreased on both samples. However, IAC showed a better trend. Our results indicate that IAC protocol was a more effective method for reducing bacterial growth in Dakgalbi.

  5. Effect of immobilization of a bacterial consortium on diuron dissipation and community dynamics.

    Science.gov (United States)

    Bazot, Stéphane; Lebeau, Thierry

    2009-09-01

    This work intended to study the relationship between diuron herbicide dissipation and the population dynamics of co-cultivated Delftia acidovorans WDL34 (WDL34) and Arthrobacter sp. N4 (N4) for different cell formulations: free cells or immobilization in Ca-alginate beads of one or both strains. GFP-tagged WDL34 and N4 Gram staining allowed analyzing the cell growth and distribution of each strain in both beads and culture medium in the course of the time. Compared to the free cell co-culture of WDL34 and N4, immobilization of WDL34 in Ca-alginate beads co-cultivated with free N4 increased the dissipation rate of diuron by 53% (0.141 mg ml(-1) h(-1)). In that case, immobilization strongly modified the final equilibrium among both strains (highest total N4 to WDL34 ratio). Our results demonstrated that the inoculant formulation played a major role in the cell growth of each cultivated strain possibly increasing diuron dissipation. This optimized cell formulation may allow improving water and soil treatment.

  6. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations.

    Science.gov (United States)

    Montenegro, Diego; Kalpana, Kriti; Chrissian, Christine; Sharma, Ashutosh; Takaoka, Anna; Iacovidou, Maria; Soll, Clifford E; Aminova, Olga; Heguy, Adriana; Cohen, Lisa; Shen, Steven; Kawamura, Akira

    2015-02-01

    Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears.

    Science.gov (United States)

    Schwab, Clarissa; Cristescu, Bogdan; Boyce, Mark S; Stenhouse, Gordon B; Gänzle, Michael

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears.

  8. Population dynamics in the high Arctic: Climate variations in time and space

    DEFF Research Database (Denmark)

    Hendrichsen, Ditte Katrine

    Climatic factors profoundly influence the population dynamics, species interactions and demography of Arctic species. Analyses of the spatio-temporal dynamics within and across species are therefore necessary to understand and predict the responses of Arctic ecosystems to climatic variability...

  9. Impact of climate change on fish population dynamics in the baltic sea: a dynamical downscaling investigation

    DEFF Research Database (Denmark)

    Mackenzie, Brian R; Meier, H E Markus; Lindegren, Martin

    2012-01-01

    Understanding how climate change, exploitation and eutrophication will affect populations and ecosystems of the Baltic Sea can be facilitated with models which realistically combine these forcings into common frameworks. Here, we evaluate sensitivity of fish recruitment and population dynamics...... and the temperature have influenced recruitment for at least 50 years. The three Baltic Sea models estimate relatively similar developments (increases) in biomass and fishery yield during twenty-first century climate change (ca. 28 % range among models). However, this uncertainty is exceeded by the one associated...... to past and future environmental forcings provided by three ocean-biogeochemical models of the Baltic Sea. Modeled temperature explained nearly as much variability in reproductive success of sprat (Sprattus sprattus; Clupeidae) as measured temperatures during 1973-2005, and both the spawner biomass...

  10. Effect of antibiotics on bacterial populations: a multi-hierachical selection process [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    José Luis Martínez

    2017-01-01

    Full Text Available Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

  11. Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

    Science.gov (United States)

    This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

  12. Population dynamics and monitoring applied to decision-making

    Directory of Open Access Journals (Sweden)

    Conroy, M. J.

    2004-06-01

    influence diagrams to capture the stochastic, temporal processes of managing cheetah population in Kenya. The model predicts likely anagement decisions made by various actors within these countries, (e.g., the President, the Environmental Protection Agency, and rural residents and the resulting probability of cheetah extinction following these decisions. By approaching the problem in both its political and ecological contexts one avoids consideration of decisions that, while beneficial from a purely conservation point of view, are unlikely to be implemented because of conflicting political objectives. Haas’s analysis demonstrates both the promise and challenges of this type of modeling, and he offers suggestions for overcoming inherent technical difficulties such as model calibration. The second paper, by Simon Hoyle and Mark Maunder (Hoyle & Maunder, 2004, uses a Bayesian approach to model population dynamics and the effects of commercial fishing bycatch for the eastern Pacific Ocean spotted dolphin (Stenella attenuata. Their paper provides a good example of why Bayesian analysis is particularly suited to many management problems. Namely, because it allows the integration of disparate pieces of monitoring data in the simultaneous estimation of population parameters; allows forincorporation of expert judgment and data from other systems and species; and provides for explicit consideration of uncertainty in decision–making. Alternative management scenarios can then be explored via forward simulations. In the third paper, Chris Fonnesbeck and Mike Conroy (Fonnesbeck & Conroy, 2004 present an integrated approach for estimating parameters and predicting abundance of American black duck (Anas rubripes populations. They also employ a ayesian approach and overcome some of the computational challenges by using Markov chain–Monte Carlo methods. Ring–recovery and harvest data are used to estimate fall age ratios under alternative reproductive models. These in turn are used to

  13. Storm-scale dynamics of bacterial community composition in throughfall and stemflow

    Science.gov (United States)

    Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

    2017-12-01

    Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

  14. Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

    Science.gov (United States)

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-04-01

    A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment

  15. Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting▿ †

    Science.gov (United States)

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-01-01

    A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment

  16. Intertidal population genetic dynamics at a microgeographic seascape scale.

    Science.gov (United States)

    Hu, Zi-Min

    2013-06-01

    The intertidal community is among the most physically harsh niches on earth, with highly heterogeneous environmental and biological factors that impose strong habitat selection on population abundance, genetic connectivity and ecological adaptation of organisms in nature. However, most genetic studies to date have concentrated on the influence of basin-wide or regional marine environments (e.g. habitat discontinuities, oceanic currents and fronts, and geographic barriers) on spatiotemporal distribution and composition of intertidal invertebrates having planktonic stages or long-distance dispersal capability. Little is known about sessile marine organisms (e.g. seaweeds) in the context of topographic tidal gradients and reproductive traits at the microgeographic scale. In this issue of Molecular Ecology, Krueger-Hadfield et al. () implemented an elaborate sampling strategy with red seaweed (Chondrus crispus) from a 90-m transect stand near Roscoff and comprehensively detected genome-scale genetic differentiation and biases in ploidy level. This study not only revealed that tidal height resulted in genetic differentiation between high- and low-shore stands and restricted the genetic exchange within the high-shore habitat, but also demonstrated that intergametophytic nonrandom fertilization in C. crispus can cause significant deviation from Hardy-Weinberg equilibrium. Such new genetic insights highlight the importance of microgeographic genetic dynamics and life history characteristics for better understanding the evolutionary processes of speciation and diversification of intertidal marine organisms. © 2013 John Wiley & Sons Ltd.

  17. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.

    Science.gov (United States)

    Pankratov, Timofey A; Ivanova, Anastasia O; Dedysh, Svetlana N; Liesack, Werner

    2011-07-01

    Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH. © 2011 Society for

  18. Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems in the Western Amazon

    Directory of Open Access Journals (Sweden)

    Paula Marcela Duque Jaramillo

    2013-12-01

    Full Text Available Cowpea (Vigna unguiculata is an important grain-producing legume that can forego nitrogen fertilization by establishing an efficient symbiosis with nitrogen-fixing bacteria. Although inoculating strains have already been selected for this species, little is known about the genotypic and symbiotic diversity of native rhizobia. Recently, Bradyrhizobium has been shown to be the genus most frequently trapped by cowpea in agricultural soils of the Amazon region. We investigated the genetic and symbiotic diversity of 148 bacterial strains with different phenotypic and cultural properties isolated from the nodules of the trap species cowpea, which was inoculated with samples from soils under agroforestry systems from the western Amazon. Sixty non-nodulating strains indicated a high frequency of endophytic strains in the nodules. The 88 authenticated strains had varying symbiotic efficiency. The SPAD (Soil Plant Analysis Development index (indirect measurement of chlorophyll content was more efficient at evaluating the contribution of symbiotic N2-fixation than shoot dry matter under axenic conditions. Cowpea-nodulating bacteria exhibited a high level of genetic diversity, with 68 genotypes identified by BOX-PCR. Sequencing of the 16S rRNA gene showed a predominance of the genus Bradyrhizobium, which accounted for 70 % of all strains sequenced. Other genera identified were Rhizobium, Ochrobactrum, Paenibacillus, Bosea, Bacillus, Enterobacter, and Stenotrophomonas. These results support the promiscuity of cowpea and demonstrate the high genetic and symbiotic diversity of rhizobia in soils under agroforestry systems, with some strains exhibiting potential for use as inoculants. The predominance of Bradyrhizobium in land uses with different plant communities and soil characteristics reflects the adaptation of this genus to the Amazon region.

  19. Population dynamics of potato cyst nematodes and associated damage to potato

    NARCIS (Netherlands)

    Schans, J.

    1993-01-01

    Population dynamics of potato cyst nematodes (PCN; Globoderarostochiensis (Woll.) Skarbilovich and G. pallida Stone) and their interactions with potato plants are insufficiently understood to explain variations of population

  20. Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm.

    Directory of Open Access Journals (Sweden)

    Jiangyu Dai

    Full Text Available Cyanobacterial blooms are a worldwide environmental problem and frequently occur in eutrophic lakes. Organophosphorus mineralization regulated by microbial alkaline phosphatase provides available nutrients for bloom regeneration. To uncover the dynamics of bacterial alkaline phosphatase activity and microbial backgrounds in relation to organophosphorus mineralization during the decomposition process of cyanobacterial blooms, the response of alkaline phosphatase PhoX-producing bacteria were explored using a 23-day mesocosm experiment with three varying densities of Microcystis biomass from eutrophic Lake Taihu. Our study found large amounts of soluble reactive phosphorus and dissolved organophosphorus were released into the lake water during the decomposition process. Bacterial alkaline phosphatase activity showed the peak values during days 5~7 in groups with different chlorophyll-a densities, and then all decreased dramatically to their initial experimental levels during the last stage of decomposition. Bacterial phoX abundances in the three experimental groups increased significantly along with the decomposition process, positively related to the dissolved organic carbon and organophosphorus released by the Microcystis blooms. The genotypes similar to the phoX genes of Alphaproteobacteria were dominant in all groups, whereas the genotypes most similar to the phoX genes of Betaproteobacteria and Cyanobacteria were also abundant in the low density (~15 μg L-1 chlorophyll-a group. At the end of the decomposition process, the number of genotypes most similar to the phoX of Betaproteobacteria and Cyanobacteria increased in the medium (~150 μg L-1 chlorophyll-a and high (~1500 μg L-1 chlorophyll-a density groups. The released organophosphorus and increased bacterial phoX abundance after decomposition of Microcystis aggregates could potentially provide sufficient nutrients and biological conditions for algal proliferation and are probably related

  1. Seasonal dynamics of bacterial biomass and production in a coastal arctic ecosystem: Franklin Bay, western Canadian Arctic

    Science.gov (United States)

    Garneau, Marie-Ã. Ve; Roy, SéBastien; Lovejoy, Connie; Gratton, Yves; Vincent, Warwick F.

    2008-07-01

    The Canadian Arctic Shelf Exchange Study (CASES) included the overwintering deployment of a research platform in Franklin Bay (70°N, 126°W) and provided a unique seasonal record of bacterial dynamics in a coastal region of the Arctic Ocean. Our objectives were (1) to relate seasonal bacterial abundance (BA) and production (BP) to physico-chemical characteristics and (2) to quantify the annual bacterial carbon flux. BA was estimated by epifluorescence microscopy and BP was estimated from 3H-leucine and 3H-thymidine assays. Mean BA values for the water column ranged from 1.0 (December) to 6.8 × 105 cells mL-1 (July). Integral BP varied from 1 (February) to 80 mg C m-2 d-1 (July). During winter-spring, BP was uncorrelated with chlorophyll a (Chl a), but these variables were significantly correlated during summer-autumn (rs = 0.68, p winter, late winter-late spring, and summer. A baseline level of BB and BP was maintained throughout late winter-late spring despite the persistent cold and darkness, with irregular fluctuations that may be related to hydrodynamic events. During this period, BP rates were correlated with colored dissolved organic matter (CDOM) but not Chl a (rs BP.CDOM∣Chl a = 0.20, p < 0.05, N = 176). Annual BP was estimated as 6 g C m-2 a-1, implying a total BP of 4.8 × 1010 g C a-1 for the Franklin Bay region. These results show that bacterial processes continue throughout all seasons and make a large contribution to the total biological carbon flux in this coastal arctic ecosystem.

  2. A spatial ecosystem and populations dynamics model (SEAPODYM) Modeling of tuna and tuna-like populations

    Science.gov (United States)

    Lehodey, Patrick; Senina, Inna; Murtugudde, Raghu

    2008-09-01

    An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical-biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack ( Katsuwonus pelamis) and bigeye ( Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization

  3. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hang; Li, Hongyi; Gilbert, Jack A.; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian; Goodrich-Blair, H.

    2015-08-21

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M),tet(O),tet(Q), andtet(W)] were reduced (P< 0.05), while those of genes encoding sulfonamide resistance (sul1andsul2) were increased (P< 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P< 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance ofFlavobacteriaceaespp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the familyRuminococcaceae, classBacilli, or phylumProteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to

  4. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem

    Directory of Open Access Journals (Sweden)

    Eric Robert Johnston

    2016-04-01

    Full Text Available How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 grams are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth by sequencing, and the recovery of twenty-seven high-quality, almost complete (>80% completeness population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity. Collectively

  5. A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination and host-mediated population structure in Pasteuria ramosa, a bacterial parasite of Daphnia.

    Science.gov (United States)

    Andras, J P; Ebert, D

    2013-02-01

    The population structure of parasites is central to the ecology and evolution of host-parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well-separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host-a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host-parasite system. © 2012 Blackwell Publishing Ltd.

  6. Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model.

    Science.gov (United States)

    Mina, Petros; Tsaneva-Atanasova, Krasimira; Bernardo, Mario di

    2016-07-15

    We extend a spatially explicit agent based model (ABM) developed previously to investigate entrainment and control of the emergent behavior of a population of synchronized oscillating cells in a microfluidic chamber. Unlike most of the work in models of control of cellular systems which focus on temporal changes, we model individual cells with spatial dependencies which may contribute to certain behavioral responses. We use the model to investigate the response of both open loop and closed loop strategies, such as proportional control (P-control), proportional-integral control (PI-control) and proportional-integral-derivative control (PID-control), to heterogeinities and growth in the cell population, variations of the control parameters and spatial effects such as diffusion in the spatially explicit setting of a microfluidic chamber setup. We show that, as expected from the theory of phase locking in dynamical systems, open loop control can only entrain the cell population in a subset of forcing periods, with a wide variety of dynamical behaviors obtained outside these regions of entrainment. Closed-loop control is shown instead to guarantee entrainment in a much wider region of control parameter space although presenting limitations when the population size increases over a certain threshold. In silico tracking experiments are also performed to validate the ability of classical control approaches to achieve other reference behaviors such as a desired constant output or a linearly varying one. All simulations are carried out in BSim, an advanced agent-based simulator of microbial population which is here extended ad hoc to include the effects of control strategies acting onto the population.

  7. A short-time scale colloidal system reveals early bacterial adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Christophe Beloin

    2008-07-01

    Full Text Available The development of bacteria on abiotic surfaces has important public health and sanitary consequences. However, despite several decades of study of bacterial adhesion to inert surfaces, the biophysical mechanisms governing this process remain poorly understood, due, in particular, to the lack of methodologies covering the appropriate time scale. Using micrometric colloidal surface particles and flow cytometry analysis, we developed a rapid multiparametric approach to studying early events in adhesion of the bacterium Escherichia coli. This approach simultaneously describes the kinetics and amplitude of early steps in adhesion, changes in physicochemical surface properties within the first few seconds of adhesion, and the self-association state of attached and free-floating cells. Examination of the role of three well-characterized E. coli surface adhesion factors upon attachment to colloidal surfaces--curli fimbriae, F-conjugative pilus, and Ag43 adhesin--showed clear-cut differences in the very initial phases of surface colonization for cell-bearing surface structures, all known to promote biofilm development. Our multiparametric analysis revealed a correlation in the adhesion phase with cell-to-cell aggregation properties and demonstrated that this phenomenon amplified surface colonization once initial cell-surface attachment was achieved. Monitoring of real-time physico-chemical particle surface properties showed that surface-active molecules of bacterial origin quickly modified surface properties, providing new insight into the intricate relations connecting abiotic surface physicochemical properties and bacterial adhesion. Hence, the biophysical analytical method described here provides a new and relevant approach to quantitatively and kinetically investigating bacterial adhesion and biofilm development.

  8. The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics

    Czech Academy of Sciences Publication Activity Database

    López-Mondéjar, Rubén; Voříšková, Jana; Větrovský, Tomáš; Baldrian, Petr

    2015-01-01

    Roč. 87, č. 1 (2015), s. 43-50 ISSN 0038-0717 R&D Projects: GA MŠk(CZ) EE2.3.30.0003; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk LD12048; GA MŠk LD12050 Institutional support: RVO:61388971 Keywords : Bacterial community * Deciduous forest * Forest soil Subject RIV: EE - Microbiology, Virology Impact factor: 4.152, year: 2015

  9. Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine.

    Science.gov (United States)

    Ding, Guo-Chun; Radl, Viviane; Schloter-Hai, Brigitte; Jechalke, Sven; Heuer, Holger; Smalla, Kornelia; Schloter, Michael

    2014-01-01

    Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.

  10. Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine.

    Directory of Open Access Journals (Sweden)

    Guo-Chun Ding

    Full Text Available Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.

  11. Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine

    Science.gov (United States)

    Ding, Guo-Chun; Radl, Viviane; Schloter-Hai, Brigitte; Jechalke, Sven; Heuer, Holger; Smalla, Kornelia; Schloter, Michael

    2014-01-01

    Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ. PMID:24671113

  12. Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine

    OpenAIRE

    Ding, Guo-Chun; Radl, Viviane; Schloter-Hai, Brigitte; Jechalke, Sven; Heuer, Holger; Smalla, Kornelia; Schloter, Michael

    2014-01-01

    Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied ...

  13. Bacterial Community Dynamics and Biodegradation Rates in Untreated and Oily Soils During PAH Exposure

    International Nuclear Information System (INIS)

    Zakaria, A.E.M.

    2008-01-01

    The approach taken in this study represents an attempt to address the possible selective effects of Polycyclic aromatic hydrocarbons (PAH) on the bacterial community structure of an untreated garden soil (S) and a chronically contaminated oily soil (CS). Untreated and chronically hydrocarbon polluted soils, collected from Egypt were enriched in shaking flasks containing 50 mg/l anthracene as a sole source of carbon over a period of 15 days. Bacterial communities in each soil were profiled by denaturing gradient gel electrophoresis (DGGE) analysis of the PCR amplified 16 S r DNA gene fragments after 0, 5, 10, and 15 days. Culture able biodegrading bacterial counts on minerals- Silica gel- Oil (MSD) plates as well as anthracene degradation for both soils were followed up at the same time intervals. Nine bacterial species were found to be dominant in the pristine soil before enrichment with the model polycyclic aromatic hydrocarbon (PAH), eight of them disappeared after live days of enrichment with the domination of one new species. It stayed dominant in soil until 15 days - exposure to anthracene. Therefore it can be used as a bio marker for PAH pollution. The chronically contaminated soil revealed a remarkable increase in the diversity directly after 5 days exposure to PAH HPLC analysis of the extracted anthracene remained in the biodegradation flasks after different degradation periods revealed that a higher biodegradation rates were accomplished by the oily soil consortium rather than by the pristine one. Before exposure to PAH, counts of culture able biodegrading bacteria were found to be higher in the untreated soil rather than in the oily one. After exposure the situation has been a bit altered as the counts in the untreated soil revealed a temporary suppression with a prolongation of the time required for growth as a result of the hydrocarbon stress

  14. Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density.

    Directory of Open Access Journals (Sweden)

    Zhaoshou Wang

    Full Text Available Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell-cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model.

  15. The effects of vaccination and immunity on bacterial infection dynamics in vivo.

    Directory of Open Access Journals (Sweden)

    Chris Coward

    2014-09-01

    Full Text Available Salmonella enterica infections are a significant global health issue, and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host. We have combined in vivo tracking of molecularly tagged bacterial subpopulations with mathematical modelling to gain a novel insight into how different classes of vaccines and branches of the immune response protect against secondary Salmonella enterica infections of the mouse. We have found that a live Salmonella vaccine significantly reduced bacteraemia during a secondary challenge and restrained inter-organ spread of the bacteria in the systemic organs. Further, fitting mechanistic models to the data indicated that live vaccine immunisation enhanced both the bacterial killing in the very early stages of the infection and bacteriostatic control over the first day post-challenge. T-cell immunity induced by this vaccine is not necessary for the enhanced bacteriostasis but is required for subsequent bactericidal clearance of Salmonella in the blood and tissues. Conversely, a non-living vaccine while able to enhance initial blood clearance and killing of virulent secondary challenge bacteria, was unable to alter the subsequent bacterial growth rate in the systemic organs, did not prevent the resurgence of extensive bacteraemia and failed to control the spread of the bacteria in the body.

  16. Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea.

    Science.gov (United States)

    De Tender, Caroline; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Vangeyte, Jürgen; Cattrijsse, André; Dawyndt, Peter; Ruttink, Tom

    2017-07-05

    Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.

  17. A Population Biology Perspective on the Stepwise Infection Process of the Bacterial Pathogen Pasteuria ramosa in Daphnia.

    Science.gov (United States)

    Ebert, Dieter; Duneau, David; Hall, Matthew D; Luijckx, Pepijn; Andras, Jason P; Du Pasquier, Louis; Ben-Ami, Frida

    2016-01-01

    The infection process of many diseases can be divided into series of steps, each one required to successfully complete the parasite's life and transmission cycle. This approach often reveals that the complex phenomenon of infection is composed of a series of more simple mechanisms. Here we demonstrate that a population biology approach, which takes into consideration the natural genetic and environmental variation at each step, can greatly aid our understanding of the evolutionary processes shaping disease traits. We focus in this review on the biology of the bacterial parasite Pasteuria ramosa and its aquatic crustacean host Daphnia, a model system for the evolutionary ecology of infectious disease. Our analysis reveals tremendous differences in the degree to which the environment, host genetics, parasite genetics and their interactions contribute to the expression of disease traits at each of seven different steps. This allows us to predict which steps may respond most readily to selection and which steps are evolutionarily constrained by an absence of variation. We show that the ability of Pasteuria to attach to the host's cuticle (attachment step) stands out as being strongly influenced by the interaction of host and parasite genotypes, but not by environmental factors, making it the prime candidate for coevolutionary interactions. Furthermore, the stepwise approach helps us understanding the evolution of resistance, virulence and host ranges. The population biological approach introduced here is a versatile tool that can be easily transferred to other systems of infectious disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Effects of demographic structure on key properties of stochastic density-independent population dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

    2012-12-01

    The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. Population Dynamics and Cost-Benefit Analysis. An Attempt to Relate Population Dynamics via Lifetime Reproductive Success to Short-Term Decisions

    NARCIS (Netherlands)

    Tinbergen, J.M.; Balen, J.H. van; Drent, P.J.; Cavé, A.J.; Mertens, J.A.L.; Boer-Hazewinkel, J. den

    1987-01-01

    1. The aim of this article is to explore whether cost-benefit analysis of behaviour may help to understand the population dynamics of a species. The Great Tit is taken as an example. 2. The lifetime reproductive success in different populations of Great Tits amounts from 0.7 (Hoge Veluwe, Wytham) to

  20. Escape from the competence state in Streptococcus mutans is governed by the bacterial population density.

    Science.gov (United States)

    Dufour, D; Villemin, C; Perry, J A; Lévesque, C M

    2016-12-01

    Horizontal gene transfer through natural DNA transformation is an important evolutionary mechanism among bacteria. Transformation requires that the bacteria are physiologically competent to take and incorporate free DNA directly from the environment. Although natural genetic transformation is a remarkable feature of many naturally competent bacteria, the process is energetically expensive for the cells. Consequently, a tight control of the competence state is necessary. The objective of the present work was to help decipher the molecular mechanisms regulating the escape from the competence state in Streptococcus mutans, the principal etiological agent responsible for tooth decay in humans. Our results showed that the cessation of competence in S. mutans was abrupt, and did not involve the accumulation of a competence inhibitor nor the depletion of a competence activator in the extracellular environment. The competence state was repressed at high cell population density via concomitant repression of sigX gene encoding the master regulator of the competence regulon. Co-culture experiments performed with oral and non-oral bacteria showed that S. mutans assesses its own population density and also the microbial density of its surroundings to regulate its competence escape. Interestingly, neither the intra-species and extra-species quorum-sensing systems nor the other 13 two-component regulatory systems identified in S. mutans were involved in the cell-density-dependent escape of the competence state. Altogether, our results suggest a complex mechanism regulating the competence shut-off involving cell-density-dependent repression of sigX through an as yet undefined system, and possibly SigX protein stability. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. The primary case is not enough: Variation among individuals, groups and social networks modify bacterial transmission dynamics.

    Science.gov (United States)

    Keiser, Carl N; Pinter-Wollman, Noa; Ziemba, Michael J; Kothamasu, Krishna S; Pruitt, Jonathan N

    2018-03-01

    The traits of the primary case of an infectious disease outbreak, and the circumstances for their aetiology, potentially influence the trajectory of transmission dynamics. However, these dynamics likely also depend on the traits of the individuals with whom the primary case interacts. We used the social spider Stegodyphus dumicola to test how the traits of the primary case, group phenotypic composition and group size interact to facilitate the transmission of a GFP-labelled cuticular bacterium. We also compared bacterial transmission across experimentally generated "daisy-chain" vs. "star" networks of social interactions. Finally, we compared social network structure across groups of different sizes. Groups of 10 spiders experienced more bacterial transmission events compared to groups of 30 spiders, regardless of groups' behavioural composition. Groups containing only one bold spider experienced the lowest levels of bacterial transmission regardless of group size. We found no evidence for the traits of the primary case influencing any transmission dynamics. In a second experiment, bacteria were transmitted to more individuals in experimentally induced star networks than in daisy-chains, on which transmission never exceeded three steps. In both experimental network types, transmission success depended jointly on the behavioural traits of the interacting individuals; however, the behavioural traits of the primary case were only important for transmission on star networks. Larger social groups exhibited lower interaction density (i.e. had a low ratio of observed to possible connections) and were more modular, i.e. they had more connections between nodes within a subgroup and fewer connections across subgroups. Thus, larger groups may restrict transmission by forming fewer interactions and by isolating subgroups that interacted with the primary case. These findings suggest that accounting for the traits of single exposed hosts has less power in predicting transmission

  2. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks

    Directory of Open Access Journals (Sweden)

    Kirsty Dougal

    2017-08-01

    Full Text Available Twelve mature (aged 5–16 years horses and ponies of mixed breed and type were fed restricted (1.25% BM Dry matter quantities of one of two fiber based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets. Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Fecal samples were collected at week 10 and week 16. DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abundant phyla found in both diets and sampling periods were the Firmicutes and Bacteroidetes. There was a clear reduction in Bacteroidetes with a concordant increase in Firmicutes over time. There was a limited degree of stability within the bacterial community of the hindgut of horses, with 65% of bacteria retained, over a 6 week period whilst on a uniform diet. The presence of a core community defined by being present in all samples (each animal/diet combination included in the study and being present at 0.1% relative abundance (or greater was identified. In total 65 operational taxonomic units (OTUs were identified that fit the definition of core making up 21–28% of the total sequences recovered. As with total population the most abundant phyla were the Bacteroidetes followed by the Firmicutes, however there was no obvious shift in phyla due to period. Indeed, when the relative abundance of OTUs was examined across diets and periods there was no significant effect of diet or period alone or in combination on the relative abundance of the core OTUs.

  3. Metastable states and quasicycles in a stochastic Wilson-Cowan model of neuronal population dynamics

    KAUST Repository

    Bressloff, Paul C.

    2010-01-01

    We analyze a stochastic model of neuronal population dynamics with intrinsic noise. In the thermodynamic limit N→∞, where N determines the size of each population, the dynamics is described by deterministic Wilson-Cowan equations. On the other hand

  4. Geographic coupling of juvenile and adult habitat shapes spatial population dynamics of a coral reef fish

    NARCIS (Netherlands)

    Huijbers, C.M.; Nagelekerken, I.; Debrot, A.O.; Jongejans, E.

    2013-01-01

    Marine spatial population dynamics are often addressed with a focus on larval dispersal, without taking into account movement behavior of individuals in later life stages. Processes occurring during demersal life stages may also drive spatial population dynamics if habitat quality is perceived

  5. Effective population size and evolutionary dynamics in outbred ...

    Indian Academy of Sciences (India)

    populations of fruit flies is not primarily driven by new mutations, but rather by changes in the frequency of ..... Drift simulation: The sex ratio, total population size and ...... Gillespie J. H. 1994a Substitution processes in molecular evolution. II.

  6. On the apllication of single specie dynamic population model | Iguda ...

    African Journals Online (AJOL)

    The Method of mathematical models of Malthus and Verhults were applied on ten years data collected from Magaram Poultry Farm to determine the nature of population growth, population decay or constant ... Keywords: Birth rate, sustainable population, overcrowding, harvesting, independent t-test and one way Anova.

  7. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

    DEFF Research Database (Denmark)

    Masoud, Wafa Mahmoud Hasan; Takamiya, Monica K Wik; Vogensen, Finn Kvist

    2011-01-01

    ripening. Other bacteria like Corynebacterium, Halomonas, Pediococcus, Micrococcus and Staphylococcus, which were encountered in some cheese samples at low percentages compared with the total bacterial populations, were only detected by pyrosequencing. 16S rRNA gene pyrosequencing is an efficient method...

  8. The Prestige oil spill: bacterial community dynamics during a field biostimulation assay

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, N; Solanas, A M [Barcelona Univ. (Spain). Dept. of Microbiology; Vinas, M [GIRO Technological Centre, Mollet del Valles (Spain); Bayona, J M; Albaiges, J [IIQAB-CSIC, Barcelona (Spain). Dept. of Environmental Chemistry

    2007-12-15

    A field bioremediation assay using the oleophilic fertilizer S200 was carried out 12 months after the Prestige heavy fuel-oil spill on a beach on the Cantabrian coast (north Spain). This assay showed that S200-enhanced oil degradation, particularly of high-molecular-weight n-alkanes and alkylated PAHs, suggesting an increase in the microbial bioavailability of these compounds. The bacterial community structure was determined by cultivation-independent analysis of polymerase chain reaction-amplified 16S rDNA by denaturing gradient gel electrophoresis. Bacterial community was mainly composed of {alpha}-Proteobacteria (Rhodobacteriaceae and Sphingomonadaceae). Representatives of {gamma}-Proteobacteria (Chromatiales, Moraxellaceae, and Halomonadaceae), Bacteroidetes (Flavobacteriaceae), and Actinobacteria group (Nocardiaceae and Corynebacteriaceae) were also found. The addition of the fertilizer led to the appearance of the bacterium Mesonia algae in the early stages, with a narrow range of growth substrates, which has been associated with the common alga Achrosiphonia sonderi. The presence of Mesonia algae may be attributable to the response of the microbial community to the addition of N and P rather than indicating a role in the biodegradation process. The Rhodococcus group appeared in both assay plots, especially at the end of the experiment. It was also found at another site on the Galician coast that had been affected by the same spill. This genus has been associated with the degradation of n-alkanes up to C{sub 36}. Taking into account the high content of heavy alkanes in the Prestige fuel, these microorganisms could play a significant role in the degradation of such fuel. A similar bacterial community structure was observed at another site that showed a similar degree of fuel weathering. (orig.)

  9. Dynamics of bacterial endospores, and microbial activities in soils and sediments

    DEFF Research Database (Denmark)

    Tamez-Hidalgo, Paulina

    Prokaryotes (Bacteria and Archaea) are essential for life on Earth. They catalyze unique and necessary chemical transformations, which shape the biogeochemical cycles, develop stable and labile pools of carbon (C) and nitrogen (N), produce essential molecules that multicellular organisms live upon...... between being considered slow growers, dormant or even immortal. Despite discussions about minimum energy requirements and metabolic categories, there is a paraphyletic group of Bacteria (the Firmicutes or low-GC Gram positive) able to create the toughest dormant forms on Earth, the endospores. Bacterial...

  10. Dynamic of population-dynamics in a medically important snail species Lymnaea (Radix Luteola (Lamarck

    Directory of Open Access Journals (Sweden)

    T. K. Misra

    1993-09-01

    Full Text Available The life-cycle parameters of the snail Lymnaea (Radix luteola and the factors influencing the same have been studied under laboratory conditions. Ins each month, from July 1990 to June 1991, a batch of 100 zero-day old individual were considered for studies. The snails of April batch survived for 19.42 days while those in December batch survived for 87.45 days. The May batch individual though survived for 65.67 days gained maximum shell size (15.84 mm in length and body weight (419.87 mg. All individuals of April batch died prior to attainment of sexual maturity. In the remaining 11 batches the snails became sexually mature between 32 and 53 days. At this stage, they were with varying shell lengths, 9.3 mm to 13,11 mm in respect to batches. The reproduction period varied from 1-67 days. An individual laid, on an average, 0,25 (March batch to 443.67 (May batch eggs in its life-span. A batch of such snails would leave 24312, 22520, 720268, 80408, 76067, 418165, 214, 9202, 0, 0, 2459386 and 127894 individuals at the end of 352nd day. Since the environmental conditions were almost similar the 'dynamic' of population dynamics seems to be involved with the 'strain' of the snail individuals of the batches concerned.

  11. Dynamics of a physiologically structured population in a time-varying environment

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

    2016-01-01

    Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

  12. Acidic Conditions in the NHE2-/- Mouse Intestine Result in an Altered Mucosa-Associated Bacterial Population with Changes in Mucus Oligosaccharides

    Directory of Open Access Journals (Sweden)

    Melinda A. Engevik

    2013-12-01

    Full Text Available Background: The mechanisms bacteria use to proliferate and alter the normal bacterial composition remain unknown. The ability to link changes in the intestinal micro-environment, such as ion composition and pH, to bacterial proliferation is clinically advantageous for diseases that involve an altered gut microbiota, such as Inflammatory Bowel Disease, obesity and diabetes. In human and mouse intestine, the apical Na+/H+ exchangers NHE2 and NHE3 affect luminal Na+, water, and pH. Loss of NHE2 results in acidic luminal pH. Since acid resistance systems in gram-positive bacteria are well documented, we hypothesize that gram-positive bacteria would increase in representation in the acidic NHE2-/- intestine. Methods: Intestinal ion composition was measured by fame photometry and chloridometry and pH measured electrochemically. DNA extracted from intestinal flushes or from mucosal scrapings was analyzed by qRT-PCR to examine luminal and mucosa-associated bacterial populations. Epithelial mucus oligosaccharide patterns were examined by histology with FIT-C labeled lectins. Results: Although total luminal and mucosa-associated bacteria were unchanged in NHE2-/- intestine, gram-positive bacterial phyla were increased in the mucosa-associated bacterial population in a region-specific manner. The genera Clostridium and Lactobacillus were increased in the cecum and colon which corresponded to changes in NHE2-/- mucus oligosaccharide composition of mannose, N-acetyglucosamine, N-acetygalactosamine and galactose. Conclusions: Together these data indicate that changes in ion transport induce region-specific bacterial changes, which alter host mucus oligosaccharide patterns. These host-bacterial interactions provide a possible mechanism of niche-development and shed insight on how certain groups proliferate in changing environments and maintain their proliferation by altering the host.

  13. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  14. Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization

    Science.gov (United States)

    Ray, J. Christian J; Igoshin, Oleg A.

    2012-01-01

    Bacterial chromosomes are organized into polycistronic cotranscribed operons, but the evolutionary pressures maintaining them are unclear. We hypothesized that operons alter gene expression noise characteristics, resulting in selection for or against maintaining operons depending on network architecture. Mathematical models for 6 functional classes of network modules showed that three classes exhibited decreased noise and 3 exhibited increased noise with same-operon cotranscription of interacting proteins. Noise reduction was often associated with a decreased chance of reaching an ultrasensitive threshold. Stochastic simulations of the lac operon demonstrated that the predicted effects of transcriptional coupling hold for a complex network module. We employed bioinformatic analysis to find overrepresentation of noise-minimizing operon organization compared with randomized controls. Among constitutively expressed physically interacting protein pairs, higher coupling frequencies appeared at lower expression levels, where noise effects are expected to be dominant. Our results thereby suggest an important role for gene expression noise, in many cases interacting with an ultrasensitive switch, in maintaining or selecting for operons in bacterial chromosomes. PMID:22956903

  15. Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach.

    Science.gov (United States)

    Bacci, Giovanni; Ceccherini, Maria Teresa; Bani, Alessia; Bazzicalupo, Marco; Castaldini, Maurizio; Galardini, Marco; Giovannetti, Luciana; Mocali, Stefano; Pastorelli, Roberta; Pantani, Ottorino Luca; Arfaioli, Paola; Pietramellara, Giacomo; Viti, Carlo; Nannipieri, Paolo; Mengoni, Alessio

    2015-03-01

    We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

  16. Dynamic chemical communication between plants and bacteria through airborne signals: induced resistance by bacterial volatiles.

    Science.gov (United States)

    Farag, Mohamed A; Zhang, Huiming; Ryu, Choong-Min

    2013-07-01

    Certain plant growth-promoting rhizobacteria (PGPR) elicit induced systemic resistance (ISR) and plant growth promotion in the absence of physical contact with plants via volatile organic compound (VOC) emissions. In this article, we review the recent progess made by research into the interactions between PGPR VOCs and plants, focusing on VOC emission by PGPR strains in plants. Particular attention is given to the mechanisms by which these bacterial VOCs elicit ISR. We provide an overview of recent progress in the elucidation of PGPR VOC interactions from studies utilizing transcriptome, metabolome, and proteome analyses. By monitoring defense gene expression patterns, performing 2-dimensional electrophoresis, and studying defense signaling null mutants, salicylic acid and ethylene have been found to be key players in plant signaling pathways involved in the ISR response. Bacterial VOCs also confer induced systemic tolerance to abiotic stresses, such as drought and heavy metals. A review of current analytical approaches for PGPR volatile profiling is also provided with needed future developments emphasized. To assess potential utilization of PGPR VOCs for crop plants, volatile suspensions have been applied to pepper and cucumber roots and found to be effective at protecting plants against plant pathogens and insect pests in the field. Taken together, these studies provide further insight into the biological and ecological potential of PGPR VOCs for enhancing plant self-immunity and/or adaptation to biotic and abiotic stresses in modern agriculture.

  17. Dynamical Properties of Transient Spatio-Temporal Patterns in Bacterial Colony of Proteus mirabilis

    Science.gov (United States)

    Watanabe, Kazuhiko; Wakita, Jun-ichi; Itoh, Hiroto; Shimada, Hirotoshi; Kurosu, Sayuri; Ikeda, Takemasa; Yamazaki, Yoshihiro; Matsuyama, Tohey; Matsushita, Mitsugu

    2002-02-01

    Spatio-temporal patterns emerged inside a colony of bacterial species Proteus mirabilis on the surface of nutrient-rich semisolid agar medium have been investigated. We observed various patterns composed of the following basic types: propagating stripe, propagating stripe with fixed dislocation, expanding and shrinking target, and rotating spiral. The remarkable point is that the pattern changes immediately when we alter the position for observation, but it returns to the original if we restore the observing position within a few minutes. We further investigated mesoscopic and microscopic properties of the spatio-temporal patterns. It turned out that whenever the spatio-temporal patterns are observed in a colony, the areas are composed of two superimposed monolayers of elongated bacterial cells. In each area they are aligned almost parallel with each other like a two-dimensional nematic liquid crystal, and move collectively and independently of another layer. It has been found that the observed spatio-temporal patterns are explained as the moiré effect.

  18. Bacterial population dynamics and sensorial quality loss in modified atmosphere packed fresh-cut iceberg lettuce

    NARCIS (Netherlands)

    Paillart, M.J.M.; Vossen, J.M.B.M.; Levin, E.; Lommen, E.; Otma, E.C.; Snels, J.C.M.A.; Woltering, E.J.

    2017-01-01

    The end of shelf life of fresh-cut iceberg lettuce packed in modified atmosphere (MA) is determined by its visual quality and by its microbial load. The total microbial load should not exceed 6–7 log CFU g−1 mesophilic counting and be free of human pathogens. Not much is known about specific

  19. An Empirical Study of AI Population Dynamics with Million-agent Reinforcement Learning

    OpenAIRE

    Yang, Yaodong; Yu, Lantao; Bai, Yiwei; Wang, Jun; Zhang, Weinan; Wen, Ying; Yu, Yong

    2017-01-01

    In this paper, we conduct an empirical study on discovering the ordered collective dynamics obtained by a population of artificial intelligence (AI) agents. Our intention is to put AI agents into a simulated natural context, and then to understand their induced dynamics at the population level. In particular, we aim to verify if the principles developed in the real world could also be used in understanding an artificially-created intelligent population. To achieve this, we simulate a large-sc...

  20. A new ODE tumor growth modeling based on tumor population dynamics

    International Nuclear Information System (INIS)

    Oroji, Amin; Omar, Mohd bin; Yarahmadian, Shantia

    2015-01-01

    In this paper a new mathematical model for the population of tumor growth treated by radiation is proposed. The cells dynamics population in each state and the dynamics of whole tumor population are studied. Furthermore, a new definition of tumor lifespan is presented. Finally, the effects of two main parameters, treatment parameter (q), and repair mechanism parameter (r) on tumor lifespan are probed, and it is showed that the change in treatment parameter (q) highly affects the tumor lifespan

  1. A new ODE tumor growth modeling based on tumor population dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Oroji, Amin; Omar, Mohd bin [Institute of Mathematical Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia amin.oroji@siswa.um.edu.my, mohd@um.edu.my (Malaysia); Yarahmadian, Shantia [Mathematics Department Mississippi State University, USA Syarahmadian@math.msstate.edu (United States)

    2015-10-22

    In this paper a new mathematical model for the population of tumor growth treated by radiation is proposed. The cells dynamics population in each state and the dynamics of whole tumor population are studied. Furthermore, a new definition of tumor lifespan is presented. Finally, the effects of two main parameters, treatment parameter (q), and repair mechanism parameter (r) on tumor lifespan are probed, and it is showed that the change in treatment parameter (q) highly affects the tumor lifespan.

  2. Intraspecific Competition and Population Dynamics of Aedes aegypti

    Science.gov (United States)

    Paixão, C. A.; Charret, I. C.; Lima, R. R.

    2012-04-01

    We report computational simulations for the evolution of the population of the dengue vector, Aedes aegypti mosquitoes. The results suggest that controlling the mosquito population, on the basis of intraspecific competition at the larval stage, can be an efficient mechanism for controlling the spread of the epidemic. The results also show the presence of a kind of genetic evolution in vector population, which results mainly in increasing the average lifespan of individuals in adulthood.

  3. Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load.

    Science.gov (United States)

    Silva, Cynthia C; Viero, Aline F; Dias, Ana Carolina F; Andreote, Fernando D; Jesus, Ederson C; De Paula, Sergio O; Torres, Ana Paula R; Santiago, Vania M J; Oliveira, Valeria M

    2010-01-01

    The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

  4. Characterization of Bacterial Community Dynamics during the Decomposition of Pig Carcasses in Simulated Soil Burial and Composting Systems.

    Science.gov (United States)

    Ki, Bo-Min; Kim, Yu Mi; Jeon, Jun Min; Ryu, Hee Wook; Cho, Kyung-Suk

    2017-12-28

    Soil burial is the most widely used disposal method for infected pig carcasses, but composting has gained attention as an alternative disposal method because pig carcasses can be decomposed rapidly and safely by composting. To understand the pig carcass decomposition process in soil burial and by composting, pilot-scale test systems that simulated soil burial and composting were designed and constructed in the field. The envelope material samples were collected using special sampling devices without disturbance, and bacterial community dynamics were analyzed by high-throughput pyrosequencing for 340 days. Based on the odor gas intensity profiles, it was estimated that the active and advanced decay stages were reached earlier by composting than by soil burial. The dominant bacterial communities in the soil were aerobic and/or facultatively anaerobic gram-negative bacteria such as Pseudomonas, Gelidibacter, Mucilaginibacter , and Brevundimonas . However, the dominant bacteria in the composting system were anaerobic, thermophilic, endospore-forming, and/or halophilic gram-positive bacteria such as Pelotomaculum, Lentibacillus, Clostridium , and Caldicoprobacter . Different dominant bacteria played important roles in the decomposition of pig carcasses in the soil and compost. This study provides useful comparative date for the degradation of pig carcasses in the soil burial and composting systems.

  5. Data Driven Approach for High Resolution Population Distribution and Dynamics Models

    Energy Technology Data Exchange (ETDEWEB)

    Bhaduri, Budhendra L [ORNL; Bright, Eddie A [ORNL; Rose, Amy N [ORNL; Liu, Cheng [ORNL; Urban, Marie L [ORNL; Stewart, Robert N [ORNL

    2014-01-01

    High resolution population distribution data are vital for successfully addressing critical issues ranging from energy and socio-environmental research to public health to human security. Commonly available population data from Census is constrained both in space and time and does not capture population dynamics as functions of space and time. This imposes a significant limitation on the fidelity of event-based simulation models with sensitive space-time resolution. This paper describes ongoing development of high-resolution population distribution and dynamics models, at Oak Ridge National Laboratory, through spatial data integration and modeling with behavioral or activity-based mobility datasets for representing temporal dynamics of population. The model is resolved at 1 km resolution globally and describes the U.S. population for nighttime and daytime at 90m. Integration of such population data provides the opportunity to develop simulations and applications in critical infrastructure management from local to global scales.

  6. High population variability and source-sink dynamics in a solitary bee species.

    Science.gov (United States)

    Franzén, Markus; Nilsson, Sven G

    2013-06-01

    Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

  7. Xylo-Oligosaccharides and Inulin Affect Genotoxicity and Bacterial Populations Differently in a Human Colonic Simulator Challenged with Soy Protein

    Science.gov (United States)

    Christophersen, Claus T.; Petersen, Anne; Licht, Tine R.; Conlon, Michael A.

    2013-01-01

    High dietary intakes of some protein sources, including soy protein, can increase colonic DNA damage in animals, whereas some carbohydrates attenuate this. We investigated whether inulin and xylo-oligosaccharides (XOS) could be protective against DNA strand breaks by adding them to a human colonic simulator consisting of a proximal vessel (PV) (pH 5.5) and a distal vessel (DV) (pH 6.8) inoculated with human faeces and media containing soy protein. Genotoxicity of the liquid phase and microbial population changes in the vessels were measured. Soy protein (3%) was fermented with 1% low amylose cornstarch for 10 day followed by soy protein with 1% XOS or 1% inulin for 10 day. Inulin did not alter genotoxicity but XOS significantly reduced PV genotoxicity and increased DV genotoxicity. Inulin and XOS significantly increased butyrate concentration in the DV but not PV. Numbers of the key butyrate-producing bacterium Faecalibacterium prausnitzii were significantly increased in the PV and DV by inulin but significantly decreased by XOS in both vessels. Other bacteria examined were also significantly impacted by the carbohydrate treatments or by the vessel (i.e., pH). There was a significant overall inverse correlation between levels of damage induced by the ferments and levels of sulphate-reducing bacteria, Bacteroides fragilis, and acetate. In conclusion, dietary XOS can potentially modulate the genotoxicity of the colonic environment and specific bacterial groups and short chain fatty acids may mediate this. PMID:24064573

  8. Bacterial community dynamics are linked to patterns of coral heat tolerance

    KAUST Repository

    Ziegler, Maren

    2017-02-10

    Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.

  9. Bacterial community dynamics are linked to patterns of coral heat tolerance

    KAUST Repository

    Ziegler, Maren; Seneca, Francois O.; Yum, Lauren; Palumbi, Stephen R.; Voolstra, Christian R.

    2017-01-01

    Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.

  10. Dynamic energy budgets in population ecotoxicology: applications and outlook.

    NARCIS (Netherlands)

    Jager, T.; Barsi, A.; Hamda, N.T.; Martin, B.; Zimmer, E.I.; Ducrot, V.

    2014-01-01

    Most of the experimental testing in ecotoxicology takes place at the individual level, but the protection goals for environmental risk assessment are at the population level (or higher). Population modelling can fill this gap, but only models on a mechanistic basis allow for extrapolation beyond the

  11. Demographic processes in a local population: seasonal dynamics of ...

    African Journals Online (AJOL)

    ... differences in daily recruitment and within-patch survival rates. Males were most abundant relative to females early in the season, indicating protandry. Total adult population size was small and showed dramatic variation between the two years, indicating how vulnerable the local population is to demographic extinction.

  12. Dynamics of buckbrush populations under simulated forest restoration alternatives

    Science.gov (United States)

    David W. Huffman; Margaret M. Moore

    2008-01-01

    Plant population models are valuable tools for assessing ecological tradeoffs between forest management approaches. In addition, these models can provide insight on plant life history patterns and processes important for persistence and recovery of populations in changing environments. In this study, we evaluated a set of ecological restoration alternatives for their...

  13. Population Dynamics and Natural Resources in the Volta in the ...

    African Journals Online (AJOL)

    Also, population growth is causing shortfalls in agricultural land, deforestation and high demand on water resources in some of the sub-basins of the Volta River Keywords: Population, Natural resources, Volta River Basin, Human Settlement Land Use/Coverage Change Ghana Journal of Development Studies Vol.

  14. Termite Population Dynamics in Arenic Kandiudults as Influenced by ...

    African Journals Online (AJOL)

    Result shows that carbofuran significantly (P=<0.0001) recorded least termite population per square meter after tuber harvest, whereas A. indica leaves and municipal waste increased termite population per square meter. Also, cassava tuber yield was significantly influenced with application of A. indica leaves and ...

  15. Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest.

    Science.gov (United States)

    Mikkelson, Kristin M; Brouillard, Brent M; Bokman, Chelsea M; Sharp, Jonathan O

    2017-12-05

    Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH 4 + concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique "tree-centric" approach, we were able to delineate plots with various tree mortality levels within the same watershed

  16. Chaos and order in stateless societies: Intercommunity exchange as a factor impacting the population dynamical patterns

    Energy Technology Data Exchange (ETDEWEB)

    Medvinsky, Alexander B., E-mail: medvinsky@iteb.ru [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation); Rusakov, Alexey V. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation)

    2011-06-15

    Highlights: > We model community dynamics in stateless societies. > Intercommunity barter is shown to be a factor impacting the societies dynamics. > Increase in the human population growth rate can lead to appearance of chaos. > Secular and millennial cycles are found to arise as a result of the barter. - Abstract: The once abstract notions of dynamical chaos now appear naturally in various systems [Kaplan D, Glass L. Understanding nonlinear dynamics. New York: Springer; 1995]. As a result, future trajectories of the systems may be difficult to predict. In this paper, we demonstrate the appearance of chaotic dynamics in model human communities, which consist of producers of agricultural product and producers of agricultural equipment. In the case of a solitary community, the horizon of predictability of the human population dynamics is shown to be dependent on both intrinsic instability of the dynamics and the chaotic attractor sizes. Since a separate community is usually a part of a larger commonality, we study the dynamics of social systems consisting of two interacting communities. We show that intercommunity barter can lead to stabilization of the dynamics in one of the communities, which implies persistence of stable equilibrium under changes of the maximum value of the human population growth rate. However, in the neighboring community, the equilibrium turns into a stable limit cycle as the maximum value of the human population growth rate increases. Following an increase in the maximum value of the human population growth rate leads to period-doubling bifurcations resulting in chaotic dynamics. The horizon of predictability of the chaotic oscillations is found to be limited by 5 years. We demonstrate that the intercommunity interaction can lead to the appearance of long-period harmonics in the chaotic time series. The period of the harmonics is of order 100 and 1000 years. Hence the long-period changes in the population size may be considered as an

  17. Chaos and order in stateless societies: Intercommunity exchange as a factor impacting the population dynamical patterns

    International Nuclear Information System (INIS)

    Medvinsky, Alexander B.; Rusakov, Alexey V.

    2011-01-01

    Highlights: → We model community dynamics in stateless societies. → Intercommunity barter is shown to be a factor impacting the societies dynamics. → Increase in the human population growth rate can lead to appearance of chaos. → Secular and millennial cycles are found to arise as a result of the barter. - Abstract: The once abstract notions of dynamical chaos now appear naturally in various systems [Kaplan D, Glass L. Understanding nonlinear dynamics. New York: Springer; 1995]. As a result, future trajectories of the systems may be difficult to predict. In this paper, we demonstrate the appearance of chaotic dynamics in model human communities, which consist of producers of agricultural product and producers of agricultural equipment. In the case of a solitary community, the horizon of predictability of the human population dynamics is shown to be dependent on both intrinsic instability of the dynamics and the chaotic attractor sizes. Since a separate community is usually a part of a larger commonality, we study the dynamics of social systems consisting of two interacting communities. We show that intercommunity barter can lead to stabilization of the dynamics in one of the communities, which implies persistence of stable equilibrium under changes of the maximum value of the human population growth rate. However, in the neighboring community, the equilibrium turns into a stable limit cycle as the maximum value of the human population growth rate increases. Following an increase in the maximum value of the human population growth rate leads to period-doubling bifurcations resulting in chaotic dynamics. The horizon of predictability of the chaotic oscillations is found to be limited by 5 years. We demonstrate that the intercommunity interaction can lead to the appearance of long-period harmonics in the chaotic time series. The period of the harmonics is of order 100 and 1000 years. Hence the long-period changes in the population size may be considered as an

  18. Methods for dynamic investigations of surface-attached in vitro bacterial and fungal biofilms

    DEFF Research Database (Denmark)

    Sternberg, Claus; Bjarnsholt, Thomas; Shirtliff, Mark

    2014-01-01

    Three dynamic models for the investigation of in vitro biofilm formation are described in this chapter. In the 6-well plate assay presented here, the placing of the plate on a rotating platform provides shear, thereby making the system dynamic with respect to the static microtiter assay.The second...... reported model, especially suitable for harvesting high amounts of cells for transcriptomic or proteomic investigations, is based on numerous glass beads placed in a flask incubated with shaking on a rotating platform, thus increasing the surface area for biofilm formation. Finally, the flow-cell system...

  19. A mechanistic analysis of density dependence in algal population dynamics

    Directory of Open Access Journals (Sweden)

    Adrian eBorlestean

    2015-04-01

    Full Text Available Population density regulation is a fundamental principle in ecology, but the specific process underlying functional expression of density dependence remains to be fully elucidated. One view contends that patterns of density dependence are largely fixed across a species irrespective of environmental conditions, whereas another is that the strength and expression of density dependence are fundamentally variable depending on the nature of exogenous or endogenous constraints acting on the population. We conducted a study investigating the expression of density dependence in Chlamydomonas spp. grown under a gradient from low to high nutrient density. We predicted that the relationship between per capita growth rate (pgr and population density would vary from concave up to concave down as nutrient density became less limiting and populations experienced weaker density regulation. Contrary to prediction, we found that the relationship between pgr and density became increasingly concave-up as nutrient levels increased. We also found that variation in pgr increased, and pgr levels reached higher maxima in nutrient-limited environments. Most likely, these results are attributable to population growth suppression in environments with high intraspecific competition due to limited nutrient resources. Our results suggest that density regulation is strongly variable depending on exogenous and endogenous processes acting on the population, implying that expression of density dependence depends extensively on local conditions. Additional experimental work should reveal the mechanisms influencing how the expression of density dependence varies across populations through space and time.

  20. Use of Mobile Device Data To Better Estimate Dynamic Population Size for Wastewater-Based Epidemiology.

    Science.gov (United States)

    Thomas, Kevin V; Amador, Arturo; Baz-Lomba, Jose Antonio; Reid, Malcolm

    2017-10-03

    Wastewater-based epidemiology is an established approach for quantifying community drug use and has recently been applied to estimate population exposure to contaminants such as pesticides and phthalate plasticizers. A major source of uncertainty in the population weighted biomarker loads generated is related to estimating the number of people present in a sewer catchment at the time of sample collection. Here, the population quantified from mobile device-based population activity patterns was used to provide dynamic population normalized loads of illicit drugs and pharmaceuticals during a known period of high net fluctuation in the catchment population. Mobile device-based population activity patterns have for the first time quantified the high degree of intraday, week, and month variability within a specific sewer catchment. Dynamic population normalization showed that per capita pharmaceutical use remained unchanged during the period when static normalization would have indicated an average reduction of up to 31%. Per capita illicit drug use increased significantly during the monitoring period, an observation that was only possible to measure using dynamic population normalization. The study quantitatively confirms previous assessments that population estimates can account for uncertainties of up to 55% in static normalized data. Mobile device-based population activity patterns allow for dynamic normalization that yields much improved temporal and spatial trend analysis.

  1. Exploring the A22-Bacterial Actin MreB Interaction through Molecular Dynamics Simulations.

    Science.gov (United States)

    Awuni, Yaw; Jiang, Shimin; Robinson, Robert C; Mu, Yuguang

    2016-09-22

    MreB is an actin-like cytoskeleton protein that plays a vital role in the maintenance of the rod-shaped morphology of many bacteria. S-(3,4-Dichlorobenzyl) isothiourea (A22) is an antibiotic-like small molecule that perturbs the rod cell shape and has been suggested to inhibit MreB by targeting ATP hydrolysis. However, without the elucidation of the structure of the ATP-bound state of MreB in the presence of A22, the mechanism of A22 inhibition is still not clear. Here we apply conventional molecular dynamics simulations to explore the dynamics of the active site of MreB in complex with A22 and different nucleotides. We observe that hydrogen bonding between A22 and the catalytic Glu140 residue is not favored in the ATP-A22-bound state of MreB. Water dynamics analysis in the MreB active site reveals that in the presence of A22 water molecules are able to occupy positions suitable for ATP hydrolysis. Overall, our results are consistent with a mechanism in which A22 affects MreB polymerization/depolymerization dynamics in part through slowing phosphate release rather than by inhibiting ATP hydrolysis. These data can be incorporated in the design/development of the next generation of MreB inhibitors.

  2. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

    Czech Academy of Sciences Publication Activity Database

    Panecka, J.; Šponer, Jiří; Trylska, J.

    112C, MAY 2015 (2015), s. 96-110 ISSN 0300-9084 R&D Projects: GA ČR(CZ) GBP305/12/G034; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS * DECODING SITE * CRYSTAL-STRUCTURE Subject RIV: BO - Biophysics Impact factor: 3.017, year: 2015

  3. Construction of a stable GFP-tagged Vibrio harveyi strain for bacterial dynamics analysis of abalone infection.

    Science.gov (United States)

    Travers, Marie-Agnès; Barbou, Annaïck; Le Goïc, Nelly; Huchette, Sylvain; Paillard, Christine; Koken, Marcel

    2008-12-01

    Vibrio harveyi is a bacterial marine pathogen that can cause fatal disease in a large range of vertebrates and invertebrates, including the commercially important marine gastropod, Haliotis tuberculata. Since 1997, strains of this bacterium have regularly been causing high mortalities in farmed and wild abalone populations. The way in which the pathogen enters into abalone and the disease transmission mechanisms are thus far unknown. Therefore, a pathogenic strain, ORM4, was green fluorescent protein-tagged and validated both for its growth characteristics and for its virulence as a genuine model for abalone disease. The strain allows V. harveyi quantification by flow cytometry in seawater and in abalone haemolymph as well as the in situ detection of the parasite inside abalone tissues.

  4. Extinction dynamics of a discrete population in an oasis.

    Science.gov (United States)

    Berti, Stefano; Cencini, Massimo; Vergni, Davide; Vulpiani, Angelo

    2015-07-01

    Understanding the conditions ensuring the persistence of a population is an issue of primary importance in population biology. The first theoretical approach to the problem dates back to the 1950s with the Kierstead, Slobodkin, and Skellam (KiSS) model, namely a continuous reaction-diffusion equation for a population growing on a patch of finite size L surrounded by a deadly environment with infinite mortality, i.e., an oasis in a desert. The main outcome of the model is that only patches above a critical size allow for population persistence. Here we introduce an individual-based analog of the KiSS model to investigate the effects of discreteness and demographic stochasticity. In particular, we study the average time to extinction both above and below the critical patch size of the continuous model and investigate the quasistationary distribution of the number of individuals for patch sizes above the critical threshold.

  5. POPULATION DYNAMICS OF SMALL MAMMALS ACROSS A NITROGEN AMENDED LANDSCAPE

    Science.gov (United States)

    Biogeochemical alterations of the nitrogen cycle from anthropogenic activities could have significant effects on ecological processes at the population, community and ecosystem levels. Nitrogen additions in grasslands have produced qualitative and quantitative changes in vegetat...

  6. Do we need demographic data to forecast plant population dynamics?

    Science.gov (United States)

    Tredennick, Andrew T.; Hooten, Mevin B.; Adler, Peter B.

    2017-01-01

    Rapid environmental change has generated growing interest in forecasts of future population trajectories. Traditional population models built with detailed demographic observations from one study site can address the impacts of environmental change at particular locations, but are difficult to scale up to the landscape and regional scales relevant to management decisions. An alternative is to build models using population-level data that are much easier to collect over broad spatial scales than individual-level data. However, it is unknown whether models built using population-level data adequately capture the effects of density-dependence and environmental forcing that are necessary to generate skillful forecasts.Here, we test the consequences of aggregating individual responses when forecasting the population states (percent cover) and trajectories of four perennial grass species in a semi-arid grassland in Montana, USA. We parameterized two population models for each species, one based on individual-level data (survival, growth and recruitment) and one on population-level data (percent cover), and compared their forecasting accuracy and forecast horizons with and without the inclusion of climate covariates. For both models, we used Bayesian ridge regression to weight the influence of climate covariates for optimal prediction.In the absence of climate effects, we found no significant difference between the forecast accuracy of models based on individual-level data and models based on population-level data. Climate effects were weak, but increased forecast accuracy for two species. Increases in accuracy with climate covariates were similar between model types.In our case study, percent cover models generated forecasts as accurate as those from a demographic model. For the goal of forecasting, models based on aggregated individual-level data may offer a practical alternative to data-intensive demographic models. Long time series of percent cover data already exist

  7. The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

    Science.gov (United States)

    Turcotte, Martin M; Reznick, David N; Hare, J Daniel

    2011-11-01

    Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

  8. Chaotic population dynamics and biology of the top-predator

    International Nuclear Information System (INIS)

    Rai, Vikas; Upadhyay, Ranjit Kumar

    2004-01-01

    We study how the dynamics of a food chain depends on the biology of the top-predator. We consider two model food chains with specialist and generalist top-predators. Both types of food chains display same type of chaotic behavior, short-term recurrent chaos; but the generating mechanisms are drastically different. Food chains with specialist top-predators are dictated by exogenous stochastic factors. On the contrary, the dynamics of those with the generalist top-predator is governed by deterministic changes in system parameters. The study also suggests that robust chaos would be a rarity

  9. Causes and consequences of complex population dynamics in an annual plant, Cardamine pensylvanica

    Energy Technology Data Exchange (ETDEWEB)

    Crone, E.E.

    1995-11-08

    The relative importance of density-dependent and density-independent factors in determining the population dynamics of plants has been widely debated with little resolution. In this thesis, the author explores the effects of density-dependent population regulation on population dynamics in Cardamine pensylvanica, an annual plant. In the first chapter, she shows that experimental populations of C. pensylvanica cycled from high to low density in controlled constant-environment conditions. These cycles could not be explained by external environmental changes or simple models of direct density dependence (N{sub t+1} = f[N{sub t}]), but they could be explained by delayed density dependence (N{sub t+1} = f[N{sub t}, N{sub t+1}]). In the second chapter, she shows that the difference in the stability properties of population growth models with and without delayed density dependence is due to the presence of Hopf as well as slip bifurcations from stable to chaotic population dynamics. She also measures delayed density dependence due to effects of parental density on offspring quality in C. pensylvanica and shows that this is large enough to be the cause of the population dynamics observed in C. pensylvanica. In the third chapter, the author extends her analyses of density-dependent population growth models to include interactions between competing species. In the final chapter, she compares the effects of fixed spatial environmental variation and variation in population size on the evolutionary response of C. pensylvanica populations.

  10. Population dynamics of Aphis gossypii Glover and in sole and intercropping systems of cotton and cowpea.

    Science.gov (United States)

    Fernandes, Francisco S; Godoy, Wesley A C; Ramalho, Francisco S; Garcia, Adriano G; Santos, Bárbara D B; Malaquias, José B

    2018-01-01

    Population dynamics of aphids have been studied in sole and intercropping systems. These studies have required the use of more precise analytical tools in order to better understand patterns in quantitative data. Mathematical models are among the most important tools to explain the dynamics of insect populations. This study investigated the population dynamics of aphids Aphis gossypii and Aphis craccivora over time, using mathematical models composed of a set of differential equations as a helpful analytical tool to understand the population dynamics of aphids in arrangements of cotton and cowpea. The treatments were sole cotton, sole cowpea, and three arrangements of cotton intercropped with cowpea (t1, t2 and t3). The plants were infested with two aphid species and were evaluated at 7, 14, 28, 35, 42, and 49 days after the infestations. Mathematical models were used to fit the population dynamics of two aphid species. There were good fits for aphid dynamics by mathematical model over time. The highest population peak of both species A. gossypii and A. craccivora was found in the sole crops, and the lowest population peak was found in crop system t2. These results are important for integrated management programs of aphids in cotton and cowpea.

  11. The demographic drivers of local population dynamics in two rare migratory birds.

    Science.gov (United States)

    Schaub, Michael; Reichlin, Thomas S; Abadi, Fitsum; Kéry, Marc; Jenni, Lukas; Arlettaz, Raphaël

    2012-01-01

    The exchange of individuals among populations can have strong effects on the dynamics and persistence of a given population. Yet, estimation of immigration rates remains one of the greatest challenges for animal demographers. Little empirical knowledge exists about the effects of immigration on population dynamics. New integrated population models fitted using Bayesian methods enable simultaneous estimation of fecundity, survival and immigration, as well as the growth rate of a population of interest. We applied this novel analytical framework to the demography of two populations of long-distance migratory birds, hoopoe Upupa epops and wryneck Jynx torquilla, in a study area in south-western Switzerland. During 2002-2010, the hoopoe population increased annually by 11%, while the wryneck population remained fairly stable. Apparent juvenile and adult survival probability was nearly identical in both species, but fecundity and immigration were slightly higher in the hoopoe. Hoopoe population growth rate was strongly correlated with juvenile survival, fecundity and immigration, while that of wrynecks strongly correlated only with immigration. This indicates that demographic components impacting the arrival of new individuals into the populations were more important for their dynamics than demographic components affecting the loss of individuals. The finding that immigration plays a crucial role in the population growth rates of these two rare species emphasizes the need for a broad rather than local perspective for population studies, and the development of wide-scale conservation actions.

  12. Consequences of population models on the dynamics of food chains.

    NARCIS (Netherlands)