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Sample records for abundant microbial growth

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

    PubMed

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

    2012-03-18

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

  2. New microbial growth factor

    NASA Technical Reports Server (NTRS)

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

    1977-01-01

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

  3. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    PubMed

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence.

  4. Stronger warming effects on microbial abundances in colder regions

    DOE PAGES

    Chen, Ji; Luo, Yiqi; Xia, Jianyang; ...

    2015-12-10

    Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra,more » and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our results therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.« less

  5. Stronger warming effects on microbial abundances in colder regions

    SciTech Connect

    Chen, Ji; Luo, Yiqi; Xia, Jianyang; Jiang, Lifen; Zhou, Xuhui; Lu, Meng; Liang, Junyi; Shi, Zheng; Shelton, Shelby; Cao, Junji

    2015-12-10

    Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra, and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our results therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.

  6. Stronger warming effects on microbial abundances in colder regions.

    PubMed

    Chen, Ji; Luo, Yiqi; Xia, Jianyang; Jiang, Lifen; Zhou, Xuhui; Lu, Meng; Liang, Junyi; Shi, Zheng; Shelton, Shelby; Cao, Junji

    2015-12-10

    Soil microbes play critical roles in regulating terrestrial carbon (C) cycle and its feedback to climate change. However, it is still unclear how the soil microbial community and abundance respond to future climate change scenarios. In this meta-analysis, we synthesized the responses of microbial community and abundance to experimental warming from 64 published field studies. Our results showed that warming significantly increased soil microbial abundance by 7.6% on average. When grouped by vegetation or soil types, tundras and histosols had the strongest microbial responses to warming with increased microbial, fungal, and bacterial abundances by 15.0%, 9.5% and 37.0% in tundra, and 16.5%, 13.2% and 13.3% in histosols, respectively. We found significant negative relationships of the response ratios of microbial, fungal and bacterial abundances with the mean annual temperature, indicating that warming had stronger effects in colder than warmer regions. Moreover, the response ratios of microbial abundance to warming were positively correlated with those of soil respiration. Our findings therefore indicate that the large quantities of C stored in colder regions are likely to be more vulnerable to climate warming than the soil C stored in other warmer regions.

  7. Prediction of Competitive Microbial Growth.

    PubMed

    Fujikawa, Hiroshi

    2016-01-01

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

  8. Teaching Microbial Growth by Simulation.

    ERIC Educational Resources Information Center

    Ruiz, A. Fernandez; And Others

    1989-01-01

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

  9. Global Distribution of Microbial Abundance and Biomass in Subseafloor Sediment

    NASA Astrophysics Data System (ADS)

    Kallmeyer, J.; Pockalny, R. A.; Adhikari, R. R.; Smith, D. C.; D'Hondt, S. L.

    2012-12-01

    Previously published cell counts were mostly from ocean margins and the eastern equatorial Pacific. Cell counts from these environments are generally similar from site to site and decrease logarithmically with sediment depth, although there can be sharp peaks of high cell densities in zones of anaerobic methane-oxidation. Recent counts from the South Pacific Gyre and the North Pacific Gyre are several orders of magnitude lower and show a more rapid decrease with depth than all previously published datasets. With these new data available, total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. The differences between cell counts from ocean margins and upwelling areas and cell counts from oceanic gyres raise three questions. First, how does the abundance of microbes in subseafloor sediment vary throughout the world ocean? Second, what property or properties are likely to control that variation? Third, how does this variation affect estimates of total subseafloor sedimentary biomass and Earth's total biomass? To address these questions, we compiled our cell counts from the South Pacific Gyre, the North Pacific Gyre and the eastern equatorial Pacific Ocean with previously published counts and parameterized the cell distribution at each site and determined two parameters, (i) cell concentration at 1 mbsf and (ii) rate of decrease in cell counts with depth. Both parameters are strongly correlated with mean sedimentation rate and distance to shore. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9*1029 cells (corresponding to 4.1 Pg C and ~0.6% of Earth's total living biomass). This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate

  10. Modeling microbial growth and dynamics.

    PubMed

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

    2015-11-01

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

  11. Microbial abundance in surface ice on the Greenland Ice Sheet

    PubMed Central

    Stibal, Marek; Gözdereliler, Erkin; Cameron, Karen A.; Box, Jason E.; Stevens, Ian T.; Gokul, Jarishma K.; Schostag, Morten; Zarsky, Jakub D.; Edwards, Arwyn; Irvine-Fynn, Tristram D. L.; Jacobsen, Carsten S.

    2015-01-01

    Measuring microbial abundance in glacier ice and identifying its controls is essential for a better understanding and quantification of biogeochemical processes in glacial ecosystems. However, cell enumeration of glacier ice samples is challenging due to typically low cell numbers and the presence of interfering mineral particles. We quantified for the first time the abundance of microbial cells in surface ice from geographically distinct sites on the Greenland Ice Sheet (GrIS), using three enumeration methods: epifluorescence microscopy (EFM), flow cytometry (FCM), and quantitative polymerase chain reaction (qPCR). In addition, we reviewed published data on microbial abundance in glacier ice and tested the three methods on artificial ice samples of realistic cell (102–107 cells ml−1) and mineral particle (0.1–100 mg ml−1) concentrations, simulating a range of glacial ice types, from clean subsurface ice to surface ice to sediment-laden basal ice. We then used multivariate statistical analysis to identify factors responsible for the variation in microbial abundance on the ice sheet. EFM gave the most accurate and reproducible results of the tested methodologies, and was therefore selected as the most suitable technique for cell enumeration of ice containing dust. Cell numbers in surface ice samples, determined by EFM, ranged from ~ 2 × 103 to ~ 2 × 106 cells ml−1 while dust concentrations ranged from 0.01 to 2 mg ml−1. The lowest abundances were found in ice sampled from the accumulation area of the ice sheet and in samples affected by fresh snow; these samples may be considered as a reference point of the cell abundance of precipitants that are deposited on the ice sheet surface. Dust content was the most significant variable to explain the variation in the abundance data, which suggests a direct association between deposited dust particles and cells and/or by their provision of limited nutrients to microbial communities on the GrIS. PMID:25852678

  12. Rapid detection of microbial cell abundance in aquatic systems.

    PubMed

    Rocha, Andrea M; Yuan, Quan; Close, Dan M; O'Dell, Kaela B; Fortney, Julian L; Wu, Jayne; Hazen, Terry C

    2016-11-15

    The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamic systems - the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10(3)-10(6) cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. This work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.

  13. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  14. Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

    PubMed

    Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

    2014-01-01

    The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

  15. Relationships between sedimentary subseafloor microbial abundance and sedimentation rate

    NASA Astrophysics Data System (ADS)

    Kallmeyer, J.

    2015-12-01

    Cell count data for estimates of global subseafloor microbial abundance need to be simplified in order to be used for model calculations All models rely on regressions of cell counts vs. depth. Different strategies are being used for simplifying the data, e.g. averaging over highly variable data from different oceanic provinces or excluding individual datasets that cannot be described by a single regression. While providing global estimates, these models fail to identify the finer details of the controls on subseafloor microbial abundance. Most subseafloor microbes are heterotrophic and gain energy by degrading buried organic matter. Because sedimentation rate is usually positively correlated with primary productivity and organic matter flux to the seafloor, it determines how much organic matter is deposited on the sea floor and how fast it is buried and reaches greater depths. At the same depth, in environments with low sed. rates the organic matter is older, more degraded and supports less metabolic activity than in those with high sed. rates. As a result, sed. rates control penetration depth of oxygen and other electron acceptors. Oxygen penetration remains in the mm to cm range over most sed. rates and it only penetrates significantly deeper at very low rates of ca. 1 mm/kyr or less. However, microbial abundance correlates with sed. rate over a wider range. In order to take a more detailed look at the influence of sed. rate and therefore sediment age on cell abundance, ages and additional geochemical information were assigned to individual cell counts. The new dataset shows the strong influence of sed. rates or rather sediment age on microbial abundance, while oxygen concentrations seem to have only a minor influence. Using data from IODP drill sites that have moved from high to low productivity zones or vice versa helps to differentiate between different factors that control microbial cell abundance.

  16. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    NASA Astrophysics Data System (ADS)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

  17. Abundance and diversity of microbial life in ocean crust.

    PubMed

    Santelli, Cara M; Orcutt, Beth N; Banning, Erin; Bach, Wolfgang; Moyer, Craig L; Sogin, Mitchell L; Staudigel, Hubert; Edwards, Katrina J

    2008-05-29

    Oceanic lithosphere exposed at the sea floor undergoes seawater-rock alteration reactions involving the oxidation and hydration of glassy basalt. Basalt alteration reactions are theoretically capable of supplying sufficient energy for chemolithoautotrophic growth. Such reactions have been shown to generate microbial biomass in the laboratory, but field-based support for the existence of microbes that are supported by basalt alteration is lacking. Here, using quantitative polymerase chain reaction, in situ hybridization and microscopy, we demonstrate that prokaryotic cell abundances on seafloor-exposed basalts are 3-4 orders of magnitude greater than in overlying deep sea water. Phylogenetic analyses of basaltic lavas from the East Pacific Rise (9 degrees N) and around Hawaii reveal that the basalt-hosted biosphere harbours high bacterial community richness and that community membership is shared between these sites. We hypothesize that alteration reactions fuel chemolithoautotrophic microorganisms, which constitute a trophic base of the basalt habitat, with important implications for deep-sea carbon cycling and chemical exchange between basalt and sea water.

  18. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    USGS Publications Warehouse

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  19. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods

    PubMed Central

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands. PMID:27140199

  20. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    PubMed

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

  1. Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges.

    PubMed

    Schmitt, Susanne; Deines, Peter; Behnam, Faris; Wagner, Michael; Taylor, Michael W

    2011-12-01

    Some marine sponges harbor dense and phylogenetically complex microbial communities [high microbial abundance (HMA) sponges] whereas others contain only few and less diverse microorganisms [low microbial abundance (LMA) sponges]. We focused on the phylum Chloroflexi that frequently occurs in sponges to investigate the different associations with three HMA and three LMA sponges from New Zealand. By applying a range of microscopical and molecular techniques a clear dichotomy between HMA and LMA sponges was observed: Chloroflexi bacteria were more abundant and diverse in HMA than in LMA sponges. Moreover, different HMA sponges contain similar Chloroflexi communities whereas LMA sponges harbor different and more variable communities which partly resemble Chloroflexi seawater communities. A comprehensive phylogenetic analysis of our own and publicly available sponge-derived Chloroflexi 16S rRNA gene sequences (> 780 sequences) revealed the enormous diversity of this phylum within sponges including 29 sponge-specific and sponge-coral clusters (SSC/SCC) as well as a 'supercluster' consisting of > 250 sponge-derived and a single nonsponge-derived 16S rRNA gene sequence. Interestingly, the majority of sequences obtained from HMA sponges, but only a few from LMA sponges, fell into SSC/SCC clusters. This indicates a much more specific association of Chloroflexi bacteria with HMA sponges and suggests an ecologically important role for these prominent bacteria.

  2. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  3. Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera

    PubMed Central

    Morris, Megan M.; Haggerty, John M.; Papudeshi, Bhavya N.; Vega, Alejandro A.; Edwards, Matthew S.; Dinsdale, Elizabeth A.

    2016-01-01

    Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community

  4. Conditioning biomass for microbial growth

    DOEpatents

    Bodie, Elizabeth A; England, George

    2015-03-31

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

  5. Well having inhibited microbial growth

    DOEpatents

    Lee, Brady D.; Dooley, Kirk J.

    2006-08-15

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

  6. A thermodynamic theory of microbial growth

    PubMed Central

    Desmond-Le Quéméner, Elie; Bouchez, Théodore

    2014-01-01

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

  7. A thermodynamic theory of microbial growth.

    PubMed

    Desmond-Le Quéméner, Elie; Bouchez, Théodore

    2014-08-01

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

  8. Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges

    PubMed Central

    Coma, Rafel; Riemann, Lasse

    2015-01-01

    Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. 15N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of 15N to 14N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology. PMID:26070678

  9. Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges.

    PubMed

    Ribes, Marta; Dziallas, Claudia; Coma, Rafel; Riemann, Lasse

    2015-09-01

    Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. (15)N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of (15)N to (14)N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology.

  10. Microbial carbonate abundance compared with fluctuations in metazoan diversity over geological time

    NASA Astrophysics Data System (ADS)

    Riding, Robert

    2006-03-01

    Secular variation in microbial carbonate abundance may be reflected by stromatolite morphotype diversity and reefal microbial carbonate abundance. These datasets reveal long-term changes over the past 3000 Myr that include a peak of abundance 1250 Myr ago, Late Proterozoic decline, Cambrian resurgence, and fluctuating decline during the remainder of the Phanerozoic. It is conceivable that Proterozoic metazoan diversification coincided with inception of stromatolite decline ˜1250 Myr ago, but microbial carbonate increase during Cambrian metazoan radiation together with failure of microbial carbonates to increase in the aftermaths of the End-Ordovician, End-Triassic and End-Cretaceous Mass Extinctions suggest that factors in addition to metazoan competition significantly influenced long-term changes in microbial carbonate abundance.

  11. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

    PubMed

    Kembel, Steven W; Wu, Martin; Eisen, Jonathan A; Green, Jessica L

    2012-01-01

    The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.

  12. Differential Abundance of Microbial Functional Groups along the Elevation Gradient from the Coast to the Luquillo Mountains

    EPA Science Inventory

    Microbial communities respond to multiple abiotic and biotic factors that change along elevation gradients. We compare changes in microbial community composition in soil and review previous research on differential abundance of microbial functional groups along an elevation gradi...

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

    PubMed Central

    Dick, Jeffrey M.; Shock, Everett L.

    2013-01-01

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

  14. 21 CFR 866.2560 - Microbial growth monitor.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbial growth monitor. 866.2560 Section 866...) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth monitor. (a) Identification. A microbial growth monitor is a device intended for medical purposes...

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

    PubMed

    Cabrol, Léa; Quéméneur, Marianne; Misson, Benjamin

    2017-02-01

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

  16. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  17. Microbial Growth under Supercritical CO2

    PubMed Central

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

    2015-01-01

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

  18. Microbial growth under supercritical CO2.

    PubMed

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

    2015-04-01

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

  19. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    PubMed

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.

  20. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities.

    PubMed

    Smith, Renee J; Paterson, James S; Sibley, Cally A; Hutson, John L; Mitchell, James G

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices.

  1. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

    PubMed Central

    Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  2. Abundance and salt tolerance of obligately aerobic, phototrophic bacteria in a marine microbial mat

    NASA Astrophysics Data System (ADS)

    Yurkov, Vladimir V.; Van Gemerden, Hans

    Data have been collected on the abundance of obligately aerobic, bacteriochlorophyll- a-containing bacteria in a marine microbial mat on the West Frisian Island of Texel, The Netherlands. Plate counts on media rich in organic matter revealed average numbers of 3 ∗10 5·cm -3 sediment in the top 10 mm of the mat; the number of purple non-sulphur bacteria was of the same magnitude. Due to the relatively small dimensions of obligately aerobic anoxygenic phototrophic bacteria and purple non-sulphur bacteria, compared to those of purple sulphur bacteria, the contributions of either of the two former groups to the biomass of Bchl- a-containing organisms was approximately 3%. The specific Bchl- a-content of the isolated obligately aerobic phototrophs was very low (0.8 to 1.0 μg·mg -1 protein) compared to that of purple non-sulphur bacteria (16 to 20 μg·mg -1 protein), and purple sulphur bacteria (27 to 30 μg·mg -1). As a consequence, the relative contribution to the total Bchl a concentration of the two former groups (0.1% and 2.1%, respectively) was negligible, compared to that of the purple sulphur bacteria (97.8%). Salinities <50 had little effect on growth rate and yield of isolates; at salinities between 50 and 100 the doubling time increased progressively with a concomitant decrease in yield; no growth occurred at salinities > 140.

  3. Microbial Abundances in Salt Marsh Soils: A Molecular Approach for Small Spatial Scales

    NASA Astrophysics Data System (ADS)

    Granse, Dirk; Mueller, Peter; Weingartner, Magdalena; Hoth, Stefan; Jensen, Kai

    2016-04-01

    The rate of biological decomposition greatly determines the carbon sequestration capacity of salt marshes. Microorganisms are involved in the decomposition of biomass and the rate of decomposition is supposed to be related to microbial abundance. Recent studies quantified microbial abundance by means of quantitative polymerase chain reaction (QPCR), a method that also allows determining the microbial community structure by applying specific primers. The main microbial community structure can be determined by using primers specific for 16S rRNA (Bacteria) and 18S rRNA (Fungi) of the microbial DNA. However, the investigation of microbial abundance pattern at small spatial scales, such as locally varying abiotic conditions within a salt-marsh system, requires high accuracy in DNA extraction and QPCR methods. Furthermore, there is evidence that a single extraction may not be sufficient to reliably quantify rRNA gene copies. The aim of this study was to establish a suitable DNA extraction method and stable QPCR conditions for the measurement of microbial abundances in semi-terrestrial environments. DNA was extracted from two soil samples (top WE{5}{cm}) by using the PowerSoil DNA Extraction Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) and applying a modified extraction protocol. The DNA extraction was conducted in four consecutive DNA extraction loops from three biological replicates per soil sample by reusing the PowerSoil bead tube. The number of Fungi and Bacteria rRNA gene copies of each DNA extraction loop and a pooled DNA solution (extraction loop 1 - 4) was measured by using the QPCR method with taxa specific primer pairs (Bacteria: B341F, B805R; Fungi: FR1, FF390). The DNA yield of the replicates varied at DNA extraction loop 1 between WE{25 and 85}{ng

  4. MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN

    SciTech Connect

    Leschine, Susan

    2009-10-31

    Our research has dealt with seven major areas of investigation: i) characterization of cellulolytic members of microbial consortia, with special attention recently given to Clostridium phytofermentans, a bacterium that decomposes cellulose and produces uncommonly large amounts of ethanol, ii) investigations of the chitinase system of Cellulomonas uda; including the purification and characterization of ChiA, the major component of this enzyme system, iii) molecular cloning, sequence and structural analysis of the gene that encodes ChiA in C. uda, iv) biofilm formation by C. uda on nutritive surfaces, v) investigations of the effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes, vi) studies of nitrogen metabolism in cellulolytic anaerobes, and vii) understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. Also, progress toward completing the research of more recent projects is briefly summarized. Major accomplishments include: 1. Characterization of Clostridium phytofermentans, a cellulose-fermenting, ethanol-producing bacterium from forest soil. The characterization of a new cellulolytic species isolated from a cellulose-decomposing microbial consortium from forest soil was completed. This bacterium is remarkable for the high concentrations of ethanol produced during cellulose fermentation, typically more than twice the concentration produced by other species of cellulolytic clostridia. 2. Examination of the use of chitin as a source of carbon and nitrogen by cellulolytic microbes. We discovered that many cellulolytic anaerobes and facultative aerobes are able to use chitin as a source of both carbon and nitrogen. This major discovery expands our understanding of the biology of cellulose-fermenting bacteria and may lead to new applications for these microbes. 3. Comparative studies of the cellulase and chitinase systems of Cellulomonas uda. Results of these studies indicate

  5. [Microbial community abundance and diversity in typical karst ecosystem to indicate soil carbon cycle].

    PubMed

    Jin, Zhen-Jiang; Tang, Hua-Feng; Li, Min; Huang, Bing-Fu; Li, Qiang; Zhang, Jia-Yu; Li, Gui-Wen

    2014-11-01

    The soil microbial characteristics were detected to clarify their indications in organic carbon cycle in karst system. Soil samples from three karst types (saddle, depression and slop) at 0-10 cm, 10-20 cm and 20-30 cm layers were collected in the Yaji Karst Experimental Site, a typical karst ecosystem. The microbial diversity and abundance were assayed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and fluorescence quantitative PCR. The data showed that the highest abundance of 16S rRNA and 18S rRNA were in depression with 1.32 x 10(11) copies x g(-1) and in saddle with 1.12 x 10(10) copies x g(-1), respectively. The abundance of 16S rRNA in saddle and depression decreased from top to bottom, while that of 18S rRNA in three karst forms decreased, which showed that the abundance changed consistently with soil organic carbon (SOC). The 3 diversity indices of 16S rRNA and 6 diversity indices of 18S rRNA increased from top to bottom in soil profiles of three karst forms. These results showed that microbial diversity changed conversely with the abundance and SOC in soil profile. It can be concluded that the abundance was more important than the diversity index for soil carbon cycle in karst system.

  6. Aboveground and belowground plant traits as drivers of microbial abundance and activity.

    NASA Astrophysics Data System (ADS)

    Baxendale, Catherine; Lavorel, Sandra; Grigulis, Karl; Legay, Nicolas; Krainer, Ute; Bahn, Michael; Kastl, Eva; Pommier, Thomas; Bardgett, Richard

    2013-04-01

    Although there is growing awareness of the roles that plant-soil interactions play in regulating ecosystem processes, our understanding of the role that specific aboveground and belowground plant traits play in defining them is limited. In this study, we aimed to develop a conceptual model linking plant functional trait impacts on soil microbial functional diversity and their coupled effects on ecosystem processes. This was done by replicating three mesocosm studies, based on model sub-alpine grasslands, across three sites in different parts of Europe as part of the pan-European project, VITAL. We manipulated community plant traits by planting communities of varying abundance and dominance of 4 common grassland species. After 1.5 years, we then measured aboveground traits (specific leaf area, leaf dry matter content, leaf nitrogen and carbon content and leaf C:N ratio), belowground traits (specific root length, average diameter, root dry matter content, root nitrogen and carbon content and root C:N ratio) microbial community abundance (using phospholipid fatty acid (PLFA) analysis and gene abundance of nitrifier and denitrifier communities), and microbial activity (via potential nitrification and denitrification rates). We present links between manipulated community traits, microbial properties and ecosystem processes, supporting the role of plant traits in driving microbial properties.

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

    NASA Astrophysics Data System (ADS)

    Pereg, Lily

    2014-05-01

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

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

    PubMed

    Ibarz, Albert; Augusto, Pedro E D

    2015-01-01

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

  9. Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

    NASA Astrophysics Data System (ADS)

    Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

    2005-12-01

    Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

  10. Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.

    PubMed

    McCoy, Connor O; Matsen, Frederick A

    2013-01-01

    In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.

  11. Pyrene biodegradation in an industrial soil exposed to simulated rhizodeposition: how does it affect functional microbial abundance?

    PubMed

    Meng, Liang; Zhu, Yong-Guan

    2011-02-15

    Rhizodeposition is an important biogeochemical process for the phytoremediation of contaminated substrates. This study investigated the effects of various rhizodeposition components from celery (Apium graveolens) on pyrene biodegradation and microbial abundance in a long-term contaminated soil. Batch microcosms simulating in situ contaminated soil were amended with lipophilic extract, water-soluble extract, or debris from celery root to mimic plant rhizodeposition within 70 days. Soil was intermittently analyzed for pyrene concentration and target gene abundance estimated by real-time PCR. Lipophilic extract was the major simulated rhizodeposit enhancing pyrene biodegradation, while water-soluble extract stimulated microbial growth most efficiently. The relative abundance of total polycyclic aromatic hydrocarbon (PAH) degraders was enhanced by lipophilic extract but inhibited by the other two rhizodeposits, indicating that these components exerted different selective pressures on PAH degrader community. Moreover, PAH catabolic pathway may involve in the pollutant detoxification and fatty acid metabolism by microorganisms, which were also affected by rhizodeposition. These results provide insights into plant-microbe interactions responsible for PAH biodegradation and offer opportunities to facilitate PAH phytoremediation in industrial sites.

  12. Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment.

    PubMed

    Luo, Ling; Gu, Ji-Dong

    2016-09-13

    Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. Bioflumology: Microbial mat growth in flumes

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  16. Microbial Diversity and Lipid Abundance in Microbial Mats from a Sulfidic, Saline, Warm Spring in Utah, USA

    NASA Astrophysics Data System (ADS)

    Gong, J.; Edwardson, C.; Mackey, T. J.; Dzaugis, M.; Ibarra, Y.; Course 2012, G.; Frantz, C. M.; Osburn, M. R.; Hirst, M.; Williamson, C.; Hanselmann, K.; Caporaso, J.; Sessions, A. L.; Spear, J. R.

    2012-12-01

    The microbial diversity of Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake was investigated. The measured pH, temperature, salinity, and sulfide concentration along the flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM to negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were dissected into depth profiles based on the color and texture of the mat layers. Genomic DNA was extracted from each layer, and the 16S rRNA gene was amplified and sequenced on the Roche 454 Titanium platform. Fatty acids were also extracted from the mat layers and analyzed by liquid chromatography and mass spectrometry. The mats at Stinking Springs were classified into roughly two morphologies with respect to their spatial distribution: loose, sometimes floating mats proximal to the spring source; and thicker, well-laminated mats distal to the spring source. Loosely-laminated mats were found in turbulent stream flow environments, whereas well-laminated mats were common in less turbulent sheet flows. Phototrophs, sulfur oxidizers, sulfate reducers, methanogens, other bacteria and archaea were identified by 16S rRNA gene sequences. Diatoms, identified by microscopy and lipid analysis were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were identified and characterized at the two fast flowing sites. These two streamer varieties were dominated by either cyanobacteria or flavobacteria. Overall, our genomic and lipid analysis suggest that the physical and chemical environment is more predictive of the community composition than mat morphology. Site Map

  17. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.

    PubMed

    Carini, Paul; Marsden, Patrick J; Leff, Jonathan W; Morgan, Emily E; Strickland, Michael S; Fierer, Noah

    2016-12-19

    Extracellular DNA from dead microorganisms can persist in soil for weeks to years(1-3). Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide(4). We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.

  18. Microbial abundance and community composition influence production performance in a low-temperature petroleum reservoir.

    PubMed

    Li, Guoqiang; Gao, Peike; Wu, Yunqiang; Tian, Huimei; Dai, Xuecheng; Wang, Yansen; Cui, Qingfeng; Zhang, Hongzuo; Pan, Xiaoxuan; Dong, Hanping; Ma, Ting

    2014-05-06

    Enhanced oil recovery using indigenous microorganisms has been successfully applied in the petroleum industry, but the role of microorganisms remains poorly understood. Here, we investigated the relationship between microbial population dynamics and oil production performance during a water flooding process coupled with nutrient injection in a low-temperature petroleum reservoir. Samples were collected monthly over a two-year period. The microbial composition of samples was determined using 16S rRNA gene pyrosequencing and real-time quantitative polymerase chain reaction analyses. Our results indicated that the microbial community structure in each production well microhabitat was dramatically altered during flooding with eutrophic water. As well as an increase in the density of microorganisms, biosurfactant producers, such as Pseudomonas, Alcaligenes, Rhodococcus, and Rhizobium, were detected in abundance. Furthermore, the density of these microorganisms was closely related to the incremental oil production. Oil emulsification and changes in the fluid-production profile were also observed. In addition, we found that microbial community structure was strongly correlated with environmental factors, such as water content and total nitrogen. These results suggest that injected nutrients increase the abundance of microorganisms, particularly biosurfactant producers. These bacteria and their metabolic products subsequently emulsify oil and alter fluid-production profiles to enhance oil recovery.

  19. Microbiome interplay: plants alter microbial abundance and diversity within the built environment.

    PubMed

    Mahnert, Alexander; Moissl-Eichinger, Christine; Berg, Gabriele

    2015-01-01

    The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria, and Eukaryota (fungi) increased on surrounding floor and wall surfaces within 6 months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g., Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  20. Organic amendments enhance microbial diversity and abundance of functional genes in Australian Soils

    NASA Astrophysics Data System (ADS)

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2016-04-01

    Food and cash crops play important roles in Australia's economy with black, grey and red clay soil, widely use for growing cotton, wheat, corn and other crops in rotation. While the majority of cotton growers use nitrogen and phosphate fertilizers only in the form of agrochemicals, a few experiment with the addition of manure or composted plant material before planting. We hypothesized that the use of such organic amendments would enhance the soil microbial function through increased microbial diversity and abundance, thus contribute to improved soil sustainability. To test the hypothesis we collected soil samples from two cotton-growing farms in close geographical proximity and with mostly similar production practices other than one grower has been using composted plants as organic amendment and the second farmer uses only agrochemicals. We applied the Biolog Ecoplate system to study the metabolic signature of microbial communities and used qPCR to estimate the abundance of functional genes in the soil. The soil treated with organic amendments clearly showed higher metabolic activity of a more diverse range of carbon sources as well as higher abundance of genes involved in the nitrogen and phosphorous cycles. Since microbes undertake a large number of soil functions, the use of organic amendments can contribute to the sustainability of agricultural soils.

  1. Microbial abundance and composition influence litter decomposition response to environmental change.

    PubMed

    Allison, Steven D; Lu, Ying; Weihe, Claudia; Goulden, Michael L; Martiny, Adam C; Treseder, Kathleen K; Martiny, Jennifer B H

    2013-03-01

    Rates of ecosystem processes such as decomposition are likely to change as a result of human impacts on the environment. In southern California, climate change and nitrogen (N) deposition in particular may alter biological communities and ecosystem processes. These drivers may affect decomposition directly, through changes in abiotic conditions, and indirectly through changes in plant and decomposer communities. To assess indirect effects on litter decomposition, we reciprocally transplanted microbial communities and plant litter among control and treatment plots (either drought or N addition) in a grassland ecosystem. We hypothesized that drought would reduce decomposition rates through moisture limitation of decomposers and reductions in plant litter quality before and during decomposition. In contrast, we predicted that N deposition would stimulate decomposition by relieving N limitation of decomposers and improving plant litter quality. We also hypothesized that adaptive mechanisms would allow microbes to decompose litter more effectively in their native plot and litter environments. Consistent with our first hypothesis, we found that drought treatment reduced litter mass loss from 20.9% to 15.3% after six months. There was a similar decline in mass loss of litter inoculated with microbes transplanted from the drought treatment, suggesting a legacy effect of drought driven by declines in microbial abundance and possible changes in microbial community composition. Bacterial cell densities were up to 86% lower in drought plots and at least 50% lower on litter derived from the drought treatment, whereas fungal hyphal lengths increased by 13-14% in the drought treatment. Nitrogen effects on decomposition rates and microbial abundances were weaker than drought effects, although N addition significantly altered initial plant litter chemistry and litter chemistry during decomposition. However, we did find support for microbial adaptation to N addition with N

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

    PubMed Central

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

    2017-01-01

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

  3. Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica

    PubMed Central

    Bézy, Vanessa S.; Valverde, Roldán A.; Plante, Craig J.

    2015-01-01

    Several studies have suggested that significant embryo mortality is caused by microbes, while high microbial loads are generated by the decomposition of eggs broken by later nesting turtles. This occurs commonly when nesting density is high, especially during mass nesting events (arribadas). However, no previous research has directly quantified microbial abundance and the associated effects on sea turtle hatching success at a nesting beach. The aim of this study was to test the hypothesis that the microbial abundance in olive ridley sea turtle nest sand affects the hatching success at Ostional, Costa Rica. We applied experimental treatments to alter the microbial abundance within the sand into which nests were relocated. We monitored temperature, oxygen, and organic matter content throughout the incubation period and quantified the microbial abundance within the nest sand using a quantitative polymerase chain reaction (qPCR) molecular analysis. The most successful treatment in increasing hatching success was the removal and replacement of nest sand. We found a negative correlation between hatching success and fungal abundance (fungal 18S rRNA gene copies g-1 nest sand). Of secondary importance in determining hatching success was the abundance of bacteria (bacterial 16S rRNA gene copies g-1 g-1 nest sand). Our data are consistent with the hypothesis that high microbial activity is responsible for the lower hatching success observed at Ostional beach. Furthermore, the underlying mechanism appears to be the deprivation of oxygen and exposure to higher temperatures resulting from microbial decomposition in the nest. PMID:25714355

  4. Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

    PubMed Central

    Smithwick, Erica A. H.; Naithani, Kusum J.; Balser, Teri C.; Romme, William H.; Turner, Monica G.

    2012-01-01

    Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R2<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21st Century. PMID:23226324

  5. Linking potential denitrification rates to microbial gene abundances in multiple boreal ecosystems

    NASA Astrophysics Data System (ADS)

    Petersen, D. G.; Blazewicz, S.; Herman, D. J.; Firestone, M. K.; Waldrop, M. P.

    2010-12-01

    The composition and functioning of boreal ecosystems are vulnerable to changes in climate, leading to changes in season length, fire regimes, and soil moisture status. To investigate the influence of vegetation and soil moisture on microbial nitrogen cycling several disparate boreal ecosystems was studied. The two primary objectives were to: (1) determine whether process rates could be predicted solely from soil physical and chemical characteristics and (2) determine if the abundance of functional genes could be an additional explanatory variable. Surface soils were sampled along an elevation-driven hydrologic gradient at the Bonanza Creek LTER that corresponds with five plant communities typical of interior Alaska. The plant communities included a black spruce stand, a deciduous stand, a tussock grassland, an emergent fen, and a rich fen. We examined the chemical composition of the surface organic moss and soil, measured gross N-mineralization, potential rates of nitrification and denitrification (DEA), and abundances of several functional groups of microorganisms from soil cores collected in mid summer. We used quantitative PCR to assess the gene abundances of ammonia oxidizers and denitrifiers based on a functional gene approach. Here, we focus on potential denitrification rates (PDR), and abundance of denitrifyers carrying NirS and NirK genes (nitrate reductase) and NosZ genes (nitrous oxide reductase). PDR increased dramatically with increasing soil moisture along the gradient, from 1 mg N/m2/h at the dry black spruce site to 300 mg N/m2/h in the rich fen, which is very high compared to other poorly drained soil environments. PDR were linearly related to the abundance of functional genes from the microorganisms responsible for this process. Abundances of NirS, NirK and NosZ genes correlated significantly to PDR (r2 = 0.61 p < 0.0001, r2 = 0.45 p < 0.0003, r2 = 0.81 p < 0.0001, respectively). In addition, PDR were better explained by functional gene abundances

  6. Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir

    PubMed Central

    Gao, Peike; Tian, Huimei; Li, Guoqiang; Sun, Hongwen; Ma, Ting

    2015-01-01

    Microbial populations associated with microbial enhanced oil recovery (MEOR) and their abundance in the Xinjiang Luliang water-flooding petroleum reservoir were investigated using 16S rRNA, nitrate reductases, dissimilatory sulfate reductase, and methyl coenzyme-M reductase-encoded genes to provide ecological information for the potential application of MEOR. 16S rRNA gene miseq sequencing revealed that this reservoir harbored large amounts of taxa, including 155 bacterial and 7 archeal genera. Among them, Arcobacter, Halomonas, Marinobacterium, Marinobacter, Sphingomonas, Rhodococcus, Pseudomonas, Dietzia, Ochrobactrum, Hyphomonas, Acinetobacter, and Shewanella were dominant, and have the potential to grow using hydrocarbons as carbon sources. Metabolic gene clone libraries indicated that the nitrate-reducing bacteria (NRB) mainly belonged to Pseudomonas, Azospirillum, Bradyrhizobium, Thauera, Magnetospirillum, Sinorhizobium, Azoarcus, and Rhodobacter; the sulfate-reducing bacteria (SRB) were Desulfarculus, Desulfomonile, Desulfosarcina, Desulfotignum, Desulfacinum, Desulfatibacillum, Desulfatibacillum, Desulfomicrobium, and Desulfovibrio; while the methanogens were archaea and belonged to Methanomethylovorans, Methanosaeta, Methanococcus, Methanolobus, and Methanobacterium. Real-time quantitative PCR analysis indicated that the number of bacterial 16S rRNA reached 106 copies/mL, while the metabolic genes of NRB, SRB, and methanogens reached 104 copies/mL. These results show that the Luliang reservoir has abundant microbial populations associated with oil recovery, suggesting that the reservoir has potential for MEOR. PMID:25641701

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

    PubMed

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

    2012-09-18

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

  8. Herbivory: effects on plant abundance, distribution and population growth

    PubMed Central

    Maron, John L; Crone, Elizabeth

    2006-01-01

    Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant–consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics. PMID:17002942

  9. Effects of biochar and elevated soil temperature on soil microbial activity and abundance in an agricultural system

    NASA Astrophysics Data System (ADS)

    Bamminger, Chris; Poll, Christian; Marhan, Sven

    2014-05-01

    As a consequence of Global Warming, rising surface temperatures will likely cause increased soil temperatures. Soil warming has already been shown to, at least temporarily, increase microbial activity and, therefore, the emissions of greenhouse gases like CO2 and N2O. This underlines the need for methods to stabilize soil organic matter and to prevent further boost of the greenhouse gas effect. Plant-derived biochar as a soil amendment could be a valuable tool to capture CO2 from the atmosphere and sequestrate it in soil on the long-term. During the process of pyrolysis, plant biomass is heated in an oxygen-low atmosphere producing the highly stable solid matter biochar. Biochar is generally stable against microbial degradation due to its chemical structure and it, therefore, persists in soil for long periods. Previous experiments indicated that biochar improves or changes several physical or chemical soil traits such as water holding capacity, cation exchange capacity or soil structure, but also biotic properties like microbial activity/abundance, greenhouse gas emissions and plant growth. Changes in the soil microbial abundance and community composition alter their metabolism, but likely also affect plant productivity. The interaction of biochar addition and soil temperature increase on soil microbial properties and plant growth was yet not investigated on the field scale. To investigate whether warming could change biochar effects in soil, we conducted a field experiment attached to a soil warming experiment on an agricultural experimental site near the University of Hohenheim, already running since July 2008. The biochar field experiment was set up as two-factorial randomized block design (n=4) with the factors biochar amendment (0, 30 t ha-1) and soil temperature (ambient, elevated=ambient +2.5° C) starting from August 2013. Each plot has a dimension of 1x1m and is equipped with combined soil temperature and moisture sensors. Slow pyrolysis biochar from the C

  10. Increasing aridity reduces soil microbial diversity and abundance in global drylands.

    PubMed

    Maestre, Fernando T; Delgado-Baquerizo, Manuel; Jeffries, Thomas C; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Quero, José Luis; García-Gómez, Miguel; Gallardo, Antonio; Ulrich, Werner; Bowker, Matthew A; Arredondo, Tulio; Barraza-Zepeda, Claudia; Bran, Donaldo; Florentino, Adriana; Gaitán, Juan; Gutiérrez, Julio R; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Mau, Rebecca L; Miriti, Maria; Naseri, Kamal; Ospina, Abelardo; Stavi, Ilan; Wang, Deli; Woods, Natasha N; Yuan, Xia; Zaady, Eli; Singh, Brajesh K

    2015-12-22

    Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

  11. Increasing aridity reduces soil microbial diversity and abundance in global drylands

    PubMed Central

    Delgado-Baquerizo, Manuel; Jeffries, Thomas C.; Eldridge, David J.; Ochoa, Victoria; Gozalo, Beatriz; Quero, José Luis; García-Gómez, Miguel; Gallardo, Antonio; Ulrich, Werner; Bowker, Matthew A.; Arredondo, Tulio; Barraza-Zepeda, Claudia; Bran, Donaldo; Florentino, Adriana; Gaitán, Juan; Gutiérrez, Julio R.; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Mau, Rebecca L.; Miriti, Maria; Naseri, Kamal; Ospina, Abelardo; Stavi, Ilan; Wang, Deli; Woods, Natasha N.; Yuan, Xia; Zaady, Eli; Singh, Brajesh K.

    2015-01-01

    Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands. PMID:26647180

  12. Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

    NASA Astrophysics Data System (ADS)

    Jeffries, T. C.; Seymour, J. R.; Newton, K.; Smith, R. J.; Seuront, L.; Mitchell, J. G.

    2012-02-01

    Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes - organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

  13. Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

    NASA Astrophysics Data System (ADS)

    Jeffries, T. C.; Seymour, J. R.; Newton, K.; Smith, R. J.; Seuront, L.; Mitchell, J. G.

    2011-07-01

    Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes - organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

  14. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  15. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient

    PubMed Central

    Fortunato, Caroline S.; Crump, Byron C.

    2015-01-01

    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance

  16. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

    PubMed

    Fortunato, Caroline S; Crump, Byron C

    2015-01-01

    Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance

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

    EPA Science Inventory

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

  18. Substrate and nutrient limitation regulating microbial growth in soil

    NASA Astrophysics Data System (ADS)

    Bååth, Erland

    2015-04-01

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

  19. Sulfate reduction and microbial abundance in saline, alkaline Lake Van (Eastern Anatolia, Turkey) - ICDP Expedition 5034

    NASA Astrophysics Data System (ADS)

    Kallmeyer, J.; Glombitza, C.; PaeloVAN Scientific Party

    2012-04-01

    Lake Van is the fourth lagest terminal lake in the world. It is located on the Eastern Anatolian High Plateau (Turkey) and surrounded by two semi-active vulcanos (Nemruth Dagi and Syphan Dagi). Evaporation processes, chemical weathering of vulcanic rocks and hydrothermal activity have created an environment of extreme alkalinity (155 m eql-1, pH 9.81) and salinity (21.4 ‰) (Kempe et al., 1991). Sediments of saline and highly alkaline soda lakes, such as Lake Van, represent one of the most extreme environments on Earth (Stam et al., 2010). These sediments host extremophilic microorganisms (alkaliphiles and halophiles) that have adapted their metabolism to these peculiar environmental conditions (Oren et al., 2002) In summer 2010 the ICDP Expedition 5034 (ICDP project PALEOVAN) retrieved long sediment cores at two sites at Lake Van, Northern Basin (5 km offshore, 245 meters below lake level, mbll) and Ahlat Ridge (12 km offshore, 357 mbll) [2]. At both sites, samples from optically undisturbed core catcher material were collected on site to investigate microbial abundance and activity. Close to both drill sites two short gravity cores (ca. 70 cm long) were retrieved to sample the sediment/water interface. We here report the first results from microbiological investigations (porewater chemistry, cell abundance and sulfate reduction rates, SRR) in samples from the two sites at Lake Van. Although the two sites are relatively close to each other, SRR differ significantly. The sedimentary microbial ecosystem in Lake Van is apparently more sensitive to environmental conditions like water depth and sedimentation rate than marine systems. The shallower Northern Basin site exhibits significantly higher SRR than Ahlat Ridge, which is located 7 km further offshore and ~100 m deeper. Microbial sedimentary abundance is similar at both sites, but cell abundance decreases linearly with depth, as compared to a logarithmic decrease with depth in marine sites. Due to the lack of

  20. Cell abundance and microbial community composition along a complete oil sand mining and reclamation process

    NASA Astrophysics Data System (ADS)

    Lappé, M.; Schneider, B.; Kallmeyer, J.

    2012-12-01

    Hydrocarbons constitute an important energy source for microbes but can also be of environmental concern. Microbial activity causes hydrocarbon degradation and thereby loss of economical value, but also helps to remove hydrocarbons from the environment. The present study characterizes the abundance of microbes along the oil sand mining process in Alberta, Canada, as a first approach to assess the impact of mining and oil extraction on the microbial population. After mining the oil is extracted from the sediment by a hot-water extraction (50-60°C), resulting in three major fractions: crude oil, tailings sand and fine tailings. The tailings sand is used as substratum for newly developing soils on the reclamation areas. The very liquid fine tailings still have a TOC content of about 4.3% and are pumped into tailings ponds, where they need up to three decades to settle and solidify. After deposition, these mature fine tailings (MFTs) are enriched in organics (TOC content between 9.6 and 16.8%) and dredged out of the ponds and put on dumps for several years for dewatering. Finally they are brought out onto the reclamation sites and deposited below the sand layer. Cells were extracted from oily sediments according to the protocol of Lappé and Kallmeyer (2011), stained with SYBR Green I and counted by fluorescence microscopy. Cell abundance in the unprocessed oil sand is around 1.6 x 107 cells cm-3. After processing the fresh fine tailings still contain around 1.6 x 107 cells cm-3. Cell counts in the processed MFTs are 5.8 x 107 cells cm-3, whereas in the sand used as substratum for newly developing soils, they are twice as high (1.4 x 108). In root-bearing horizons, cell counts reach 1.1 x 109 cell cm-3. Cell numbers calculated from cultivation experiments are in the same range. Higher cell counts in the tailings sand are probably due to a higher nitrogen supply through the addition of a 35 cm top layer of a peat-mineral mix. In the sand nitrate concentrations are high

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  2. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System.

    PubMed

    Li, Shuqing; Song, Lina; Gao, Xiang; Jin, Yaguo; Liu, Shuwei; Shen, Qirong; Zou, Jianwen

    2017-01-01

    Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4(+) together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.

  3. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System

    PubMed Central

    Li, Shuqing; Song, Lina; Gao, Xiang; Jin, Yaguo; Liu, Shuwei; Shen, Qirong; Zou, Jianwen

    2017-01-01

    Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models. PMID:28373862

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2016-10-01

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

  6. Do associated microbial abundances impact marine demosponge pumping rates and tissue densities?

    PubMed

    Weisz, Jeremy B; Lindquist, Niels; Martens, Christopher S

    2008-03-01

    The evolution of marine demosponges has led to two basic life strategies: one involving close associations with large and diverse communities of microorganisms, termed high microbial abundance (HMA) species, and one that is essentially devoid of associated microorganisms, termed low microbial abundance (LMA) species. This dichotomy has previously been suggested to correlate with morphological differences, with HMA species having a denser mesohyl and a more complex aquiferous systems composed of longer and narrower water canals that should necessitate slower seawater filtration rates. We measured mesohyl density for a variety of HMA and LMA sponges in the Florida Keys, and seawater pumping rates for a select group of these sponges using an in situ dye technique. HMA sponges were substantially denser than LMA species, and had per unit volume pumping rates 52-94% slower than the LMA sponges. These density and pumping rate differences suggest that evolutionary differences between HMA and LMA species may have resulted in profound morphological and physiological differences between the two groups. The LMA sponge body plan moves large quantities of water through their porous tissues allowing them to rapidly acquire the small particulate organic matter (POM) that supplies the majority of their nutritional needs. In contrast, the HMA sponge body plan is suited to host large and tightly packed communities of microorganisms and has an aquiferous system that increases contact time between seawater and the sponge/microbial consortium that feeds on POM, dissolved organic matter and the raw inorganic materials for chemolithotrophic sponge symbionts. The two evolutionary patterns represent different, but equally successful patterns and illustrate how associated microorganisms can potentially have substantial effects on host evolution.

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

    PubMed

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

    2013-07-01

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

  8. Inherited microbial symbionts increase herbivore abundances and alter arthropod diversity on a native grass.

    PubMed

    Faeth, Stanley H; Shochat, Eyal

    2010-05-01

    Some microbial symbionts of plants are maternally inherited and thus functionally increase genetic and phenotypic variation within plant populations. This variation, coupled with that of the host plant and environment, may alter abundances, diversity, and trophic structure of associated plant and animal communities. Fungal endophytes in the genus Neotyphodium are vertically transmitted, asexual microbial symbionts of grasses that remain asymptomatic and rely upon their hosts for resources and transmission via seeds, often providing benefits to their hosts, including protection against herbivores. Endophyte infections may influence associated arthropod communities in agronomic grasses, but the long-term effects of endophytes and variation in host genotype and resource availability on arthropod communities in native grass populations are unknown. We conducted a long-term field experiment with four maternal genotypes of an infected (E+) native grass (Festuca arizonica) from whence the endophyte was experimentally removed (E-) and water availability was controlled, to test the effects of infection, plant genotype, and resources on abundances, biomass, diversity (richness and evenness), and trophic structure of the arthropod community. Generally, E+ grasses harbored more arthropods, including more herbivores, predators, and detritivores, suggesting that the effects of endophytes cascaded upward through trophic levels in terms of abundances, at least in early ontogeny of the host. That E+ plants harbored more herbivorous insects than E- plants suggests that infection does not increase but instead decreases resistance to herbivores, contrary to prevailing concepts of endophytes as defensive mutualists. Infection did not alter overall species richness of the arthropod community or richness of herbivores but reduced natural enemy richness, especially that of parasites, and increased richness of detritivores. Reduced richness and shifts in evenness of natural enemies on E

  9. Abundance and Genetic Diversity of Microbial Polygalacturonase and Pectate Lyase in the Sheep Rumen Ecosystem

    PubMed Central

    Wang, Yaru; Luo, Huiying; Huang, Huoqing; Shi, Pengjun; Bai, Yingguo; Yang, Peilong; Yao, Bin

    2012-01-01

    Background Efficient degradation of pectin in the rumen is necessary for plant-based feed utilization. The objective of this study was to characterize the diversity, abundance, and functions of pectinases from microorganisms in the sheep rumen. Methodology/Principal Findings A total of 103 unique fragments of polygalacturonase (PF00295) and pectate lyase (PF00544 and PF09492) genes were retrieved from microbial DNA in the rumen of a Small Tail Han sheep, and 66% of the sequences of these fragments had low identities (<65%) with known sequences. Phylogenetic tree building separated the PF00295, PF00544, and PF09492 sequences into five, three, and three clades, respectively. Cellulolytic and noncellulolytic Butyrivibrio, Prevotella, and Fibrobacter species were the major sources of the pectinases. The two most abundant pectate lyase genes were cloned, and their protein products, expressed in Escherichia coli, were characterized. Both enzymes probably act extracellularly as their nucleotide sequences contained signal sequences, and they had optimal activities at the ruminal physiological temperature and complementary pH-dependent activity profiles. Conclusion/Significance This study reveals the specificity, diversity, and abundance of pectinases in the rumen ecosystem and provides two additional ruminal pectinases for potential industrial use under physiological conditions. PMID:22815874

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

    PubMed

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

    2010-04-01

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

  11. The use of microbial gene abundance in the development of fuel remediation guidelines in polar soils.

    PubMed

    Richardson, Elizabeth L; King, Catherine K; Powell, Shane M

    2015-04-01

    Terrestrial fuel spills in Antarctica commonly occur on ice-free land around research stations as the result of human activities. Successful spill clean-ups require appropriate targets that confirm contaminated sites are no longer likely to pose environmental risk following remediation. These targets are based on knowledge of the impacts of contaminants on the soil ecosystem and on the response of native biota to contamination. Our work examined the response of soil microbial communities to fuel contamination by measuring the abundance of genes involved in critical soil processes, and assessed the use of this approach as an indicator of soil health in the presence of weathered and fresh fuels. Uncontaminated and contaminated soils were collected from the site of remediation treatment of an aged diesel spill at Casey Station, East Antarctica in December 2012. Uncontaminated soil was spiked with fresh Special Antarctic Blend (SAB) diesel to determine the response of the genes to fresh fuel. Partly remediated soil containing weathered SAB diesel was diluted with uncontaminated soil to simulate a range of concentrations of weathered fuel and used to determine the response of the genes to aged fuel. Quantitative PCR (qPCR) was used to measure the abundance of rpoB, alkB, cat23, and nosZ in soils containing SAB diesel. Differences were observed between the abundance of genes in control soils versus soils containing weathered and fresh fuels. Typical dose-response curves were generated for genes in response to the presence of fresh fuel. In contrast, the response of these genes to the range of weathered fuel appeared to be due to dilution, rather than to the effect of the fuel on the microbial community. Changes in microbial genes in response to fresh contamination have potential as a sensitive measure of soil health and for assessments of the effect of fuel spills in polar soils. This will contribute to the development of remediation guidelines to assist in management

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

    PubMed

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

    2003-03-01

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

  13. Microbial growth and physiology in space - A review

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

  15. Obesity-Dependent Increases in Oocyte mRNAs Are Associated With Increases in Proinflammatory Signaling and Gut Microbial Abundance of Lachnospiraceae in Female Mice.

    PubMed

    Xie, Fang; Anderson, Christopher L; Timme, Kelsey R; Kurz, Scott G; Fernando, Samodha C; Wood, Jennifer R

    2016-04-01

    RNAs stored in the metaphase II-arrested oocyte play important roles in successful embryonic development. Their abundance is defined by transcriptional activity during oocyte growth and selective degradation of transcripts during LH-induced oocyte maturation. Our previous studies demonstrated that mRNA abundance is increased in mature ovulated oocytes collected from obese humans and mice and therefore may contribute to reduced oocyte developmental competence associated with metabolic dysfunction. In the current study mouse models of diet-induced obesity were used to determine whether obesity-dependent increases in proinflammatory signaling regulate ovarian abundance of oocyte-specific mRNAs. The abundance of oocyte-specific Bnc1, Dppa3, and Pou5f1 mRNAs as well as markers of proinflammatory signaling were significantly increased in ovaries of obese compared with lean mice which were depleted of fully grown preovulatory follicles. Chromatin-immunoprecipitation analyses also demonstrated increased association of phosphorylated signal transducer and activator of transcription 3 with the Pou5f1 promoter in ovaries of obese mice suggesting that proinflammatory signaling regulates transcription of this gene in the oocyte. The cecum microbial content of lean and obese female mice was subsequently examined to identify potential relationships between microbial composition and proinflammatory signaling in the ovary. Multivariate Association with Linear Models identified significant positive correlations between cecum abundance of the bacterial family Lachnospiraceae and ovarian abundance of Tnfa as well as Dppa3, Bnc1, and Pou5f1 mRNAs. Together, these data suggest that diet-induced changes in gut microbial composition may be contributing to ovarian inflammation which in turn alters ovarian gene expression and ultimately contributes to obesity-dependent reduction in oocyte quality and development of infertility in obese patients.

  16. [Effects of Slope Position and Soil Horizon on Soil Microbial Biomass and Abundance in Karst Primary Forest of Southwest China].

    PubMed

    Feng, Shu-zhen; Su, Yi-rong; Zhang, Wei; Chen, Xiang-bi; He, Xun-yang

    2015-10-01

    To explore the effects of slope position and soil horizon on soil microbial biomass and abundance, chloroform fumigation extraction methods and real-time fluorescence-based quantitative PCR (Real-time PCR) were adopted to quantify the changes of soil microbial biomass C, N and abundance of bacteria and fungi, respectively. Soil samples were harvested from three horizons along profile, i. e., leaching horizon (A, 0-10 cm), transitional horizon (AB, 30-50 cm) and alluvial horizon (B, 70-100 cm), which were collected from the upper, middle and lower slope positions of a karst primary forest ecosystem. The results showed that slope position, soil horizon and their interaction significantly influenced the soil microbial biomass and abundance (P < 0.05). Different from A horizon, where SMBC was greater in lower than in upper slope position (P < 0.05), SMBC in AB and B horizons were highest in middle slope position. Similarly, SMBN was greater in lower than in upper slope position for A, AB and B horizons. Besides soil bacterial abundance in B horizon and fungal abundance in AB layer, the middle slope position had the highest value for all the three soil horizons (P < 0.05). Stepwise regression analysis showed that soil organic carbon, available nitrogen and pH were the key factors responsible for SMBC and SMBN variation, respectively, while the important factors responsible for the variation of bacteria abundance were available nitrogen and available phosphorus, and that for fungi abundance variation were available potassium.

  17. Solid and Aqueous Geochemical Controls on Phylogenetic Diversity and Abundance of Microbial Biofilms

    NASA Astrophysics Data System (ADS)

    Jones, A. A.; Bennett, P. C.

    2015-12-01

    In the subsurface, the vast majority of microorganisms are found in biofilms attached to mineral surfaces. The fickle nature of these environments (chemically and physically) likely causes dynamic ecological shifts in these microbial communities. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the role of mineralogy as part of a microbe-mineral-water ecosystem under variable pressures (mineralogy, pH, carbon, phosphate). Following multivariate analyses, pH was identified as the key physicochemical property associated with variation in both phylogenetic and taxonomic diversity as well as overall community structure (P<0.05). In particular, the ability of minerals, media, or a combination of the two to buffer metabolically generated acidity impacted community structure under oligotrophic and eutrophic conditions. Additionally, we found that media phosphate limitations were significantly correlated to greater biofilm accumulation (P<0.002), but lower species richness (P<0.001) and Shannon diversity (P<0.001); while mineral-bound phosphate limitations were significantly correlated to lesser biofilm accumulation (P<0.05) but not to species richness or diversity. Carbon (as acetate, lactate, or formate) added to the media was correlated with a significant increase in biofilm accumulation (P<0.04), and overall Shannon diversity (P<0.006), but not significantly correlated with overall species richness. Although variable in magnitude, the effect of surface chemistry on microbial diversity (both phylogenetic and taxonomic) was statistically significant, in all reactors, regardless of environmental pressures. Phylogenetically, surface type (carbonate, silicate, or Al-silicate) controlled ~70-90%, meaning that organisms attached to similar surfaces were significantly more genetically similar. Taxonomy and proportional abundance was significantly sensitive to variations in media chemistry with consistent patterns emerging among

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed

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

    2011-02-01

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

  20. High Ozone (O3) Affects the Fitness Associated with the Microbial Composition and Abundance of Q Biotype Bemisia tabaci

    PubMed Central

    Hong, Yanyun; Yi, Tuyong; Tan, Xiaoling; Zhao, Zihua; Ge, Feng

    2016-01-01

    Ozone (O3) affects the fitness of an insect, such as its development, reproduction and protection against fungal pathogens, but the mechanism by which it does so remains unclear. Here, we compared the fitness (i.e., the growth and development time, reproduction and protection against Beauveria bassiana (B. bassiana) of Q biotype whiteflies fumigated under hO3 (280 ± 20 ppb) and control O3 (50 ± 10 ppb) concentrations. Moreover, we determined that gene expression was related to development, reproduction and immunity to B. bassiana and examined the abundance and composition of bacteria and fungi inside of the body and on the surface of the Q biotype whitefly. We observed a significantly enhanced number of eggs that were laid by a female, shortened developmental time, prolonged adult lifespan, decreased weight of one eclosion, and reduced immunity to B. bassiana in whiteflies under hO3, but hO3 did not significantly affect the expression of genes related to development, reproduction and immunity. However, hO3 obviously changed the composition of the bacterial communities inside of the body and on the surface of the whiteflies, significantly reducing Rickettsia and enhancing Candidatus_Cardinium. Similarly, hO3 significantly enhanced Thysanophora penicillioides from the Trichocomaceae family and reduced Dothideomycetes (at the class level) inside of the body. Furthermore, positive correlations were found between the abundance of Candidatus_Cardinium and the female whitefly ratio and the fecundity of a single female, and positive correlations were found between the abundance of Rickettsia and the weight of adult whiteflies just after eclosion and immunity to B. bassiana. We conclude that hO3 enhances whitefly development and reproduction but impairs immunity to B. bassiana, and our results also suggest that the changes to the microbial environments inside of the body and on the surface could be crucial factors that alter whitefly fitness under hO3. PMID:27799921

  1. Microbial communities on glacier surfaces in Svalbard: impact of physical and chemical properties on abundance and structure of cyanobacteria and algae.

    PubMed

    Stibal, Marek; Sabacká, Marie; Kastovská, Klára

    2006-11-01

    Microbial communities occurring in three types of supraglacial habitats--cryoconite holes, medial moraines, and supraglacial kames--at several glaciers in the Arctic archipelago of Svalbard were investigated. Abundance, biovolume, and community structure were evaluated by using epifluorescence microscopy and culturing methods. Particular emphasis was laid on distinctions in the chemical and physical properties of the supraglacial habitats and their relation to the microbial communities, and quantitative multivariate analyses were used to assess potential relationships. Varying pH (4.8 in cryoconite; 8.5 in a moraine) and texture (the proportion of coarse fraction 2% of dry weight in cryoconite; 99% dw in a kame) were found, and rather low concentrations of organic matter (0.3% of dry weight in a kame; 22% dw in cryoconite) and nutrients (nitrogen up to 0.4% dw, phosphorus up to 0.8% dw) were determined in the samples. In cryoconite sediment, the highest numbers of bacteria, cyanobacteria, and algae were found, whereas relatively low microbial abundances were recorded in moraines and kames. Cyanobacterial cells were significantly more abundant than microalgal ones in cryoconite and supraglacial kames. Different species of the cyanobacterial genus Leptolyngbya were by far the most represented in all samples, and cyanobacteria of the genera Phormidium and Nostoc prevailed in cultures isolated from cryoconite samples. These species are considered opportunistic organisms with wide ecological valency and strong colonizing potential rather than glacial specialists. Statistical analyses suggest that fine sediment with higher water content is the most suitable condition for bacteria, cyanobacteria, and algae. Also, a positive impact of lower pH on microbial growth was found. The fate of a microbial cell deposited on the glacier surface seems therefore predetermined by the physical and chemical factors such as texture of sediment and water content rather than spatial factors

  2. Microbial distribution and abundance in the digestive system of five shipworm species (Bivalvia: Teredinidae).

    PubMed

    Betcher, Meghan A; Fung, Jennifer M; Han, Andrew W; O'Connor, Roberta; Seronay, Romell; Concepcion, Gisela P; Distel, Daniel L; Haygood, Margo G

    2012-01-01

    Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose.

  3. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

    SciTech Connect

    Yagi, J.M.; Madsen, E.L.

    2009-10-15

    The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ni Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72: 4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low (similar to 10{sup 2} ppb; similar to 1 {mu} M) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

  4. Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression

    PubMed Central

    Henne, Karsten; Fuchs, Felix; Kruth, Sebastian; Horz, Hans-Peter; Conrads, Georg

    2014-01-01

    Background Oral Campylobacter species have been found to be associated with periodontitis progression. While the etiological significance of Campylobacter rectus is quite established, the association of C. gracilis, C. concisus, and C. curvus with health or disease remains contradictory. Objectives This study hypothesizes that the proportion of species within the Campylobacter genus rather than the absolute abundance of a single species is a suitable indicator for periodontitis progression. Design Subgingival plaque from 90 periodontitis patients and gingival sulcus fluid of 32 healthy individuals were subjected to a newly developed nested PCR approach, in which all Campylobacter spp. were amplified simultaneously. The resulting mixture of 16S-rRNA-gene-amplicons were separated by single-stranded conformation polymorphism (SSCP) gel electrophoresis, followed by sequencing and identification of excised bands and relative quantification of band intensities. In all samples, the abundance of selected periodontitis marker species was determined based on DNA hybridization on a microarray. Results The highly prevalent Campylobacter community was composed of varying proportions of C. rectus, C. gracilis, C. concisus, and C. curvus. Cluster analysis based on SSCP-banding pattern resulted in distinct groups which in turn coincided with significant differences in abundance of established periodontitis marker species (Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum) and progression. Conclusions The shift in the Campylobacter community composition seems to display the general microbial community shift during clinical progression in a simplified manner. The focus on members of the Campylobacter in this study suggests that this genus can be an indicator of ecological changes in the subgingival oral microflora. PMID:25412608

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

    PubMed

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

    2015-06-01

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

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

    PubMed Central

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

    2010-01-01

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

  7. Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

    PubMed

    Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

    2014-01-01

    Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions.

  8. Dynamic speckle study of microbial growth

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  9. Kinetics of microbial growth on pentachlorophenol.

    PubMed Central

    Klecka, G M; Maier, W J

    1985-01-01

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

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

    PubMed

    Demeyer, D; Van Nevel, C

    1986-01-01

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

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

    EPA Science Inventory

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

  12. Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales.

    PubMed

    Hendershot, J Nicholas; Read, Quentin D; Henning, Jeremiah A; Sanders, Nathan J; Classen, Aimée T

    2017-04-05

    Macroecology seeks to understand broad-scale patterns in the diversity and abundance of organisms, but macroecologists typically study aboveground macroorganisms. Belowground organisms regulate numerous ecosystem functions, yet we lack understanding of what drives their diversity. Here, we examine the controls on belowground diversity along latitudinal and elevational gradients. We performed a global meta-analysis of 325 soil communities across 20 studies conducted along temperature and soil pH gradients. Belowground taxa, whether bacterial or fungal, observed along a given gradient of temperature or soil pH were equally likely to show a linear increase, linear decrease, humped pattern, trough-shaped pattern, or no pattern in diversity along the gradient. Land-use intensity weakly affected the diversity-temperature relationship, but no other factor did so. Our study highlights disparities among diversity patterns of soil microbial communities. Belowground diversity may be controlled by the associated climatic and historical contexts of particular gradients, by factors not typically measured in community-level studies, or by processes operating at scales that do not match the temporal and spatial scales under study. Because these organisms are responsible for a suite of key processes, understanding the drivers of their distribution and diversity is fundamental to understanding the functioning of ecosystems. This article is protected by copyright. All rights reserved.

  13. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield

    PubMed Central

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-01-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions. PMID:21124490

  14. Microplastic is an abundant and distinct microbial habitat in an urban river.

    PubMed

    McCormick, Amanda; Hoellein, Timothy J; Mason, Sherri A; Schluep, Joseph; Kelly, John J

    2014-10-21

    Recent research has documented microplastic particles (< 5 mm in diameter) in ocean habitats worldwide and in the Laurentian Great Lakes. Microplastic interacts with biota, including microorganisms, in these habitats, raising concerns about its ecological effects. Rivers may transport microplastic to marine habitats and the Great Lakes, but data on microplastic in rivers is limited. In a highly urbanized river in Chicago, Illinois, USA, we measured concentrations of microplastic that met or exceeded those measured in oceans and the Great Lakes, and we demonstrated that wastewater treatment plant effluent was a point source of microplastic. Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter. Several taxa that include plastic decomposing organisms and pathogens were more abundant on microplastic. These results demonstrate that microplastic in rivers are a distinct microbial habitat and may be a novel vector for the downstream transport of unique bacterial assemblages. In addition, this study suggests that urban rivers are an overlooked and potentially significant component of the global microplastic life cycle.

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

    PubMed

    Stoffel, Joseph; Bernatchez, Stéphanie F

    2017-03-01

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

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

    PubMed Central

    Stoffel, Joseph; Bernatchez, Stéphanie F.

    2017-01-01

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

  17. Microbial physiology and ecology of slow growth.

    PubMed Central

    Koch, A L

    1997-01-01

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

  18. Spatial and temporal variation in enterococcal abundance and its relationship to the microbial community in Hawaii beach sand and water.

    PubMed

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn; Yan, Tao

    2013-06-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.

  19. Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

    PubMed Central

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn

    2013-01-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

  20. Effects of Spatial Localization on Microbial Consortia Growth.

    PubMed

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

    2017-01-01

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

  1. Effects of Spatial Localization on Microbial Consortia Growth

    PubMed Central

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

    2017-01-01

    Microbial consortia are commonly observed in natural and synthetic systems, and these consortia frequently result in higher biomass production relative to monocultures. The focus here is on the impact of initial spatial localization and substrate diffusivity on the growth of a model microbial consortium consisting of a producer strain that consumes glucose and produces acetate and a scavenger strain that consumes the acetate. The mathematical model is based on an individual cell model where growth is described by Monod kinetics, and substrate transport is described by a continuum-based, non-equilibrium reaction-diffusion model where convective transport is negligible (e.g., in a biofilm). The first set of results focus on a single producer cell at the center of the domain and surrounded by an initial population of scavenger cells. The impact of the initial population density and substrate diffusivity is examined. A transition is observed from the highest initial density resulting in the greatest cell growth to cell growth being independent of initial density. A high initial density minimizes diffusive transport time and is typically expected to result in the highest growth, but this expected behavior is not predicted in environments with lower diffusivity or larger length scales. When the producer cells are placed on the bottom of the domain with the scavenger cells above in a layered biofilm arrangement, a similar critical transition is observed. For the highest diffusivity values examined, a thin, dense initial scavenger layer is optimal for cell growth. However, for smaller diffusivity values, a thicker, less dense initial scavenger layer provides maximal growth. The overall conclusion is that high density clustering of members of a food chain is optimal under most common transport conditions, but under some slow transport conditions, high density clustering may not be optimal for microbial growth. PMID:28045924

  2. Effects of Grain Growth on Molecular Abundances in Young Stellar Objects

    NASA Astrophysics Data System (ADS)

    Harada, Nanase; Hasegawa, Yasuhiro; Aikawa, Yuri; Hirashita, Hiroyuki; Liu, Haoyu Baobab; Hirano, Naomi

    2017-03-01

    Recent observations suggested that the growth of dust grains may have already occurred in class 0/I young stellar objects (YSOs). Since chemical reactions on dust grain surfaces are important in determining molecular abundances, the dust size growth may affect chemical compositions in YSOs significantly. In this work, we aim to determine how grain growth affects chemical abundances. We use a time-dependent gas-grain chemical model for a star-forming core to calculate the gas-phase and grain-surface chemical abundances with variation of surface areas of grains to imitate grain growth. We also perform parameter studies in which the initial molecular abundances vary. Our results show that a smaller extent of the surface areas caused by grain growth changes the dominant form of sulfur-bearing molecules by decreasing H2S abundances and increasing SO and/or SO2 abundances. We also find that complex organic molecules such as CH3CN decrease in abundances with larger grain sizes, while the abundance of other species such as CH3OCH3 is dependent on other parameters such as the initial conditions. Comparisons with observations of a class 0 protostar, IRAS 16293-2422, indicate that the observed abundance ratios between sulfur-bearing molecules H2S, SO, and SO2 can be reproduced very well when dust grains grow to a maximum grain size of a max = 10–100 μm.

  3. Pan-Arctic patterns of planktonic heterotrophic microbial abundance and processes: Controlling factors and potential impacts of warming

    NASA Astrophysics Data System (ADS)

    Maranger, Roxane; Vaqué, Dolors; Nguyen, Dan; Hébert, Marie-Pier; Lara, Elena

    2015-12-01

    The Arctic Ocean is rapidly changing where increasing water temperatures and rapid loss of summer sea-ice will likely influence the structure and functioning of the entire ecosystem. The aim of this study was to synthesize the current state of knowledge on microbial abundances and processes from a regional Pan-Arctic perspective, characterize regulating factors and attempt to predict how patterns may change under a warming scenario. Here we identify some generalized patterns of different microbial variables between the Pacific-fed and the Atlantic-fed sectors of the Arctic Ocean. Bacterial production (BP), abundance and grazing rates by protists (GT) were all higher in the Atlantic-fed region. Bacterial loss by viral lyses (VL) was proportionally more important in the Pacific-fed sector, suggesting a reduced C transfer efficiency within the microbial loop of that region. Using a cross-comparative approach and all available data to build Arrhenius plots, we found a differential response to warming temperatures among various microbial processes. BP and GT responded similarly and more strongly to increases in temperature than VL did, suggesting a shift in the overall influence of viral mortality under a warming scenario. However, together with temperature, resource-related factors also exerted an influence in regulating these rates. We identified large information gaps for more classically studied microbial variable from several Arctic seas. Furthermore, there is limited information on less conventional pathways such as grazing by mixotrophic species, which may be playing a significant role in Arctic microbial trophodynamics. Although generalized patterns could be elucidated, more information is needed to predict and understand how a changing Arctic will alter microbial C pathways and major biogeochemical cycles on regional and seasonal scales.

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

    PubMed

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

    2009-06-01

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

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

    PubMed Central

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

    1997-01-01

    As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone. PMID:16535670

  6. Heavy metal immobilization and microbial community abundance by vegetable waste and pine cone biochar of agricultural soils.

    PubMed

    Igalavithana, Avanthi Deshani; Lee, Sung-Eun; Lee, Young Han; Tsang, Daniel C W; Rinklebe, Jörg; Kwon, Eilhann E; Ok, Yong Sik

    2017-05-01

    In order to determine the efficacy of vegetable waste and pine cone biochar for immobilization of metal/metalloid (lead and arsenic) and abundance of microbial community in different agricultural soils, we applied the biochar produced at two different temperatures to two contaminated soils. Biochar was produced by vegetable waste, pine cone, and their mixture (1:1 ww(-1)) at 200 °C (torrefied biomass) and 500 °C (biochar). Contaminated soils were incubated with 5% (ww(-1)) torrefied biomass or biochar. Sequential extraction, thermodynamic modeling, and scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy were used to evaluate the metal immobilization. Microbial communities were characterized by microbial fatty acid profiles and microbial activity was assessed by dehydrogenase activity. Vegetable waste and the mixture of vegetable waste and pine cone biochar exhibited greater ability for Pb immobilization than pine cone biochar and three torrefied biomass, and vegetable waste biochar was found to be most effective. However, torrefied biomass was most effective in increasing both microbial community and dehydrogenase activity. This study confirms that vegetable waste could be a vital biomass to produce biochar to immobilize Pb, and increase the microbial communities and enzyme activity in soils. Biomass and pyrolytic temperature were not found to be effective in the immobilization of As in this study.

  7. Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

    SciTech Connect

    Classen, Aimee T; Overby, Stephen; Hart, Stephen C; Koch, George W; Whitham, Thomas G

    2007-01-01

    Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltration (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.

  8. Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats.

    PubMed

    Metzler-Zebeli, Barbara U; Schmitz-Esser, Stephan; Klevenhusen, Fenja; Podstatzky-Lichtenstein, Leopold; Wagner, Martin; Zebeli, Qendrim

    2013-04-01

    High grain feeding has been associated with ruminal pH depression and microbial dysbiosis in cattle. Yet, the impact of high grain feeding on the caprine rumen and hindgut microbial community and lipopolysaccharide (LPS) release is largely unknown. Therefore, the objective was to investigate the effect of increasing dietary levels of barley grain on the microbial composition and LPS concentrations in the rumen and colon of goats. Effects were compared with respect to the responses of ruminal and colonic pH and short-chain fatty acid (SCFA) generation. Growing goats (n = 5-6) were fed diets containing 0, 30, or 60% coarsely ground barley grain for 6 weeks. Ruminal ciliate protozoa were counted with Bürker counting chamber, and quantitative PCR was used to compare bacterial populations. Increasing dietary grain level linearly increased (P < 0.05) ruminal numbers of entodiniomorphids. With the 60% grain diet, there was a reduction in ruminal abundance of the genus Prevotella and Fibrobacter succinogenes, whereas the ruminal abundance of Lactobacillus spp. increased compared to the 0 and 30% grain diets (P < 0.05). In the colon, abundance of the genus Prevotella and F. succinogenes increased (P < 0.05) in goats fed the 60% grain diet compared to those fed the other diets. Colonic abundance of Clostridium cluster I was related to the presence of grain in the diet. Ruminal LPS concentration decreased (P < 0.05) in response to the 60% grain diet, whereas its colonic concentration increased in response to the same diet (P < 0.05). Present results provide first insight on the adaptive response of rumen protozoa and rumen and colonic bacterial populations to increasing dietary levels of grain in goats. Although luminal pH largely affects microbial populations, fermentable substrate flow to the caprine hindgut may have played a greater role for colonic bacterial populations in the present study.

  9. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea.

    PubMed

    Moitinho-Silva, Lucas; Bayer, Kristina; Cannistraci, Carlo V; Giles, Emily C; Ryu, Taewoo; Seridi, Loqmane; Ravasi, Timothy; Hentschel, Ute

    2014-03-01

    Marine sponges are generally classified as high microbial abundance (HMA) and low microbial abundance (LMA) species. Here, 16S rRNA amplicon sequencing was applied to investigate the diversity, specificity and transcriptional activity of microbes associated with an LMA sponge (Stylissa carteri), an HMA sponge (Xestospongia testudinaria) and sea water collected from the central Saudi Arabia coast of the Red Sea. Altogether, 887 068 denoised sequences were obtained, of which 806 661 sequences remained after quality control. This resulted in 1477 operational taxonomic units (OTUs) that were assigned to 27 microbial phyla. The microbial composition of S. carteri was more similar to that of sea water than to that of X. testudinaria, which is consistent with the observation that the sequence data set of S. carteri contained many more possibly sea water sequences (~24%) than the X. testudinaria data set (~6%). The most abundant OTUs were shared between all three sources (S. carteri, X. testudinaria, sea water), while rare OTUs were unique to any given source. Despite this high degree of overlap, each sponge species contained its own specific microbiota. The X. testudinaria-specific bacterial taxa were similar to those already described for this species. A set of S. carteri-specific bacterial taxa related to Proteobacteria and Nitrospira was identified, which are likely permanently associated with S. carteri. The transcriptional activity of sponge-associated microorganisms correlated well with their abundance. Quantitative PCR revealed the presence of Poribacteria, representing typical sponge symbionts, in both sponge species and in sea water; however, low transcriptional activity in sea water suggested that Poribacteria are not active outside the host context.

  10. [Effects of adding straw carbon source to root knot nematode diseased soil on soil microbial biomass and protozoa abundance].

    PubMed

    Zhang, Si-Hui; Lian, Jian-Hong; Cao, Zhi-Ping; Zhao, Li

    2013-06-01

    A field experiment with successive planting of tomato was conducted to study the effects of adding different amounts of winter wheat straw (2.08 g x kg(-1), 1N; 4.16 g x kg(-1), 2N; and 8.32 g x kg(-1), 4N) to the soil seriously suffered from root knot nematode disease on the soil microbial biomass and protozoa abundance. Adding straw carbon source had significant effects on the contents of soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) and the abundance of soil protozoa, which all decreased in the order of 4N > 2N > 1N > CK. The community structure of soil protozoa also changed significantly under straw addition. In the treatments with straw addition, the average proportion of fagellate, amoeba, and ciliates accounted for 36.0%, 59.5%, and 4.5% of the total protozoa, respectively. Under the same adding amounts of wheat straw, there was an increase in the soil MBC and MBN contents, MBC/MBN ratio, and protozoa abundance with increasing cultivation period.

  11. Microbial abundance in the deep subsurface of the Chesapeake Bay impact crater: Relationship to lithology and impact processes

    USGS Publications Warehouse

    Cockell, Charles S.; Gronstal, Aaron L.; Voytek, Mary A.; Kirshtein, Julie D.; Finster, Kai; Sanford, Ward E.; Glamoclija, Mihaela; Gohn, Gregroy S.; Powars, David S.; Horton, J. Wright

    2009-01-01

    Asteroid and comet impact events are known to cause profound disruption to surface ecosystems. The aseptic collection of samples throughout a 1.76-km-deep set of cores recovered from the deep subsurface of the Chesapeake Bay impact structure has allowed the study of the subsurface biosphere in a region disrupted by an impactor. Microbiological enumerations suggest the presence of three major microbiological zones. The upper zone (127–867 m) is characterized by a logarithmic decline in microbial abundance from the surface through the postimpact section of Miocene to Upper Eocene marine sediments and across the transition into the upper layers of the impact tsunami resurge sediments and sediment megablocks. In the middle zone (867–1397 m) microbial abundances are below detection. This zone is predominantly quartz sand, primarily composed of boulders and blocks, and it may have been mostly sterilized by the thermal pulse delivered during impact. No samples were collected from the large granite block (1096–1371 m). The lowest zone (below 1397 m) of increasing microbial abundance coincides with a region of heavily impact-fractured, hydraulically conductive suevite and fractured schist. These zones correspond to lithologies influenced by impact processes. Our results yield insights into the influence of impacts on the deep subsurface biosphere.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Chi; Keating, Kristina; Revil, Andre

    2015-04-01

    clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets was also observed. These results will provide a basis for understanding the effect of microbes within geologic media on SIP and low-field NMR measurements. This research suggests that both SIP and NMR have the potential to monitor microbial growth and activities in the subsurface and could provide spatiotemporal variations in bacterial abundance in porous media.

  13. Nanomechanical sensors for single microbial cell growth monitoring

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  14. Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

    PubMed Central

    Highton, Matthew P.; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E.

    2016-01-01

    Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI, and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns. PMID:27826296

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

    PubMed

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

    2011-01-01

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

  16. Growth and abundance of Pacific Sand Lance, Ammodytes hexapterus, under differing oceanographic regimes

    USGS Publications Warehouse

    Robards, Martin D.; Gray, Floyd; Piatt, John F.

    2002-01-01

    Dramatic changes in seabird and marine mammal stocks in the Gulf of Alaska have been linked to shifts in abundance and composition of forage fish stocks over the past 20 years. The relative value (e.g., size and condition of individual fish, abundance) of specific forage fish stocks to predators under temporally changing oceanographic regimes is also expected to vary. We inferred potential temporal responses in abundance, growth, and age structure of a key forage fish, sand lance, by studying across spatially different oceanographic regimes. Marked meso-scale differences in abundance, growth, and mortality existed in conjunction with these differing regimes. Growth rate within stocks (between years) was positively correlated with temperature. However, this relationship did not exist among stocks (locations) and differing growth rates were better correlated to marine productivity. Sand lance were least abundant and grew slowest at the warmest site (Chisik Island), an area of limited habitat and low food abundance. Abundance and growth of juvenile sand lance was highest at the coolest site (Barren Islands), an area of highly productive upwelled waters. Sand lance at two sites located oceanographically between the Barren Islands and Chisik Island (inner- and outer-Kachemak Bay) displayed correspondingly intermediate abundance and growth. Resident predators at these sites are presented with markedly different numbers and quality of this key prey species. Our results suggest that at the decadal scale, Gulf of Alaska forage fish such as sand lance are probably more profoundly affected by changes in abundance and quality of their planktonic food, than by temperature alone.

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

    EPA Science Inventory

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

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

    PubMed

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

    2016-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    1.2-1.9-fold higher than under ambient CO2. This indicates the increased activity of microorganisms, which leads to accelerated C turnover in soil under elevated CO2. Our results clearly showed that the functional characteristics of the soil microbial community (i.e. specific growth rates and enzymes activity) rather than total microbial biomass amount are sensitive to increased atmospheric CO2. We conclude that the more abundant available organics released by roots at elevated CO2 altered the ecological strategy of the soil microbial community specifically a shift to a higher contribution of fast-growing r-selected species was observed. These changes in functional structure of the soil microbial community may counterbalance higher C input into the soil under elevated atmospheric CO2 concentration.

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

    PubMed

    Yan, Jinyao; Deller, J R

    2014-01-01

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

  2. Modeling of a compost biofilter incorporating microbial growth

    SciTech Connect

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

    1995-11-01

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

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

    PubMed

    Juška, Alfonsas

    2011-01-21

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

  4. Perception and regulatory principles of microbial growth control.

    PubMed

    Khonsari, Armin S; Kollmann, Markus

    2015-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  6. Microbial plankton abundance and heterotrophic activity across the Central Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Vázquez-Domínguez, Evaristo; Duarte, Carlos M.; Agustí, Susana; Jürgens, Klaus; Vaqué, Dolors; Gasol, Josep M.

    2008-10-01

    The role of microorganisms in the transfer of carbon of marine systems is very important in open oligotrophic oceans. Here, we analyze the picoplankton structure, the heterotrophic bacterioplankton activity, and the predator-prey relationships between heterotrophic bacteria and nanoflagellates during two large scale cruises in the Central Atlantic Ocean (∼29°N to ∼40°S). Latitud cruises were performed in 1995 between March-April and October-November. During both cruises we crossed the regions of different trophic statuses; where we measured different biological variables both at the surface and at the deep chlorophyll maximum (DCM). The concentration of chlorophyll a varied between 0.1 and 0.8 mg m -3, the abundance of heterotrophic bacteria varied between <1.0 × 10 5 and >1.0 × 10 6 cells ml -1, and that of heterotrophic nanoflagellates between <100 and >1.0 × 10 4 cells ml -1. The production of heterotrophic bacteria varied more than three orders of magnitude between <0.01 and 24 μgC L -1 d -1; and the growth rates were in the range <0.01-2.1 d -1. In the Latitud-II cruise, Prochlorococcus ranged between <10 3 and >3 × 10 5 cells ml -1, Synechococcus between <100 and >1.0 × 10 4 cells ml -1, and picoeukaryotes between <100 and >10 4 cells ml -1. Two empirical models were used to learn more about the relationship between heterotrophic bacteria and nanoflagellates. Most bacterial production was ingested when this production was low, the heterotrophic nanoflagellates could be controlled by preys during Latitud-I cruise at the DCM, and by predators in the surface and in the Latitud-II cruise. Our results were placed in context with others about the structure and function of auto- and heterotrophic picoplankton and heterotrophic nanoplankton in the Central Atlantic Ocean.

  7. Temporal trends in microbial abundance and biodegradation in Louisiana salt marshes following the Deepwater Horizon oil spill

    NASA Astrophysics Data System (ADS)

    Mahmoudi, N.; Fulthorpe, R. R.; Zimmerman, A. R.; Silliman, B. R.; Slater, G. F.

    2012-12-01

    The Deepwater Horizon oil spill that began in April 2010 released approximately 4.9 million barrels of crude oil into the Gulf of Mexico waters. Coastal salt marshes experienced moderate to heavy oiling as spilled oils washed ashore and threatened economically important habitats. In situ biodegradation of petroleum by microbes is one of the most effective methods used to remediate oil spills. However, demonstrating biodegradation can be challenging due to heterogeneous distributions of contaminants and dynamic conditions of coastal ecosystems. Salt marshes provide a unique opportunity in which variations in the natural abundance of δ13C can be used to confirm in situ biodegradation of petroleum. Marsh grasses, specifically Spartina sp., have δ13C values of -12 to -14‰ whereas the BP crude oil has a δ13C signature of -27‰. Thus, the 13C content of microbial membrane lipids (which reflects their carbon source) can be used to detect incorporation of petroleum-derived carbon. We investigated biodegradation in marsh sediments in oiled and non-oiled portions of Barataria Bay, Louisiana which experienced some of the most extensive oil contamination. Samples were collected 3, 9 and 15 months following Deepwater Horizon oil intrusion to assess biodegradation over time. Total alkane and PAH analyses confirmed that by Oct 2011 (15 months), concentrations had been significantly reduced (by up to 50,000 ug/kg at some sites). Microbial phospholipid fatty acids (PLFA) analysis revealed that cell densities decreased over the 1 year sampling period across both oil-impacted and non-impacted sites indicating that, rather than petroleum presence, seasonal variability was likely the primary control on microbial abundance. The ranges of δ13C PLFA values in oil-impacted (-26.7 to -30.5‰ ± 1.0) and non-impacted sediments (-24.5 to -33.3‰ ± 0.7) in Oct 2010 overlap, thereby reducing confidence in confirmation of biodegradation at this time point. However, in Oct 2011, PLFA

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

    PubMed

    Fujikawa, Hiroshi; Kano, Yoshihiro

    2009-06-01

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

  9. Slow pyrolyzed biochars from crop residues for soil metal(loid) immobilization and microbial community abundance in contaminated agricultural soils.

    PubMed

    Igalavithana, Avanthi Deshani; Park, Jinje; Ryu, Changkook; Lee, Young Han; Hashimoto, Yohey; Huang, Longbin; Kwon, Eilhann E; Ok, Yong Sik; Lee, Sang Soo

    2017-06-01

    This study evaluated the feasibility of using biochars produced from three types of crop residues for immobilizing Pb and As and their effects on the abundance of microbial community in contaminated lowland paddy (P-soil) and upland (U-soil) agricultural soils. Biochars were produced from umbrella tree [Maesopsis eminii] wood bark [WB], cocopeat [CP], and palm kernel shell [PKS] at 500 °C by slow pyrolysis at a heating rate of 10 °C min(-1). Soils were incubated with 5% (w w(-1)) biochars at 25 °C and 70% water holding capacity for 45 d. The biochar effects on metal immobilization were evaluated by sequential extraction of the treated soil, and the microbial community was determined by microbial fatty acid profiles and dehydrogenase activity. The addition of WB caused the largest decrease in Pb in the exchangeable fraction (P-soil: 77.7%, U-soil: 91.5%), followed by CP (P-soil: 67.1%, U-soil: 81.1%) and PKS (P-soil: 9.1%, U-soil: 20.0%) compared to that by the control. In contrast, the additions of WB and CP increased the exchangeable As in U-soil by 84.6% and 14.8%, respectively. Alkalinity and high phosphorous content of biochars might be attributed to the Pb immobilization and As mobilization, respectively. The silicon content in biochars is also an influencing factor in increasing the As mobility. However, no considerable effects of biochars on the microbial community abundance and dehydrogenase activity were found in both soils.

  10. General calibration of microbial growth in microplate readers

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    1983-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  13. Weed seed persistence and microbial abundance in long-term organic and conventional cropping systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weed seed persistence in soil can be influenced by many factors, including crop management. This research was conducted to determine whether organic management systems with higher organic amendments and soil microbial biomass could reduce weed seed persistence compared to conventional management sy...

  14. Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

    PubMed

    Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

    2013-02-01

    Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

  15. High abundances of viruses in a deep-sea hydrothermal vent system indicates viral mediated microbial mortality

    NASA Astrophysics Data System (ADS)

    Ortmann, Alice C.; Suttle, Curtis A.

    2005-08-01

    Little is known about the distribution and abundance of viruses at deep-sea hydrothermal vents. Based on estimates made using epifluorescence microscopy and the dye YoPro-1, much higher viral abundances were observed at active hydrothermal vents than in the surrounding deep sea. This indicates that viral production was occurring and that viruses were a source of microbial mortality. Samples collected from three actively venting sites (Clam Bed, S&M and Salut) within the Endeavour Ridge system off the west coast of North America had viral abundances ranging from 1.45×10 5 to 9.90×10 7 ml -1, while the abundances of prokaryotes ranged from 1.30×10 5 to 4.46×10 6 ml -1. The abundances of viruses and prokaryotes in samples collected along the neutrally buoyant plume associated with the Main Endeavour Field were lower than at actively venting sites, with a mean of 5.3×10 5 prokaryotes ml -1 (s.d. 2.9×10 5, n=64) and 3.50×10 6 viruses ml -1 (s.d. 1.89×10 6, n=64), but were higher than non-plume samples (2.7×10 5 prokaryotes ml -1, s.d. 5.0×10 4, n=15 and 2.94×10 6 viruses ml -1, s.d. 1.08×10 6, n=15). Prokaryotic and viral abundances in non-hydrothermal regions were as much as 10-fold higher than found in previous studies, in which sample fixation likely resulted in underestimates. This suggests that viral infection may be a greater source of prokaryotic mortality throughout the deep sea than previously recognized. Overall, our results indicate that virus-mediated mortality of prokaryotes at these hydrothermal-vent environments is significant and may reduce energy flow to higher trophic levels.

  16. Evaluating microbial carbon sources in Athabasca oil sands tailings ponds using natural abundance stable and radiocarbon isotopes

    NASA Astrophysics Data System (ADS)

    Ahad, J. M.; Pakdel, H.

    2013-12-01

    Natural abundance stable (δ13C) and radiocarbon (Δ14C) isotopes of phospholipid fatty acids (PLFAs) were used to evaluate the carbon sources utilized by the active microbial populations in surface sediments from Athabasca oil sands tailings ponds. The absence of algal-specific PLFAs at three of the four sites investigated, in conjunction with δ13C signatures for PLFAs that were generally within ~3‰ of that reported for oil sands bitumen (~ -30‰), indicated that the microbial communities growing on petroleum constituents were dominated by aerobic heterotrophs. The Δ14C values of PLFAs ranged from -906 to -586‰ and pointed to a significant uptake of fossil carbon (up to ~90% of microbial carbon derived from petroleum), particularly in PLFAs (e.g., cy17:0 and cy19:0) often associated with petroleum hydrocarbon degrading bacteria. The comparatively higher levels of 14C in other, less specific PLFAs (e.g., 16:0) indicated the preferential uptake of younger organic matter by the general microbial population (~50-80% of microbial carbon derived from petroleum). Since the main carbon pools in tailings sediment were essentially 'radiocarbon dead' (i.e., no detectable 14C), the principal source for this modern carbon is considered to be the Athabasca River, which provides the bulk of the water used in the bitumen extraction process. The preferential uptake of the minor amount of young and presumably more biodegradable material present in systems otherwise dominated by recalcitrant petroleum constituents has important implications for remediation strategies. On the one hand, it implies that mining-related organic contaminants could persist in the environment long after tailings pond reclamation has begun. Alternatively, it may be that the young, labile organic matter provided by the Athabasca River plays an important role in stimulating or supporting the microbial utilization of petroleum carbon in oil sands tailings ponds via co-metabolism or priming processes

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

    PubMed

    Lawrence, J; Turner, M; Gilbert, P

    1988-04-01

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

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

    PubMed

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

    2013-01-14

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

  19. Anodic biofilms in microbial fuel cells harbor low numbers of higher-power-producing bacteria than abundant genera.

    PubMed

    Kiely, Patrick D; Call, Douglas F; Yates, Matthew D; Regan, John M; Logan, Bruce E

    2010-09-01

    Microbial fuel cell (MFC) anode communities often reveal just a few genera, but it is not known to what extent less abundant bacteria could be important for improving performance. We examined the microbial community in an MFC fed with formic acid for more than 1 year and determined using 16S rRNA gene cloning and fluorescent in situ hybridization that members of the Paracoccus genus comprised most (approximately 30%) of the anode community. A Paracoccus isolate obtained from this biofilm (Paracoccus denitrificans strain PS-1) produced only 5.6 mW/m(2), whereas the original mixed culture produced up to 10 mW/m(2). Despite the absence of any Shewanella species in the clone library, we isolated a strain of Shewanella putrefaciens (strain PS-2) from the same biofilm capable of producing a higher-power density (17.4 mW/m(2)) than the mixed culture, although voltage generation was variable. Our results suggest that the numerical abundance of microorganisms in biofilms cannot be assumed a priori to correlate to capacities of these predominant species for high-power production. Detailed screening of bacterial biofilms may therefore be needed to identify important strains capable of high-power generation for specific substrates.

  20. Impact of Microbial Growth on Subsurface Perfluoroalkyl Acid Transport

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  1. Comparing growth patterns among field populations of cereal aphids reveals factors limiting their maximum abundance.

    PubMed

    Honek, A; Jarosik, V; Dixon, A F G

    2006-06-01

    Cereal stands in central Europe are commonly infested with three species of aphids that may become serious pests. With increasing abundance, the proportion of a particular species in the total aphid population may remain constant, suggesting a density-independent exponential growth, or the proportion can change, suggesting density-dependent constraints on growth. The constraints that affect particular species, and thus their relative abundance, were studied. The proportionality between maximum abundances of the cereal aphids was studied using a 10-year census of the numbers of aphids infesting 268 winter wheat plots. For two species their abundance on leaves and ears was compared. With increasing aphid density the maximum abundance of Rhopalosiphum padi (Linnaeus) remained proportional, but not that of Sitobion avenae (Fabricius), which was constrained by the smaller surface area of ears compared to leaves. There was no evidence of inter-specific competition. Maximum abundance of R. padi and Metopolophium dirhodum (Walker) on leaves did not change proportionally as the proportion of M. dirhodum decreased with increasing overall aphid density. This decrease was probably caused by the restricted distribution of M. dirhodum, which is confined to leaves, where space is limiting. No change in proportion between populations was detected when the average densities were below 0.54 aphids per leaf or ear. Non-proportional relationships between aphid populations appeared to be due to spatial constraints, acting upon the more abundant population. Detecting the limitation of population growth can help with the assessment of when density-independent exponential growth is limited by density-dependent factors. This information may help in the development of models of cereal aphid population dynamics.

  2. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    PubMed

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial

  3. Nutrient utilization, ruminal fermentation, microbial nitrogen flow, microbial abundances, and methane emissions in goats fed diets including tomato and cucumber waste fruits.

    PubMed

    Romero-Huelva, M; Molina-Alcaide, E

    2013-02-01

    The effects of replacing 50% of cereals-based concentrate with feed blocks (FB) including wastes of tomato fruits (diet ACT), wastes of cucumber fruits (diet ACC), or barley grain (diet ACB) on nutrient use, ruminal fermentation, microbial N flow to the duodenum, methane emissions, and abundances of total bacteria and methanogen were studied in goats. Four adult, dry, nonpregnant, rumen-fistulated Granadina goats (32.1 ± 5.52 kg BW) were used and 4 diets were studied in 4 trials by using a 4 × 4 Latin square experimental design. Diets consisted of alfalfa hay plus concentrate in a 1:1 ratio (AC) or 1:0.5 plus FB including wastes of ACT, ACC, or ACB. In each trial, goats were randomly assigned to 1 of the diets. Intake of each FB including ACT, ACC, and ACB were 203 ± 73, 179 ± 39, and 144 ± 68 g·animal(-1)·d(-1), respectively. The ACT and ACC diets did not (P > 0.05) compromise digestible and metabolizable energy, but reduced N retention by up to 29% (P = 0.03). Cucumber-based FB decreased the purine bases (PB):N ratio (P = 0.02) in total bacterial pellets isolated from the rumen content. Tomato-based FB decreased purine derivatives urinary excretion (P = 0.04) and microbial N flow (P = 0.03) without affecting the efficiency of synthesis but decreased methane emission by 28% (P < 0.001) compared with the other diets. Tomato and cucumber-based FB resulted in greater (P < 0.001) rumen VFA concentration and molar proportions of propionate and butyrate (P ≤ 0.02) than AC and ACB diets. No effect (P = 0.07) of diet on total bacteria abundance was observed whereas the abundance of methanogens increased (P = 0.01) with wastes-based FB. Our study suggests that ACC-based FB could replace one-half of the amount of concentrate in goat diet without compromising rumen fermentation and nutrient and energy use and without increasing methane emissions. Blocks including ACT showed an antimethanogenic effect but reduced microbial N flow to the duodenum. Further research is

  4. Linkages between Alaskan sockeye salmon abundance, growth at sea, and climate, 1955 2002

    NASA Astrophysics Data System (ADS)

    Ruggerone, G. T.; Nielsen, J. L.; Bumgarner, J.

    2007-11-01

    We tested the hypothesis that increased growth of salmon during early marine life contributed to greater survival and abundance of salmon following the 1976/1977 climate regime shift and that this, in turn, led to density-dependent reductions in growth during late marine stages. Annual measurements of Bristol Bay (Bering Sea) and Chignik (Gulf of Alaska) sockeye salmon scale growth from 1955 to 2002 were used as indices of body growth. During the first and second years at sea, growth of both stocks tended to be higher after the 1976-1977 climate shift, whereas growth during the third year and homeward migration was often below average. Multiple regression models indicated that return per spawner of Bristol Bay sockeye salmon and adult abundance of western and central Alaska sockeye salmon were positively correlated with growth during the first 2 years at sea and negatively correlated with growth during later life stages. After accounting for competition between Bristol Bay sockeye and Asian pink salmon, age-specific adult length of Bristol Bay salmon increased after the 1976-1977 regime shift, then decreased after the 1989 climate shift. Late marine growth and age-specific adult length of Bristol Bay salmon was exceptionally low after 1989, possibly reducing their reproductive potential. These findings support the hypothesis that greater marine growth during the first 2 years at sea contributed to greater salmon survival and abundance, which in turn led to density-dependent growth during later life stages when size-related mortality was likely lower. Our findings provide new evidence supporting the importance of bottom-up control in marine ecosystems and highlight the complex dynamics of species interactions that continually change as salmon grow and mature in the ocean.

  5. Linkages between Alaskan sockeye salmon abundance, growth at sea, and climate, 1955-2002

    USGS Publications Warehouse

    Ruggerone, G.T.; Nielsen, J.L.; Bumgarner, J.

    2007-01-01

    We tested the hypothesis that increased growth of salmon during early marine life contributed to greater survival and abundance of salmon following the 1976/1977 climate regime shift and that this, in turn, led to density-dependent reductions in growth during late marine stages. Annual measurements of Bristol Bay (Bering Sea) and Chignik (Gulf of Alaska) sockeye salmon scale growth from 1955 to 2002 were used as indices of body growth. During the first and second years at sea, growth of both stocks tended to be higher after the 1976-1977 climate shift, whereas growth during the third year and homeward migration was often below average. Multiple regression models indicated that return per spawner of Bristol Bay sockeye salmon and adult abundance of western and central Alaska sockeye salmon were positively correlated with growth during the first 2 years at sea and negatively correlated with growth during later life stages. After accounting for competition between Bristol Bay sockeye and Asian pink salmon, age-specific adult length of Bristol Bay salmon increased after the 1976-1977 regime shift, then decreased after the 1989 climate shift. Late marine growth and age-specific adult length of Bristol Bay salmon was exceptionally low after 1989, possibly reducing their reproductive potential. These findings support the hypothesis that greater marine growth during the first 2 years at sea contributed to greater salmon survival and abundance, which in turn led to density-dependent growth during later life stages when size-related mortality was likely lower. Our findings provide new evidence supporting the importance of bottom-up control in marine ecosystems and highlight the complex dynamics of species interactions that continually change as salmon grow and mature in the ocean. ?? 2007 Elsevier Ltd. All rights reserved.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    PubMed

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

    2015-10-15

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

  8. Abundance and biomass responses of microbial food web components to hydrology and environmental gradients within a floodplain of the River Danube.

    PubMed

    Palijan, Goran

    2012-07-01

    This study investigated the relationships of time-dependent hydrological variability and selected microbial food web components. Samples were collected monthly from the Kopački Rit floodplain in Croatia, over a period of 19 months, for analysis of bacterioplankton abundance, cell size and biomass; abundance of heterotrophic nanoflagellates and nanophytoplankton; and concentration of chlorophyll a. Similar hydrological variability at different times of the year enabled partition of seasonal effects from hydrological changes on microbial community properties. The results suggested that, unlike some other studies investigating sites with different connectivity, bacterioplankton abundance, and phytoplankton abundance and biomass increased during lentic conditions. At increasing water level, nanophytoplankton showed lower sensitivity to disturbance in comparison with total phytoplankton biomass: this could prolong autotrophic conditions within the floodplain. Bacterioplankton biomass, unlike phytoplankton, was not impacted by hydrology. The bacterial biomass less affected by hydrological changes can be an important additional food component for the floodplain food web. The results also suggested a mechanism controlling bacterial cell size independent of hydrology, as bacterial cell size was significantly decreased as nanoflagellate abundance increased. Hydrology, regardless of seasonal sucession, has the potential to structure microbial food webs, supporting microbial development during lentic conditions. Conversely, other components appear unaffected by hydrology or may be more strongly controlled by biotic interactions. This research, therefore, adds to understanding on microbial food web interactions in the context of flood and flow pulses in river-floodplain ecosystems.

  9. Factors Affecting Growth of Tengmalm's Owl (Aegolius funereus) Nestlings: Prey Abundance, Sex and Hatching Order.

    PubMed

    Zárybnická, Markéta; Riegert, Jan; Brejšková, Lucie; Šindelář, Jiří; Kouba, Marek; Hanel, Jan; Popelková, Alena; Menclová, Petra; Tomášek, Václav; Šťastný, Karel

    2015-01-01

    In altricial birds, energy supply during growth is a major predictor of the physical condition and survival prospects of fledglings. A number of experimental studies have shown that nestling body mass and wing length can vary with particular extrinsic factors, but between-year observational data on this topic are scarce. Based on a seven-year observational study in a central European Tengmalm's owl population we examine the effect of year, brood size, hatching order, and sex on nestling body mass and wing length, as well as the effect of prey abundance on parameters of growth curve. We found that nestling body mass varied among years, and parameters of growth curve, i.e. growth rate and inflection point in particular, increased with increasing abundance of the owl's main prey (Apodemus mice, Microtus voles), and pooled prey abundance (Apodemus mice, Microtus voles, and Sorex shrews). Furthermore, nestling body mass varied with hatching order and between sexes being larger for females and for the first-hatched brood mates. Brood size had no effect on nestling body mass. Simultaneously, we found no effect of year, brood size, hatching order, or sex on the wing length of nestlings. Our findings suggest that in this temperate owl population, nestling body mass is more sensitive to prey abundance than is wing length. The latter is probably more limited by the physiology of the species.

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

    PubMed

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

    2014-06-15

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

  11. Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

    PubMed

    Merlin, Chloé; Devers, Marion; Béguet, Jérémie; Boggio, Baptiste; Rouard, Nadine; Martin-Laurent, Fabrice

    2016-03-01

    The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2009-08-01

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

  14. Fermentable non-starch polysaccharides increases the abundance of Bacteroides-Prevotella-Porphyromonas in ileal microbial community of growing pigs.

    PubMed

    Ivarsson, E; Roos, S; Liu, H Y; Lindberg, J E

    2014-11-01

    Most plant-origin fiber sources used in pig production contains a mixture of soluble and insoluble non-starch polysaccharides (NSP). The knowledge about effects of these sources of NSP on the gut microbiota and its fermentation products is still scarce. The aim of this study was to investigate effects of feeding diets with native sources of NSP on the ileal and fecal microbial composition and the dietary impact on the concentration of short-chain fatty acids (SCFA) and lactic acid. The experiment comprised four diets and four periods in a change-over design with seven post valve t-cecum cannulated growing pigs. The four diets were balanced to be similar in NSP content and included one of four fiber sources, two diets were rich in pectins, through inclusion of chicory forage (CFO) and sugar beet pulp, and two were rich in arabinoxylan, through inclusion of wheat bran (WB) and grass meal. The gut microbial composition was assessed with terminal restriction fragment (TRF) length polymorphism and the abundance of Lactobacillus spp., Enterobacteriaceae, Bacteroides-Prevotella-Porphyromonas and the β-xylosidase gene, xynB, were assessed with quantitative PCR. The gut microbiota did not cluster based on NSP structure (arabinoxylan or pectin) rather, the effect was to a high degree ingredient specific. In pigs fed diet CFO, three TRFs related to Prevotellaceae together consisted of more than 25% of the fecal microbiota, which is about 3 to 23 times higher (P<0.05) than in pigs fed the other diets. Whereas pigs fed diet WB had about 2 to 22 times higher abundance (P<0.05) of Megasphaera elsdenii in feces and about six times higher abundance (P<0.05) of Lactobacillus reuteri in ileal digesta than pigs fed the other diets. The total amount of digested NSP (r=0.57; P=0.002), xylose (r=0.53; P=0.004) and dietary fiber (r=0.60; P=0.001) in ileal digesta were positively correlated with an increased abundance of Bacteroides-Prevotella-Porphyromonas. The effect on SCFA was

  15. Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass

    NASA Astrophysics Data System (ADS)

    Caron, David A.; Connell, Paige E.; Schaffner, Rebecca A.; Schnetzer, Astrid; Fuhrman, Jed A.; Countway, Peter D.; Kim, Diane Y.

    2017-03-01

    Biogeochemistry in marine plankton communities is strongly influenced by the activities of microbial species. Understanding the composition and dynamics of these assemblages is essential for modeling emergent community-level processes, yet few studies have examined all of the biological assemblages present in the plankton, and benchmark data of this sort from time-series studies are rare. Abundance and biomass of the entire microbial assemblage and mesozooplankton (>200 μm) were determined vertically, monthly and seasonally over a 3-year period at a coastal time-series station in the San Pedro Basin off the southwestern coast of the USA. All compartments of the planktonic community were enumerated (viruses in the femtoplankton size range [0.02-0.2 μm], bacteria + archaea and cyanobacteria in the picoplankton size range [0.2-2.0 μm], phototrophic and heterotrophic protists in the nanoplanktonic [2-20 μm] and microplanktonic [20-200 μm] size ranges, and mesozooplankton [>200 μm]. Carbon biomass of each category was estimated using standard conversion factors. Plankton abundances varied over seven orders of magnitude across all categories, and total carbon biomass averaged approximately 60 μg C l-1 in surface waters of the 890 m water column over the study period. Bacteria + archaea comprised the single largest component of biomass (>1/3 of the total), with the sum of phototrophic protistan biomass making up a similar proportion. Temporal variability at this subtropical station was not dramatic. Monthly depth-specific and depth-integrated biomass varied 2-fold at the station, while seasonal variances were generally <50%. This study provides benchmark information for investigating long-term environmental forcing on the composition and dynamics of the microbes that dominate food web structure and function at this coastal observatory.

  16. Abundance and structure of microbial loop components (bacteria and protists) in lakes of different trophic status.

    PubMed

    Ryszard, Chrost J; Tomasz, Adamczewski; Kalinowska, Krystyna; Skowronska, Agnieszka

    2009-09-01

    The abundance, biomass, size distribution, and taxonomic composition of bacterial and protistan (heterotrophic and autotrophic nanoflagellates and ciliates) communities were investigated in six lakes of Masurian Lake District (north-eastern Poland) differing in trophic state. Samples were taken from the trophogenic water layer during summer stratification periods in the years of 2004 and 2006. Image analysis techniques with fluorescent in situ hybridization (FISH) as well as [3H]-methyl-thymidine incorporation methods were applied to analyze differences in the composition and activity of bacterial communities. The greatest differences in trophic parameters were found between the humic lake and remaining non-humic ones. The same bacterial and heterotrophic nanoflagellate (HNF) cell size classes dominated in all the studied lakes. However, distinct increases in the contributions of large bacterial (>1.0 microm) and HNF (>10 microm) cells were observed in eutrophic lakes. The bacterial community was dominated by the beta-Proteobacteria group, which accounted for 27% of total DAPI counts. Ciliate communities were largely composed of Oligotrichida. Positive correlations between bacteria and protists, as well as between nanoflagellates (both heterotrophic and autotrophic) and ciliates, suggest that concentrations of food sources may be important in determining the abundance of protists in the studied lakes.

  17. Environmental variability in a transitional Mediterranean system (Oliveri-Tindari, Italy): Focusing on the response of microbial activities and prokaryotic abundance

    NASA Astrophysics Data System (ADS)

    Caruso, Gabriella; Azzaro, Filippo; Azzaro, Maurizio; Decembrini, Franco; La Ferla, Rosabruna; Maimone, Giovanna; De Pasquale, Francesca; Monticelli, Luis Salvador; Zaccone, Renata; Zappalà, Giuseppe; Leonardi, Marcella

    2013-12-01

    The response of both microbial activities and prokaryotic abundances to environmental variability was studied in a transitional Mediterranean system (Oliveri-Tindari, Italy) during two yearly surveys (1997-'98 and 2005-'06). The total enzymatic (leucine aminopeptidase, β-glucosidase, alkaline phosphatase) and respiratory activity rates as well as of the abundances of total prokaryotes, culturable heterotrophic bacteria, faecal coliforms and enterococci were measured in surface waters of four brackish ponds, together with temperature, salinity, dissolved oxygen, pH, inorganic nutrients, chlorophyll-a and particulate organic carbon and particulate nitrogen determinations. The seasonal and interannual patterns of microbial parameters were investigated in relation to environmental variations.

  18. Diversity, abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant.

    PubMed

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-09-01

    The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment.

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

    PubMed

    Narang, A

    1998-07-05

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

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

    PubMed

    Long, Tao; Or, Dani

    2009-08-01

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

  1. Microbial Prevalence, Diversity and Abundance in Amniotic Fluid During Preterm Labor: A Molecular and Culture-Based Investigation

    PubMed Central

    DiGiulio, Daniel B.; Romero, Roberto; Amogan, Harold P.; Kusanovic, Juan Pedro; Bik, Elisabeth M.; Gotsch, Francesca; Kim, Chong Jai; Erez, Offer; Edwin, Sam; Relman, David A.

    2008-01-01

    Background Preterm delivery causes substantial neonatal mortality and morbidity. Unrecognized intra-amniotic infections caused by cultivation-resistant microbes may play a role. Molecular methods can detect, characterize and quantify microbes independently of traditional culture techniques. However, molecular studies that define the diversity and abundance of microbes invading the amniotic cavity, and evaluate their clinical significance within a causal framework, are lacking. Methods and Findings In parallel with culture, we used broad-range end-point and real-time PCR assays to amplify, identify and quantify ribosomal DNA (rDNA) of bacteria, fungi and archaea from amniotic fluid of 166 women in preterm labor with intact membranes. We sequenced up to 24 rRNA clones per positive specimen and assigned taxonomic designations to approximately the species level. Microbial prevalence, diversity and abundance were correlated with host inflammation and with gestational and neonatal outcomes. Study subjects who delivered at term served as controls. The combined use of molecular and culture methods revealed a greater prevalence (15% of subjects) and diversity (18 taxa) of microbes in amniotic fluid than did culture alone (9.6% of subjects; 11 taxa). The taxa detected only by PCR included a related group of fastidious bacteria, comprised of Sneathia sanguinegens, Leptotrichia amnionii and an unassigned, uncultivated, and previously-uncharacterized bacterium; one or more members of this group were detected in 25% of positive specimens. A positive PCR was associated with histologic chorioamnionitis (adjusted odds ratio [OR] 20; 95% CI, 2.4 to 172), and funisitis (adjusted OR 18; 95% CI, 3.1 to 99). The positive predictive value of PCR for preterm delivery was 100 percent. A temporal association between a positive PCR and delivery was supported by a shortened amniocentesis-to-delivery interval (adjusted hazard ratio 4.6; 95% CI, 2.2 to 9.5). A dose-response association was

  2. Inconsistent Changes in Microbial Community Structure and Abundance with Biochar Amendment in Rice Paddy Soils from South China

    NASA Astrophysics Data System (ADS)

    Chen, J.; Qu, J.; Liu, X.; Zheng, J.; Li, L.; Pan, G.

    2012-04-01

    Effects of biochar amendment on soil microbiota had not yet been well understood. We conducted a cross site field study on biochar amendment to rice paddies from south China in 2010. The experiment was performed with four treatments including N fertilization only (C0N), N fertilization plus biochar at 20t/ha (C1N) and at 40t/ha (C2N) as well as a control without N fertilization and biochar (C0N0) consistently with three sites. Biochar was spread at soil surface and incorporated into soil and thoroughly mixed to depth of about 12cm before padding for rice seedling transplantation. Rice production was conducted with conventional water and nutrient management practices adapting to local climate and cultivar conditions. Topsoil samples were collected from each treatment plot across sites for chemical properties and molecular analysis after rice harvest in autumn of 2010. Contents of organic carbon, total N as well as soil microbial biomass carbon were determined with recommended methods. Quantitative real-time PCR coupled with 16S rRNA gene and 18S rRNA gene denaturing gradient gel electrophoresis (DGGE) were respectively employed to trace changes in abundance and structure of bacteria and fungi community with biochar amendment. Increase in microbial biomass carbon (SMBC) was not observed in one site but by 10-20% in other two sites while SOC contents were increased by 25-45% in all sites under biochar treatments. Copy numbers of bacterial genes were different between the sites but no changes with biochar treatment in a single site. However, cluster analysis revealed a more or less decreased similarity of bacterial community to the control (ranging from 75% to 85%) by biochar treatment in a single site. Nevertheless, a number of special bands appeared both in bacterial and fungal DGGE patterns under biochar treatments, though varying with site also. While the fungi copy numbers markedly varied both with sites and with biochar treatments, lower similarity and greater

  3. Field population abundance of leafhopper (Homoptera: Cicadelidae) and planthopper (Homoptera: Delphacidae) as affected by rice growth stages

    NASA Astrophysics Data System (ADS)

    Hafizal, M. M.; Idris, A. B.

    2013-11-01

    The leafhopper (Homoptera: Delphacidae) and planthopper (Homoptera: Cicadelidae) are considered as important rice pest in Asia including Malaysia. As phloem-feeders, they can cause loss to rice growth development and their population abundance is thought to be influenced by rice growth stages. This study was conducted to examine the population of Delphacidae and Cicadelidae between different rice growth stages, i.e. before and after rice planting periods. Monthly sampling was conducted in three sites in Kuala Selangor at before planting, vegetative, reproductive, maturing stages and post-harvest period using sweeping net and light traps. Population abundance of Delphacidae and Cicadelidae were found to be significantly different and positively correlated with different rice growth stages (p<0.05). Delphacidae was most abundance during maturing stages, while the abundance of Cicadelidae peaked during reproductive stage of rice growth. Differences in temporal abundance of the population of these two homopterans indicated adaptive feeding strategy to reduce food competition.

  4. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms.

    PubMed

    Dominiak, Dominik Marek; Nielsen, Jeppe Lund; Nielsen, Per Halkjaer

    2011-03-01

    A new approach for quantification of extracellular DNA (eDNA) in mixed biofilms at microscale resolution was developed and combined with other staining techniques to assess the origin, abundance and role of eDNA in activated sludge biofilms. Most eDNA was found in close proximity to living cells in microcolonies, suggesting that most of it originated from an active secretion or alternatively, by lysis of a sub-population of cells. When the staining was combined with fluorescence in situ hybridization for identification of the microorganisms, it was found that the eDNA content varied among the different probe-defined species. The highest amount of eDNA was found in and around the microcolonies of denitrifiers belonging to the genera Curvibacter and Thauera, the ammonium-oxidizing Nitrosomonas and the nitrite-oxidizing Nitrospira. Other floc-formers also produced eDNA, although in lower amounts. The total eDNA content in activated sludge varied from 4 to 52 mg per gram volatile suspended solids in different wastewater treatment plants. Very high local concentrations within some microcolonies were found with up to approximately 300 mg of eDNA per g of organic matter. DNase digestion of activated sludge led to general floc disintegration and disruption of the microcolonies with high eDNA content, implying that eDNA was an important structural component in activated sludge biofilms.

  5. Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces.

    PubMed

    Smriga, Steven; Sandin, Stuart A; Azam, Farooq

    2010-07-01

    Feces and distal gut contents were collected from three coral reef fish species. Bacteria cell abundances, as determined via epifluorescence microscopy, ranged two orders of magnitude among the fishes. Mass-specific and apparent cell-specific hydrolytic enzyme activities in feces from Chlorurus sordidus were very high, suggesting that endogenous fish enzymes were egested into feces. Denaturing gradient gel electrophoresis profiles of 16S rRNA genes were more similar among multiple individuals of the surgeonfish Acanthurus nigricans than among individuals of the parrotfish C. sordidus or the snapper Lutjanus bohar. Analyses of feces-derived 16S rRNA gene clones revealed that at least five bacterial phyla were present in A. nigricans and that Vibrionaceae comprised 10% of the clones. Meanwhile, C. sordidus contained at least five phyla and L. bohar three, but Vibrionaceae comprised 71% and 76% of the clones, respectively. Many sequences clustered phylogenetically to cultured Vibrio spp. and Photobacterium spp. including Vibrio ponticus and Photobacterium damselae. Other Vibrionaceae-like sequences comprised a distinct phylogenetic group that may represent the presence of 'feces-specific' bacteria. The observed differences among fishes may reflect native gut microbiota and/or bacterial assemblages associated with ingested prey.

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

    PubMed

    Szczotko, Maciej

    2007-01-01

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

  7. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils.

    PubMed

    Lammel, Daniel R; Feigl, Brigitte J; Cerri, Carlos C; Nüsslein, Klaus

    2015-01-01

    Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world's largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our

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

    PubMed

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

    2013-06-05

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

  9. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

    PubMed Central

    Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; McKain, Nest; Ross, Dave W.; Hyslop, Jimmy J.; Waterhouse, Anthony; Freeman, Tom C.

    2016-01-01

    Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism

  10. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

    PubMed

    Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

    2016-02-01

    Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism

  11. Reconstruction of Pacific salmon abundance from riparian tree-ring growth.

    PubMed

    Drake, D C; Naiman, Robert J

    2007-07-01

    We use relationships between modern Pacific salmon (Oncorhynchus spp.) escapement (migrating adults counted at weirs or dams) and riparian tree-ring growth to reconstruct the abundance of stream-spawning salmon over 150-350 years. After examining nine sites, we produced reconstructions for five mid-order rivers and four salmon species over a large geographic range in the Pacific Northwest: chinook (O. tschwatcha) in the Umpqua River, Oregon, USA; sockeye (O. nerka) in Drinkwater Creek, British Columbia, Canada; pink (O. gorbuscha) in Sashin Creek, southeastern Alaska, USA; chum (O. keta) in Disappearance Creek, southeastern Alaska, USA; and pink and chum in the Kadashan River, southeastern Alaska, USA. We first derived stand-level, non-climatic growth chronologies from riparian trees using standard dendroecology methods and differencing. When the chronologies were compared to 18-55 years of adult salmon escapement we detected positive, significant correlations at five of the nine sites. Regression models relating escapement to tree-ring growth at the five sites were applied to the differenced chronologies to reconstruct salmon abundance. Each reconstruction contains unique patterns characteristic of the site and salmon species. Reconstructions were validated by comparison to local histories (e.g., construction of dams and salmon canneries) and regional fisheries data such as salmon landings and aerial surveys and the Pacific Decadal Oscillation climate index. The reconstructions capture lower-frequency cycles better than extremes and are most useful for determination and comparison of relative abundance, cycles, and the effects of interventions. Reconstructions show lower population cycle maxima in both Umpqua River chinook and Sashin Creek pink salmon in recent decades. The Drinkwater Creek reconstruction suggests that sockeye abundance since the mid-1990s has been 15-25% higher than at any time since 1850, while no long-term deviations from natural cycles are

  12. Spatial scaling of avian population dynamics: population abundance, growth rate, and variability.

    PubMed

    Jones, Jason; Doran, Patrick J; Holmes, Richard T

    2007-10-01

    Synchrony in population fluctuations has been identified as an important component of population dynamics. In a previous study, we determined that local-scale (<15-km) spatial synchrony of bird populations in New England was correlated with synchronous fluctuations in lepidopteran larvae abundance and with the North Atlantic Oscillation. Here we address five questions that extend the scope of our earlier study using North American Breeding Bird Survey data. First, do bird populations in eastern North America exhibit spatial synchrony in abundances at scales beyond those we have documented previously? Second, does spatial synchrony depend on what population metric is analyzed (e.g., abundance, growth rate, or variability)? Third, is there geographic concordance in where species exhibit synchrony? Fourth, for those species that exhibit significant geographic concordance, are there landscape and habitat variables that contribute to the observed patterns? Fifth, is spatial synchrony affected by a species' life history traits? Significant spatial synchrony was common and its magnitude was dependent on the population metric analyzed. Twenty-four of 29 species examined exhibited significant synchrony in population abundance: mean local autocorrelation (rho)= 0.15; mean spatial extent (mean distance where rho=0) = 420.7 km. Five of the 29 species exhibited significant synchrony in annual population growth rate (mean local autocorrelation = 0.06, mean distance = 457.8 km). Ten of the 29 species exhibited significant synchrony in population abundance variability (mean local autocorrelation = 0.49, mean distance = 413.8 km). Analyses of landscape structure indicated that habitat variables were infrequent contributors to spatial synchrony. Likewise, we detected no effects of life history traits on synchrony in population abundance or growth rate. However, short-distance migrants exhibited more spatially extensive synchrony in population variability than either year

  13. Seasonal Abundance, Spatial Distribution, Spawning and Growth of Astropecten irregularis (Echinodermata: Asteroidea)

    NASA Astrophysics Data System (ADS)

    Freeman, S. M.; Richardson, C. A.; Seed, R.

    2001-07-01

    Seasonal trends in the abundance, spatial distribution, spawning and growth of a population of Astropecten irregularis inhabiting the coastal waters of North Wales are described. Population densities of A. irregularis varied seasonally with starfish attaining their maximum and minimum abundances in summer and winter respectively. Changes in their spatial distribution strongly suggests that A. irregularis migrates offshore into deeper waters during the winter months probably to avoid strong onshore wave surges. High population densities of starfish which occur during the summer months may be associated with spawning aggregations or the availability of suitable prey species; a smaller peak in starfish abundance occurred during autumn 1997 coinciding with the settlement of the bivalve Spisula subtruncata and the cumacean Diastylis rugosa , prey species which are readily consumed by A. irregularis. Astropecten irregularis spawned during late spring-early summer, but thereafter the gonad somatic index remained at a low level until late autumn; the index increased throughout winter and starfish attained peak reproductive condition by late spring. Small starfish (arm length <24 mm), showed little evidence of reproductive development. Limited recruitment of A. irregularis (<8 mm) occurred during October-November 1996, and the integration of this small cohort into the main population occurred within one year. Locomotory activity and burrowing depth of starfish maintained in laboratory aquaria correlated with changes in seawater temperature; activity was largely inhibited and burrowing depth significantly increased at temperatures <8 °C. Seawater temperature is probably an important factor regulating the abundance and distribution of A. irregularis in coastal waters.

  14. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation.

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

    PubMed

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

    2015-10-01

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

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

    PubMed

    Fujikawa, Hiroshi

    2011-06-01

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

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

    PubMed Central

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

  19. Bathyal meiobenthos of the western Coral Sea: distribution and abundance in relation to microbial standing stocks and environmental factors

    NASA Astrophysics Data System (ADS)

    Alongi, Daniel M.; Pichon, Michel

    1988-04-01

    The distribution and abundance of meiobenthos in relation to microbial densities and environmental factors were examined at 24 stations in a bathyal (298-1610 m) region of the western Coral Sea. Densities of metazoan meiofauna were low ( overlinex = 57 ; range: 19-170 individuals 10 cm -2) compared with other bathyal communtiesm but when densities of living Foraminifera ( overlinex = 560 ; range: 0-3410 individuals 10 cm -2) were included, total faunal densities were high ( overlinex = 610 10 cm-2) and ranged from 73 to 3465 individuals 10 cm -2. Soft-bodied (non-chitinous) taxa (e.g. turbellarians) were not detected beyond the continental slope. Densities of all metazoan taxa, excluding nematodes, decreased significantly with bathymetric depth. When the effect of ocean depth was held constant, only a few significant correlations of meiobenthos with microbes and sediment characteristics were found. Our data, coupled with earlier findings of low bacterial densities and organic conditions, suggest that low densities of metazoan meiobenthos in the western Coral Sea are due to low rates of detrital input. However, densities of Foraminifera and other protozoans increased with bathymetric depth ( ALONGI, 1987, Deep-Sea Research, 34, 1245-1254), indicating their ability to exploit oligotrophic conditions and to gain numerical dominance in benthic food webs of the deep sea.

  20. Age, growth, mortality, and abundance of lake sturgeon in the Grasse River, New York, USA

    USGS Publications Warehouse

    Trested, D.G.; Isely, J.J.

    2011-01-01

    An increased understanding of lake sturgeon (Acipenser fulvescens) population dynamics is a key requirement for successful management efforts. Little is known regarding the Grasse River population of lake sturgeon except that it is one of a few populations in New York State where spawning has been documented. Thus our purpose was to assess the current status of lake sturgeon in the Grasse River system, including age, growth, mortality, and abundance. Age was determined for 196 of 211 lake sturgeon by examination of sectioned pectoral fin rays. Ages ranged from 0 to 32 years and the annual mortality rate for fish between ages 7 and 14 was 16.8%. The weight (W, g) to total length (TL, mm) relationship was W = 1.281 x 10-6TL3.202. The von Bertalanffy growth equation was TL = 1913(1-e-0.0294(t+9.5691)). While the range of observed ages was similar to that of nearby St. Lawrence River populations, mean weight at age for an individual at 1000 mm TL was lower than that observed for lake sturgeon within Lake St. Francis of the St. Lawrence River. Predicted growth based on von Bertalanffy parameters was similar to that observed for the nearby Lake St. Francis. An open population estimator using the POPAN sub-module in the Program MARK produced an abundance estimate of 793 lake sturgeon (95% CI = 337-1249).

  1. Inhibition of microbial growth by carbon nanotube networks

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  2. Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

    NASA Technical Reports Server (NTRS)

    Huang, Jonathan; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Bej, Asim K.

    2010-01-01

    Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

  3. Comparison of the microbial diversity and abundance between the freshwater land-locked lakes of Schirmacher Oasis, and the perennially ice-covered Lake Untersee in East Antarctica

    NASA Astrophysics Data System (ADS)

    Huang, Jonathan P.; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Andersen, Dale T.; Bej, Asim K.

    2010-09-01

    Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors to the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed an abundant and diverse group of microorganisms compared to Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27C had a richer microbial diversity representing 4 different phyla and 7 different genera. In contrast L47 consisted of 3 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

  4. Rumen microbial abundance and fermentation profile during severe subacute ruminal acidosis and its modulation by plant derived alkaloids in vitro.

    PubMed

    Mickdam, Elsayed; Khiaosa-Ard, Ratchaneewan; Metzler-Zebeli, Barbara U; Klevenhusen, Fenja; Chizzola, Remigius; Zebeli, Qendrim

    2016-06-01

    Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and fermentation profiles using a severe subacute ruminal acidosis (SARA) in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA), containing quaternary benzophenanthridine and protopine alkaloids, of which sanguinarine and chelerythrine were the major bioactive compounds. Induction of severe SARA strongly affected the rumen microbial composition and fermentation variables without suppressing the abundance of total bacteria. Protozoa and fungi were more sensitive to the low ruminal pH condition than bacteria. Induction of severe SARA clearly depressed degradation of fiber (P < 0.001), which came along with a decreased relative abundance of fibrolytic Ruminococcus albus and Fibrobacter succinogenes (P < 0.001). Under severe SARA conditions, the genus Prevotella, Lactobacillus group, Megasphaera elsdenii, and Entodinium spp. (P < 0.001) were more abundant, whereas Ruminobacter amylophilus was less abundant. SARA largely suppressed methane formation (-70%, P < 0.001), although total methanogenic 16S rRNA gene abundance was not affected. According to principal component analysis, Methanobrevibacter spp. correlated to methane concentration. Addition of PDA modulated ruminal fermentation under normal conditions such as enhanced (P < 0.05) concentration of total SCFA, propionate and valerate, and increased (P < 0.05) degradation of crude protein compared with the unsupplemented control diet. Our results indicate strong shifts in the microbial community during severe SARA compared to normal conditions. Supplementation of PDA positively modulates ruminal fermentation under normal ruminal pH conditions.

  5. Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem ▿ †

    PubMed Central

    Boyd, Eric S.; Lange, Rachel K.; Mitchell, Andrew C.; Havig, Jeff R.; Hamilton, Trinity L.; Lafrenière, Melissa J.; Shock, Everett L.; Peters, John W.; Skidmore, Mark

    2011-01-01

    Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Although archaeal amoA genes were detected, they were less abundant and less diverse than bacterial amoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur in situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ∼210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of nifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales. PMID:21622799

  6. Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem.

    PubMed

    Boyd, Eric S; Lange, Rachel K; Mitchell, Andrew C; Havig, Jeff R; Hamilton, Trinity L; Lafrenière, Melissa J; Shock, Everett L; Peters, John W; Skidmore, Mark

    2011-07-01

    Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Although archaeal amoA genes were detected, they were less abundant and less diverse than bacterial amoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur in situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ~210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of nifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    S.M. Frank

    2009-02-01

    A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 × 103 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments.

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

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

    PubMed

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

    2015-07-01

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

  12. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

    PubMed Central

    Lammel, Daniel R.; Feigl, Brigitte J.; Cerri, Carlos C.; Nüsslein, Klaus

    2015-01-01

    Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve

  13. Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

    PubMed Central

    Liu, Xing; Zhang, Junlian; Gu, Tianyu; Zhang, Wenming; Shen, Qirong; Yin, Shixue; Qiu, Huizhen

    2014-01-01

    Background Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Methodology/Principal Findings Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (HShannon) and richness (SChao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Conclusions Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait

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

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

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

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

    PubMed

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

    2006-12-01

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

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

    PubMed

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

    2015-01-01

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

  17. Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis

    PubMed

    Blackburn; Hagstrom; Wikner; Cuadros-Hansson; Bjornsen

    1998-09-01

    Annual bacterial plankton dynamics at several depths and locations in the Baltic Sea were studied by image analysis. Individual bacteria were classified by using an artificial neural network which also effectively identified nonbacterial objects. Cell counts and frequencies of dividing cells were determined, and the data obtained agreed well with visual observations and previously published values. Cell volumes were measured accurately by comparison with bead standards. The survey included 690 images from a total of 138 samples. Each image contained approximately 200 bacteria. The images were analyzed automatically at a rate of 100 images per h. Bacterial abundance exhibited coherent patterns with time and depth, and there were distinct subsurface peaks in the summer months. Four distinct morphological classes were resolved by the image analyzer, and the dynamics of each could be visualized. The bacterial growth rates estimated from frequencies of dividing cells were different from the bacterial growth rates estimated by the thymidine incorporation method. With minor modifications, the image analysis technique described here can be used to analyze other planktonic classes.

  18. Rapid Determination of Bacterial Abundance, Biovolume, Morphology, and Growth by Neural Network-Based Image Analysis

    PubMed Central

    Blackburn, Nicholas; Hagström, Åke; Wikner, Johan; Cuadros-Hansson, Rocio; Bjørnsen, Peter Koefoed

    1998-01-01

    Annual bacterial plankton dynamics at several depths and locations in the Baltic Sea were studied by image analysis. Individual bacteria were classified by using an artificial neural network which also effectively identified nonbacterial objects. Cell counts and frequencies of dividing cells were determined, and the data obtained agreed well with visual observations and previously published values. Cell volumes were measured accurately by comparison with bead standards. The survey included 690 images from a total of 138 samples. Each image contained approximately 200 bacteria. The images were analyzed automatically at a rate of 100 images per h. Bacterial abundance exhibited coherent patterns with time and depth, and there were distinct subsurface peaks in the summer months. Four distinct morphological classes were resolved by the image analyzer, and the dynamics of each could be visualized. The bacterial growth rates estimated from frequencies of dividing cells were different from the bacterial growth rates estimated by the thymidine incorporation method. With minor modifications, the image analysis technique described here can be used to analyze other planktonic classes. PMID:9726867

  19. Optimising Microbial Growth with a Bench-Top Bioreactor

    ERIC Educational Resources Information Center

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

    2006-01-01

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

  20. Estrogenic compounds decrease growth hormone receptor abundance and alter osmoregulation in Atlantic salmon

    USGS Publications Warehouse

    Lerner, Darren T.; Sheridan, Mark A.; McCormick, Stephen D.

    2012-01-01

    Exposure of Atlantic salmon smolts to estrogenic compounds is shown to compromise several aspects of smolt development. We sought to determine the underlying endocrine mechanisms of estrogen impacts on the growth hormone (GH)/insulin-like growth factor I (IGF-I) axis. Smolts in freshwater (FW) were either injected 3 times over 10 days with 2 μg g−1 17β-estradiol (E2) or 150 μg g−1 4-nonylphenol (NP). Seawater (SW)-acclimated fish received intraperitoneal implants of 30 μg g−1 E2 over two weeks. Treatment with these estrogenic compounds increased hepatosomatic index and total plasma calcium. E2 and NP reduced maximum growth hormone binding by 30–60% in hepatic and branchial membranes in FW and SW, but did not alter the dissociation constant. E2 and NP treatment decreased plasma levels of IGF-I levels in both FW and SW. In FW E2 and NP decreased plasma GH whereas in SW plasma GH increased after E2 treatment. Compared to controls, plasma chloride concentrations of E2-treated fish were decreased 5.5 mM in FW and increased 10.5 mM in SW. There was no effect of NP or E2 on gill sodium–potassium adenosine triphosphatase (Na+/K+-ATPase) activity in FW smolts, whereas E2 treatment in SW reduced gill Na+/K+-ATPase activity and altered the number and size of ionocytes. Our data indicate that E2 downregulates the GH/IGF-I-axis and SW tolerance which may be part of its normal function for reproduction and movement into FW. We conclude that the mechanism of endocrine disruption of smolt development by NP is in part through alteration of the GH/IGF-I axis via reduced GH receptor abundance.

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

    PubMed Central

    Roden, Eric E.; Jin, Qusheng

    2011-01-01

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

  2. Influence of Land Use, Nutrients, and Geography on Microbial Communities and Fecal Indicator Abundance at Lake Michigan Beaches.

    PubMed

    Cloutier, Danielle D; Alm, Elizabeth W; McLellan, Sandra L

    2015-08-01

    Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, fine-scale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress.

  3. Evaluation of the microbial growth response to inorganic nanoparticles

    PubMed Central

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

    2006-01-01

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

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

    PubMed

    Fujikawa, Hiroshi

    2010-09-01

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

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

    PubMed

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

    2014-09-01

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

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

    DTIC Science & Technology

    1983-03-01

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

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

    PubMed

    Peleg, Micha; Corradini, Maria G

    2011-12-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2016-06-01

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

  11. Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes.

    PubMed

    Zhang, Ximei; Liu, Wei; Schloter, Michael; Zhang, Guangming; Chen, Quansheng; Huang, Jianhui; Li, Linghao; Elser, James J; Han, Xingguo

    2013-01-01

    Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.

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

    SciTech Connect

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

    2012-01-01

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

  13. Immune indexes of larks from desert and temperate regions show weak associations with life history but stronger links to environmental variation in microbial abundance.

    PubMed

    Horrocks, Nicholas P C; Hegemann, Arne; Matson, Kevin D; Hine, Kathryn; Jaquier, Sophie; Shobrak, Mohammed; Williams, Joseph B; Tinbergen, Joost M; Tieleman, B Irene

    2012-01-01

    Immune defense may vary as a result of trade-offs with other life-history traits or in parallel with variation in antigen levels in the environment. We studied lark species (Alaudidae) in the Arabian Desert and temperate Netherlands to test opposing predictions from these two hypotheses. Based on their slower pace of life, the trade-off hypothesis predicts relatively stronger immune defenses in desert larks compared with temperate larks. However, as predicted by the antigen exposure hypothesis, reduced microbial abundances in deserts should result in desert-living larks having relatively weaker immune defenses. We quantified host-independent and host-dependent microbial abundances of culturable microbes in ambient air and from the surfaces of birds. We measured components of immunity by quantifying concentrations of the acute-phase protein haptoglobin, natural antibody-mediated agglutination titers, complement-mediated lysis titers, and the microbicidal ability of whole blood. Desert-living larks were exposed to significantly lower concentrations of airborne microbes than temperate larks, and densities of some bird-associated microbes were also lower in desert species. Haptoglobin concentrations and lysis titers were also significantly lower in desert-living larks, but other immune indexes did not differ. Thus, contrary to the trade-off hypothesis, we found little evidence that a slow pace of life predicted increased immunological investment. In contrast, and in support of the antigen exposure hypothesis, associations between microbial exposure and some immune indexes were apparent. Measures of antigen exposure, including assessment of host-independent and host-dependent microbial assemblages, can provide novel insights into the mechanisms underlying immunological variation.

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

    PubMed

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

    2015-02-01

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

  15. mRNA Transcript abundance during plant growth and the influence of Li(+) exposure.

    PubMed

    Duff, M C; Kuhne, W W; Halverson, N V; Chang, C-S; Kitamura, E; Hawthorn, L; Martinez, N E; Stafford, C; Milliken, C E; Caldwell, E F; Stieve-Caldwell, E

    2014-12-01

    Lithium (Li) toxicity in plants is, at a minimum, a function of Li(+) concentration, exposure time, species and growth conditions. Most plant studies with Li(+) focus on short-term acute exposures. This study examines short- and long-term effects of Li(+) exposure in Arabidopsis with Li(+) uptake studies and measured shoot mRNA transcript abundance levels in treated and control plants. Stress, pathogen-response and arabinogalactan protein genes were typically more up-regulated in older (chronic, low level) Li(+)-treatment plants and in the much younger plants from acute high-level exposures. The gene regulation behavior of high-level Li(+) resembled prior studies due to its influence on: inositol synthesis, 1-aminocyclopropane-1-carboxylate synthases and membrane ion transport. In contrast, chronically-exposed plants had gene regulation responses that were indicative of pathogen, cold, and heavy-metal stress, cell wall degradation, ethylene production, signal transduction, and calcium-release modulation. Acute Li(+) exposure phenocopies magnesium-deficiency symptoms and is associated with elevated expression of stress response genes that could lead to consumption of metabolic and transcriptional energy reserves and the dedication of more resources to cell development. In contrast, chronic Li(+) exposure increases expression signal transduction genes. The identification of new Li(+)-sensitive genes and a gene-based "response plan" for acute and chronic Li(+) exposure are delineated.

  16. mRNA Transcript Abundance during Plant Growth and the Influence of Li+ Exposure

    DOE PAGES

    Duff, M. C.; Kuhne, W. W.; Halverson, N. V.; ...

    2014-10-23

    Lithium (Li) toxicity in plants is, at a minimum, a function of Li+ concentration, exposure time, species and growth conditions. Most plant studies with Li+ focus on short-term acute exposures. This study examines short- and long-term effects of Li+ exposure in Arabidopsis with Li+ uptake studies and measured shoot mRNA transcript abundance levels in treated and control plants. Stress, pathogen-response and arabinogalactan protein genes were typically more up-regulated in older (chronic, low level) Li+-treatment plants and in the much younger plants from acute high-level exposures. The gene regulation behavior of high-level Li+ resembled prior studies due to its influence on:more » inositol synthesis, 1-aminocyclopropane-1-carboxylate synthases and membrane ion transport. In contrast, chronically-exposed plants had gene regulation responses that were indicative of pathogen, cold, and heavy-metal stress, cell wall degradation, ethylene production, signal transduction, and calcium-release modulation. Acute Li+ exposure phenocopies magnesium-deficiency symptoms and is associated with elevated expression of stress response genes that could lead to consumption of metabolic and transcriptional energy reserves and the dedication of more resources to cell development. In contrast, chronic Li+ exposure increases expression signal transduction genes. The identification of new Li+-sensitive genes and a gene-based “response plan” for acute and chronic Li+ exposure are delineated.« less

  17. Settlement, abundance, growth and mortality of juvenile flatfish in a subtropical tidal estuary (Georgia, U.S.A.)

    NASA Astrophysics Data System (ADS)

    Reichert, Marcel J. M.; van der Veer, Henk W.

    The population dynamics of juveniles of some flatfish species were studied in the Duplin River, a tidal creek in a subtropical salt-marsh area in Georgia, U.S.A. from April until September 1990. Seven species were found. Paralichthys dentatus, Paralichthys lethostigma, Paralichthys oblongus and Trinectus maculatus were relatively rare. Etropus crossotus, Citharichthys spilopterus and Symphurus plagiusa were abundant and settled during the period studied. E. crossotus was the most abundant species with a mean abundance of 18 ind·10 -2 m -2 (max. 287). Demersal settlement of E. crossotus took place in shallow areas and over sandy bottoms from mid-May to August. Prolonged settlement hampered the calculation of growth rate and instantaneous mortality rate. However, laboratory growth experiments indicated a mean growth of about 0.50 mm·d -1 at 24-28°C. Juveniles of C. spilopterus were already present in the Duplin River in March. Settling continued until the end of April with a mean abundance of 3.5 ind·10 -2 m -2 (max. 183). With increasing size the juveniles of this species tended to migrate to deeper waters and to the mouth of the river, possibly as a reaction to increasing water temperatures. Maximum growth rate was 1.4 mm·d -1 at about 26°C. The mean instantaneous mortality rate (z) was estimated at 0.03·d -1. Settling of S. plagiusa occurred from mid-May onwards. The mean abundance was 10.3 ind·10 -2 m -2 (max. 98.3). Newly settled juveniles were most abundant on muddy sediments in the shallow river areas. The maximum growth rate was 1.3 mm·d -1 at about 28°C. The mean instantaneous mortality rate (Z) decreased from 0.04·d -1 in April to 0.01·d -1 in August. At all sites the abundance of juveniles of this species decreased with increasing water depth. Predation experiments indicated that blue crabs ( Callinectes similis and C. sapidus) and sea robins ( Prionotus sp.) are potential predators on juvenile flatfish. The high abundances of juvenile flatfish

  18. Influence of Land Use, Nutrients, and Geography on Microbial Communities and Fecal Indicator Abundance at Lake Michigan Beaches

    PubMed Central

    Cloutier, Danielle D.; Alm, Elizabeth W.

    2015-01-01

    Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, fine-scale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress. PMID:25979888

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

    PubMed

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

    1966-01-01

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

  20. What's on the menu? Assessing microbial carbon sources and cycling in soils using natural abundance radiocarbon analysis

    NASA Astrophysics Data System (ADS)

    Mahmoudi, N.; Burns, L.; Mancini, S.; Fulthorpe, R.; Slater, G. F.

    2011-12-01

    Organic matter in soils is composed of diverse materials in various stages of decomposition. Soil organic matter is not in a single pool but rather in multiple carbon pools with different intrinsic turnover times that can be on annual to decadal and even millennial timescales. Microorganisms can influence the total amount of carbon stored in soils and the turnover rates of these different pools. However, the links between microbes and their ability to utilize these various carbon pools are not well understood. Moreover, microbes have been shown to co-utilize a number of available carbon sources rather than a single carbon source under soil conditions which creates difficulties in identifying microbial carbon sources in the natural environment. Compound-specific radiocarbon analysis of microbial phospholipid fatty acids (PLFA) has become a useful tool in elucidating microbial carbon sources in complex environments with multiple carbon sources. We investigated microbial carbon cycling at an industrial site in Ontario which included a variety of carbon sources including vegetation, PAHs and natural organic matter (NOM). Using this approach, the 14C content of microbial membrane lipids (which reflects their carbon source) can be compared to surrounding carbon sources in order to assess which carbon source they are metabolizing and incorporating into their lipids. In addition, we assessed microbial community structure and diversity by analyzing amplified bacterial, eukaryotic and archaeal rDNA fragments with denaturing gel gradient electrophoresis (DGGE). The Δ14C value for PLFAs ranged from +54 to -697% which indicates that microbial carbon sources across soils differ. The Δ14CPLFA for some soils is consistent with modern carbon sources while Δ14CPLFA for other soils is consistent with natural organic matter including older pools of carbon. The microbial communities at this site are not metabolizing PAHs but rather they are utilizing various pools of natural organic

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

    PubMed

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

    2009-10-01

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

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

    PubMed

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

    2015-08-01

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

  3. Decline in topsoil microbial quotient, fungal abundance and C utilization efficiency of rice paddies under heavy metal pollution across South China.

    PubMed

    Liu, Yongzhuo; Zhou, Tong; Crowley, David; Li, Lianqing; Liu, Dawen; Zheng, Jinwei; Yu, Xinyan; Pan, Genxing; Hussain, Qaiser; Zhang, Xuhui; Zheng, Jufeng

    2012-01-01

    Agricultural soils have been increasingly subject to heavy metal pollution worldwide. However, the impacts on soil microbial community structure and activity of field soils have been not yet well characterized. Topsoil samples were collected from heavy metal polluted (PS) and their background (BGS) fields of rice paddies in four sites across South China in 2009. Changes with metal pollution relative to the BGS in the size and community structure of soil microorganisms were examined with multiple microbiological assays of biomass carbon (MBC) and nitrogen (MBN) measurement, plate counting of culturable colonies and phospholipids fatty acids (PLFAs) analysis along with denaturing gradient gel electrophoresis (DGGE) profile of 16S rRNA and 18S rRNA gene and real-time PCR assay. In addition, a 7-day lab incubation under constantly 25°C was conducted to further track the changes in metabolic activity. While the decrease under metal pollution in MBC and MBN, as well as in culturable population size, total PLFA contents and DGGE band numbers of bacteria were not significantly and consistently seen, a significant reduction was indeed observed under metal pollution in microbial quotient, in culturable fungal population size and in ratio of fungal to bacterial PLFAs consistently across the sites by an extent ranging from 6% to 74%. Moreover, a consistently significant increase in metabolic quotient was observed by up to 68% under pollution across the sites. These observations supported a shift of microbial community with decline in its abundance, decrease in fungal proportion and thus in C utilization efficiency under pollution in the soils. In addition, ratios of microbial quotient, of fungal to bacterial and qCO(2) are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO(2) production in the polluted rice paddies deserve further field studies.

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

    PubMed

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

    2012-09-01

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

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

    NASA Technical Reports Server (NTRS)

    Macatangay, Ariel V.; Bruce, Rebekah J.

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Macatangay, Ariel V.; Bruce, Rebekah J.

    2009-01-01

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

  7. Factors Affecting Growth of Tengmalm’s Owl (Aegolius funereus) Nestlings: Prey Abundance, Sex and Hatching Order

    PubMed Central

    Zárybnická, Markéta; Riegert, Jan; Brejšková, Lucie; Šindelář, Jiří; Kouba, Marek; Hanel, Jan; Popelková, Alena; Menclová, Petra; Tomášek, Václav; Šťastný, Karel

    2015-01-01

    In altricial birds, energy supply during growth is a major predictor of the physical condition and survival prospects of fledglings. A number of experimental studies have shown that nestling body mass and wing length can vary with particular extrinsic factors, but between-year observational data on this topic are scarce. Based on a seven-year observational study in a central European Tengmalm’s owl population we examine the effect of year, brood size, hatching order, and sex on nestling body mass and wing length, as well as the effect of prey abundance on parameters of growth curve. We found that nestling body mass varied among years, and parameters of growth curve, i.e. growth rate and inflection point in particular, increased with increasing abundance of the owl’s main prey (Apodemus mice, Microtus voles), and pooled prey abundance (Apodemus mice, Microtus voles, and Sorex shrews). Furthermore, nestling body mass varied with hatching order and between sexes being larger for females and for the first-hatched brood mates. Brood size had no effect on nestling body mass. Simultaneously, we found no effect of year, brood size, hatching order, or sex on the wing length of nestlings. Our findings suggest that in this temperate owl population, nestling body mass is more sensitive to prey abundance than is wing length. The latter is probably more limited by the physiology of the species. PMID:26444564

  8. Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this report we use Terminal Restriction Fragment Length Polymorphisms (TRFLP) in a tomato production system to “finger printing” the soil microbial community structure with Phylum specific primer sets. Factors influencing the soil microbes are a cover crop of Hairy Vetch (Vicia villosa) or Rye (...

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

    PubMed

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

    2014-07-01

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

  10. Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

    PubMed Central

    Francioli, Davide; Schulz, Elke; Lentendu, Guillaume; Wubet, Tesfaye; Buscot, François; Reitz, Thomas

    2016-01-01

    Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    PubMed

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

    2015-11-01

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

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

    PubMed

    Gimkiewicz, Carla; Harnisch, Falk

    2013-12-29

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

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

    PubMed Central

    Gimkiewicz, Carla; Harnisch, Falk

    2013-01-01

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

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

    PubMed

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

    2013-05-15

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

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

    PubMed Central

    Li, W K

    1984-01-01

    The uptake of [3H]glucose and a mixture of 3H-labeled amino acids was measured, in time course fashion, in planktonic microbial assemblages of the eastern tropical Pacific Ocean. The average generation times of those portions of the assemblages able to utilize these substrates were estimated from a simple exponential growth model. Other workers have independently used this model in its integrated or differential form. A mathematical verification and an experimental demonstration of the equivalence of the two approaches are presented. A study was made of the size distribution of heterotrophic activity, using time course measurements. It was found that the size distribution and the effect of sample filtration before radiolabeling were dependent on time of incubation. In principle, it was possible to ascribe these time dependences to differences in the specific growth rate and initial standing stock of the microbial assemblages. PMID:6696414

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

    PubMed Central

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

    1992-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  20. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

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

    PubMed

    Meier, Courtney L; Bowman, William D

    2008-11-01

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

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

    PubMed

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

    2010-07-15

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

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

    SciTech Connect

    Lau, Ming Woei

    2015-12-08

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

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

    PubMed Central

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

    2016-01-01

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

  5. Enough is enough: the effects of symbiotic ant abundance on herbivory, growth, and reproduction in an African acacia.

    PubMed

    Palmer, Todd M; Brody, Alison K

    2013-03-01

    Understanding how cooperative interactions evolve and persist remains a central challenge in biology. Many mutualisms are thought to be maintained by "partner fidelity feedback," in which each partner bases their investment on the benefits they receive. Yet, we know little about how benefits change as mutualists vary their investment, which is critical to understanding the balance between mutualism and antagonism in any given partnership. Using an obligate ant-plant mutualism, we manipulated the density of symbiotic acacia ants (Crematogaster mimosae) and examined how the costs and benefits to Acacia drepanolobium trees scaled with ant abundance. Benefits of ants to plants saturated with increasing ant abundance for protection from branch browsing by elephants and attack by branch galling midges, while varying linearly for protection from cerambycid beetles. In addition, the risk of catastrophic whole-tree herbivory by elephants was highest for trees with very low ant abundance. However, there was no relationship between ant abundance and herbivory by leaf-feeding invertebrates, nor by vertebrate browsers such as giraffe, steinbuck, and Grant's gazelle. Ant abundance did not significantly influence rates of branch growth on acacias, but there was a significant negative relationship between ant abundance and the number of fruits produced by host plants, suggesting that maintaining high-density ant colonies is costly. Because benefits to plants largely saturated with increasing colony size, while costs to plant reproduction increased, we suggest that ant colonies may achieve abundances that are higher than optimal for host plants. Our results highlight the conflicts of interest inherent in many mutualisms, and demonstrate the value of examining the shape of curves relating costs and benefits within these globally important interactions.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2001-05-01

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

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

    PubMed

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

    2012-07-01

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

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

    PubMed

    Gendugov, V M; Glazunov, G P

    2013-01-01

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

  10. Experimental Manipulation of Soil Moisture Regime Impacts Soil Microbial Community Abundance, Diversity, and Function in a Semi-Arid Sagebrush Steppe

    NASA Astrophysics Data System (ADS)

    Sorensen, P. O.; Feris, K. P.; Germino, M. J.

    2010-12-01

    Rising global temperatures are predicted to alter regional climate regimes, including the spatial and temporal distribution of precipitation. In water-limited (e.g. arid and semi-arid) ecosystems annual precipitation is low and shows a high degree of variability. In these environments, soil microbes occupy a pivotal seat coupling the effects of water availability and plant productivity to biogeochemical cycling and ecosystem function. Using a long running ecological field experiment (>15 years) sited in Idaho’s sagebrush steppe, effects of experimentally manipulated precipitation regime on microbial diversity, abundance, and terrestrial carbon cycling are being explored. Soils were sampled in January (winter) of 2009. Replicate cores collected at 15-20cm and 95-100cm, were taken from field plots planted with native vegetation under three different precipitation amendments; Ambient, Summer (+200mm in June), or Fall/Spring (+200mm in April or October). Bacterial and Fungal community structure was analyzed by high-resolution 454 pyrosequencing. Edaphic properties (soil moisture, pH, total C, total N, organic C, inorganic N, ortho P) were measured and used as factors for general linear modeling of Bacterial and Fungal community structure against field treatments. Labile soil carbon pools were measured as C mineralization rates by gas chromatography using long term soil incubations. Pyrosequencing analysis of soil Bacterial communities has revealed greater Bacterial community abundance and diversity across all treatments relative to Archaeal and Fungal communities. General linear modeling of sequences obtained from 454 pyrosequencing showed significant interactions of phyla-level Bacterial and Fungal abundance with experimental precipitation regime and depth of sampling. Edaphic properties such as soil moisture and pH also showed significant interactions with phyla-level Bacterial and Fungal abundance. Long-term soil incubation studies revealed treatment effects on

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2010-09-01

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

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

    PubMed

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

    2002-01-01

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

  14. El Niño, host plant growth, and migratory butterfly abundance in a changing climate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the wet forests of Panama, El Niño typically brings a more prolonged and severe dry season. Interestingly, many trees and lianas that comprise the wet forests increase their productivity as a response to El Niño. Here we quantify the abundance of migrating Marpesia chiron butterflies over 17 yea...

  15. Effects of planting Phragmites australis on nitrogen removal, microbial nitrogen cycling, and abundance of ammonia-oxidizing and denitrifying microorganisms in sediments.

    PubMed

    Toyama, Tadashi; Nishimura, Yoshiko; Ogata, Yuka; Sei, Kazunari; Mori, Kazuhiro; Ike, Michihiko

    2015-10-21

    We examined the effect of planting an emergent aquatic plant (Phragmites australis) on nitrogen removal from sediments using a 42-d pot experiment. The experimental pot systems comprised two types of sediments planted with and without young P. australis. Total nitrogen (total N), total dissolved N, and NH4-N in the sediments decreased markedly after planting. In contrast, those levels decreased only slightly in the unplanted sediments. The decrease in total N in the P. australis-planted sediments was 7-20 times those in the unplanted sediments. Abundances of bacterial 16S rRNA, archaeal 16S rRNA, ammonia-oxidizing bacterial ammonia monooxygenase (amoA), ammonia-oxidizing archaeal amoA, and denitrifying bacterial nitrite reductase (nirK) genes increased significantly in sediments after planting. Phragmites australis appears to have released oxygen and created a repeating cycle of oxidizing and reducing conditions in the sediments. These conditions should promote mineralization of organic N, nitrification, and denitrification in the sediments. Phragmites australis absorbed bioavailable nitrogen generated by microbial nitrogen metabolism. During the 42-d period after planting, 31-44% of total N was removed by microbial nitrogen cycling, and 56-69% was removed via absorption by P. australis. These results suggest that planting P. australis can increase microbial populations and their activities, and that nitrogen removal can be accelerated by the combined functions of P. australis and microorganisms in the sediment. Thus, planting P. australis has considerable potential as an effective remediation technology for eutrophic sediments.

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

    PubMed Central

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

    2015-01-01

    Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial–plants and microbial–microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use. PMID:25821453

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

    PubMed

    Saravanan, Pichiah; Pakshirajan, K; Saha, Prabirkumar

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Juarez, Gabriel; Stocker, Roman

    2015-11-01

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

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

    PubMed

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

    2014-01-01

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

  20. Bioremediation of PAH-contamined soils: Consequences on formation and degradation of polar-polycyclic aromatic compounds and microbial community abundance.

    PubMed

    Biache, Coralie; Ouali, Salma; Cébron, Aurélie; Lorgeoux, Catherine; Colombano, Stéfan; Faure, Pierre

    2017-05-05

    A bioslurry batch experiment was carried out over five months on three polycyclic aromatic compound (PAC) contaminated soils to study the PAC (PAH and polar-PAC) behavior during soil incubation and to evaluate the impact of PAC contamination on the abundance of microbial communities and functional PAH-degrading populations. Organic matter characteristics and reactivity, assessed through solvent extractable organic matter and PAC contents, and soil organic matter mineralization were monitored during 5 months. Total bacteria and fungi, and PAH-ring hydroxylating dioxygenase genes were quantified. Results showed that PAHs and polar-PACs were degraded with different degradation dynamics. Differences in degradation rates were observed among the three soils depending on PAH distribution and availability. Overall, low molecular weight compounds were preferentially degraded. Degradation selectivity between isomers and structurally similar compounds was observed which could be used to check the efficiency of bioremediation processes. Bacterial communities were dominant over fungi and were most likely responsible for PAC degradation. Abundance of PAH-degrading bacteria increased during incubations, but their proportion in the bacterial communities tended to decrease. The accumulation of some oxygenated-PACs during the bioslurry experiment underlines the necessity to monitor these compounds during application of remediation treatment on PAH contaminated soils.

  1. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

    PubMed Central

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-01-01

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies. PMID:27886221

  2. Arsenic methylation in soils and its relationship with microbial arsM abundance and diversity, and as speciation in rice.

    PubMed

    Zhao, Fang-Jie; Harris, Eleanor; Yan, Jia; Ma, Jincai; Wu, Liyou; Liu, Wenju; McGrath, Steve P; Zhou, Jizhong; Zhu, Yong-Guan

    2013-07-02

    Methylation of arsenic in soil influences its environmental behavior and accumulation by plants, but little is known about the factors affecting As methylation. As speciation was determined in the pore waters of six soils from diverse geographical locations over 54 days of incubation under flooded conditions. The concentration of methylated As (monomethylarsonic acid, MMA, and dimethylarsinic acid, DMA) varied from 0 to 85 μg L(-1) (0 - 69% of the total As in pore water). Two Bangladeshi paddy soils contaminated by irrigation of As-laden groundwater produced large concentrations of inorganic As but relatively little methylated As. Two contaminated paddy soils from China produced a transient peak of DMA during the early phase of incubation. Methylated As represented considerable proportions of the total soluble As in the two uncontaminated soils from the UK and U.S. The copy number of the microbial arsenite methyltransferase gene (arsM) correlated positively with soil pH. However, pore-water methylated As correlated negatively with pH or arsM copy number, and positively with dissolved organic C. GeoChip assay revealed considerable arsM diversity among the six soils, with 27-35 out of 66 sequences in the microarray being detected. As speciation in rice plants grown in the soils generally mirrored that in the pore water. The results suggest that methylated As species in plants originated from the soil and As methylation in soil was influenced strongly by the soil conditions.

  3. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

    PubMed

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-11-25

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

  4. Effects of initial moisture content of Korean traditional wheat-based fermentation starter nuruk on microbial abundance and diversity.

    PubMed

    Bal, Jyotiranjan; Yun, Suk-Hyun; Yeo, Soo-Hwan; Kim, Jung-Mi; Kim, Beom-Tae; Kim, Dae-Hyuk

    2017-03-01

    The brewing of makgeolli, one of Korea's most popular alcoholic beverages that is gaining popularity globally, is facilitated by nuruk, a traditional Korean cereal starter. The nuruk microbiome greatly influences the fermentation process as well as the nutritional, hygienic, and aromatic qualities of the product. This study is a continuation of our efforts to examine nuruk biodiversity at a depth previously unattainable. In this study, microfloral dynamics in wheat-based nuruk C, composed of traditional ingredients such as barley, green gram, and wheat and fermented under various internal moisture contents of 20% (C20), 26% (C26), and 30% (C30), was evaluated using 454 pyrosequencing during the 30-day fermentation process. Rarefaction analysis and alpha diversity parameters indicated adequate sampling. C20 showed the greatest fungal richness and diversity, C20 and C26 exhibited similar bacterial richness and diversity, while C30 had low fungal and bacterial richness. Fungal taxonomic assignments revealed that the initial moisture content caused selective enrichment of Aspergillus candidus with a decreasing trend during fermentation, whereas Saccharomycetales sp. exhibited increasing relative abundance with increasing moisture content from day 6 of the fermentation process. Depending on initial moisture level, changes in bacterial communities were also observed in the genera Streptomyces, Bacillus, and Staphylococcus, with decreasing trends whereas Saccharopolyspora exhibited a sigmoidal trend with the highest abundance in C26. These findings demonstrate the possible impact of initial moisture content of nuruk on microfloral richness, diversity, and dynamics; this study is thus a step toward our ultimate goal of enhancing the quality of nuruk.

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

    PubMed

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

    2012-01-01

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

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

    PubMed

    Yönten, Vahap; Aktaş, Nahit

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-01-01

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

  8. Spatio-temporal distribution of organic and inorganic pollutants from Lake Geneva (Switzerland) reveals strong interacting effects of sewage treatment plant and eutrophication on microbial abundance.

    PubMed

    Thevenon, Florian; Graham, Neil D; Herbez, Aline; Wildi, Walter; Poté, John

    2011-07-01

    Variation with depth and time of organic matter (carbon, nitrogen, phosphorus), inorganic pollutant (mercury), as well as bacterial abundance and activity, were investigated for the first time in sediment profiles of different parts of Lake Geneva (Switzerland) over the last decades. The highest organic contents (about 32%), mercury concentration (27 mg kg(-1)), bacterial abundance (in order of 9×10(9) cell g(-1) dry sediment), and bacterial activity (1299 Relative Light Units (RLU)) were found in the highly polluted sediments contaminated by the waste water treatment plant (WWTP) discharge, which deposited during the period of cultural eutrophication. Such data, which contrast with the other sampled sites from deeper and more remote parts of the lake, prove that the organic matter and nutrients released from the municipal WWTP have considerable effects on bacterial abundance and activities in freshwater sediments. In fact, the relatively unpolluted deepwater sites and the coastal polluted site show large synchronous increases in bacterial densities linked to the anoxic conditions in the 1970s (lake eutrophication caused by external nutrient input) that subsequently increased the nutrient loading fluxes. These results show that the microbial activities response to natural or human-induced changing limnological conditions (e.g., nutrient supply, oxygen availability, redox conditions) constitutes a threat to the security of water resources, which in turn poses concerns for the world's freshwater resources in the context of global warming and the degradation of water quality (oxygen depletion in the bottom water due to reduced deep waters mixing). Moreover, the accumulation of inorganic pollutants such as high mercury (methyl-mercury) concentration may represent a significant source of toxicity for sediment dwelling organisms.

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

    NASA Astrophysics Data System (ADS)

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

    2006-10-01

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

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

    SciTech Connect

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

    2006-10-05

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed

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

    2010-03-01

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

  13. Impact of mycorrhization on the abundance, growth and leaf nutrient status of ferns along a tropical elevational gradient.

    PubMed

    Kessler, Michael; Güdel, Ramona; Salazar, Laura; Homeier, Jürgen; Kluge, Jürgen

    2014-07-01

    Mycorrhizal fungi are crucial for the ecological success of land plants, providing their hosts with nutrients in exchange for organic C. However, not all plants are mycorrhizal, especially ferns, of which about one-third of the species lack this symbiosis. Because the mycorrhizal status is evolutionarily ancestral, this lack of mycorrhizae must have ecological advantages, but what these advantages are and how they affect the competitive ability of non-mycorrhizal plants under natural conditions is currently unknown. To address this uncertainty, we studied terrestrial fern assemblages and species abundances as well as their mycorrhization status, leaf nutrient concentration and relative annual growth along an elevational gradient in the Ecuadorian Andes (500-4,000 m). We surveyed the mycorrhizal status of 375 root samples belonging to 85 species, and found mycorrhizae in 89% of the samples. The degree of mycorrhization decreased with elevation but was unrelated to soil nutrients. Species with mycorrhizae were significantly more abundant than non-mycorrhizal species, but non-mycorrhizal species had significantly higher relative growth and concentrations of leaf N, P, Mg, and Ca. Our study thus shows that despite lower abundances, non-mycorrhizal fern species did not appear to be limited in their growth or nutrient supply relative to mycorrhizal ones. As a basis for future studies, we hypothesize that non-mycorrhizal fern species may be favoured in special microhabitats of the forest understory with high soil nutrient or water availability, or that the ecological benefit of mycorrhizae is not related to nutrient uptake but rather to, for example, pathogen resistance.

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

    PubMed

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

    2013-04-09

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  16. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11).

    PubMed

    Logares, Ramiro; Bråte, Jon; Heinrich, Friederike; Shalchian-Tabrizi, Kamran; Bertilsson, Stefan

    2010-02-01

    The aquatic bacterial group SAR11 is one of the most abundant organisms on Earth, with an estimated global population size of 2.4 x 10(28) cells in the oceans. Members of SAR11 have also been detected in brackish and fresh waters, but the evolutionary relationships between the species present in the different environments have been ambiguous. In particular, it was not clear how frequently this lineage has crossed the saline-freshwater boundary during its evolutionary diversification. Due to the huge population size of SAR11 and the potential of microbes for long-distance dispersal, we hypothesized that environmental transitions could have occurred repeatedly during the evolutionary diversification of this group. Here, we have constructed extensive 16S rDNA-based molecular phylogenies and undertaken metagenomic data analyses to assess the frequency of saline-freshwater transitions in SAR11 and to investigate the evolutionary implications of this process. Our analyses indicated that very few saline-freshwater transitions occurred during the evolutionary diversification of SAR11, generating genetically distinct saline and freshwater lineages that do not appear to exchange genes extensively via horizontal gene transfer. In contrast to lineages from saline environments, extant freshwater taxa from diverse, and sometimes distant, geographic locations were very closely related. This points to a rapid diversification and dispersal in fresh waters or to slower evolutionary rates in fresh water SAR11 when compared with marine counterparts. In addition, the colonization of both saline and fresh waters appears to have occurred early in the evolution of SAR11. We conclude that the different biogeochemical conditions that prevail in saline and fresh waters have likely prevented the environmental transitions in SAR11, promoting the evolution of clearly distinct lineages in each environment.

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

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Rousk, Johannes

    2015-04-01

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

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

    PubMed

    Huang, Lihan; Hwang, Andy; Phillips, John

    2011-10-01

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

  19. Statistical Modeling to Predict N2O Production Within the Hyporheic Zone by Coupling Denitrifying Microbial Community Abundance to Geochemical and Hydrological Parameters

    NASA Astrophysics Data System (ADS)

    Farrell, T. B.; Quick, A. M.; Reeder, W. J.; Benner, S. G.; Tonina, D.; Feris, K. P.

    2015-12-01

    The hyporheic zone (HZ) of streams may be a significant source of nitrous oxide (N2O). However, the biogeochemical processes controlling N2O emissions remain poorly constrained due to difficulties in obtaining high-resolution chemical, physical, and biological data from streams. Our research elucidates specific controls on N2O production within the HZ by coupling the distribution of denitrifying microbial communities to flow dynamics (i.e. hydraulics and streambed morphology) and biogeochemical processes. We conducted a large-scale flume experiment that allowed us to constrain streambed morphology, flow rate, organic carbon loading, grain size distribution, and exogenous nitrate loading while enabling regular monitoring of dissolved oxygen, pH, alkalinity, nitrogen species, and elemental concentrations in the HZ. We also employed real-time PCR (qPCR) to quantify the distribution of denitrifying functional genes (nirS and nosZ, nitrite reductase and nitrous oxide reductase genes, respectively) in HZ sediment cores as a measure of denitrifying microorganism abundance. A steady increase in N2O was observed after 8 hours of residence time with a peak in concentration (9.5 μg-N/L) recorded at hour 18. Abundance of nosZ increased an order of magnitude between hours 8 and 18 (2.6x106 to 2.1x107 gene copy #/g dry sediment). nirS abundance remained within the same order of magnitude between hours 8 and 18 (1.7x107 to 3.8x107). Linear and nonlinear mixed-effects models were used to investigate N2O production in the HZ as a function of total nitrogen, nirS, nosZ, residence time, and dissolved oxygen. N2O production was localized at redox-controlled hotspots within the subsurface and concentrations were strongly correlated with the availability of nitrogen when an interaction with nosZ abundance was considered. On-going analysis will provide predictions of N2O production and support for conditions under which the HZ could be a significant contributor of N2O emissions. These

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

    PubMed

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

    2008-06-10

    Thirteen storage trials and ten challenge tests were carried out to examine microbial changes, spoilage and the potential growth of Listeria monocytogenes in brined shrimp (Pandalus borealis). Shrimp in brine as well as brined and drained shrimp in modified atmosphere packaging (MAP) were produced and studied. Different recipes were used to study the effect of preserving parameters (organic acids, pH and NaCl) on growth of microorganisms and shelf life at 7-8 degrees C or 12 degrees C. Particularly, brines with different concentrations of (i) benzoic, citric and sorbic acids or (ii) acetic, citric and lactic acids were studied. Furthermore, the effect of adding diacetate to brined shrimp was evaluated. A single batch of cooked and peeled shrimp was used to study both industrially and manually processed brined shrimp with respect to the effect of process hygiene on microbial changes and the shelf life of products. Concentrations of microorganisms on newly produced brined shrimp from an industrial scale processing line were 1.0-2.3 log (CFU g(-1)) higher than comparable concentrations in manually processed samples. This resulted in a substantially shorter shelf life and a more diverse spoilage microflora of the industrially processed brined shrimp. In addition, shelf life of brined shrimp was affected by the types and concentrations of organic acids and by the storage temperature as expected. The effect of MAP was less pronounced. Eighty-two isolates from the spoilage microflora of brined shrimp were identified and they included 53 lactic acid bacteria, 6 coagulase negative Staphylococcus spp., 18 Pseudomonas fluorescens and 5 yeast isolates. After storage at 7 degrees C, P. fluorescens, Enterococcus-like isolates, E. malodoratus, Carnobacterium maltaromaticum, coagulase negative Staphylococcus spp. and Lactobacillus sakei constituted the dominating microflora of shrimp in brines that contained benzoic, citric and sorbic acids as preservatives. L. sakei dominated the

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

    NASA Astrophysics Data System (ADS)

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

    1995-01-01

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

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

    SciTech Connect

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

    2014-02-09

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2017-01-10

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

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

    PubMed

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

    2008-05-01

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

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

    PubMed

    An, Youn-Joo; Kim, Minjin

    2009-02-01

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

  7. Nutrient utilization, ruminal fermentation, microbial abundances, and milk yield and composition in dairy goats fed diets including tomato and cucumber waste fruits.

    PubMed

    Romero-Huelva, M; Ramos-Morales, E; Molina-Alcaide, E

    2012-10-01

    The effects of replacing 35% of cereals-based concentrate with feed blocks (FB) containing waste fruits of tomato, cucumber, or barley grain in diets for lactating goats on nutrient utilization, ruminal fermentation, microbial N flow to the duodenum, milk yield and quality, methane emissions, and abundances of total bacteria and methanogens were studied. Eight Murciano-Granadina goats (39.4 ± 5.39 kg of body weight, mean ± SD) in the middle of the third lactation were used and 4 diets were studied in a replicated 4×4 Latin square experimental design. Diets consisted of alfalfa hay (A) plus concentrate (C) in a 1:1 ratio (diet AC) or diets in which 35% of the concentrate was replaced with FB including wastes of tomato fruit, cucumber, or barley. In each period, 2 goats were randomly assigned to 1 of the dietary treatments. Intakes of FB including tomato, cucumber, and barley were 208 ± 65, 222 ± 52, and 209 ± 83 g of dry matter per animal and day, respectively. The replacement of 35% of concentrate with FB did not compromise nutrient apparent digestibility, total purine derivative urinary excretion, milk yield and composition, and total bacteria and methanogen abundances. Digestible energy and that in methane and urine were higher for AC than for FB-containing diets, whereas the metabolizable energy value was not affected by diet. The inclusion of tomato and cucumber fruits in FB decreased N in urine and CH(4) emissions compared with AC, which is environmentally relevant. However, tomato-based FB decreased microbial N flow in the rumen, whereas goats fed cucumber-based FB had the highest values for this measurement. Moreover, FB containing barley or tomato and cucumber led to lower rumen volatile fatty acid and NH(3)-N concentrations, respectively. Milk from goats fed diets including tomato and cucumber-based FB had higher linoleic, linolenic, and total polyunsaturated fatty acid concentrations than that from goats fed AC. Overall, our study suggests that

  8. The use of amino acid indices for assessing organic matter quality and microbial abundance in deep-sea Antarctic sediments of IODP Expedition 318

    USGS Publications Warehouse

    Carr, Stephanie A; Mills, Christopher; Mandernack, Kevin W

    2016-01-01

    The Adélie Basin, located offshore of the Wilkes Land margin, experiences unusually high sedimentation rates (~ 2 cm yr− 1) for the Antarctic coast. This study sought to compare depthwise changes in organic matter (OM) quantity and quality with changes in microbial biomass with depth at this high-deposition site and an offshore continental margin site. Sediments from both sites were collected during the International Ocean Drilling (IODP) Program Expedition 318. Viable microbial biomass was estimated from concentrations of bacterial-derived phospholipid fatty acids, while OM quality was assessed using four different amino acid degradation proxies. Concentrations of total hydrolysable amino acids (THAA) measured from the continental margin suggest an oligotrophic environment, with THAA concentrations representing only 2% of total organic carbon with relative proportions of non-protein amino acids β-alanine and γ-aminobutyric acid as high as 40%. In contrast, THAA concentrations from the near-shore Adélie Basin represent 40%–60% of total organic carbon. Concentrations of β-alanine and γ-aminobutyric acid were often below the detection limit and suggest that the OM of the basin as labile. DI values in surface sediments at the Adélie and margin sites were measured to be + 0.78 and − 0.76, reflecting labile and more recalcitrant OM, respectively. Greater DI values in deeper and more anoxic portions of both cores correlated positively with increased relative concentrations of phenylalanine plus tyrosine and may represent a change of redox conditions, rather than OM quality. This suggests that DI values calculated along chemical profiles should be interpreted with caution. THAA concentrations, the percentage of organic carbon (CAA%) and total nitrogen (NAA%) represented by amino acids at both sites demonstrated a significant positive correlation with bacterial abundance estimates. These data suggest that the selective degradation of amino acids, as

  9. Two different late embryogenesis abundant proteins from Arabidopsis thaliana contain specific domains that inhibit Escherichia coli growth.

    PubMed

    Campos, Francisco; Zamudio, Fernando; Covarrubias, Alejandra A

    2006-04-07

    Late embryogenesis abundant (LEA) proteins constitute a set of proteins widespread in the plant kingdom that show common physicochemical properties such as high hydrophilicity and high content of small amino acid residues such as glycine, alanine, and serine. Typically, these proteins accumulate in response to water deficit conditions imposed by the environment or during plant normal development. In this work, we show that the over-expression in Escherichia coli of proteins of the LEA 2 and the LEA 4 families from Arabidopsis thaliana leads to inhibition of bacterial growth and that this effect is dependent on discrete regions of the proteins. Our data indicate that their antimicrobial effect is achieved through their interaction with intracellular targets. The relevance of the cationic nature and the predicted structural organization of particular protein domains in this detrimental effect on the bacteria growth process is discussed.

  10. Microbial growth under humic-free conditions in a supraglacial stream system on the Cotton Glacier, Antarctica

    NASA Astrophysics Data System (ADS)

    Foreman, Christine M.; Cory, Rose M.; Morris, Cindy E.; SanClements, Michael D.; Smith, Heidi J.; Lisle, John T.; Miller, Penney L.; Chin, Yu-Ping; McKnight, Diane M.

    2013-09-01

    During the austral summers of 2004 and 2009, we sampled a supraglacial stream on the Cotton Glacier, Antarctica. The stream dissolved organic matter (DOM) was low (44-48 μM C) and lacked detectable humic fluorescence signatures. Analysis of the excitation emissions matrices (EEMs) indicated that amino-acid fluorophores dominated, consistent with DOM of microbial origin, with little humic-like fluorescence. In most aquatic ecosystems, humic DOM attenuates harmful UV radiation and its absence may represent an additional stressor influencing the microbial community. Nonetheless, the stream contained an active microbial assemblage with bacterial cell abundances from 2.94 × 104 to 4.97 × 105 cells ml-1, and bacterial production ranging from 58.8 to 293.2 ng C l-1 d-1. Chlorophyll-a concentrations ranged from 0.3 to 0.53 μg l-1 indicating that algal phototrophs were the probable source of the DOM. Microbial isolates produced a rainbow of pigment colors, suggesting adaptation to stress, and were similar to those from other cryogenic systems (Proteobacteria and Bacteroidetes lineages). Supraglacial streams provide an example of contemporary microbial processes on the glacier surface and a natural laboratory for studying microbial adaptation to the absence of humics.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    PubMed

    Battley, Edwin H

    2013-06-01

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

  13. Gibberellin regulates PIN-FORMED abundance and is required for auxin transport-dependent growth and development in Arabidopsis thaliana.

    PubMed

    Willige, Björn C; Isono, Erika; Richter, René; Zourelidou, Melina; Schwechheimer, Claus

    2011-06-01

    Plants integrate different regulatory signals to control their growth and development. Although a number of physiological observations suggest that there is crosstalk between the phytohormone gibberellin (GA) and auxin, as well as with auxin transport, the molecular basis for this hormonal crosstalk remains largely unexplained. Here, we show that auxin transport is reduced in the inflorescences of Arabidopsis thaliana mutants deficient in GA biosynthesis and signaling. We further show that this reduced auxin transport correlates with a reduction in the abundance of PIN-FORMED (PIN) auxin efflux facilitators in GA-deficient plants and that PIN protein levels recover to wild-type levels following GA treatment. We also demonstrate that the regulation of PIN protein levels cannot be explained by a transcriptional regulation of the PIN genes but that GA deficiency promotes, at least in the case of PIN2, the targeting of PIN proteins for vacuolar degradation. In genetic studies, we reveal that the reduced auxin transport of GA mutants correlates with an impairment in two PIN-dependent growth processes, namely, cotyledon differentiation and root gravitropic responses. Our study thus presents evidence for a role of GA in these growth responses and for a GA-dependent modulation of PIN turnover that may be causative for these differential growth responses.

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

    PubMed

    Ledezma, Pablo; Greenman, John; Ieropoulos, Ioannis

    2012-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2015-03-18

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Merchant, Sabeeha S.; Helmann, John D.

    2014-01-01

    Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility at fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental-sparing and elemental-recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels; including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes. PMID:22633059

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

    PubMed

    Merchant, Sabeeha S; Helmann, John D

    2012-01-01

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

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

    PubMed

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

    2011-07-01

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

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

    PubMed

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

    2008-10-01

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

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

    PubMed

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

    2006-05-05

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

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

    PubMed

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

    2015-01-01

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

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

    DOE PAGES

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

    2016-01-07

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-06-01

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

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

    PubMed

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

    2013-07-10

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

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

    DOEpatents

    Lee, Brady D.; Dooley, Kirk J.

    2004-11-02

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

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

    PubMed

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

    2014-05-15

    Sulfate-reducing bacteria (SRB) can produce iron sulfide (FeS) solids with mineralogical characteristics that may be beneficial for a variety of biogeochemical applications, such as long-term immobilization of uranium. In this study, the growth and metabolism of Desulfovibrio vulgaris, one of the best-studied SRB species, were comprehensively monitored in batch studies, and the biogenic FeS solids were characterized by X-ray diffraction. Controlling the pH by varying the initial pH, the iron-to-sulfate ratio, or the electron donor - affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH (from initial conditions or a decrease caused by less sulfate reduction, FeS precipitation, or using pyruvate as the electron donor) produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and particularly stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3mM. Furthermore, sufficient free Fe(2+) led to the additional formation of vivianite [Fe3(PO4)2·8(H2O)]. Thus, microbially relevant conditions (initial pH, choice of electron donor, and excess or deficiency of sulfide) are tools to generate biogenic FeS solids of different characteristics.

  10. Growth Arrest Specific 1 (GAS1) Is Abundantly Expressed in the Adult Mouse Central Nervous System

    PubMed Central

    Zarco, Natanael; Bautista, Elizabeth; Cuéllar, Manola; Vergara, Paula; Flores-Rodriguez, Paola; Aguilar-Roblero, Raúl

    2013-01-01

    Growth arrest specific 1 (GAS1) is a pleiotropic protein that induces apoptosis and cell arrest in different tumors, but it is also involved in the development of the nervous system and other tissues and organs. This dual ability is likely caused by its capacity to interact both by inhibiting the intracellular signaling cascade induced by glial cell-line derived neurotrophic factor and by facilitating the activity of the sonic hedgehog pathway. The presence of GAS1 mRNA has been described in adult mouse brain, and here we corroborated this observation. We then proceeded to determine the distribution of the protein in the adult central nervous system (CNS). We detected, by western blot analysis, expression of GAS1 in olfactory bulb, caudate-putamen, cerebral cortex, hippocampus, mesencephalon, medulla oblongata, cerebellum, and cervical spinal cord. To more carefully map the expression of GAS1, we performed double-label immunohistochemistry and noticed expression of GAS1 in neurons in all brain areas examined. We also observed expression of GAS1 in astroglial cells, albeit the pattern of expression was more restricted than that seen in neurons. Briefly, in the present article, we report the widespread distribution and cellular localization of the GAS1 native protein in adult mammalian CNS. PMID:23813868

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

    PubMed Central

    Price, P. Buford; Sowers, Todd

    2004-01-01

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

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

    PubMed

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

    2013-02-01

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

  13. Microbial community abundance and biomass along a 180° transect in the equatorial Pacific during an El Niño-Southern Oscillation cold phase

    NASA Astrophysics Data System (ADS)

    Brown, Susan L.; Landry, Michael R.; Neveux, Jacques; Dupouy, CéCile

    2003-12-01

    As part of the French Joint Global Ocean Flux Study Etude du Broutage en Zone Equatoriale program, we investigated the distributions of microorganisms (bacteria and protists <200 μm) in the upper 120 m of the equatorial Pacific from 8°S to 8°N, along 180°. Population distributions, determined by a combination of flow cytometry, microscopy and spectrofluorometry, were closely related to physical features across the study site. Phytoplankton biomass, ranging from 1.2 to 34.2 μg C L-1 and averaging 15.5 μg C L-1, was most enhanced in the divergence zone. Carbon to chlorophyll ratios were also enhanced in the divergence zone and showed distinct latitudinal variations. Heterotrophic biomass, excluding ciliates, was patchy across the area, ranging from 5 to 36 μg C L-1 and averaging 13 μg C L-1. Prokaryotic species (Prochlorococcus spp., Synechococcus spp., and heterotrophic bacteria) showed similar patterns of abundance, with the main feature being their distributional asymmetry to the south of the equator. Both autotrophic and heterotrophic biomass were enriched in the convergent zone at 4°-5°N between the South Equatorial Current and the North Equatorial Counter Current. Heterotrophic biomass exceeded phytoplankton biomass in the more nutrient-impoverished waters to the north and in the branch of a tropical instability wave eddy. Microplankton represented only a small portion of the total autotrophic carbon and was comprised mostly of dinoflagellates. Large species dominated the relatively modest diatom biomass. Food web interactions and biogeochemical fluxes in the central equatorial Pacific may be significantly influenced by temporal and spatial variability of the microbial community associated with physical features of the region.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  15. Natural Abundance 43Ca NMR as a Tool for Exploring Calcium Biomineralization: Renal Stone Formation and Growth

    SciTech Connect

    Bowers, Geoffrey M.; Kirkpatrick, Robert J.

    2011-12-07

    Renal stone diseases are a global health issue with little effective therapeutic recourse aside from surgery and shock-wave lithotripsy, primarily because the fundamental chemical mechanisms behind calcium biomineralization are poorly understood. In this work, we show that natural abundance 43Ca NMR at 21.1 T is an effective means to probe the molecular-level Ca2+ structure in oxalate-based kidney stones. We find that the 43Ca NMR resonance of an authentic oxalate-based kidney stone cannot be explained by a single pure phase of any common Ca2+-bearing stone mineral. Combined with XRD results, our findings suggest an altered calcium oxalate monohydrate-like Ca2+ coordination environment for some fraction of Ca2+ in our sample. The evidence is consistent with existing literature hypothesizing that nonoxalate organic material interacts directly with Ca2+ at stone surfaces and is the primary driver of renal stone aggregation and growth. Our findings show that 43Ca NMR spectroscopy may provide unique and crucial insight into the fundamental chemistry of kidney stone formation, growth, and the role organic molecules play in these processes.

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

    PubMed Central

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

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

    2008-10-01

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

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

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

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

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

    SciTech Connect

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

    2000-05-01

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

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

    PubMed

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

    2010-08-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

    Bajaj, Neeti; Tandon, Shobha

    2011-01-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-03-13

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

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

    SciTech Connect

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

    2016-01-07

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

  7. Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

    PubMed

    Alvaro, J J; Clausen, S

    2010-03-01

    The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.

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

    PubMed

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

    2012-10-01

    This study evaluated the potential of silver nanoparticles (AgNano) as an antimicrobial growth-promoting supplement for broiler chickens. One hundred forty-four seven-day-old broiler chicks were distributed randomly to AgNano treatments at 0, 10 and 20 mg/kg (Control, Group AgNano10, and Group AgNano20, respectively) provided via the drinking water from day 7 to 36 post-hatching. Body weight and feed consumption were measured weekly. In addition, balance and respiration experiments were carried out to determine nitrogen (N) utilisation and energy retention. At days 22 and 36, blood samples and intestinal content were collected to evaluate the effects of AgNano on plasma concentration of immunoglobulins and the intestinal microflora, respectively. The provision of water solutions containing different concentrations of AgNano had no effect on postnatal growth performance and the energy metabolism of broiler chickens. However, in Group AgNano10 N intake (p = 0.05) and retention (p = 0.03) was increased, but N excretion and efficiency of utilisation was not affected. The populations of bacteria in the intestinal samples were not affected by AgNano supplementation. The concentration of immunoglobulin (IgG) in the blood plasma of broilers supplemented with AgNano decreased at day 36 (p = 0.012). The results demonstrated that AgNano affects N utilisation and plasma IgG concentration; however, it does not influence the microbial populations in the digestive tract, the energy metabolism and growth performance of chickens.

  9. Bacterial Growth, Necromass Turnover, And Endospore Abundance In The Deep Subseafloor Sediments Of The Greenland Shelf Using D:L Amino Acid Model.

    NASA Astrophysics Data System (ADS)

    Mhatre, S. S.; Braun, S.; Jaussi, M.; Røy, H.; Jørgensen, B. B.; Lomstein, B. A.

    2015-12-01

    The subsurface realm is colonized by a large number of microorganisms- about 3 × 1029. Microbial cells in these very stable and oligotrophic settings catabolize at a much slower rate than model organisms in nutrient rich cultures. The aim of this work was to use recently developed D:L-amino acid racemization model for studying the turnover times of microbial biomass and microbial necromass in a ~12,000 years old Greenland shelf marine sediment samples. Sediments were analyzed for total hydrolysable amino acids (THAA), the bacterial endospore marker dipicolinic acid (DPA), and amino acid enantiomers of aspartic acid. The percentage amino acid carbon content (%TAAC) and the percentage amino acid nitrogen content (%TAAN) were used for determining the degradation state of the organic matter. Endospores quantified using DPA quantification method were found to be as abundant as vegetative cells. The microbial necromass turnover times were thousand years, and biomass turnover times were in the range of tens to hundred years. Studies with deeper sediment cores will further improve our understanding of the energetic limits of life in the deep biosphere.

  10. An Economic Framework of Microbial Trade

    PubMed Central

    Mee, Michael T.

    2015-01-01

    A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century. PMID:26222307

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed

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

    2011-04-01

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

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

    PubMed

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

    2013-08-01

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

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

    PubMed

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

    2015-01-01

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

  15. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

    PubMed Central

    Zheng, Qiupeng; Bao, Chunyang; Guo, Weijie; Li, Shuyi; Chen, Jie; Chen, Bing; Luo, Yanting; Lyu, Dongbin; Li, Yan; Shi, Guohai; Liang, Linhui; Gu, Jianren; He, Xianghuo; Huang, Shenglin

    2016-01-01

    Circular RNAs (circRNAs) represent a class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates. Many of these circRNAs are differently expressed between the normal and cancerous tissues. We further characterize one abundant circRNA derived from Exon2 of the HIPK3 gene, termed circHIPK3. The silencing of circHIPK3 but not HIPK3 mRNA significantly inhibits human cell growth. Via a luciferase screening assay, circHIPK3 is observed to sponge to 9 miRNAs with 18 potential binding sites. Specifically, we show that circHIPK3 directly binds to miR-124 and inhibits miR-124 activity. Our results provide evidence that circular RNA produced from precursor mRNA may have a regulatory role in human cells. PMID:27050392

  16. Proteome profiling of the growth phases of Leishmania pifanoi promastigotes in axenic culture reveals differential abundance of immunostimulatory proteins.

    PubMed

    Alcolea, Pedro J; Alonso, Ana; García-Tabares, Francisco; Mena, María del Carmen; Ciordia, Sergio; Larraga, Vicente

    2016-06-01

    Leishmaniasis is a term that encompasses a compendium of neglected tropical diseases caused by dimorphic and digenetic protozoan parasites from the genus Leishmania (Kinetoplastida: Trypanosomatidae). The clinical manifestations of neotropical cutaneous leishmaniasis (NCL) caused by Leishmania pifanoi and other species of the "Leishmania mexicana complex" mainly correspond to anergic diffuse cutaneous leishmaniasis (ADCL), which is the origin of considerable morbidity. Despite the outstanding advances in the characterization of the trypanosomatid genomes and proteomes, the biology of this species has been scarcely explored. However, the close relation of L. pifanoi to the sequenced species L. mexicana and others included in the "L. mexicana complex" allowed us to perform a two-dimension electrophoresis (2DE) approach to the promastigote proteome at the differential expression level. Protein identifications were performed by matrix-assisted laser desorption-ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). This insight has revealed similarities and differences between L. pifanoi and other species responsible for cutaneous and visceral leishmaniasis. Interestingly, certain proteins that were previously described as immunostimulatory (elongation factor 1β, trypanothione peroxidase, heat shock protein 70, enolase, GDP-forming succinyl-CoA and aldehyde dehydrogenase) are more abundant in the final growth stages of promastigotes (late-logarithmic and/or stationary phase) in the case of L. pifanoi.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    PubMed

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

    2008-03-01

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

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

    PubMed

    Christner, Brent C

    2010-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2013-05-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

    Al-Hussaini, Reema; Mahasneh, Adel M

    2009-09-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

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

    PubMed

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

    1997-01-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

    Klamt, Steffen; Mahadevan, Radhakrishnan

    2015-07-01

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

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

    PubMed Central

    Horváthová, Terézia; Babik, Wiesław; Bauchinger, Ulf

    2016-01-01

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

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

    PubMed

    Pouillot, Régis; Lubran, Meryl B

    2011-06-01

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

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

    PubMed

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

    2009-10-01

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

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

    PubMed

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

    2017-01-01

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

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

    PubMed

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

    2006-12-01

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

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

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  17. mRNA Transcript Abundance during Plant Growth and the Influence of Li+ Exposure

    SciTech Connect

    Duff, M. C.; Kuhne, W. W.; Halverson, N. V.; Chang, C. -S.; Kitamura, E.; Hawthorn, L.; Martinez, N. E.; Stafford, C.; Milliken, C. E.; Caldwell, E. F.; Stieve-Caldwell, E.

    2014-10-23

    Lithium (Li) toxicity in plants is, at a minimum, a function of Li+ concentration, exposure time, species and growth conditions. Most plant studies with Li+ focus on short-term acute exposures. This study examines short- and long-term effects of Li+ exposure in Arabidopsis with Li+ uptake studies and measured shoot mRNA transcript abundance levels in treated and control plants. Stress, pathogen-response and arabinogalactan protein genes were typically more up-regulated in older (chronic, low level) Li+-treatment plants and in the much younger plants from acute high-level exposures. The gene regulation behavior of high-level Li+ resembled prior studies due to its influence on: inositol synthesis, 1-aminocyclopropane-1-carboxylate synthases and membrane ion transport. In contrast, chronically-exposed plants had gene regulation responses that were indicative of pathogen, cold, and heavy-metal stress, cell wall degradation, ethylene production, signal transduction, and calcium-release modulation. Acute Li+ exposure phenocopies magnesium-deficiency symptoms and is associated with elevated expression of stress response genes that could lead to consumption of metabolic and transcriptional energy reserves and the dedication of more resources to cell development. In contrast, chronic Li+ exposure increases expression signal transduction genes. The identification of new Li+-sensitive genes and a gene-based “response plan” for acute and chronic Li+ exposure are delineated.

  18. Impacts of oxidation aging on secondary organic aerosol formation, particle growth rate, cloud condensation nuclei abundance, and aerosol climate forcing

    NASA Astrophysics Data System (ADS)

    Yu, F.; Luo, G.

    2014-12-01

    Particle composition measurements indicate that organic aerosol (OA) makes up ~20-90% of submicron particulate mass and secondary OA (SOA) accounts for a large fraction (~ 72 ±21%) of these OA masses at many locations around the globe. The volatility changes of secondary organic gases (SOG) associated with oxidation aging as well as the contribution of highly oxidized low volatile SOG (LV-SOG) to the condensational growth of secondary particles have been found to be important in laboratory and field measurements but are poorly represented in global models. A novel scheme to extend the widely used two-product SOA formation model, by adding a third product arising from the oxidation aging (i.e., LV-SOG) and considering the dynamic transfer of mass from higher to lower volatile products, has been developed and implemented into a global chemical transport model (GEOS-Chem) and a community atmosphere model (CESM-CAM5). The scheme requires only minor changes to the existing two-product SOA formation model and is computationally efficient. With the oxidation rate constrained by laboratory measurements, we show that the new scheme predicts a much higher SOA mass concentrations, improving the agreement with aerosol mass spectrometer SOA measurements. The kinetic condensation of LV-SOG on ultrafine particles, simulated by a size-resolved (sectional) advanced particle microphysics (APM) model incorporated into in GEOS-Chem and CAM5, increases the particle growth rate substantially and improves the agreement of simulated cloud condensation nuclei (CCN) concentrations with observations. Based on GEOS-Chem-APM simulations, the new SOA formation scheme increases global mean low troposphere SOA mass concentration by ~130% and CCN abundance by ~ 15%, and optical depth of secondary particles and coated black carbon and primary organic carbon particles by ~10%. As a result, aerosol radiative cooling effect (direct + first indirect) is enhanced by -0.9 W/m2, with large spatial

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed

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

    2008-09-01

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

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2014-12-01

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

  3. Siderophile and chalcophile element abundances in oceanic basalts, Pb isotope evolution and growth of the earth's core

    NASA Technical Reports Server (NTRS)

    Newsom, H. E.; White, W. M.; Jochum, K. P.; Hofmann, A. W.

    1986-01-01

    The hypothesis that the mantle Pb isotope ratios reflect continued extraction of Pb into the earth's core over geologic time is evaluated by studying the depeletion of chalcophile and siderophile elements in the mantle. Oceanic basalt samples are analyzed in order to determine the Pb, Sr, and Nd isotropic compositions and the abundances of siderophile and chalcophile elements and incompatible lithophile elements. The data reveal that there is no systematic variation of siderophile or chalcophile element abundances relative to abundances of lithophile elements and the Pb/Ce ratio of the mantle is constant. It is suggested that the crust formation involves nonmagmatic and magmatic processes.

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

    PubMed

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

    2016-10-01

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

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

    PubMed Central

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

    2017-01-01

    The microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation. PMID:28367963

  6. Impact of Reed Canary Grass Cultivation and Mineral Fertilisation on the Microbial Abundance and Genetic Potential for Methane Production in Residual Peat of an Abandoned Peat Extraction Area.

    PubMed

    Espenberg, Mikk; Truu, Marika; Truu, Jaak; Maddison, Martin; Nõlvak, Hiie; Järveoja, Järvi; Mander, Ülo

    This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an abandoned peat extraction area. The archaeal proportion was 0.67-39.56% in the prokaryotic community and the methanogens proportion was 0.01-1.77% in the archaeal community. When bacterial abundance was higher in the top 20 cm of peat, the archaea were more abundant in the 20-60 cm layer and methanogens in the 40-60 cm layer of the residual peat. The bacterial abundance was significantly increased, but archaeal abundance was not affected by cultivation. The fertiliser application had a slight effect on peat properties and on archaeal and methanogen abundances in the deeper layer of cultivated peat. The CH4 emission was positively related to mcrA abundance in the 20-60 cm of the bare peat, while in case of reed canary grass cultivation these two parameters were not correlated. Reed canary grass cultivation mitigated CH4 emission, although methanogen abundance remained approximately the same or even increased in different layers of residual peat under cultivated sites over time. This study supports the outlook of using abandoned peat extraction areas to produce reed canary grass for energy purposes as an advisable land-use practice from the perspective of atmospheric impact in peatland-rich Northern Europe.

  7. Impact of Reed Canary Grass Cultivation and Mineral Fertilisation on the Microbial Abundance and Genetic Potential for Methane Production in Residual Peat of an Abandoned Peat Extraction Area

    PubMed Central

    Espenberg, Mikk; Truu, Marika; Truu, Jaak; Maddison, Martin; Nõlvak, Hiie; Järveoja, Järvi; Mander, Ülo

    2016-01-01

    This study examined physiochemical conditions and prokaryotic community structure (the bacterial and archaeal 16S rRNA genes and mcrA gene abundances and proportions), and evaluated the effect of reed canary grass cultivation and mineral fertilisation on these factors, in the 60 cm thick residual peat layer of experimental plots located on an abandoned peat extraction area. The archaeal proportion was 0.67–39.56% in the prokaryotic community and the methanogens proportion was 0.01–1.77% in the archaeal community. When bacterial abundance was higher in the top 20 cm of peat, the archaea were more abundant in the 20–60 cm layer and methanogens in the 40–60 cm layer of the residual peat. The bacterial abundance was significantly increased, but archaeal abundance was not affected by cultivation. The fertiliser application had a slight effect on peat properties and on archaeal and methanogen abundances in the deeper layer of cultivated peat. The CH4 emission was positively related to mcrA abundance in the 20–60 cm of the bare peat, while in case of reed canary grass cultivation these two parameters were not correlated. Reed canary grass cultivation mitigated CH4 emission, although methanogen abundance remained approximately the same or even increased in different layers of residual peat under cultivated sites over time. This study supports the outlook of using abandoned peat extraction areas to produce reed canary grass for energy purposes as an advisable land-use practice from the perspective of atmospheric impact in peatland-rich Northern Europe. PMID:27684377

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2017-01-01

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

  12. Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass

    SciTech Connect

    Giannone, Richard J; Lochner, Adriane; Keller, Martin; Antranikian, Garabed; Graham, David E; Hettich, Robert {Bob} L

    2011-01-01

    Mass spectrometric analysis of Caldicellulosiruptor obsidiansis cultures grown on four different carbon sources identified 65% of the cells predicted proteins in cell lysates and supernatants. Biological and technical replication together with sophisticated statistical analysis were used to reliably quantify protein abundances and their changes as a function of carbon source. Extracellular, multifunctional glycosidases were significantly more abundant on cellobiose than on the crystalline cellulose substrates Avicel and filter paper, indicating either disaccharide induction or constitutive protein expression. Highly abundant flagellar, chemotaxis, and pilus proteins were detected during growth on insoluble substrates, suggesting motility or specific substrate attachment. The highly abundant extracellular binding protein COB47-0549 together with the COB47-1616 ATPase might comprise the primary ABC-transport system for cellooligosaccharides, while COB47-0096 and COB47-0097 could facilitate monosaccharide uptake. Oligosaccharide degradation can occur either via extracellular hydrolysis by a GH1 {beta}-glycosidase or by intracellular phosphorolysis using two GH94 enzymes. When C. obsidiansis was grown on switchgrass, the abundance of hemicellulases (including GH3, GH5, GH51, and GH67 enzymes) and certain sugar transporters increased significantly. Cultivation on biomass also caused a concerted increase in cytosolic enzymes for xylose and arabinose fermentation.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    Saravanan, Pichiah; Pakshirajan, K; Saha, Prabirkumar

    2009-02-15

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

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

    PubMed

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

    2013-12-12

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

    PubMed

    Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

    2016-12-15

    Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study.

  19. Increased Abundance of Proteins Involved in Resistance to Oxidative and Nitrosative Stress at the Last Stages of Growth and Development of Leishmania amazonensis Promastigotes Revealed by Proteome Analysis

    PubMed Central

    Alonso, Ana; García-Tabares, Francisco; Mena, María C.; Ciordia, Sergio; Larraga, Vicente

    2016-01-01

    Leishmania amazonensis is one of the major etiological agents of the neglected, stigmatizing disease termed american cutaneous leishmaniasis (ACL). ACL is a zoonosis and rodents are the main reservoirs. Most cases of ACL are reported in Brazil, Bolivia, Colombia and Peru. The biological cycle of the parasite is digenetic because sand fly vectors transmit the motile promastigote stage to the mammalian host dermis during blood meal intakes. The amastigote stage survives within phagocytes of the mammalian host. The purpose of this study is detection and identification of changes in protein abundance by 2DE/MALDI-TOF/TOF at the main growth phases of L. amazonensis promastigotes in axenic culture and the differentiation process that takes place simultaneously. The average number of proteins detected per gel is 202 and the non-redundant cumulative number is 339. Of those, 63 are differentially abundant throughout growth and simultaneous differentiation of L. amazonensis promastigotes. The main finding is that certain proteins involved in resistance to nitrosative and oxidative stress are more abundant at the last stages of growth and differentiation of cultured L. amazonensis promastigotes. These proteins are the arginase, a light variant of the tryparedoxin peroxidase, the iron superoxide dismutase, the regulatory subunit of the protein kinase A and a light HSP70 variant. These data taken together with the decrease of the stress-inducible protein 1 levels are additional evidence supporting the previously described pre-adaptative hypothesis, which consists of preparation in advance towards the amastigote stage. PMID:27776144

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

    SciTech Connect

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

    1993-12-31

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

  1. Spatial and temporal changes in microbial diversity of the Marmara Sea sediments.

    PubMed

    Kolukirik, M; Ince, O; Cetecioglu, Z; Celikkol, S; Ince, B K

    2011-11-01

    Spatial (10 different locations) and temporal (2 years) changes in characteristics of the Marmara Sea Sediments were monitored to determine interactions between the chemical and microbial diversity. The sediments were rich in terms of hydrocarbon, nitrate, Ni and microbial cell content. Denitrifying, sulfate reducing, fermentative and methanogenic organisms were co-abundant in 15 cm below the sea floor. The local variations in the sediments' characteristics were more distinctive than the temporal ones. The sulfate and nitrate contents were the main drivers of the changes in the microbial community compositions. N and P were limited for microbial growth in the sediments, and their levels determined the total cell abundance and activity. Seasonal shifts in temperatures of the shallow sediments were also reflected in the active cell abundances. It was concluded that the Marmara Sea is a promising ecosystem for the further investigation of the ecologically important microbial processes.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Controls and dynamics of biochar decay and soil microbial abundance, carbon use efficiency during long-term biochar-amended soil incubations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar addition to soil has been proposed as a management strategy to sequester a recalcitrant form of carbon (C). However, there is growing evidence that biochar can be degraded by soil microbes and modify their abundance, community composition and activity. Yet we lack an understanding of how mic...

  4. Nanoporous microscale microbial incubators.

    PubMed

    Ge, Zhifei; Girguis, Peter R; Buie, Cullen R

    2016-02-07

    Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals abundant microbial diversity that has not been cultured in the laboratory. Many attribute this so-called 'great plate count anomaly' to traditional microbial cultivation techniques, which largely facilitate the growth of a single species. Yet, it is widely recognized that bacteria in nature exist in complex communities. One technique to increase the pool of cultivated bacterial species is to co-culture multiple species in a simulated natural environment. Here, we present nanoporous microscale microbial incubators (NMMI) that enable high-throughput screening and real-time observation of multi-species co-culture. The key innovation in NMMI is that they facilitate inter-species communication while maintaining physical isolation between species, which is ideal for genomic analysis. Co-culture of a quorum sensing pair demonstrates that the NMMI can be used to culture multiple species in chemical communication while monitoring the growth dynamics of individual species.

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

    PubMed

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

    2007-01-01

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

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

    PubMed

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

    2015-07-01

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

  7. Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

    PubMed

    Bengtson, Per; Sterngren, Anna E; Rousk, Johannes

    2012-08-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

  8. Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico.

    PubMed

    Williams, Alicia K; McInnes, Allison S; Rooker, Jay R; Quigg, Antonietta

    2015-01-01

    Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific 'microbial signature' (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM.

  9. Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico

    PubMed Central

    Williams, Alicia K.; McInnes, Allison S.; Rooker, Jay R.; Quigg, Antonietta

    2015-01-01

    Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific ‘microbial signature’ (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM. PMID:26375709

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

    PubMed

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

    2017-03-27

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2008-06-01

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

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

    PubMed

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

    2008-01-01

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

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

    PubMed

    Mohamed, M; Hatfield, K

    2011-09-01

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

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

    PubMed

    Koseki, Shigenobu; Itoh, Kazuhiko

    2002-02-01

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

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

    PubMed

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

    2014-03-17

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

  17. Influence of Growth Phase, pH, and Temperature on the Abundance and Composition of Tetraether Lipids in the Thermoacidophile Picrophilus torridus

    PubMed Central

    Feyhl-Buska, Jayme; Chen, Yufei; Jia, Chengling; Wang, Jin-Xiang; Zhang, Chuanlun L.; Boyd, Eric S.

    2016-01-01

    The abundance and composition of glycerol dibiphytanyl glycerol tetraether (GDGT) and glycerol tribiphytanyl glycerol tetraether (GTGT) lipids were determined as a function of growth phase as a proxy for nutrient availability, the pH of growth medium, and incubation temperature in cultures of the thermoacidophile Picrophilus torridus. Regardless of the cultivation condition, the abundance of GDGTs and GTGTs was greater in the polar than core fraction, with a marked decrease in core GDGTs in cultures harvested during log phase growth. These data are consistent with previous suggestions indicating that core GDGTs are re-functionalized during polar lipid synthesis. Under all conditions examined, polar lipids were enriched in a GDGT with 2 cyclopentyl rings (GDGT-2), indicating GDGT-2 is the preferred lipid in this taxon. However, lag or stationary phase grown cells or cells subjected to pH or thermal stress were enriched in GDGTs with 4, 5, or 6 rings and depleted in GDGTs with 1, 2, 3, rings relative to log phase cells grown under optimal conditions. Variation in the composition of polar GDGT lipids in cells harvested during various growth phases tended to be greater than in cells cultivated over a pH range of 0.3–1.1 and a temperature range of 53–63°C. These results suggest that the growth phase, the pH of growth medium, and incubation temperature are all important factors that shape the composition of tetraether lipids in Picrophilus. The similarity in enrichment of GDGTs with more rings in cultures undergoing nutrient, pH, and thermal stress points to GDGT cyclization as a generalized physiological response to stress in this taxon. PMID:27625636

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

    PubMed

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

    2015-05-01

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

  19. Effects of abundance and water temperature on recruitment and growth of alewife (Alosa pseudoharengus) near South Bay, Lake Huron, 1954-82

    USGS Publications Warehouse

    Henderson, Bryan A.; Brown, Edward H.

    1985-01-01

    Analysis of catches in pound nets provided indices of population size (ages 2–6) and of recruitment (ages 4–6) for alewives (Alosa pseudoharengus) spawning in South Bay (1954–82). Four hypotheses concerning the effects of stock size and water temperature on growth and recruitment were tested statistically. The number of recruits per spawner was not a function of parental stock size, but was dependent on surface-water temperatures in June and July. Although the size of both males and females at age 3 yr was positively related to surface-water temperatures in the three preceding summers, growth rates were only a function of water temperatures during the second year of growth (age 1). However, growth rates during the first, second, and third years of growth were all related to year-class strength. Thus, population abundance, through recruitment, was determined by an abiotic factor (water temperature), but growth was mostly affected by intraspecific competition for, presumably, food.

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed Central

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

    2014-01-01

    Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by t