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Sample records for abundant microbial growth

  1. Global distribution of microbial abundance and biomass in subseafloor sediment

    PubMed Central

    Kallmeyer, Jens; Pockalny, Robert; Adhikari, Rishi Ram; Smith, David C.; D’Hondt, Steven

    2012-01-01

    The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅1029 cells [corresponding to 4.1 petagram (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 Earth’s total number of microbes and total living biomass to be, respectively, 50–78% and 10–45% lower than previous estimates. PMID:22927371

  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. Stronger warming effects on microbial abundances in colder regions

    DOE PAGESBeta

    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,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

  4. 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.

  5. Stronger warming effects on microbial abundances in colder regions

    PubMed Central

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

    2015-01-01

    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. PMID:26658882

  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

    2015-01-01

    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. PMID:26658882

  7. 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)

  8. 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. PMID:26298697

  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. Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT ).

    PubMed

    Chakrabarti, Anirikh; Siddharth, Jay; Lauber, Christian L; Membrez, Mathieu; Betrisey, Bertrand; Loyer, Carole; Chou, Chieh Jason; Pataky, Zoltan; Golay, Alain; Parkinson, Scott J

    2016-01-01

    Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, 'AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized 'AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios. PMID:27530237

  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. PMID:27315516

  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. 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.

  15. 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. PMID:25772872

  16. Soil microbial abundance and diversity along a low precipitation gradient.

    PubMed

    Bachar, Ami; Al-Ashhab, Ashraf; Soares, M Ines M; Sklarz, Menachem Y; Angel, Roey; Ungar, Eugene D; Gillor, Osnat

    2010-08-01

    The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem. PMID:20683588

  17. New Abundant Microbial Groups in Aquatic Hypersaline Environments

    PubMed Central

    Ghai, Rohit; Pašić, Lejla; Fernández, Ana Beatriz; Martin-Cuadrado, Ana-Belen; Mizuno, Carolina Megumi; McMahon, Katherine D.; Papke, R. Thane; Stepanauskas, Ramunas; Rodriguez-Brito, Beltran; Rohwer, Forest; Sánchez-Porro, Cristina; Ventosa, Antonio; Rodríguez-Valera, Francisco

    2011-01-01

    We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. Metagenomic assembly revealed three new abundant microbes: a low-GC euryarchaeon with the lowest GC content described for any euryarchaeon, a high-GC euryarchaeon and a gammaproteobacterium related to Alkalilimnicola and Nitrococcus. Multiple displacement amplification and sequencing of the genome from a single archaeal cell of the new low GC euryarchaeon suggest a photoheterotrophic and polysaccharide-degrading lifestyle and its relatedness to the recently described lineage of Nanohaloarchaea. These discoveries reveal the combined power of an unbiased metagenomic and single cell genomic approach. PMID:22355652

  18. 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

  19. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater.

    PubMed

    Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz; Cannistraci, Carlo V; Ravasi, Timothy; Hentschel, Ute

    2014-12-01

    The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater. PMID:25318900

  20. Conditioning biomass for microbial growth

    SciTech Connect

    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.

  1. 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.

  2. Temperature affects microbial abundance, activity and interactions in anaerobic digestion.

    PubMed

    Lin, Qiang; De Vrieze, Jo; Li, Jiabao; Li, Xiangzhen

    2016-06-01

    Temperature is a major factor determining the performance of the anaerobic digestion process. The microbial abundance, activity and interactional networks were investigated under a temperature gradient from 25°C to 55°C through amplicon sequencing, using 16S ribosomal RNA and 16S rRNA gene-based approaches. Comparative analysis of past accumulative elements presented by 16S rRNA gene-based analysis, and the in-situ conditions presented by 16S rRNA-based analysis, provided new insights concerning the identification of microbial functional roles and interactions. The daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. Increased methanogenesis and hydrolysis at 50°C were main factors causing higher methane production which was also closely related with more well-defined methanogenic and/or related modules with comprehensive interactions and increased functional orderliness referred to more microorganisms participating in interactions. This research demonstrated the importance of evaluating functional roles and interactions of microbial community. PMID:26970926

  3. 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. PMID:24522260

  4. Abundance and functional diversity of riboswitches in microbial communities

    PubMed Central

    Kazanov, Marat D; Vitreschak, Alexey G; Gelfand, Mikhail S

    2007-01-01

    Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. Results Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198). Conclusion This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes. PMID:17908319

  5. 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

  6. 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. PMID:26070678

  7. 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...

  8. 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

  9. A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring.

    PubMed

    Dick, Jeffrey M; Shock, Everett L

    2013-01-01

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

  10. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.

    PubMed

    Paula, Fabiana S; Rodrigues, Jorge L M; Zhou, Jizhong; Wu, Liyou; Mueller, Rebecca C; Mirza, Babur S; Bohannan, Brendan J M; Nüsslein, Klaus; Deng, Ye; Tiedje, James M; Pellizari, Vivian H

    2014-06-01

    Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale. PMID:24806276

  11. Fractal scaling of microbial colonies affects growth

    NASA Astrophysics Data System (ADS)

    Károlyi, György

    2005-03-01

    The growth dynamics of filamentary microbial colonies is investigated. Fractality of the fungal or actinomycetes colonies is shown both theoretically and in numerical experiments to play an important role. The growth observed in real colonies is described by the assumption of time-dependent fractality related to the different ages of various parts of the colony. The theoretical results are compared to a simulation based on branching random walks.

  12. Re-examination of the relationship between marine virus and microbial cell abundances.

    PubMed

    Wigington, Charles H; Sonderegger, Derek; Brussaard, Corina P D; Buchan, Alison; Finke, Jan F; Fuhrman, Jed A; Lennon, Jay T; Middelboe, Mathias; Suttle, Curtis A; Stock, Charles; Wilson, William H; Wommack, K Eric; Wilhelm, Steven W; Weitz, Joshua S

    2016-01-01

    Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10(8) per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,671 microbial cell and virus abundance estimates from 25 distinct marine surveys and find substantial variation in the virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from 'representative' abundances require substantial refinement to be extrapolated to regional or global scales. PMID:27572161

  13. 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

  14. Microbial abundance in lacustrine sediments: a case study from Lake Van, Turkey

    NASA Astrophysics Data System (ADS)

    Kallmeyer, Jens; Grewe, Sina; Glombitza, Clemens; Kitte, J. Axel

    2015-09-01

    The ICDP "PaleoVan" drilling campaign at Lake Van, Turkey, provided a long (>100 m) record of lacustrine subsurface sedimentary microbial cell abundance. After the ICDP campaign at Potrok Aike, Argentina, this is only the second time deep lacustrine cell counts have been documented. Two sites were cored and revealed a strikingly similar cell distribution despite differences in organic matter content and microbial activity. Although shifted towards higher values, cell counts from Lake Potrok Aike, Argentina, reveal very similar distribution patterns with depth. The lacustrine cell count data are significantly different from published marine records; the most probable cause is differences in sedimentary organic matter composition with marine sediments containing a higher fraction of labile organic matter. Previous studies showed that microbial activity and abundance increase centimetres to metres around geologic interfaces. The finely laminated Lake Van sediment allowed studying this phenomenon on the microscale. We sampled at the scale of individual laminae, and in some depth intervals, we found large differences in microbial abundance between the different laminae. This small-scale heterogeneity is normally overlooked due to much larger sampling intervals that integrate over several centimetres. However, not all laminated intervals exhibit such large differences in microbial abundance, and some non-laminated horizons show large variability on the millimetre scale as well. The reasons for such contrasting observations remain elusive, but indicate that heterogeneity of microbial abundance in subsurface sediments has not been taken into account sufficiently. These findings have implications not just for microbiological studies but for geochemistry as well, as the large differences in microbial abundance clearly show that there are distinct microhabitats that deviate considerably from the surrounding layers.

  15. 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. PMID:26787774

  16. Resolving microbial membership using Abundance and Variability In Taxonomy (‘AVIT )

    PubMed Central

    Chakrabarti, Anirikh; Siddharth, Jay; Lauber, Christian L.; Membrez, Mathieu; Betrisey, Bertrand; Loyer, Carole; Chou, Chieh Jason; Pataky, Zoltan; Golay, Alain; Parkinson, Scott J.

    2016-01-01

    Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce ‘AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, ‘AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized ‘AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios. PMID:27530237

  17. 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. PMID:25764538

  18. 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. PMID:26083532

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. Bioflumology: Microbial mat growth in flumes

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  5. 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.

  6. Investigating microbial carbon cycling using natural abundance isotope analysis of PLFA

    NASA Astrophysics Data System (ADS)

    Slater, G. G.; Brady, A.; Cowie, B.

    2008-12-01

    Understanding microbial carbon sources and cycling is fundamental to our conceptualization of microbial ecosystems and their role in biogeochemical cycling in natural systems. Achieving this understanding requires application of a wide range of approaches. Natural abundance isotope analysis of individual compounds, particularly cellular components such as Phospholipids Fatty Acids (PLFA) can provide insights into the carbon sources and metabolic activities of the in situ microbial community from environmental samples. This is primarily because specific PLFA can be well resolved by gas chromatography even from complex matrices where confounding biological/organic compound abound. These PLFA can then be attributed to the viable microbial community, in some cases to specific components of this community and due to characteristic biosynthetic fractionations of stable isotope ratios, δ13C analysis of PLFA can: differentiate isotopically distinct primary carbon sources of heterotrophic communities; identify isotopic patterns characteristic of autotrophic versus heterotrophic processes; and elucidate microbial biosynthetic pathways. In cases where there δ13C cannot provide resolution of carbon sources, new approaches in Δ14C of PLFA can be applied. The vast range in Δ14C of ancient and modern carbon provides an easily traceable signal that can differentiate uptake and utilization of these carbon sources. This is particularly useful in cases such as contaminated sites where petroleum based contamination has occurred, or in natural systems where microbial communities may be utilizing geologic versus recently photosynthetically fixed carbon. This talk will present several examples demonstrating the utility of this approach.

  7. 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

  8. 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

    2014-05-01

    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. PMID:24730445

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

    PubMed Central

    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. PMID:26379656

  10. 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.

  11. 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

  12. 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

  13. Post-fire spatial patterns of soil nitrogen mineralization and microbial abundance.

    PubMed

    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 21(st) Century. PMID:23226324

  14. 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...

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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. PMID:26647180

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Microbial mat controls on infaunal abundance and diversity in modern marine microbialites.

    PubMed

    Tarhan, L G; Planavsky, N J; Laumer, C E; Stolz, J F; Reid, R P

    2013-09-01

    Microbialites are the most abundant macrofossils of the Precambrian. Decline in microbialite abundance and diversity during the terminal Proterozoic and early Phanerozoic has historically been attributed to the concurrent radiation of complex metazoans. Similarly, the apparent resurgence of microbialites in the wake of Paleozoic and Mesozoic mass extinctions is frequently linked to drastic declines in metazoan diversity and abundance. However, it has become increasing clear that microbialites are relatively common in certain modern shallow, normal marine carbonate environments-foremost the Bahamas. For the first time, we present data, collected from the Exuma Cays, the Bahamas, systematically characterizing the relationship between framework-building cyanobacteria, microbialite fabrics, and microbialite-associated metazoan abundance and diversity. We document the coexistence of diverse microbialite and infaunal metazoan communities and demonstrate that the predominant control upon both microbialite fabric and metazoan community structure is microbial mat type. These findings necessitate that we rethink prevalent interpretations of microbialite-metazoan interactions and imply that microbialites are not passive recipients of metazoan-mediated alteration. Additionally, this work provides support for the theory that certain Precambrian microbialites may have been havens of early complex metazoan life, rather than bereft of metazoans, as has been traditionally envisaged. PMID:23889904

  9. 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.

  10. T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut

    PubMed Central

    Brugman, Sylvia; Schneeberger, Kerstin; Witte, Merlijn; Klein, Mark R; van den Bogert, Bartholomeus; Boekhorst, Jos; Timmerman, Harro M; Boes, Marianne L; Kleerebezem, Michiel; Nieuwenhuis, Edward ES

    2014-01-01

    Dysbiosis of the intestinal microbial community is considered a risk factor for development of chronic intestinal inflammation as well as other diseases such as diabetes, obesity and even cancer. Study of the innate and adaptive immune pathways controlling bacterial colonization has however proven difficult in rodents, considering the extensive cross-talk between bacteria and innate and adaptive immunity. Here, we used the zebrafish to study innate and adaptive immune processes controlling the microbial community. Zebrafish lack a functional adaptive immune system in the first weeks of life, enabling study of the innate immune system in the absence of adaptive immunity. We show that in wild type zebrafish, the initial lack of adaptive immunity associates with overgrowth of Vibrio species (a group encompassing fish and human pathogens), which is overcome upon adaptive immune development. In Rag1-deficient zebrafish (lacking adaptive immunity) Vibrio abundance remains high, suggesting that adaptive immune processes indeed control Vibrio species. Using cell transfer experiments, we confirm that adoptive transfer of T lymphocytes, but not B lymphocytes into Rag1-deficient recipients suppresses outgrowth of Vibrio. In addition, ex vivo exposure of intestinal T lymphocytes to Rag1-deficient microbiota results in increased interferon-gamma expression by these T lymphocytes, compared to exposure to wild type microbiota. In conclusion, we show that T lymphocytes control microbial composition by effectively suppressing the outgrowth of Vibrio species in the zebrafish intestine. PMID:25536157

  11. T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut.

    PubMed

    Brugman, Sylvia; Schneeberger, Kerstin; Witte, Merlijn; Klein, Mark R; van den Bogert, Bartholomeus; Boekhorst, Jos; Timmerman, Harro M; Boes, Marianne L; Kleerebezem, Michiel; Nieuwenhuis, Edward E S

    2014-01-01

    Dysbiosis of the intestinal microbial community is considered a risk factor for development of chronic intestinal inflammation as well as other diseases such as diabetes, obesity and even cancer. Study of the innate and adaptive immune pathways controlling bacterial colonization has however proven difficult in rodents, considering the extensive cross-talk between bacteria and innate and adaptive immunity. Here, we used the zebrafish to study innate and adaptive immune processes controlling the microbial community. Zebrafish lack a functional adaptive immune system in the first weeks of life, enabling study of the innate immune system in the absence of adaptive immunity. We show that in wild type zebrafish, the initial lack of adaptive immunity associates with overgrowth of Vibrio species (a group encompassing fish and human pathogens), which is overcome upon adaptive immune development. In Rag1-deficient zebrafish (lacking adaptive immunity) Vibrio abundance remains high, suggesting that adaptive immune processes indeed control Vibrio species. Using cell transfer experiments, we confirm that adoptive transfer of T lymphocytes, but not B lymphocytes into Rag1-deficient recipients suppresses outgrowth of Vibrio. In addition, ex vivo exposure of intestinal T lymphocytes to Rag1-deficient microbiota results in increased interferon-gamma expression by these T lymphocytes, compared to exposure to wild type microbiota. In conclusion, we show that T lymphocytes control microbial composition by effectively suppressing the outgrowth of Vibrio species in the zebrafish intestine. PMID:25536157

  12. 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.

  13. 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.

  14. 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

  15. Afforestation impacts microbial biomass and its natural (13)C and (15)N abundance in soil aggregates in central China.

    PubMed

    Wu, Junjun; Zhang, Qian; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

    2016-10-15

    We investigated soil microbial biomass and its natural abundance of δ(13)C and δ(15)N in aggregates (>2000μm, 250-2000μm, 53-250μm and <53μm) of afforested (implementing woodland and shrubland plantations) soils, adjacent croplands and open area (i.e., control) in the Danjiangkou Reservoir area of central China. The afforested soils averaged higher microbial biomass carbon (MBC) and nitrogen (MBN) levels in all aggregates than in open area and cropland, with higher microbial biomass in micro-aggregates (<250μm) than in macro-aggregates (>2000μm). The δ(13)C of soil microbial biomass was more enriched in woodland soils than in other land use types, while δ(15)N of soil microbial biomass was more enriched compared with that of organic soil in all land use types. The δ(13)C and δ(15)N of microbial biomass were positively correlated with the δ(13)C and δ(15)N of organic soil across aggregates and land use types, whereas the (13)C and (15)N enrichment of microbial biomass exhibited linear decreases with the corresponding C:N ratio of organic soil. Our results suggest that shifts in the natural (13)C and (15)N abundance of microbial biomass reflect changes in the stabilization and turnover of soil organic matter (SOM) and thereby imply that afforestation can greatly impact SOM accumulation over the long-term. PMID:27285796

  16. 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

  17. 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. PMID:26881311

  18. 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

  19. 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

  20. 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

  1. 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.

  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. PMID:23028923

  3. Microbial Distribution and Abundance in the Digestive System of Five Shipworm Species (Bivalvia: Teredinidae)

    PubMed Central

    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. PMID:23028923

  4. 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...

  5. 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

  6. Effects of suspended matter quality and virus abundance on microbial parameters: experimental evidence from a large European river

    PubMed Central

    Kernegger, Lisa; Zweimüller, Irene; Peduzzi, Peter

    2014-01-01

    In riverine water, both suspended particulate material and viruses are prominent ecological factors. The existence of various particle types and differences in viral abundance impose variability in microenvironments. Particulates and their microbial surrounding may interact in several ways, this interaction being strongly dependent on particle quality and the abundance of organisms involved. In laboratory experiments, we used different suspended matter types (fresh and aged mineral sediment and leaf litter, river snow) that typically occur in riverine environments as model particles. We investigated the effects of particle quality and different ambient viral abundances (×1, ×2 enrichments, and inactivated viruses) on several microbial parameters (changes in bacterial and viral abundances, bacterial production, specific bacterial production) of both the free-living and particle-attached fractions using water from a floodplain system of the Danube River (Austria). Both seston quality and variable viral abundances in the bulk water influenced some microbial parameters. The average abundance of bacteria and viruses was significantly higher on organic than on inorganic particles and on aged particles (for both sediment and leaf litter). Changes in bacterial abundance during the course of the experiments were also influenced by particle quality, with, for example, aged sediment favoring increasing abundances. Virus:bacterium ratios (VBR) were significantly higher on organic than on inorganic particles, but significantly lower on suspended particles than in the plank-tonic fraction. Typically, bacterial secondary production (overall and cell-specific) was higher on particles than in bulk water. Bacterial productivity in the ambient water was negatively affected by the abundance of planktonic viruses but positively affected by that of attached viruses. These findings from experimental systems may foster in situ studies of particle-rich environments. PMID:24707113

  7. 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

  8. 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

  9. Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment.

    PubMed

    Luo, Ling; Gu, Ji-Dong

    2016-11-01

    Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention. PMID:27454094

  10. 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. PMID:25230146

  11. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities

    SciTech Connect

    Podar, Mircea; Abulencia, Carl; Walcher, Marion; Hutchinson, Don; Zengler, Karsten; Garcia, Joseph; Holland, Trevin; Cotton, Dave; Hauser, Loren John; Keller, Martin

    2007-01-01

    Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.

  12. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR.

    PubMed

    Bayer, Kristina; Kamke, Janine; Hentschel, Ute

    2014-09-01

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. PMID:24942664

  13. 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. PMID:23563940

  14. Microbial growth and physiology: a call for better craftsmanship

    PubMed Central

    Egli, Thomas

    2015-01-01

    Virtually every microbiological experiment starts with the cultivation of microbes. Consequently, as originally pointed out by Monod (1949), handling microbial cultures is a fundamental methodology of microbiology and mastering different cultivation techniques should be part of every microbiologist’s craftsmanship. This is particularly important for research in microbial physiology, as the composition and behavior of microbes is strongly dependent on their growth environment. It has been pointed out repeatedly by eminent microbiologists that we should give more attention to the media and culturing conditions. However, this is obviously not adhered to with sufficient rigor as mistakes in basic cultivation principles are frequently found in the published research literature. The most frequent mistakes are the use of inappropriate growth media and little or no control of the specific growth rate, and some examples will be discussed here in detail. Therefore, this is a call for better microbiological craftsmanship when cultivating microbial cultures for physiological experiments. This call is not only addressed to researchers but it is probably even more important for the teaching of our discipline. PMID:25926822

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

    NASA Astrophysics Data System (ADS)

    Sumner, D. Y.

    2014-12-01

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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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...

  1. Microbial growth and biofilm formation in geologic media is detected with complex conductivity measurements

    NASA Astrophysics Data System (ADS)

    Davis, Caroline A.; Atekwana, Estella; Atekwana, Eliot; Slater, Lee D.; Rossbach, Silvia; Mormile, Melanie R.

    2006-09-01

    Complex conductivity measurements (0.1-1000 Hz) were obtained from biostimulated sand-packed columns to investigate the effect of microbial growth and biofilm formation on the electrical properties of porous media. Microbial growth was verified by direct microbial counts, pH measurements, and environmental scanning electron microscope imaging. Peaks in imaginary (interfacial) conductivity in the biostimulated columns were coincident with peaks in the microbial cell concentrations extracted from sands. However, the real conductivity component showed no discernible relationship to microbial cell concentration. We suggest that the observed dynamic changes in the imaginary conductivity (σ″) arise from the growth and attachment of microbial cells and biofilms to sand surfaces. We conclude that complex conductivity techniques, specifically imaginary conductivity measurements are a proxy indicator for microbial growth and biofilm formation in porous media. Our results have implications for microbial enhanced oil recovery, CO2 sequestration, bioremediation, and astrobiology studies.

  2. 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. PMID:23957633

  3. 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.

  4. In Scarcity and Abundance: Metabolic Signals Regulating Cell Growth

    PubMed Central

    Saad, Shady; Peter, Matthias

    2013-01-01

    Although nutrient availability is a major driver of cell growth, and continuous adaptation to nutrient supply is critical for the development and survival of all organisms, the molecular mechanisms of nutrient sensing are only beginning to emerge. Here, we highlight recent advances in the field of nutrient sensing and discuss arising principles governing how metabolism might regulate growth-promoting pathways. In addition, we discuss signaling functions of metabolic enzymes not directly related to their metabolic activity. PMID:23997189

  5. Addition of activated switchgrass biochar to an aridic subsoil increases microbial nitrogen cycling gene abundances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It has been demonstrated that soil amended with biochar, designed specifically for use as a soil conditioner, results in changes to the microbial populations that reside therein. These changes have been reflected in studies measuring variations in microbial activity, biomass, and community structure...

  6. Growth dynamics and the evolution of cooperation in microbial populations

    NASA Astrophysics Data System (ADS)

    Cremer, Jonas; Melbinger, Anna; Frey, Erwin

    2012-02-01

    Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

  7. Arsenic as an energy source for microbial growth. (Invited)

    NASA Astrophysics Data System (ADS)

    Oremland, R. S.

    2009-12-01

    Arsenic, although known for millenia to be a potent poison, can also constitute the basis for energy metabolism by a number of Bacteria and Archaea. Hence, the oxyanion arsenate [As(V)] can serve as a respiratory electron acceptor for the growth of anaerobes, resulting in the accumulation of arsenite [As(III)]. Conversely, As(III) can serve as an electron donor for the growth of aerobic and anaerobic (e.g., nitrate-respiring) chemoautotrophs, as well as photoautotrophs that grow via anoxygenic photosynthesis. Collectively, these microbes carry out these redox reactions between the +3 and +5 oxidation states that have profound importance for the mobility of As in the environment, and perhaps for the pattern of microbial evolution on Earth. I will focus upon the occurrence of these microbes in extreme environments that are rich in naturally-occurring arsenic.

  8. 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.

  9. Microbial growth on hydrocarbons: terminal branching inhibits biodegradation.

    PubMed Central

    Schaeffer, T L; Cantwell, S G; Brown, J L; Watt, D S; Fall, R R

    1979-01-01

    A variety of octane-utilizing bacteria and fungi were screened for growth on some terminally branched dimethyloctane derivatives to explore the effects of iso- and anteiso-termini on the biodegradability of such hydrocarbons. Of 27 microbial strains tested, only 9 were found to use any of the branched hydrocarbons tested as a sole carbon source, and then only those hydrocarbons containing at least one iso-terminus were susceptible to degradation. Anteiso-or isopropenyl termini prevented biodegradation. None of the hydrocarbonoclastic yeasts tested was able to utilize branched-hydrocarbon growth sustrates. In the case of pseudomonads containing the OCT plasmid, whole-cell oxidation of n-octane was poorly induced by terminally branched dimethyloctanes. In the presence of a gratuitous inducer of the octane-oxidizing enzymes, the iso-branched 2,7-dimethyloctane was slowly oxidized by whole cells, whereas the anteiso-branched 3,6-dimethyloctane was not oxidized at all. This microbial sampling dramatically illustrated the deleterious effect of alkyl branching, especially anteiso-terminal branching, on the biodegradation of hydrocarbons. PMID:539824

  10. 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

  11. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  12. 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

  13. 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.

  14. Inhibition of microbial growth on chitosan membranes by plasma treatment.

    PubMed

    de Oliveira Cardoso Macêdo, Marina; de Macêdo, Haroldo Reis Alves; Gomes, Dayanne Lopes; de Freitas Daudt, Natália; Rocha, Hugo Alexandre Oliveira; Alves, Clodomiro

    2013-11-01

    The use of polymeric medical devices has stimulated the development of new sterilization methods. The traditional techniques rely on ethylene oxide, but there are many questions concerning the carcinogenic properties of the ethylene oxide residues adsorbed on the materials after processing. Another common technique is the gamma irradiation process, but it is costly, its safe operation requires an isolated site, and it also affects the bulk properties of the polymers. The use of gas plasma is an elegant alternative sterilization technique. The plasma promotes efficient inactivation of the microorganisms, minimizes damage to the materials, and presents very little danger for personnel and the environment. In this study we used plasma for microbial inhibition of chitosan membranes. The membranes were treated with oxygen, methane, or argon plasma for different time periods (15, 30, 45, or 60 min). For inhibition of microbial growth with oxygen plasma, the time needed was 60 min. For the methane plasma, samples were successfully treated after 30, 45, and 60 min. For argon plasma, all treatment periods were effective. PMID:24251774

  15. Detecting Microbial Growth and Metabolism in Geologic Media with Complex Conductivity Measurements

    NASA Astrophysics Data System (ADS)

    Davis, C. A.; Atekwana, E. A.; Slater, L. D.; Bottrell, P. M.; Chasten, L. E.; Heidenreich, J. D.

    2006-05-01

    Complex conductivity measurements between 0.1-1000 Hz were obtained from biostimulated sand-packed (coarse and mixed fine and medium grain) columns to investigate microbial growth, biofilm formation, and microbial metabolism on the electrical properties of porous media. Microbial growth and metabolism was verified by direct microbial counts, pH changes, and environmental scanning electron microscope imaging. Peaks in imaginary (interfacial) conductivity in the coarse grain columns occurred concurrently with peaks in the microbial cell concentrations. The magnitude of the imaginary conductivity response in the mixed fine and medium grain columns, however, was low compared to the coarse grain sand columns, consistent with lower microbial cell concentrations. It is possible that the pore size in the mixed fine and medium grain sand restricted bacteria cell division, inhibiting microbial growth, and thus the smaller magnitude imaginary conductivity response. The biostimulated columns for both grain sizes displayed similar trends and showed an increase in the real (electrolytic) conductivity and decrease in pH over time. Dynamic changes in the imaginary conductivity arises from the growth and attachment of microbial cells and biofilms to surfaces, whereas, changes in the real conductivity arises from the release of byproducts (ionic species) of microbial metabolism. We conclude that complex conductivity techniques are feasible sensors for detecting microbial growth (imaginary conductivity measurements) and metabolism (real conductivity measurements) with implications for bioremediation and astrobiology studies.

  16. 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 bacteria…

  17. 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. PMID:25957076

  18. 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. PMID:24685456

  19. 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...

  20. 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

  1. 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.

  2. 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

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Skidmore, M. L.; Boyd, E. S.; Lange, R. K.; Mitchell, A. C.; Havig, J. R.; Hamilton, T. L.; Lafreniere, M. J.; Shock, E.; Peters, J.

    2011-12-01

    Ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of the planet during Earth's history. Significant microbial populations have been documented in all subglacial settings sampled to date. Recent research has demonstrated sizable volumes of subglacial sediment beneath the Antarctic Ice Sheet that are greater than 1km thick in places and where sampled active microbial populations have been documented. Collectively this suggests subglacial microbial populations may impact global biogeochemical cycles on glacial-interglacial timescales, however, nitrogen cycling in subglacial systems is poorly understood. Subglacial sediments sampled from beneath Robertson Glacier, Alberta, Canada harbor a diverse assemblage of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Archaeal amoA genes were less abundant and less diverse than bacterial amoA. Nitrification and nitrate reduction were measured in microcosms incubated at 4 degrees Celsius indicating the potential for these processes to occur in situ. Subglacial sediment porewaters and bulk meltwaters have low concentrations of dissolved inorganic and organic nitrogen compounds and a high C/N ratio of dissolved organic matter in sediment porewaters, indicating that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence for N limitation and detection of nifH, biological nitrogen fixation was not detected in subglacial sediment microcosm experiments at 4 degrees Celsius. Collectively, our results suggest a role for nitrification and nitrate reduction in sustaining microbial communities in subglacial environments.

  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. 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.

  7. 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

  8. SOYBEAN APHID ABUNDANCE AMONG CONTEMPORARY SOYBEAN LINES IN A GROWTH-CHAMBER TEST, 2005

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The abundance of soybean aphid was compared among eight contemporary soybean lines in a growth chamber test. All soybean lines had >500 soybean aphids per plant 2 wks after infestation. The number of soybean aphids per plant differed among lines, with Surge and 91B91 having more soybean aphids tha...

  9. 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

  10. Population-specific shifts in viral and microbial abundance within a cryptic upwelling

    NASA Astrophysics Data System (ADS)

    Paterson, James S.; Nayar, Sasi; Mitchell, James G.; Seuront, Laurent

    2013-03-01

    Coastal upwelling systems play an essential role in bringing cold and nutrient-rich water into the euphotic zone, hence enhancing the biological productivity of the world's oceans. We describe a "cryptic" upwelling occurring in South Australian waters, in which cold upwelled waters do not reach surface waters and do not exhibit a sea surface temperature (SST) signature. Due to the wide continental shelf (ca. 100 km), upwelled waters form a sub-surface cold water pool and are forced north-west after a secondary event. Using flow cytometry we investigated the abundance and composition of viruses, heterotrophic bacteria and pico-phytoplankton within upwelling affected and unaffected waters. Our results identified the presence of upwelled waters at and below the Deep-Chlorophyll Maximum (DCM), where water temperature was at least 4 °C colder than surface waters. In contrast to previous studies, no significant differences were observed between upwelled and non-upwelled waters for most individual viral, bacterial and pico-phytoplankton sub-groups. However, one viral, one bacterial and two pico-phytoplankton sub-groups were significantly more abundant at the DCM. This indicates the presence of depth- and population-specific shifts in abundance and potential niche partitioning of these cytometrically-defined sub-groups that may be related to their host organisms and/or resource availability.

  11. A Thermodynamically-Based Model For Predicting Microbial Growth And Community Composition Coupled To System Geochemistry

    NASA Astrophysics Data System (ADS)

    Istok, J. D.

    2007-12-01

    We present an approach that couples thermodynamic descriptions for microbial growth and geochemical reactions to provide quantitative predictions for the effects of substrate addition or other enviornmental perturbations on microbial community composition. A synthetic microbial community is defined as a collection of defined microbial groups; each with a growth equation derived from bioenergetic principles. The growth equations and standard-state free energy yields are appended to a thermodynamic database for geochemical reactions and the combined equations are solved simultaneously to predict coupled changes in microbial biomass, community composition, and system geochemistry. This approach, with a single set of thermodynamic parameters (one for each growth equation), was used to predict the results of laboratory and field experiments at three geochemically diverse research sites. Predicted effects of ethanol or acetate addition on radionuclide and heavy metal solubility, major ion geochemistry, mineralogy, microbial biomass and community composition were in general agreement with experimental observations although the available experimental data precluded rigorous model testing. Model simulations provide insight into the long-standing difficulty in transferring experimental results from the laboratory to the field and from one site to the next, especially if the form, concentration, or delivery of growth substrate is varied from one experiment to the next. Although originally developed for use in better understanding bioimmobilization of radionuclides and heavy metals via reductive precipitation, the modeling approach is potentially useful for exploring the coupling of microbial growth and geochemical reactions in a variety of basic and applied biotechnology research settings.

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

    PubMed Central

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

    2014-01-01

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

  13. 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

  14. 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.

  15. Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas.

    PubMed

    Yang, Yuyin; Wang, Jie; Liao, Jingqiu; Xie, Shuguang; Huang, Yi

    2015-02-01

    Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems. PMID:25236802

  16. MICROBIALLY MEDIATED GROWTH SUPPRESSION AND DEATH OF SALMONELLA IN COMPOSTED SEWAGE SLUDGE

    EPA Science Inventory

    The role of compost microflora in the suppression of salmonella regrowth in composted sewage sludge was investigated. Microbial inhibition studies of salmonella growth were conducted on nutrient agar, in composts that had been subjected to different temperatures in compost piles,...

  17. 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. PMID:24818690

  18. 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

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

    PubMed Central

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

    1983-01-01

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

  20. 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.

  1. 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. PMID:20455942

  2. 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

  3. 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

  4. Effect of temperature and zooplankton abundance on growth and survival of larval threadfin shad

    USGS Publications Warehouse

    Betsill, R.K.; Van Den Avyle, M.J.

    1997-01-01

    As a test of the match-mismatch hypothesis, we examined the effects of prey availability and water temperature on growth and survival of weekly cohorts of larval threadfin shad Dorosoma petenense in J. Strom Thurmond Reservoir, Georgia-South Carolina. Hatching dates were estimated from otolith increments, and availability of prey was estimated from the abundance of zooplankton size-classes commonly eaten by larval threadfin shad. Growth rates of 31 cohorts ranged from 0.39 to 0.78 mm/d, demonstrating the potential for stage-duration effects on cohort survival. Daily growth rate was related to water temperature and prey availability for larvae up to 21 d old. Growth increased linearly with water temperature up to 28??C, but the relation between growth and prey availability was more complex. Growth rate increased with prey density up to 160-290 organisms/L; at higher densities, growth rate decreased or was unchanged. Cohort survival ranged from 0.65 to 0.96 (per millimeter increase in length) and was significantly correlated with water temperature and growth rate but not with prey availability.

  5. 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.

  6. 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

  7. 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.

  8. Elevated bacterial abundance and exopolymers in saline frost flowers and implications for atmospheric chemistry and microbial dispersal

    NASA Astrophysics Data System (ADS)

    Bowman, J. S.; Deming, J. W.

    2010-07-01

    Frost flowers (FF) have been studied for their potential influence on ice-surface reflectivity and roles in atmospheric chemistry, but not as microbial habitats. We examined FF grown in a freezer laboratory from a bacteria-containing saline solution and FF formed naturally in the coastal (April) and central Arctic Ocean (September). All FF contained bacteria (up to 3.46 × 106 ml-1 in natural FF) with densities 3-6-fold higher than in underlying ice. Bacterial abundance correlated strongly with salinity in FF (p values ≤ 0.001), a correlation that held for all components of the surface-ice environment (p < 0.0001, coastal samples). Concentrations of extracellular polysaccharides were also elevated in FF and brine skim relative to underlying ice (up to 74-fold higher). Here we consider implications of finding microbes and exopolymers within the chemically reactive surface-ice environment to the photolytic production of oxidants and long-range transport of potential ice-nucleating particles in the atmosphere.

  9. Use of abundance ratios of somatic coliphages and bacteriophages of Bacteroides thetaiotaomicron GA17 for microbial source identification.

    PubMed

    Muniesa, Maite; Lucena, Francisco; Blanch, Anicet R; Payán, Andrey; Jofre, Juan

    2012-12-01

    Water contaminated with human faeces is a risk to human health and management of water bodies can be improved by determining the sources of faecal pollution. Field studies show that existing methods are insufficient and that different markers are required. This study proposes the combined use of two microbial indicators, the concentrations of which are presented as ratios. This provides a more reliable approach to identifying faecal sources as it avoids variation due to treatment or ageing of the contamination. Among other indicators, bacteriophages have been proposed as rapid and cheap indicators of faecal pollution. Samples analysed in this study were derived from wastewater treatment plants (raw sewage, secondary and tertiary effluents and raw sewage sludge) river water, seawater and animal related wastewater. The abundance ratios of faecal coliforms and Bacteroides phages, either strain RYC2056 (non-specific for faecal origin) or strain GA17 (specific for human pollution), and among somatic coliphages and phages infecting both Bacteroides strains, were evaluated. The results indicate that the ratio of somatic coliphages and phages infecting Bacteroides strain GA17, which is specific to human faecal sources, provides a robust method for discriminating samples, even those presenting different levels and ages of pollution, and allows samples polluted with human faeces to be distinguished from those containing animal faecal pollution. This method allows the generation of numerical data that can be further applied to numerical methods for faecal pollution discrimination. PMID:23039916

  10. 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

  11. 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. PMID:26539483

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    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 × 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments.

  14. 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.

  15. Effects of fertilization on microbial abundance and emissions of greenhouse gases (CH4 and N2O) in rice paddy fields.

    PubMed

    Fan, Xianfang; Yu, Haiyang; Wu, Qinyan; Ma, Jing; Xu, Hua; Yang, Jinghui; Zhuang, Yiqing

    2016-02-01

    This study is to explore effects of nitrogen application and straw incorporation on abundance of relevant microbes and CH 4 and N2O fluxes in a midseason aerated rice paddy field. Fluxes of CH 4 and N2O were recorded, and abundance of relevant soil microbial functional genes was determined during rice-growing season in a 6-year-long fertilization experiment field in China. Results indicate that application of urea significantly changed the functional microbial composition, while the influence of straw incorporation was not significant. Application of urea significantly decreased the gene abundances of archaeal amoA and mcrA, but it significantly increased the gene abundances of bacterial amoA. CH 4 emission was significantly increased by fresh straw incorporation. Incorporation of burnt straw tended to increase CH 4 emission, while the urea application had no obvious effect on CH 4 emission. N2O emission was significantly increased by urea application, while fresh or burnt straw incorporation tended to decrease N2O emission. The functional microbial composition did not change significantly over time, although the abundances of pmoA, archaeal amoA, nirS, and nosZ genes changed significantly. The change of CH 4 emission showed an inverse trend with the one of the N2O emissions over time. To some extent, the abundance of some functional genes in this study can explain CH 4 and N2O emissions. However, the correlation between CH 4 and N2O emissions and the abundance of related functional genes was not significant. Environmental factors, such as soil Eh, may be more related to CH 4 and N2O emissions. PMID:26811747

  16. Microbial Growth Inside Insulated External Walls as an Indoor Air Biocontamination Source

    PubMed Central

    Pessi, Anna-Mari; Suonketo, Jommi; Pentti, Matti; Kurkilahti, Mika; Peltola, Kaija; Rantio-Lehtimäki, Auli

    2002-01-01

    The association between moisture-related microbial growth (mesophilic fungi and bacteria) within insulated exterior walls and microbial concentrations in the indoor air was studied. The studied apartment buildings with precast concrete external walls were situated in a subarctic zone. Actinomycetes in the insulation layer were found to have increased concentrations in the indoor air. The moisture content of the indoor air significantly affected all measurable airborne concentrations. PMID:11823245

  17. 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).

  18. 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. PMID:25674807

  19. Multikinase inhibitor regorafenib inhibits the growth and metastasis of colon cancer with abundant stroma.

    PubMed

    Takigawa, Hidehiko; Kitadai, Yasuhiko; Shinagawa, Kei; Yuge, Ryo; Higashi, Yukihito; Tanaka, Shinji; Yasui, Wataru; Chayama, Kazuaki

    2016-05-01

    Interaction between tumor cells and stromal cells plays an important role in the growth and metastasis of colon cancer. We previously found that carcinoma-associated fibroblasts (CAFs) expressed platelet-derived growth factor receptor-β (PDGFR-β) and that PDGFR targeted therapy using imatinib or nilotinib inhibited stromal reaction. Bone marrow-derived mesenchymal stem cells (MSCs) migrate to tumor stroma and differentiate into CAFs. A novel oral multikinase inhibitor regorafenib inhibits receptor tyrosine kinases expressed on stromal cells (vascular endothelial growth factor receptor 1-3, TIE2, PDGFR-β, and fibroblast growth factors) and tumor cells (c-KIT, RET, and BRAF). These molecules are involved in tumor growth, angiogenesis, lymphangiogenesis, and stromal activation. Therefore, we examined whether regorafenib impaired the tumor-promoting effect of CAFs/MSCs. KM12SM human colon cancer cells alone or KM12SM cells with MSCs were transplanted into the cecal wall of nude mice. Co-implantation of KM12SM cells with MSCs into the cecal wall of nude mice produced tumors with abundant stromal component and promoted tumor growth and lymph node metastasis. Single treatment with regorafenib inhibited tumor growth and metastasis by inhibiting both tumor cells and stromal reaction. This tumor-inhibitory effect of regorafenib was more obvious in tumors developed by co-implanting KM12SM cells with MSCs. Our data suggested that targeting of the tumor microenvironment with regorafenib affected tumor cell-MSC interaction, which in turn inhibited the growth and metastasis of colon cancer. PMID:26865419

  20. 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.

  1. An antibody to amphiregulin, an abundant growth factor in patients' fluids, inhibits ovarian tumors.

    PubMed

    Carvalho, S; Lindzen, M; Lauriola, M; Shirazi, N; Sinha, S; Abdul-Hai, A; Levanon, K; Korach, J; Barshack, I; Cohen, Y; Onn, A; Mills, G; Yarden, Y

    2016-01-28

    Growth factors of the epidermal growth factor (EGF)/neuregulin family are involved in tumor progression and, accordingly, antibodies that intercept a cognate receptor, epidermal growth factor receptor (EGFR)/ERBB1, or a co-receptor, HER2, have been approved for cancer therapy. Although they might improve safety and delay onset of chemoresistance, no anti-ligand antibodies have been clinically approved. To identify suitable ligands, we surveyed fluids from ovarian and lung cancer patients and found that amphiregulin (AREG) is the most abundant and generalized ligand secreted by advanced tumors. AREG is a low affinity EGFR ligand, which is upregulated following treatment with chemotherapeutic drugs. Because AREG depletion retarded growth of xenografted ovarian tumors in mice, we generated a neutralizing monoclonal anti-AREG antibody. The antibody inhibited growth of ovarian cancer xenografts and strongly enhanced chemotherapy efficacy. Taken together, these results raise the possibility that AREG and other low- or high-affinity binders of EGFR might serve as potential targets for cancer therapy. PMID:25915843

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

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

    Prediction of microbial growth in mixed culture was studied with a competition model that we had developed recently. The model, which is composed of the new logistic model and the Lotka-Volterra model, is shown to successfully describe the microbial growth of two species in mixed culture using Staphylococcus aureus, Escherichia coli, and Salmonella. With the parameter values of the model obtained from the experimental data on monoculture and mixed culture with two species, it then succeeded in predicting the simultaneous growth of the three species in mixed culture inoculated with various cell concentrations. To our knowledge, it is the first time for a prediction model for multiple (three) microbial species to be reported. The model, which is not built on any premise for specific microorganisms, may become a basic competition model for microorganisms in food and food materials. PMID:24975413

  3. Modeling Microbial Growth Dynamics, Patterns, and Coexistence on Partially Saturated Rough Surfaces

    NASA Astrophysics Data System (ADS)

    Long, T.; Or, D.

    2005-12-01

    A new modeling tool was developed to study the impact of variations in matric potential on aquatic pathways and substrate diffusion, and on microbial growth and movement on unsaturated rough surfaces. The modeling domain is composed of prescribed distributions of conical pits (sites) connected by prismatic channels (bonds) representing rough surfaces of soils or rocks. The well-defined geometry facilitates exact description of aqueous phase distribution within the roughness for a given matric potential. Microbial growth within the resulting highly variable diffusion network architectures (vary with matric potential) and interactions with nutrient diffusion patterns are simulated by coupling Reaction-Diffusion Method (RDM) and the Active Walker Method (AWM). Simulation results show direct impact of wetness conditions (matric potential values) on microbial growth rates and expansion patters for the same surface roughness. In addition to modification of mean diffusion rates for drier or wetter conditions, the network connectivity may induce significant changes in spatial patters of microbial growth. Impact of these changes on coexistence of two competing microbial species will be discussed.

  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. PMID:26868619

  5. Using PLFA Biomarkers and Natural Abundance Stable and Radiocarbon Isotopes to Characterize the Microbial Ecology and Metabolism of Methane Cycling

    NASA Astrophysics Data System (ADS)

    Mills, C. T.; Mandernack, K. W.; Slater, G. F.; Dias, R. F.

    2008-12-01

    Methane generated in the subsurface is a major source of atmospheric CH4, but its release is mitigated by CH4-oxidizing bacteria (methanotrophs). Therefore, it is important to understand the ecology of methanotroph communities in various environments. Phospholipid fatty acid (PLFA) analyses are a particularly useful method for characterizing these communities for two reasons: (1) Many type I and II methanotrophs produce specific PLFA biomarkers that can be used to estimate their populations, and (2) because CH4 is often very depleted in 13C and sometimes 14C, natural abundance δ13CPLFA and Δ14CPLFA values can be used to trace the flow of CH4- derived carbon through microbial ecosystems. We used these tools to evaluate the role of methanotrophs in carbon flow in three different environments: (1) a soil column overlying a coal bed methane (CBM) seep in southwest CO, and pristine, oligotrophic groundwaters within (2) sedimentary and (3) granitic host rocks in Japan. In the soil column impacted by CBM seepage, concentrations of the biomarker PLFAs for type I (16:1ω8cis) and type II (18:1ω8cis) methanotrophs were as high as 13 and 18 nmoles (g dry soil)-1, respectively. Depth profiles of methanotroph PLFA concentrations varied over different sampling dates indicating dynamic populations. δ13CPLFA values of the CBM soils (-25.1 to - 66.9‰) were substantially more negative than those for the control soil (-14.5 to -32.5‰) indicating that CBM is an important carbon source for the CBM-impacted soil microbial community. Δ14CPLFA values (-351 to -936‰) indicate the importance of 14C-dead CBM as a carbon source to the microbial communities, contributing 32 to 66% of total carbon in PLFA structures isolated from shallow soils and 67 to 97% for those isolated from deeper soils. The biomarker for type II methanotrophs, comprised 3 and 18% of total PLFAs in sedimentary and granitic groundwaters, respectively. The Δ14C values determined for type II methanotroph PLFAs

  6. 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

  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. 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

  9. 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…

  10. 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

  11. [Evaluation of microbial growth on single-use vitrectomy probes reprocessed in healthcare practice].

    PubMed

    Pinto, Flávia Morais Gomes; Araújo, Valéria Garcia Lopes; Souza, Rafael Queiroz de; Goveia, Vânia Regina; Missali, Carmen Castilho; Luz, Reginaldo Adalberto de; Graziano, Kazuko Uchikawa

    2012-06-01

    The aim of this study was to evaluate the microbial growth on single-use vitrectomy probes reprocessed in healthcare practice. We investigated nine vitrectomy probes that had been reused and reprocessed using different methods. The samples were sectioned, individually, in portions of 3.5 cm, totaling 979 sampling units (extensions, connectors and vitrectomy cutters), which were inoculated in culture medium and incubated at 37º C for 14 days. The results showed microbial growth on 57 (5.8%) sample units, 25 of which had been sterilized using ethylene oxide, 16 by hydrogen peroxide plasma, and 16 by low-temperature steam and formaldehyde. Seventeen microbial species were identified. The most prevalent were: Micrococcus spp., coagulase-negative Staphylococcus, Pseudomonas spp., and Bacillus subtilis. The reuse of single-use vitrectomy probes was shown to be unsafe, therefore this practice is not recommended. PMID:22773479

  12. Abundance, biomass and growth rates of Synechococcus sp. in a tropical coastal ecosystem (Philippines, South China Sea)

    NASA Astrophysics Data System (ADS)

    Agawin, N. S. R.; Duarte, C. M.; Agustí, S.; McManus, L.

    2003-03-01

    The abundance, biomass and growth rates of Synechococcus sp. were estimated in a tropical coastal ecosystem (Philippines, South China Sea). The patterns of change of these parameters were further examined in relation to human-derived disturbance such as siltation, and by short-term episodic disturbances such as the typhoons, which are frequent in the region. The average abundance and biomass of Synechococcus sp. in the coastal ecosystem ranged from 0.13 to 21×10 6 cells l -1, and from 0.01 to l.6 mg C m -3, respectively, with higher biomass occurring near river sources rich in inorganic nutrients. There was, however, a significant decline of specific growth rates and maximum frequency of cells in division with increasing siltation, which suggests a deterioration of the environmental conditions to support picocyanobacterial populations. The low biomass of Synechococcus sp. in more pristine sites, in spite of relatively high growth rates there suggests that loss factors (i.e. grazing) are important in controlling the biomass in the area. The temporal pattern of picocyanobacterial abundance in the tropical ecosystem studied was tightly coupled with their temporal patterns of growth indicating that changes in abundance may result from changes in growth rate. There was not, however, a clear annual pattern of Synechococcus sp. abundance in the study site but there was some evidence for effects of storms on Synechococcus sp. abundance.

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

    PubMed

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

    2014-09-01

    The suitability of indirect impedance to accurately measure microbial growth in real food matrices was investigated. A variety of semi-solid and liquid food products were inoculated with Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Lactobacillus plantarum, Pseudomonas aeruginosa, Escherichia coli, Salmonella enteriditis, Candida tropicalis or Zygosaccharomyces rouxii and CO2 production was monitored using a conductimetric (Don Whitely R.A.B.I.T.) system. The majority (80%) of food and microbe combinations produced a detectable growth signal. The linearity of conductance responses in selected food products was investigated and a good correlation (R(2) ≥ 0.84) was observed between inoculum levels and times to detection. Specific growth rate estimations from the data were sufficiently accurate for predictive modeling in some cases. This initial evaluation of the suitability of indirect impedance to generate microbial growth data in complex food matrices indicates significant potential for the technology as an alternative to plating methods. PMID:24929710

  14. Hot water treatment reduces microbial growth and improves quality of packaged fresh-cut tables grapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Packaged fresh-cut table grape (Vitis vinifera L.) has emerged as a popular snack food because it offers freshness, nutrition, and convenience. However, tissue injury sustained during stem removal, and the openings created after stem removal make grapes susceptible to microbial growth, product deca...

  15. 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 ...

  16. 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. PMID:27060444

  17. 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

  18. Plant growth and soil microbial community structure of legumes and grasses grown in monoculture or mixture.

    PubMed

    Chen, Meimei; Chen, Baodong; Marschner, Petra

    2008-01-01

    A greenhouse pot experiment was conducted to investigate the influence of soil moisture content on plant growth and the rhizosphere microbial community structure of four plant species (white clover, alfalfa, sudan grass, tall fescue), grown individually or in a mixture. The soil moisture content was adjusted to 55% or 80% water holding capacity (WHC). The results indicated that the total plant biomass of one pot was lower at 55% WHC. At a given soil moisture, the total plant biomass of white clover and tall fescue in the mixture was lower than that in a monoculture, indicating their poor competitiveness. For leguminous plants, the decrease in soil moisture reduced the total microbial biomass, bacterial biomass, fungal biomass, and fungal/bacterial ratio in soil as assessed by the phospholipid fatty acid analysis, whereas, lower soil moisture increased those parameters in the tall fescue. The microbial biomass in the soil with legumes was higher than that in the soil with grasses and the two plant groups differed in soil microbial community composition. At high soil moisture content, microbial communities of the plant mixture were similar to those of the legume monoculture, and the existence of legumes in the mixture enhanced the bacterial and fungal biomass in the soil compared to the grasses grown in the monoculture, indicating that legumes played a dominant role in the soil microbial community changes in the plant mixture. PMID:19143348

  19. 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.

  20. Numerical solution of a microbial growth model applied to dynamic environments.

    PubMed

    Zhu, Si; Chen, Guibing

    2015-05-01

    The Baranyi and Roberts model is one of the most frequently used microbial growth models. It has been successfully applied to numerous studies of various microorganisms in different food products. Under dynamic conditions, the model is implicitly formulated as a set of two coupled differential equations which could be numerically solved using the Runge-Kutta method. In this study, a simplified numerical solution of the coupled differential equations was derived and used to simulate microbial growth under dynamic conditions in Microsoft Excel. As expected, the results obtained were the same as those from solving the coupled differential equations using a MATLAB Solver. In addition, model parameters were accurately identified by fitting the numerical solution to simulated growth curves under dynamic (time-varying) temperature conditions using the Microsoft Excel Solver. PMID:25765150

  1. Soil microbial abundance, activity and diversity response in two different altitude-adapted plant communities affected by wildfire in Sierra Nevada National Park (Granada, Spain)

    NASA Astrophysics Data System (ADS)

    Bárcenas-Moreno, Gema; Zavala, Lorena; Jordan, Antonio; Bååth, Erland; Mataix-Beneyto, Jorge

    2013-04-01

    Plant communities can play an important role in fire severity and post-fire ecosystem recovery due to their role as combustible and different plant-soil microorganisms interactions. Possible differences induced by plant and microorganisms response after fire could affect the general ecosystem short and long-term response and its sustainability. The main objective of this work was the evaluation of the effect of wildfire on soil microbial abundance, activity and diversity in two different plant communities associated to different altitudes in Sierra Nevada National Park (Granada, Spain). Samples were collected in two areas located on the Sierra Nevada Mountain between 1700 and 2000 m above sea level which were affected by a large wildfire in 2005. Two samplings were carried out 8 and 20 months after fire and samples were collected in both burned and unburned (control) zones in each plant community area. Area A is located at 1700m and it is formed by Quercus rotundifolia forest while area B is located at 2000 m altitude and is composed of alpine vegetation formed by creeping bearing shrubs. Microbial biomass measured by Fumigation-Extraction method followed the same trend in both areas showing slight and no significant differences between burned and unburned area during the study period while viable and cultivable bacteria abundance were markedly higher in fire affected samples than in the control ones in both samplings. Viable and cultivable filamentous fungi had different behavior depending of plant vegetation community studied showing no differences between burned and unburned area in area A while was significantly higher in burned samples than in the control ones in area B. Microbial activity monitoring with soil microbial respiration appears to had been affected immediately after fire since microbial respiration was lower in burned samples from area A than in unburned one only 8 months after fire and no significant differences were observed between burned and

  2. 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

  3. 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.

  4. Effect of refrigeration on microbial growth in the Blairex Water Purifier.

    PubMed

    Harris, M G; Meng, K E; Frank, L J; Mamalis, G

    1987-05-01

    The Blairex Water Purifier is designed to make tap water into purified water that can be used to make saline solution for soft contact lens disinfection and rinsing. The micropore filters of eight Purifiers were perforated to allow a controlled contamination by either Pseudomonas aeruginosa or Serratia marcescens. The bacterial growth was evaluated in these altered Blairex Water Purifiers under refrigerated and unrefrigerated conditions. Those Purifiers that were refrigerated showed significantly less bacterial growth than those Purifiers that were kept at room temperature between samplings. Our findings imply that soft contact lens wearers may reduce the level of microbial growth in undamaged Purifiers by refrigerating the Purifiers between uses. PMID:3111265

  5. 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.

  6. Response of the Abundance of Key Soil Microbial Nitrogen-Cycling Genes to Multi-Factorial Global Changes

    PubMed Central

    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. PMID:24124568

  7. Comparative analysis of some models of gene regulation in mixed-substrate microbial growth.

    PubMed

    Narang, Atul

    2006-09-21

    Mixed-substrate microbial growth is of fundamental interest in microbiology and bioengineering. Several mathematical models have been developed to account for the genetic regulation of such systems, especially those resulting in diauxic growth. In this work, we compare the dynamics of three such models (Narang, 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121; Thattai and Shraiman, 2003. Metabolic switching in the sugar phosphotransferase system of Escherichia coli. Biophys. J. 85(2), 744-754; Brandt et al., 2004. Modelling microbial adaptation to changing availability of substrates. Water Res. 38, 1004-1013). We show that these models are dynamically similar--the initial motion of the inducible enzymes in all the models is described by the Lotka-Volterra equations for competing species. In particular, the prediction of diauxic growth corresponds to "extinction" of one of the enzymes during the first few hours of growth. The dynamic similarity occurs because in all the models, the inducible enzymes possess properties characteristic of competing species: they are required for their own synthesis, and they inhibit each other. Despite this dynamic similarity, the models vary with respect to the range of dynamics captured. The Brandt et al. model always predicts the diauxic growth pattern, whereas the remaining two models exhibit both diauxic and non-diauxic growth patterns. The models also differ with respect to the mechanisms that generate the mutual inhibition between the enzymes. In the Narang model, mutual inhibition occurs because the enzymes for each substrate enhance the dilution of the enzymes for the other substrate. The Brandt et al. model superimposes upon this dilution effect an additional mechanism of mutual inhibition. In the Thattai and Shraiman model, the mutual inhibition is entirely due to competition for the phosphoryl groups. For quantitative

  8. 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. PMID:22902379

  9. Bifunctional silver nanoparticle cathode in microbial fuel cells for microbial growth inhibition with comparable oxygen reduction reaction activity.

    PubMed

    An, Junyeong; Jeon, Hongrae; Lee, Jaeyoung; Chang, In Seop

    2011-06-15

    Organic contamination of water bodies in which benthic microbial fuel cells (benthic MFCs) are installed, and organic crossover from the anode to the cathode of membraneless MFCs, is a factor causing oxygen depletion and substrate loss in the cathode due to the growth of heterotrophic aerobic bacteria. This study examines the possible use of silver nanoparticles (AgNPs) as a cathodic catalyst for MFCs suffering from organic contamination and oxygen depletion. Four treated cathodes (AgNPs-coated, Pt/C-coated, Pt/C+AgNPs-coated, and plain graphite cathodes) were prepared and tested under high levels of organics loading. During operation (fed with 50 mM acetate), the AgNPs-coated system showed the highest DO concentration (0.8 mg/L) in the cathode area as well as the highest current (ranging from 0.04 to 0.12 mA). Based on these results, we concluded that (1) the growth of oxygen-consuming heterotrophic microbes could be inhibited by AgNPs, (2) the function of AgNPs as a bacterial growth inhibitor resulted in a greater increase of DO concentration in the cathode than the other tested cathode systems, (3) AgNPs could be applied as a cathode catalyst for oxygen reduction, and as a result (4) the MFC with the AgNPs-coated cathode led to the highest current generation among the tested MFCs. PMID:21585217

  10. 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.

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

    PubMed

    Amirdivani, Shabboo; Baba, Ahmad Salihin Hj

    2015-07-01

    The purpose of this study was to evaluate fermentation of milk in the presence of green tea (Camellia sinensis) with respect to changes in antioxidant activity, phenolic compounds and the growth of lactic acid bacteria. Pasteurized full fat cow's milk and starter culture were incubated at 41 °C in the presence of two different types of green tea extracts. The yogurts formed were refrigerated (4 °C) for further analysis. The total phenolic content was highest (p < 0.05) in air-dried green tea-yogurt (MGT) followed by steam-treated green tea (JGT) and plain yogurts. Four major compounds in MGTY and JGTY were detected. The highest concentration of major phenolic compounds in both samples was related to quercetin-rhamnosylgalactoside and quercetin-3-O-galactosyl-rhamnosyl-glucoside for MGTY and JGTY respectively during first 7 day of storage. Diphenyl picrylhydrazyl and ferric reducing antioxidant power methods showed highest antioxidant capacity in MGTY, JGTY and PY. Streptococcus thermophillus and Lactobacillus spp. were highest in MGTY followed by JGTY and PY. This paper evaluates the implementation of green tea yogurt as a new product with functional properties and valuable component to promote the growth of beneficial yogurt bacteria and prevention of oxidative stress by enhancing the antioxidant activity of yogurt. PMID:26139940

  12. Monitoring of microbial adhesion and biofilm growth using electrochemical impedancemetry.

    PubMed

    Dheilly, A; Linossier, I; Darchen, A; Hadjiev, D; Corbel, C; Alonso, V

    2008-05-01

    Electrochemical impedance spectroscopy was tested to monitor the cell attachment and the biofilm proliferation in order to identify characteristic events induced on the metal surface by Gram-negative (Pseudomonas aeruginosa PAO1) and Gram-positive (Bacillus subtilis) bacteria strains. Electrochemical impedance spectra of AISI 304 electrodes during cell attachment and initial biofilm growth for both strains were obtained. It can be observed that the resistance increases gradually with the culture time and decreases with the biofilm detachment. So, the applicability of electric cell-substrate impedance sensing (ECIS) for studying the attachment and spreading of cells on a metal surface has been demonstrated. The biofilm formation was also characterized by the use of scanning electron microscopy and confocal laser scanning microscopy and COMSTAT image analysis. The electrochemical results roughly agree with the microscope image observations. The ECIS technique used in this study was used for continuous real-time monitoring of the initial bacterial adhesion and the biofilm growth. It provides a simple and non-expensive electrochemical method for in vitro assessment of the presence of biofilms on metal surfaces. PMID:18330564

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

    PubMed Central

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

    2012-01-01

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

  14. 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

  15. Using coagulation to restrict microbial re-growth in tap water by phosphate limitation in water treatment.

    PubMed

    Wen, Gang; Ma, Jun; Huang, Ting-Lin; Egli, Thomas

    2014-09-15

    Extensive microbial re-growth in a drinking water distribution system can deteriorate water quality. The limiting factor for microbial re-growth in a tap water produced by a conventional drinking water treatment plant in China was identified by determining the microbial re-growth potential (MRP) by adding different nutrients to stimulate growth of a natural microbial consortium as inoculum and flow-cytometric enumeration. No obvious change of MRP was found in tap water after addition of carbon, whereas, a 1- to 2-fold increase of MRP was observed after addition of phosphate (P). This clearly demonstrated that microbial re-growth in this tap water was limited by P. Most of the re-grown microbial flora (>85%) consisted of high nucleic acid content cells. A subsequent investigation of the MRP in the actual water treatment plant demonstrated that coagulation was the crucial step for decreasing MRP and producing P-limited water. Therefore, a comparison concerning the control of MRP by three different coagulants was conducted. It showed that all the three coagulants efficiently reduced the MRP and shifted the limitation regime from C to P, but the required dose was different. The study shows that it is feasible to restrict microbial re-growth by P limitation using coagulation in water treatment. PMID:25179107

  16. 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

  17. Decline in Topsoil Microbial Quotient, Fungal Abundance and C Utilization Efficiency of Rice Paddies under Heavy Metal Pollution across South China

    PubMed Central

    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 qCO2 are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO2 production in the polluted rice paddies deserve further field studies. PMID:22701725

  18. 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

  19. 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

  20. Effect of vapor phase corrosion inhibitor on microbial corrosion of aluminum alloys.

    PubMed

    Yang, S S; Ku, C H; Bor, H J; Lin, Y T

    1996-02-01

    Vapor phase corrosion inhibitors were used to investigate the antimicrobial activities and anticorrosion of aluminum alloy. Aspergillus flavus, A. niger, A. versicolor, Chaetomium globosum and Penicillium funiculosum had moderate to abundant growth on the aluminum alloy AA 1100 at Aw 0.901, while there was less growth at Aw 0.842. High humidity stimulated microbial growth and induced microbial corrosion. Dicyclohexylammonium carbonate had a high inhibitory effect on the growth of test fungi and the microbial corrosion of aluminum alloy, dicyclohexylammonium caprate and dicyclohexylammonium stearate were the next. Aluminum alloy coating with vapor phase corrosion inhibitor could prevent microbial growth and retard microbial corrosion. PMID:10592784

  1. 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.

  2. 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. PMID:25443852

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

    DOE PAGESBeta

    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.; et al

    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

  4. Effects of ion abundances on electromagnetic ion cyclotron wave growth rate in the vicinity of the plasmapause

    SciTech Connect

    Henning, F. D. Mace, R. L.

    2014-04-15

    Electromagnetic ion cyclotron (EMIC) waves in multi-ion species plasmas propagate in branches. Except for the branch corresponding to the heaviest ion species, which has only a resonance at its gyrofrequency, these branches are bounded below by a cutoff frequency and above by a resonant gyrofrequency. The condition for wave growth is determined by the thermal anisotropies of each ion species, j, which sets an upper bound, ω{sub j}{sup ∗}, on the wave frequency below which that ion species contributes positively to the growth rate. It follows that the relative positions of the cutoffs and the critical frequencies ω{sub j}{sup ∗} play a crucial role in determining whether a particular wave branch will be unstable. The effect of the magnetospheric ion abundances on the growth rate of each branch of the EMIC instability in a model where all the ion species have kappa velocity distributions is investigated by appealing to the above ideas. Using the variation of the cutoff frequencies predicted by cold plasma theory as a guide, optimal ion abundances that maximise the EMIC instability growth rate are sought. When the ring current is comprised predominantly of H{sup +} ions, all branches of the EMIC wave are destabilised, with the proton branch having the maximum growth rate. When the O{sup +} ion abundance in the ring current is increased, a decrease in the growth rate of the proton branch and cyclotron damping of the helium branch are observed. The oxygen branch, on the other hand, experiences an increase in the maximum growth rate with an increase in the O{sup +} ion abundance. When the ring current is comprised predominantly of He{sup +} ions, only the helium and oxygen branches of the EMIC wave are destabilised, with the helium branch having the maximum growth rate.

  5. 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 (...

  6. The perils and promises of microbial abundance: novel natures and model ecosystems, from artisanal cheese to alien seas.

    PubMed

    Paxson, Heather; Helmreich, Stefan

    2014-04-01

    Microbial life has been much in the news. From outbreaks of Escherichia coli to discussions of the benefits of raw and fermented foods to recent reports of life forms capable of living in extreme environments, the modest microbe has become a figure for thinking through the presents and possible futures of nature, writ large as well as small. Noting that dominant representations of microbial life have shifted from an idiom of peril to one of promise, we argue that microbes--especially when thriving as microbial communities--are being upheld as model ecosystems in a prescriptive sense, as tokens of how organisms and human ecological relations with them could, should, or might be. We do so in reference to two case studies: the regulatory politics of artisanal cheese and the speculative research of astrobiology. To think of and with microbial communities as model ecosystems offers a corrective to the scientific determinisms we detect in some recent calls to attend to the materiality of scientific objects. PMID:24941610

  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. 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.

  9. 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. PMID

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

    PubMed

    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

  11. 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

  12. 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

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

    PubMed

    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

  14. 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

  15. 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. PMID:27416509

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  17. Development and evaluation of formulations of microbial biotransformed extract of tobacco leaves for hair growth potential

    PubMed Central

    Murkute, Ashlesh V.; Sahu, Mahesh S.; Mali, Prashant Y.; Rangari, Vinod D.

    2010-01-01

    Background: Extensive researches are going on to explore the effective and safe drug for their hair growth. Tobacco leaves are traditionally known to potentiate hair growth promotion. Therefore, the aim of present study was to formulate and evaluate the microbial biotransformed extract of tobacco leaves for hair growth potential in male albino wister rats. Materials and Methods: The extract of was prepared by microbial biotransformation of tobacco leaves in cow urine for 28 days. The herbal formulations (lotion) were formulated by general method using o/w type base in various rations or concentrations such as 10%, 20% and 30% of extract. These lotions were applied on shaved skin area of rats for 30 days once in a day and hair length, serum total protein, and total testosterone were measured. Results: Our formulations show increase in hair growth and serum total protein at concentration dependent manner with effect to standard and control groups. Serum total testosterone decreases according to a concentration dependent manner. Conclusion: Further, series of investigations are, however, necessary to remain exploration, which includes their structural elucidation, characterization, clinical safety, reliability and molecular mechanism involved in this pharmacological activity. PMID:21589756

  18. Bacterial abundance and aerobic microbial activity across natural and oyster aquaculture habitats during summer conditions in a northeastern Pacific estuary.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We measured sediment properties and the abundance and functional diversity of microbes in Willapa Bay, Washington, USA, to test the response of sediment microbes to oyster aquaculture. Sites spanned the estuary gradient (salinity 24-30) and six different habitat types: eelgrass (Zostera marina), uns...

  19. 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

  20. Cultural management of microbial community structure to enhance growth of apple in replant soils.

    PubMed

    Mazzola, Mark; Granatstein, David M; Elfving, Don C; Mullinix, Kent; Gu, Yu-Huan

    2002-12-01

    ABSTRACT Apple replant disease typically is managed through pre-plant application of broad-spectrum soil fumigants including methyl bromide. The impending loss or restricted use of soil fumigants and the needs of an expanding organic tree fruit industry necessitate the development of alternative control measures. The microbial community resident in a wheat field soil was shown to suppress components of the microbial complex that incites apple replant disease. Pseudomonas putida was the primary fluorescent pseudomonad recovered from suppressive soil, whereas Pseudomonas fluorescens bv. III was dominant in a conducive soil; the latter developed within 3 years of orchard establishment at the same site. In greenhouse studies, cultivation of wheat in replant orchard soils prior to planting apple suppressed disease development. Disease suppression was induced in a wheat cultivar-specific manner. Wheat cultivars that enhanced apple seedling growth altered the dominant fluorescent pseudo-monad from Pseudomonas fluorescens bv. III to Pseudomonas putida. The microbial community resident in replant orchard soils after growing wheat also was suppressive to an introduced isolate of Rhizoctonia solani anastomosis group 5, which causes root rot of apple. Incorporation of high glucosinolate containing rapeseed ('Dwarf Essex') meal also enhanced growth of apple in replant soils through suppression of Rhizoc-tonia spp., Cylindrocarpon spp., and Pratylenchus penetrans. Integration of these methods will require knowledge of the impact of the biofumigant component on the wheat-induced disease-suppressive microbial community. Implementation of these control strategies for management of apple replant disease awaits confirmation from ongoing field validation trials. PMID:18943894

  1. Rumen degradable protein supply affects microbial efficiency in continuous culture and growth in steers.

    PubMed

    Brooks, M A; Harvey, R M; Johnson, N F; Kerley, M S

    2012-12-01

    We hypothesized that microbial efficiency and output from fermentation in the rumen would be optimized when peptide supply was balanced with peptide requirement of ruminal microflora. This study was conducted to measure response of varying rumen degradable peptide (RDPep) supply on ruminal fermentation characteristics and steer growth. A continuous culture experiment was conducted with diets formulated to achieve a predicted RDPep balance (RDPep supplied above RDPep required) of -0.30 to 1.45% CP with rumen degradable N (RDN) balance (RDN supplied above RDN required) above dietary ammonia-N requirement of microbes. Two additional treatments had RDPep balances of -0.30 and 0.78% CP with insufficient ammonia-N supply to meet microbial requirements. Single-flow fermenters (N = 24; n = 6) were inoculated with rumen fluid and maintained anaerobically at 39°C with a 0.06 h(-1) dilution rate. Inadequate RDN decreased OM digestion and microbial N flow, and increased rumen undegradable N (P < 0.01). Microbial efficiency decreased in RDN-deficient diets and was greatest when RDPep balance did not excessively exceed microbial requirement of RDPep predicted (P < 0.01). A growth study was conducted with 49 yearling, crossbred, Angus steers (initial BW 370 ± 34 kg). Animals were assigned to 1 of 4 treatment groups by BW and further divided into 3 pens with 4 steers per pen to achieve similar initial pen weights. Treatments consisted of 4 isonitrogenous diets balanced for RDN but varying in predicted RDPep balance (0.55%, -0.02%, -0.25%, and -0.65% CP). Animals were maintained on treatment for 70 d with individual BW taken on d 0, 1, 21, 42, 70, and 71. Final BW decreased linearly with decreasing RDPep (P = 0.05). Average daily gain and G:F displayed a quadratic effect with greater ADG and G:F at greater and lesser RDPep levels (P = 0.02). We concluded that balancing RDPep supply to predicted requirement improved fermentation efficiency and microbial output, which in turn

  2. 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.

  3. 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. PMID:24975409

  4. 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.

  5. 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

  6. 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. PMID:23687894

  7. 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.

  8. Growth Kinetics of Suspended Microbial Cells: From Single-Substrate-Controlled Growth to Mixed-Substrate Kinetics

    PubMed Central

    Kovárová-Kovar, Karin; Egli, Thomas

    1998-01-01

    Growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. However, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. For pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. The low quality of experimental data has so far hampered the comparison and validation of the different growth models proposed, and only recently have data collected from nutrient-controlled chemostat cultures allowed us to compare different kinetic models on a statistical basis. The problems are mainly due to (i) the analytical difficulty in measuring substrates at growth-controlling concentrations and (ii) the fact that during a kinetic experiment, particularly in batch systems, microorganisms alter their kinetic properties because of adaptation to the changing environment. For example, for Escherichia coli growing with glucose, a physiological long-term adaptation results in a change in KS for glucose from some 5 mg liter−1 to ca. 30 μg liter−1. The data suggest that a dilemma exists, namely, that either “intrinsic” KS (under substrate-controlled conditions in chemostat culture) or μmax (under substrate-excess conditions in batch culture) can be measured but both cannot be determined at the same time. The above-described conventional growth kinetics derived from single-substrate-controlled laboratory experiments have invariably been used for describing both growth and substrate utilization in ecosystems. However, in nature, microbial cells are exposed to a wide spectrum of potential substrates, many of which they utilize simultaneously (in particular carbon sources). The kinetic data available to date for growth of pure cultures in carbon-controlled continuous culture

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

    NASA Astrophysics Data System (ADS)

    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

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

    SciTech Connect

    Istok, Jonathan D.; Park, Melora M.; Michalsen, Mandy M.; Spain, A. M.; Krumholz, Lee R.; Liu, Chongxuan; McKinley, James P.; Long, Philip E.; Roden, Eric E.; Peacock, Aaron D.; Baldwin, Brett R.

    2010-04-01

    ‘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 databasse 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 added incrementally to a defined geochemical environment and the coupled equations are solved simultaneously to predict 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 concentration and speciation, major ion

  11. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-08-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  12. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed Central

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-01-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  13. A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters.

    PubMed

    Gerstgrasser, Matthias; Nicholls, Sarah; Stout, Michael; Smart, Katherine; Powell, Chris; Kypraios, Theodore; Stekel, Dov

    2016-06-01

    Biolog phenotype microarrays (PMs) enable simultaneous, high throughput analysis of cell cultures in different environments. The output is high-density time-course data showing redox curves (approximating growth) for each experimental condition. The software provided with the Omnilog incubator/reader summarizes each time-course as a single datum, so most of the information is not used. However, the time courses can be extremely varied and often contain detailed qualitative (shape of curve) and quantitative (values of parameters) information. We present a novel, Bayesian approach to estimating parameters from Phenotype Microarray data, fitting growth models using Markov Chain Monte Carlo (MCMC) methods to enable high throughput estimation of important information, including length of lag phase, maximal "growth" rate and maximum output. We find that the Baranyi model for microbial growth is useful for fitting Biolog data. Moreover, we introduce a new growth model that allows for diauxic growth with a lag phase, which is particularly useful where Phenotype Microarrays have been applied to cells grown in complex mixtures of substrates, for example in industrial or biotechnological applications, such as worts in brewing. Our approach provides more useful information from Biolog data than existing, competing methods, and allows for valuable comparisons between data series and across different models. PMID:26762475

  14. Microbial abundance and activities in relation to water potential in the vadose zones of arid and semiarid sites.

    PubMed

    Kieft, T L; Amy, P S; Brockman, F J; Fredrickson, J K; Bjornstad, B N; Rosacker, L L

    1993-07-01

    Numbers and activities of microorganisms were measured in the vadose zones of three arid and semiarid areas of the western United States, and the influence of water availability was determined. These low-moisture environments have vadose zones that are commonly hundreds of meters thick. The specific sampling locations chosen were on or near U.S. Department of Energy facilities: the Nevada Test Site (NTS), the Idaho National Engineering Laboratory (INEL), and the Hanford Site (HS) in southcentral Washington State. Most of the sampling locations were uncontaminated, but geologically representative of nearby locations with storage and/or leakage of waste compounds in the vadose zone. Lithologies of samples included volcanic tuff, basalt, glaciofluvial and fluvial sediments, and paleosols (buried soils). Samples were collected aseptically, either by drilling bore-holes (INEL and HS), or by excavation within tunnels (NTS) and outcrop faces (paleosols near the HS). Total numbers of microorganisms were counted using direct microscopy, and numbers of culturable microorganisms were determined using plate-count methods. Desiccation-tolerant microorganisms were quantified by plate counts performed after 24 h desiccation of the samples. Mineralization of (14)C-labeled glucose and acetate was quantified in samples at their ambient moisture contents, in dried samples, and in moistened samples, to test the hypothesis that water limits microbial activities in vadose zones. Total numbers of microorganisms ranged from log 4.5 to 7.1 cells g(-1) dry wt. Culturable counts ranged from log <2 to 6.7 CFU g(-1) dry wt, with the highest densities occurring in paleosol (buried soil) samples. Culturable cells appeared to be desiccation-tolerant in nearly all samples that had detectable viable heterotrophs. Water limited mineralization in some, but not all samples, suggesting that an inorganic nutrient or other factor may limit microbial activities in some vadose zone environments. PMID

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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 ([14C]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 pgṡmL-1 sedimentṡy-1 at the surface to 0.2 pgṡmL-1ṡy-1 at 1 km depth, equivalent to production of 7 × 105 to 140 archaeal cellsṡmL-1 sedimentṡy-1, respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

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

    PubMed Central

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

    2013-01-01

    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 ([14C]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 × 105 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. PMID:23530229

  18. 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

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

    PubMed

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

    2008-06-10

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

  20. 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...

  1. 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.

  2. MediaDB: A Database of Microbial Growth Conditions in Defined Media

    PubMed Central

    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. PMID:25098325

  3. 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

    2013-07-01

    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. PMID:23750559

  4. Microbial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant Defense Responses

    PubMed Central

    Song, Junqi; Bent, Andrew F.

    2014-01-01

    Immune responses and DNA damage repair are two fundamental processes that have been characterized extensively, but the links between them remain largely unknown. We report that multiple bacterial, fungal and oomycete plant pathogen species induce double-strand breaks (DSBs) in host plant DNA. DNA damage detected by histone γ-H2AX abundance or DNA comet assays arose hours before the disease-associated necrosis caused by virulent Pseudomonas syringae pv. tomato. Necrosis-inducing paraquat did not cause detectable DSBs at similar stages after application. Non-pathogenic E. coli and Pseudomonas fluorescens bacteria also did not induce DSBs. Elevation of reactive oxygen species (ROS) is common during plant immune responses, ROS are known DNA damaging agents, and the infection-induced host ROS burst has been implicated as a cause of host DNA damage in animal studies. However, we found that DSB formation in Arabidopsis in response to P. syringae infection still occurs in the absence of the infection-associated oxidative burst mediated by AtrbohD and AtrbohF. Plant MAMP receptor stimulation or application of defense-activating salicylic acid or jasmonic acid failed to induce a detectable level of DSBs in the absence of introduced pathogens, further suggesting that pathogen activities beyond host defense activation cause infection-induced DNA damage. The abundance of infection-induced DSBs was reduced by salicylic acid and NPR1-mediated defenses, and by certain R gene-mediated defenses. Infection-induced formation of γ-H2AX still occurred in Arabidopsis atr/atm double mutants, suggesting the presence of an alternative mediator of pathogen-induced H2AX phosphorylation. In summary, pathogenic microorganisms can induce plant DNA damage. Plant defense mechanisms help to suppress rather than promote this damage, thereby contributing to the maintenance of genome integrity in somatic tissues. PMID:24699527

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Dev, Subhabrata; Roy, Shantonu; Bhattacharya, Jayanta

    2016-07-15

    A novel marine waste extract (MWE) as alternative nitrogen source was explored for the growth of sulfate reducing bacteria (SRB). Variation of sulfate and nitrogen (MWE) showed that SRB growth follows an uncompetitive inhibition model. The maximum specific growth rates (μmax) of 0.085 and 0.124 h(-1) and inhibition constants (Ki) of 56 and 4.6 g/L were observed under optimized sulfate and MWE concentrations, respectively. The kinetic data shows that MWE improves the microbial growth by 27%. The packed bed bioreactor (PBR) under optimized sulfate and MWE regime showed sulfate removal efficiency of 62-66% and metals removal efficiency of 66-75% on using mine wastewater. The microbial community analysis using DGGE showed dominance of SRB (87-89%). The study indicated the optimum dosing of sulfate and cheap organic nitrogen to promote the growth of SRB over other bacteria. PMID:27085153

  7. 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.

  8. 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

  9. 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

  10. 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

  11. Effects of Essential Oils on Methane Production and Fermentation by, and Abundance and Diversity of, Rumen Microbial Populations

    PubMed Central

    Patra, Amlan K.

    2012-01-01

    Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were tested in vitro at 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e., Fibrobacter succinogenes, Ruminococcus flavefaciens, and R. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H′) was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds. PMID:22492451

  12. Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations.

    PubMed

    Patra, Amlan K; Yu, Zhongtang

    2012-06-01

    Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were tested in vitro at 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e., Fibrobacter succinogenes, Ruminococcus flavefaciens, and R. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H') was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds. PMID:22492451

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

    DOE PAGESBeta

    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. 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

  14. 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

  15. 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

  16. Growth performance and intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel.

    PubMed

    Orban, J I; Patterson, J A; Adeola, O; Sutton, A L; Richards, G N

    1997-01-01

    Four experiments were conducted to determine growth performance and changes in intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel (STOC). Ninety-six barrows and 96 gilts were group-fed experimental nursery diets for 32 d after weaning in both Exp. 1 and 2. For each experiment, pigs were divided into four groups of 48 pigs and were fed either control, antibiotic (Apramycin sulfate, 34 mg/kg), 1% STOC, or 2% STOC diets for 32 d after weaning. Each diet was replicated six times with eight pigs per replication. Pigs were either orally gavaged (Exp 1) with water of STOC (2 g per pig) or pigs were creep-fed (Exp 2) either a control diet or a 2% STOC diet for 5 d before weaning (33 d). At the end of Exp 1 and 2, cecal material was collected for enumeration of total aerobes, total anaerobes, coliforms, lactobacilli, and bifidobacteria. Gilts (96 per experiment) used in Exp. 3 and 4 were weaned at 26 d and fed experimental nursery diets for 32 d. They were fed either a control or 1% STOC diet and were otherwise treated as previously described. There were no significant effects of STOC or antibiotic on ADG, ADFI, feed efficiency, or cecal microbial populations in pigs in this study. Feeding diets containing either antibiotic of STOC did not improve animal performance or change intestinal bacterial populations in the present study. PMID:9027562

  17. Reduced methane growth rate explained by decreased Northern Hemisphere microbial sources.

    PubMed

    Kai, Fuu Ming; Tyler, Stanley C; Randerson, James T; Blake, Donald R

    2011-08-11

    Atmospheric methane (CH(4)) increased through much of the twentieth century, but this trend gradually weakened until a stable state was temporarily reached around the turn of the millennium, after which levels increased once more. The reasons for the slowdown are incompletely understood, with past work identifying changes in fossil fuel, wetland and agricultural sources and hydroxyl (OH) sinks as important causal factors. Here we show that the late-twentieth-century changes in the CH(4) growth rates are best explained by reduced microbial sources in the Northern Hemisphere. Our results, based on synchronous time series of atmospheric CH(4) mixing and (13)C/(12)C ratios and a two-box atmospheric model, indicate that the evolution of the mixing ratio requires no significant change in Southern Hemisphere sources between 1984 and 2005. Observed changes in the interhemispheric difference of (13)C effectively exclude reduced fossil fuel emissions as the primary cause of the slowdown. The (13)C observations are consistent with long-term reductions in agricultural emissions or another microbial source within the Northern Hemisphere. Approximately half (51 ± 18%) of the decrease in Northern Hemisphere CH(4) emissions can be explained by reduced emissions from rice agriculture in Asia over the past three decades associated with increases in fertilizer application and reductions in water use. PMID:21833086

  18. 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. PMID:25575970

  19. Coupling Microbial Growth with Nanoparticles: A Universal Strategy To Produce Functional Fungal Hyphae Macrospheres.

    PubMed

    Zhu, Wen-Kun; Cong, Huai-Ping; Guan, Qing-Fang; Yao, Wei-Tang; Liang, Hai-Wei; Wang, Wei; Yu, Shu-Hong

    2016-05-25

    Macroscale assembly of nanoscale building blocks is an intriguing way to translate the unique characteristics of individual nanoparticles into macroscopic materials. However, the lack of the efficient universal assembly strategy seriously hinders the possibility of macroscale architectures in practical applications. Herein, we develop a general, environment-friendly, and scalable microbial growth method for the construction of macroscopic composite assemblies with excellent mechanical strength by in situ integrating various types of nanoparticles into fungal hyphae (FH) macrospheres. Notably, the size of the FH-based composite spheres and the loading amount of the nanoparticles with different dimensions can be well tuned by controlling the cultivation time and the dosage of nanoparticles, respectively. Interestingly, bifunctional FH-based core-shell macrospheres can also be achieved by programmed assembling two different kinds of nanoparticles in the cultivation process. The produced multifunctional FH-based composite spheres exhibit wide potential applications in magnetic actuation, photothermal therapy, and contaminant adsorption, etc. PMID:27148809

  20. 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.

  1. Volatile organic compounds associated with microbial growth in automobile air conditioning systems.

    PubMed

    Rose, L J; Simmons, R B; Crow, S A; Ahearn, D G

    2000-09-01

    Volatile organic compounds from Penicillium viridicatum and Methylobacterium mesophilicum growing on laboratory media and on component materials of automobile air conditioners were analyzed with gas chromatography and mass spectrometry. P. viridicatum produced compounds such as 4-methyl thiazole, terpenes and alcohols, whereas M. mesophilicum produced dimethyl disulfide, dimethyl trisulfide, and chlorophenol with growth on laboratory media. In comparison with laboratory media, fewer volatiles were detected from colonized foam insulation materials. Biofilms of M. mesophilicum on aluminum evaporator components produced mainly dimethyl disulfide. These biofilms, after inoculation with P. viridicatum, produced offensive smelling alcohols and esters such as 2-methyl propanol, 3-penten-2-ol, and the ethyl ester of butanoic acid. The moisture and substrates innate to the automobile air conditioning systems provided an environment suitable for microbial biofilm development and odor production. Reduction of retained moisture in the air conditioning system coupled with use of less susceptible or antimicrobial substrates are advised for remediation of the noxious odors. PMID:10915209

  2. 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. PMID:24675611

  3. Global microbialization of coral reefs.

    PubMed

    Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

    2016-01-01

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC. PMID:27572833

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

    PubMed

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

    2014-02-01

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site (a largely decommissioned nuclear production complex) in eastern Washington state, USA, and have been shown to change significantly 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 micro-organisms. 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 extracellular 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, which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic micro-organisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area (in the south-eastern corner of the site) subsurface and biogeochemical shifts associated with Columbia River water intrusion. PMID:24324032

  5. Abundance, breeding and growth of the ocypodid crab Dotilla myctiroides (Milne-Edwards) on a West Malaysian beach

    NASA Astrophysics Data System (ADS)

    Hails, A. J.; Yaziz, S.

    1982-08-01

    The ocypodid crab, Dotilla myctiroides, was studied on the south-west coast of peninsular Malaysia. The mean numbers and biomass over a year along a transect from high to low water ranged from 37·5 to 579 crabs m -2 and from 2·22 to 50·79 g m -2 (wet weight) respectively. Berried females were found in all months of the year but two peaks of activity were apparent, from November to February and May to July. It is suggested that this may be related to changes in food abundance associated with the effects of monsoon winds on sea currents. Laboratory growth studies indicated that maximum life span was approximately 13 months (from first crab stage) for males and 10 months for females. Growth rate decreased with increasing size of crab. Egg number increased with size of female.

  6. Invading rainbow trout usurp a terrestrial prey subsidy from native charr and reduce their growth and abundance.

    PubMed

    Baxter, Colden V; Fausch, Kurt D; Murakami, Masashi; Chapman, Phillip L

    2007-08-01

    Movements of prey organisms across ecosystem boundaries often subsidize consumer populations in adjacent habitats. Human disturbances such as habitat degradation or non-native species invasions may alter the characteristics or fate of these prey subsidies, but few studies have measured the direct effects of this disruption on the growth and local abundance of predators in recipient habitats. Here we present evidence, obtained from a combined experimental and comparative study in northern Japan, that an invading stream fish usurped the flux of allochthonous prey to a native fish, consequently altering the diet and reducing the growth and abundance of the native species. A large-scale field experiment showed that excluding terrestrial invertebrates that fell into the stream with a mesh greenhouse reduced terrestrial prey in diets of native Dolly Varden charr (Salvelinus malma) by 46-70%, and reduced their growth by 25% over six weeks. However, when nonnative rainbow trout (Oncorhynchus mykiss) were introduced, they monopolized these prey and caused an even greater reduction of terrestrial prey in charr diets of 82-93%, and reduced charr growth by 31% over the same period. Adding both greenhouse and rainbow trout treatments together produced similar results to adding either alone. Results from a comparative field study of six other stream sites in the region corroborated the experimental findings, showing that at invaded sites rainbow trout usurped the terrestrial prey subsidy, causing a more than 75% decrease in the biomass of terrestrial invertebrates in Dolly Varden diets and forcing them to shift their foraging to insects on the stream bottom. Moreover, at sites with even low densities of rainbow trout, biomass of Dolly Varden was more than 75% lower than at sites without rainbow trout. Disruption of resource fluxes between habitats may be a common, but unidentified, consequence of invasions, and an additional mechanism contributing to the loss of native species

  7. Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth

    PubMed Central

    Grivennikov, Sergei I.; Wang, Kepeng; Mucida, Daniel; Stewart, C. Andrew; Schnabl, Bernd; Jauch, Dominik; Taniguchi, Koji; Yu, Guann-Yi; Osterreicher, Christoph H.; Hung, Kenneth E.; Datz, Christian; Feng, Ying; Fearon, Eric R.; Oukka, Mohamed; Tessarollo, Lino; Coppola, Vincenzo; Yarovinsky, Felix; Cheroutre, Hilde; Eckmann, Lars; Trinchieri, Giorgio; Karin, Michael

    2013-01-01

    Approximately 2% of colorectal cancer is linked to pre-existing inflammation known as colitis-associated cancer, but most develops in patients without underlying inflammatory bowel disease. Colorectal cancer often follows a genetic pathway whereby loss of the adenomatous polyposis coli (APC) tumour suppressor and activation of β-catenin are followed by mutations in K-Ras, PIK3CA and TP53, as the tumour emerges and progresses1,2. Curiously, however, ‘inflammatory signature’ genes characteristic of colitis-associated cancer are also upregulated in colorectal cancer3,4. Further, like most solid tumours, colorectal cancer exhibits immune/inflammatory infiltrates5, referred to as ‘tumour elicited inflammation’6. Although infiltrating CD4+ TH1 cells and CD8+ cytotoxic T cells constitute a positive prognostic sign in colorectal cancer7,8, myeloid cells and T-helper interleukin (IL)-17-producing (TH17) cells promote tumorigenesis5,6, and a ‘TH17 expression signature’ in stage I/II colorectal cancer is associated with a drastic decrease in disease-free survival9. Despite its pathogenic importance, the mechanisms responsible for the appearance of tumour-elicited inflammation are poorly understood. Many epithelial cancers develop proximally to microbial communities, which are physically separated from immune cells by an epithelial barrier10. We investigated mechanisms responsible for tumour-elicited inflammation in a mouse model of colorectal tumorigenesis, which, like human colorectal cancer, exhibits upregulation of IL-23 and IL-17. Here we show that IL-23 signalling promotes tumour growth and progression, and development of a tumoural IL-17 response. IL-23 is mainly produced by tumour-associated myeloid cells that are likely to be activated by microbial products, which penetrate the tumours but not adjacent tissue. Both early and late colorectal neoplasms exhibit defective expression of several barrier proteins. We propose that barrier deterioration induced by

  8. Goldeye, Hiodon alosoides, in Lake Oahe: abundance, age, growth, maturity, food, and the fishery, 1963-69

    USGS Publications Warehouse

    Miller, Grant L.; Nelson, William R.

    1974-01-01

    Reproductive success was relatively consistent, and adequate to maintain species abundance at a nearly constant level, during 1963-69. Both abundance and growth in length increased from the lower to the upper portion of the reservoir. In most characteristics -- growth in length, length-weight relation, age at maturity, and food -- goldeye in Lake Oahe were similar to those from other Missouri River impoundments. Experimental gill nets samples all lengths (range 80-460 mm; median, 320 mm) of goldeye, bottom trawls sampled mostly small fish, (median, 215 mm) and trap nets large ones (median, 345 mm). Commercial gill nets were highly size selective (median, 375 mm); fish of ages IV-VII made up 90% of the catch. Survival rates were 57 to 52% for ages II-X. Estimated survival rates for ages V-IX declined from 44 to 35% after the inception of the commercial fishery in 1966. The peak commercial catch was 151,432 kg (1.2 kg/hectare) in 1969. Unless recruitment declines, the population can support a fishery of that magnitude.

  9. Reducing microbial growth and improving quality of fresh-cut table grapes using a mild heat treatment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Packaged fresh-cut table grapes (Vitis vinifera L.) have emerged as a popular snack food because they offer freshness, nutrition, and convenience. However, tissue injury sustained during stem removal, and the openings created after stem removal make the grapes susceptible to microbial growth, produ...

  10. BIODEGRADATION DURING CONTAMINANT TRANSPORT IN POROUS MEDIA. 4. IMPACT OF MICROBIAL LAG AND BACTERIAL CELL GROWTH. (R825415)

    EPA Science Inventory

    Abstract

    Miscible-displacement experiments were conducted to examine the impact of microbial lag and bacterial cell growth on the transport of salicylate, a model hydrocarbon compound. The impacts of these processes were examined separately, as well as jointly, to dete...

  11. Effects of Direct-Fed Microbials on Growth Performance, Gut Morphometry, and Immune Characteristics in Broiler Chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to compare growth performance, gut morphometry, and parameters of local and systemic immunity in broiler chickens fed for 22 consecutive days with a diet supplemented with one of eight Bacillus spp. as a direct-fed microbial (DFM), a commercial product incorporating three DF...

  12. Effects of direct-fed microbials on growth performance, gut morphometry, and immune characteristics in broiler chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to compare growth performance, gut morphometry, and parameters of local and systemic immunity in broiler chickens fed for 22 consecutive days with a diet supplemented with one of eight Bacillus spp. as a direct-fed microbial (DFM), a commercial product incorporating three DF...

  13. 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.

  14. Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis

    PubMed Central

    Soy, Judit; Leivar, Pablo; González-Schain, Nahuel; Sentandreu, Maria; Prat, Salomé; Quail, Peter H.; Monte, Elena

    2012-01-01

    SUMMARY Arabidopsis seedlings display rhythmic growth when grown under diurnal conditions, with maximal elongation rates occurring at the end of the night under short-day photoperiods. Current evidence indicates that this behavior involves the action of the growth-promoting bHLH factors PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) at the end of the night, through a coincidence mechanism that combines their transcriptional regulation by the circadian clock with control of protein accumulation by light. To assess the possible role of PIF3 in this process, we have analyzed hypocotyl responses and marker gene expression in pif single- and higher-order mutants. The data show that PIF3 plays a prominent role as a promoter of seedling growth under diurnal light/dark conditions, in conjunction with PIF4 and PIF5. In addition, we provide evidence that PIF3 functions in this process through its intrinsic transcriptional regulatory activity, at least in part by directly targeting growth-related genes, and independently of its ability to regulate phytochrome B (phyB) levels. Furthermore, in sharp contrast to PIF4 and PIF5, our data show that the PIF3 gene is not subject to transcriptional regulation by the clock, but that PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period. Collectively, the data suggest that phyB-mediated, post-translational regulation allows PIF3 accumulation to peak just before dawn, at which time it accelerates hypocotyl growth, together with PIF4 and PIF5, by directly regulating the induction of growth-related genes. PMID:22409654

  15. 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

  16. 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.

  17. 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. PMID:15895736

  18. 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.

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

    PubMed

    Liu, Feng; Ying, Guang-Guo; Tao, Ran; Zhao, Jian-Liang; Yang, Ji-Feng; Zhao, Lan-Feng

    2009-05-01

    The potential impact of six antibiotics (chlortetracycline, tetracycline and tylosin; sulfamethoxazole, sulfamethazine and trimethoprim) on plant growth and soil quality was studied by using seed germination test on filter paper and plant growth test in soil, soil respiration and phosphatase activity tests. The phytotoxic effects varied between the antibiotics and between plant species (sweet oat, rice and cucumber). Rice was most sensitive to sulfamethoxazole with the EC10 value of 0.1 mg/L. The antibiotics tested inhibited soil phosphatase activity during the 22 days' incubation. Significant effects on soil respiration were found for the two sulfonamides (sulfamethoxazole and sulfamethazine) and trimethoprim, whereas little effects were observed for the two tetracyclines and tylosin. The effective concentrations (EC10 values) for soil respiration in the first 2 days were 7 mg/kg for sulfamethoxazole, 13 mg/kg for sulfamethazine and 20 mg/kg for trimethoprim. Antibiotic residues in manure and soils may affect soil microbial and enzyme activities. PMID:19157661

  20. 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

  1. Dietary Nisin Modulates the Gastrointestinal Microbial Ecology and Enhances Growth Performance of the Broiler Chickens

    PubMed Central

    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 for broiler

  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

    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. 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

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

    PubMed

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

    2012-10-01

    This study evaluated the potential of silver nanoparticles (AgNano) as an antimicrobial growth-promoting supplement for broiler chickens. One hundred forty-four seven-day-old broiler chicks were distributed randomly to AgNano treatments at 0, 10 and 20 mg/kg (Control, Group AgNano10, and Group AgNano20, respectively) provided via the drinking water from day 7 to 36 post-hatching. Body weight and feed consumption were measured weekly. In addition, balance and respiration experiments were carried out to determine nitrogen (N) utilisation and energy retention. At days 22 and 36, blood samples and intestinal content were collected to evaluate the effects of AgNano on plasma concentration of immunoglobulins and the intestinal microflora, respectively. The provision of water solutions containing different concentrations of AgNano had no effect on postnatal growth performance and the energy metabolism of broiler chickens. However, in Group AgNano10 N intake (p = 0.05) and retention (p = 0.03) was increased, but N excretion and efficiency of utilisation was not affected. The populations of bacteria in the intestinal samples were not affected by AgNano supplementation. The concentration of immunoglobulin (IgG) in the blood plasma of broilers supplemented with AgNano decreased at day 36 (p = 0.012). The results demonstrated that AgNano affects N utilisation and plasma IgG concentration; however, it does not influence the microbial populations in the digestive tract, the energy metabolism and growth performance of chickens. PMID:22889095

  6. 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

  7. 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

  8. 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

  9. Alterations in transcript abundance of bovine oocytes recovered at growth and dominance phases of the first follicular wave

    PubMed Central

    Ghanem, Nasser; Hölker, Michael; Rings, Franca; Jennen, Danyel; Tholen, Ernst; Sirard, Marc-André; Torner, Helmut; Kanitz, Wilhelm; Schellander, Karl; Tesfaye, Dawit

    2007-01-01

    Background Oocyte developmental competence is highly affected by the phase of ovarian follicular wave. Previous studies have shown that oocytes from subordinate follicles recovered at growth phase (day 3 after estrus) are developmentally more competent than those recovered at dominance phase (day 7 after estrus). However, the molecular mechanisms associated with these differences are not well elucidated. Therefore, the objective of this study was to investigate transcript abundance of bovine oocytes retrieved from small follicles at growth and dominance phases of the first follicular wave and to identify candidate genes related to oocyte developmental competence using cDNA microarray. Results Comparative gene expression analysis of oocytes from growth and dominance phases and subsequent data analysis using Significant Analysis of Microarray (SAM) revealed a total of 51 differentially regulated genes, including 36 with known function, 6 with unknown function and 9 novel transcripts. Real-time PCR has validated 10 transcripts revealed by microarray analysis and quantified 5 genes in cumulus cells derived from oocytes of both phases. The expression profile of 8 (80%) transcripts (ANAXA2, FL396, S100A10, RPL24, PP, PTTG1, MSX1 and BMP15) was in agreement with microarray data. Transcript abundance of five candidate genes in relation to oocyte developmental competence was validated using Brilliant Cresyl Blue (BCB) staining as an independent model. Furthermore, localization of mRNA and protein product of the candidate gene MSX1 in sections of ovarian follicles at days 0, 1, 3 and 7 of estrous cycle showed a clear fluorescent signal in both oocytes and cumulus cells with higher intensity in the former. Moreover, the protein product was detected in bovine oocytes and early cleavage embryos after fertilization with higher intensity around the nucleus. Conclusion This study has identified distinct sets of differentially regulated transcripts between bovine oocytes recovered

  10. An investigation of the sensitivity of low-field nuclear magnetic resonance to microbial growth and activity

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Keating, K.

    2014-12-01

    Microbes and microbial processes play a significant role in shaping subsurface environments and are involved in applications ranging from microbially enhanced oil recovery to soil and groundwater contaminant remediation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface; however, due to the complexity of subsurface systems,it is difficult to monitor the growth of microbes and microbial activity in porous media. The focus of this research is to determine if low-field nuclear magnetic resonance (NMR), a method used in well logging to characterize fluids in hydrocarbon reservoirs or water in aquifers, can be used to directly detect the presence and the growth of microbes in geologic media. In this laboratory study, low-field NMR (2 MHz) relaxation measurements were collected on microbial suspensions with measured densities (i.e. biomasses), microbial pellets (live and dead), and inoculated silica. We focus on the direct contribution of microbes to the NMR signals in the absence of biomineralization. Shewanella oneidensis (MR-1), a facultative metal reducer known to play an important role in subsurface environments, were used as a model organism and were inoculated under aerobic condition. Data were collected using a CPMG pulse sequence, which was to determine the T2-distribution, and using a gradient spin-echo (PGSE) plus CPMG pulse sequence, which was used to encode diffusion properties and determine the effective diffusion-spin-spin relaxation correlation (D-T2) plot. Our data show no obvious change in the T2-distribution as S. oneidensis density varied in suspension, but show a clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets. A decrease in the T2-distribution is observed in the inoculated sand column. These results will provide a basis for understanding the effect of microbes within geologic media on low-field NMR measurements. This

  11. 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

  12. 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

  13. 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. PMID:25483720

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

    PubMed

    Al-Hussaini, Reema; Mahasneh, Adel M

    2009-01-01

    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. PMID:19783935

  15. Macroscopic models for predicting changes in saturated porous media properties caused by microbial growth

    SciTech Connect

    Clement, T.P.; Hooker, B.S.; Skeen, R.S.

    1996-09-01

    Analytical equations are developed to model changes in porosity, specific surface area, and permeability caused by biomass accumulation in porous media. The proposed equations do not assume any specific pattern for microbial growth but instead are based on macroscopic estimates of average biomass concentrations. For porous media with a pore-size distribution index value ({lambda}) equal to 3, the macroscopic model predictions of porosity, specific surface area, and permeability changes are in exact agreement with biofilm-model predictions. At other values of {lambda} between 2 and 5, simulated porosity profiles are identical and relative specific surface area and permeability profiles show minor deviations. In comparison to biofilm-based models, the macroscopic models are relatively simple to implement and are computationally more efficient. Simulations of biologically reactive flow in a one-dimensional column show that the macroscopic and biofilm approach based transport codes predict almost identical porosity and permeability profiles. The macroscopic models are simple and useful tools for estimating changes in various porous media properties during bioremediation of contaminated aquifers.

  16. 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). PMID:26330315

  17. Evaluation of americium-241 toxicity influence on the microbial growth of organic wastes

    SciTech Connect

    Takehiro Marumo, Julio; Padua Ferreira, Rafael Vicente de; Keiko Isiki, Vera Lucia; Miyamoto, Hissae; Sayuri Takara, Aline; Kazumi Sakata, Solange; Bellini, Maria Helena; Cardoso Pedroso de Lima, Luis Filipe

    2007-07-01

    Available in abstract form only. Full text of publication follows: Since the licenses for using radioactive sources in radioactive lightning rods were lifted by the Brazilian national nuclear authority, in 1989, the radioactive devices have been replaced by Franklin type and collected as radioactive waste. However, only 20 percent of the estimated total number of installed rods was delivered to Brazilian Nuclear Commission. This situation causes concern, due to, first, the possibility of the rods being disposed as domestic waste, and second, the americium, the most commonly employed radionuclide, is classified as a high-toxicity element. In the present study, Am-241 migration experiments were performed by a lysimeter system, in order to evaluate the risk of contamination caused by radioactive lightning rods disposed as a common solid waste. Besides the risk evaluation, it is important to know the mechanism of the Am-241 release or retention in waste as well as its influence in the waste decomposition processes. Many factors are involved, but microorganisms present in the waste play an important role in its degradation, which control the physical and chemical processes. The objective of this work was to evaluate the Am-241 influence on the microbial population by counting number of cells in lysimeters leachate. Preliminary results suggest that americium may influence significantly the bacteria growth in organic waste, evidenced by culture under aerobiosis and an-aerobiosis and the antimicrobial resistance test. (authors)

  18. 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.

  19. 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. PMID:25198844

  20. 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.

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

    PubMed

    Horváthová, Terézia; Babik, Wiesław; Bauchinger, Ulf

    2016-01-01

    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

  2. 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

  3. 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

  4. 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.

  5. Correlations of Gut Microbial Community Shift with Hepatic Damage and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure.

    PubMed

    Kan, Haifeng; Zhao, Fuzheng; Zhang, Xu-Xiang; Ren, Hongqiang; Gao, Shixiang

    2015-10-01

    Goldfish (Carassius auratus) were exposed to 0-100 μg/L pentachlorophenol (PCP) for 28 days to investigate the correlations of fish gut microbial community shift with the induced toxicological effects. PCP exposure caused accumulation of PCP in the fish intestinal tract in a time- and dose-dependent manner, while hepatic PCP reached the maximal level after a 21 day exposure. Under the relatively higher PCP stress, the fish body weight and liver weight were reduced and hepatic CAT and SOD activities were inhibited, demonstrating negative correlations with the PCP levels in liver and gut content (R < -0.5 and P < 0.05 each). Pyrosequencing of the 16S rRNA gene indicated that PCP exposure increased the abundance of Bacteroidetes in the fish gut. Within the Bacteroidetes phylum, the Bacteroides genus had the highest abundance, which was significantly correlated with PCP exposure dosage and duration (R > 0.5 and P < 0.05 each). Bioinformatic analysis revealed that Bacteroides showed quantitatively negative correlations with Chryseobacterium, Microbacterium, Arthrobacter, and Legionella in the fish gut, and the Bacteroidetes abundance, Bacteroides abundance, and Firmicutes/Bacteroidetes ratio played crucial roles in the reduction of body weight and liver weight under PCP stress. The results may extend our knowledge regarding the roles of gut microbiota in ecotoxicology. PMID:26378342

  6. 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

  7. 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

  8. 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. PMID:26992294

  9. 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

  10. 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

  11. 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

  12. Validation of a predictive model coupling gas transfer and microbial growth in fresh food packed under modified atmosphere.

    PubMed

    Guillard, V; Couvert, O; Stahl, V; Hanin, A; Denis, C; Huchet, V; Chaix, E; Loriot, C; Vincelot, T; Thuault, D

    2016-09-01

    Predicting microbial safety of fresh products in modified atmosphere packaging implies to take into account the dynamic of O2, CO2 and N2 exchanges in the system and its effect on microbial growth. In this paper a mechanistic model coupling gas transfer and predictive microbiology was validated using dedicated challenge-tests performed on poultry meat, fresh salmon and processed cheese, inoculated with either Listeria monocytogenes or Pseudomonas fluorescens and packed in commercially used packaging materials (tray + lid films). The model succeeded in predicting the relative variation of O2, CO2 and N2 partial pressure in headspace and the growth of the studied microorganisms without any parameter identification. This work highlighted that the respiration of the targeted microorganism itself and/or that of the naturally present microflora could not be neglected in most of the cases, and could, in the particular case of aerobic microbes contribute to limit the growth by removing all residual O2 in the package. This work also confirmed the low sensitivity of L. monocytogenes toward CO2 while that of P. fluorescens permitted to efficiently prevent its growth by choosing the right combination of packaging gas permeability value and initial % of CO2 initially flushed in the pack. PMID:27217358

  13. 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

  14. 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

  15. 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. PMID:25145227

  16. 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.

  17. Cell abundance and fluorescence of picoplankton in relation to growth irradiance and nitrogen availability in the red sea

    NASA Astrophysics Data System (ADS)

    Veldhuis, Marcel J. W.; Kraay, Gijsbert W.

    The vertical distribution and cellular fluorescence characteristics (chlorophyll and phycoerythrin, PE) of picoplankton (cyanobacteria and prochlorophytes) in the southern Red Sea were investigated in relation to physico-chemical properties of the water column. At all stations two subpopulations of Synechococcus sp. (type A and B) co-occurred, with maximal numbers up to 75 000·cm -3. Type B, with dim fluorescence signals, dominated the surface waters whereas type A, with bright fluorescence signals, dominated at greater depth. The divinyl a and b containing Prochlorococcus sp. peaked below the cyanobacteria at the deep chlorophyll maximum (DCM) with maximal cell numbers of 276 000·cm -3. Due to thermal stratification the cellular fluorescence (chlorophyll and phycoerythrin) increased with decreasing growth (PAR) irradiance, in an S-shaped manner, but magnitude and slope for the three picoplankters differed. The Synechococcus sp. type B had only a moderate increase in chlorophyll and phycoerythrin fluorescence signals with depth (3.4 and 6.6 fold, respectively), with values saturating at 3% (L d) of the surface irradiance. The deeper-water type not only possessed much higher values for cellular fluorescence than the B type, but the increase with decreasing light level was also much higer (for chlorophyll by a factor of 11 and PE increased by a factor of 23). In addition, maximal values for these fluorescence signals occurred at an isolume of 1 to 0.5%. These differences in concentrations and responses of the pigment content to the prevailing light climate explain the variation in abundance of both types over the water column. Although the prochlorophytes dominated almost the entire euphotic zone, their adaptation to low light levels was even better than in the two types of cyanobacteria. With depth their increase in chlorophyll fluorescence was similar to that observed in the cyanobacteria (with an increase from surface to bottom of the euphotic zone by a factor

  18. 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

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

    PubMed

    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

  20. {sup 210}Pb atmospheric flux and growth rates of a microbial mat from the northwestern Mediterranean Sea (Ebro River Delta)

    SciTech Connect

    Sanchez-Cabeza, J.A.; Masque, P.; Martinez-Alonso, M.; Mir, J.; Esteve, I.

    1999-11-01

    Environmental archives are needed to study the variability of natural systems and the impact of man on them. Microbial mats, modern homologues of stromatolites, can be found in extreme environments such as the Ebro River Delta and were studied as potential environmental archives of atmospheric deposition. {sup 210}Pb, a radiotracer widely used in geochronology studies, was used both to determine the growth rates of a microbial mat from this environment and to estimate the {sup 210}Pb atmospheric flux in the northwestern Mediterranean Sea. The {sup 210}Pb profile showed the presence of three distinct peaks related to low growth-rate periods. This variability indicted the sensitivity of the system to external forcing. The annual atmospheric flux of {sup 210}Pb was 81.2 {+-} 1.4 B1 m{sup {minus}2}yr{sup {minus}1}, which is similar to other values found in the literature. The age profile showed two layers of differing growth rates, being 0.99 {+-} 0.10 mm yr{sup {minus}1} from the surface down to 10 mm depth. The accumulated mass profile showed a change at about 9 mm depth, corresponding to year 1983 {+-} 1. It is noteworthy that this is coincident with a strong El Nino Southern Oscillation event during 1982--1983, which has been shown to affect other ecosystems, including some in the Mediterranean area.

  1. 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

  2. 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

    2013-01-01

    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

  3. 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.

  4. 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. PMID:21962921

  5. Nanoporous microscale microbial incubators.

    PubMed

    Ge, Zhifei; Girguis, Peter R; Buie, Cullen R

    2016-02-01

    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. PMID:26584739

  6. 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.

  7. 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

  8. GROWTH MEASUREMENTS OF TERRESTRIAL MICROBIAL SPECIES BY A CONTINUOUS-FLOW TECHNIQUE (JOURNAL VERSION)

    EPA Science Inventory

    A continuous nutrient flow system has been developed to measure microbial activity in soil with various concentrations of added substrate. The system consists of a thin soil layer through which substrate was added continuously over periods up to 4.5 days. Substrate utilization wa...

  9. 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...

  10. Wash operations affect water quality and packaged fresh-cut romaine lettuce quality and microbial growth

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Washing during the preparation of fresh-cut produce is an important step to maintaining the quality and safety of the finished products. It is often the only step aimed at reducing microbial populations and removing tissue fluids from cut produce. However, little is known about the effects of washi...

  11. 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. PMID:26375709

  12. 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

  13. Maternal undernutrition around the time of conception and embryo number each impact on the abundance of key regulators of cardiac growth and metabolism in the fetal sheep heart.

    PubMed

    Lie, S; Sim, S M; McMillen, I C; Williams-Wyss, O; MacLaughlin, S M; Kleemann, D O; Walker, S K; Roberts, C T; Morrison, J L

    2013-10-01

    Poor maternal nutrition before and during pregnancy is associated with an increased risk of cardiovascular disease in later life. To determine the impact of maternal undernutrition during the periconceptional (PCUN: -45 days to 6 days) and preimplantation (PIUN: 0-6 days) periods on cardiac growth and metabolism, we have quantified the mRNA and protein abundance of key regulators of cardiac growth and metabolism in the left ventricle of the sheep fetus in late gestation. The cardiac protein abundance of AMP-activated protein kinase (AMPK), phospho-acetyl CoA carboxykinase (ACC) and pyruvate dehydrogenase kinase-4 (PDK-4) were decreased, whereas ACC was increased in singletons in the PCUN and PIUN groups. In twins, however, cardiac ACC was decreased in the PCUN and PIUN groups, and carnitine palmitoyltransferase-1 (CPT-1) was increased in the PIUN group. In singletons, the cardiac abundance of insulin receptor β (IRβ) was decreased in the PCUN group, and phosphoinositide-dependent protein kinase-1 (PDPK-1) was decreased in the PCUN and PIUN groups. In twins, however, the cardiac abundance of IRβ and phospho-Akt substrate 160kDa (pAS160) were increased in the PIUN group. The cardiac abundance of insulin-like growth factor-2 receptor (IGF-2R), protein kinase C alpha (PKCα) and mammalian target of rapamycin (mTOR) were decreased in PCUN and PIUN singletons and extracellular-signal-regulated kinase (ERK) was also decreased in the PIUN singletons. In contrast, in twins, cardiac abundance of IGF-2R and PKCα were increased in the PCUN and PIUN groups, phospho-ribosomal protein S6 (pRPS6) was increased in the PCUN group, and ERK and eukaryotic initiation factor 4E (eIF4E) were also increased in the PIUN fetuses. In conclusion, maternal undernutrition limited to around the time of conception is sufficient to alter the abundance of key factors regulating cardiac growth and metabolism and this may increase the propensity for cardiovascular diseases in later life. PMID

  14. Modeling and optimization of Newfoundland shrimp waste hydrolysis for microbial growth using response surface methodology and artificial neural networks.

    PubMed

    Zhang, Kedong; Zhang, Baiyu; Chen, Bing; Jing, Liang; Zhu, Zhiwen; Kazemi, Khoshrooz

    2016-08-15

    The hydrolyzed protein derived from seafood waste is regarded as a premium and low-cost nitrogen source for microbial growth. In this study, optimization of enzymatic shrimp waste hydrolyzing process was investigated. The degree of hydrolysis (DH) with four processing variables including enzyme/substrate ratio (E/S), hydrolysis time, initial pH value and temperature, were monitored. The DH values were used for response surface methodology (RSM) optimization through central composite design (CCD) and for training artificial neural network (ANN) to make a process prediction. Results indicated that the optimum levels of variables are: E/S ratio at 1.64%, hydrolysis time at 3.59h, initial pH at 9 and temperature at 52.57°C. Hydrocarbon-degrading bacteria Bacillus subtilis N3-1P was cultivated using different DHs of hydrolysate. The associated growth curves were generated. The research output facilitated effective shrimp waste utilization. PMID:27312986

  15. 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. PMID:18444073

  16. Efficacy of sodium hypochlorite and acidified sodium chlorite in preventing browning and microbial growth on fresh-cut produce.

    PubMed

    Sun, Shih Hui; Kim, Su Jin; Kwak, Soo Jin; Yoon, Ki Sun

    2012-09-01

    The use of suitable sanitizers can increase the quality of fresh-cut produce and reduce the risk of foodborne illnesses. The objective of this study was to compare the washing effects of 100 mg/L sodium hypochlorite (SH) and 500 mg/L acidified sodium chlorite (ASC) on the prevention of enzymatic browning and the growth of microbial populations, including aerobic plate counts, E. coli, and coliforms, throughout storage at 4°C and 10°C. Fresh-cut zucchini, cucumbers, green bell peppers, and root vegetables such as potatoes, sweet potatoes, carrots, and radishes were used. Compared to SH washing, ASC washing significantly (p<0.05) reduced microbial contamination on the fresh-cut produce and prevented browning of fresh-cut potatoes and sweet potatoes during storage. More effective inhibition of aerobic plate counts and coliforms growth was observed on fresh-cut produce treated with ASC during storage at 10°C. Polyphenol oxidase (PPO) activity of fresh-cut potatoes and sweet potatoes was more effectively inhibited after washing with ASC. The use of 500 mg/L ASC can provide effective antimicrobial and anti-browning treatments of fresh-cut produce, including processed root vegetables. PMID:24471086

  17. Efficacy of Sodium Hypochlorite and Acidified Sodium Chlorite in Preventing Browning and Microbial Growth on Fresh-Cut Produce

    PubMed Central

    Sun, Shih Hui; Kim, Su Jin; Kwak, Soo Jin; Yoon, Ki Sun

    2012-01-01

    The use of suitable sanitizers can increase the quality of fresh-cut produce and reduce the risk of foodborne illnesses. The objective of this study was to compare the washing effects of 100 mg/L sodium hypochlorite (SH) and 500 mg/L acidified sodium chlorite (ASC) on the prevention of enzymatic browning and the growth of microbial populations, including aerobic plate counts, E. coli, and coliforms, throughout storage at 4°C and 10°C. Fresh-cut zucchini, cucumbers, green bell peppers, and root vegetables such as potatoes, sweet potatoes, carrots, and radishes were used. Compared to SH washing, ASC washing significantly (p<0.05) reduced microbial contamination on the fresh-cut produce and prevented browning of fresh-cut potatoes and sweet potatoes during storage. More effective inhibition of aerobic plate counts and coliforms growth was observed on fresh-cut produce treated with ASC during storage at 10°C. Polyphenol oxidase (PPO) activity of fresh-cut potatoes and sweet potatoes was more effectively inhibited after washing with ASC. The use of 500 mg/L ASC can provide effective antimicrobial and anti-browning treatments of fresh-cut produce, including processed root vegetables. PMID:24471086

  18. Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters.

    PubMed

    Wong, Wilson W; Liao, James C

    2009-11-01

    Understanding how growth rates changes under different perturbations is fundamental to many aspect of microbial physiology. In this work, we experimentally showed that maximal specific growth rate is a square-root function of the biomass yield, the substrate turnover number, and the maximum synthesis rate of the substrate transporter under that condition. We used Escherichia coli cultures in lactose minimal medium as a model system by introducing genetic modifications, in vitro evolution, and ethanol stress to the cell. Deletion of crr affected all three parameters in different directions while deletion of ptsG decreased only the biomass yield. Ethanol stress negatively impacted all three parameters, while anaerobicity decreased biomass yield and transporter synthesis rate. In addition, laboratory evolution increased the growth rate in lactose mostly through enhancing the expression rate of the lac operon. Despite all these changes, the growth rate of the perturbed strain was successfully related to the three parameters by the square-root equation. Thus, this square-root relationship provides insight into how growth rate is altered by different physiological parameters. PMID:19712746

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

    PubMed

    Gandhi, Saurabh R; Yurtsev, Eugene Anatoly; Korolev, Kirill S; Gore, Jeff

    2016-06-21

    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

  20. 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

  1. 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

  2. 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.

  3. Increased abundance and growth of the suspension-feeding bivalve corbula gibba in a shallow part of the eutrophic Limfjord, Denmark

    NASA Astrophysics Data System (ADS)

    Jensen, Jørgen Nørrevang

    The abundance, growth and production of Corbula gibba have been studied by intensive sampling over a 2-year period in a shallow part of the eutrophied Limfjord (Denmark). Size-frequency distributions and growth marks on the shells were used to follow successive cohorts over time. The abundance of Corbula gibba was high, the highest density found in 1-mm sieve samples (≈53 000) being one order of magnitude higher than previously recorded. The analysis of samples sieved through 250-μm sieves revealed that settling took place in August. The mortality of newly settled individuals was high, followed by low and constant mortality during the following winter. The growth of C. gibba was fast compared with records from the Irish Sea and the Sound and the specimens reached a mean size of 6 to 7 mm one year after settlement. It is suggested that the between-year-variation in growth rate was caused by variable frequences of wind-induced resuspension of settled organic matter. The production of C. gibba varied between stations but was generally high (mean: 26.8 g AFDW·y -1·m -2) compared with previous records from subtidal areas. The P/B ratio is among the highest recorded (mean: 4.2 y -1). Growth seems to be higher at present than during the first part of this century, probably due to the increased eutrophication of the Limfjord. It is suggested that growth rate may be a good complement to the use of total abundance and biomass in monitoring, as the latter parameters are more variable due to stochastic events such as sampling variance and inter- seasonal variations in settlement succes caused by physical factors.

  4. Low frequency electromagnetic waves as a supplemental energy source to sustain microbial growth?

    NASA Astrophysics Data System (ADS)

    Gusev, Victor A.; Schulze-Makuch, Dirk

    2005-03-01

    Microbial populations in tetra-distilled water collapsed when cultured in a permalloy chamber shielding the populations from the sun's and earth's electromagnetic field, but thrived when cultured in an ordinary thermostat open to the electromagnetic field. Theoretically, protons in liquid water can be excited at their natural resonance frequencies through Langmuir oscillations and obtain enough kinetic energy to charge the transmembrane potential of a cell. Microbes may be capable of converting this energy into chemical energy to supplement their energy needs.

  5. 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. PMID:26020314

  6. 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...

  7. 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. PMID:24430486

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

    PubMed Central

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

    2014-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2016-06-01

    The present study evaluated the effects of dietary microbial phytase on the growth and gut health of hybrid tilapia (Oreochromis niloticus ♀×Oreochromis aureus ♂), focusing on the effect on intestinal histology, adhesive microbiota and expression of immune-related cytokine genes. Tilapia were fed either control diet or diet supplemented with microbial phytase (1000 U/kg). Each diet was randomly assigned to four groups of fish reared in cages (3×3×2 m). After 12 weeks of feeding, weight gain and feed conversion ratio of tilapia were not significantly improved by dietary microbial phytase supplementation. However, significantly higher level of P content in the scales, tighter and more regular intestinal mucosa folds were observed in the microbial phytase group and the microvilli density was significantly increased. The adhesive gut bacterial communities were strikingly altered by microbial phytase supplementation (0·41microbial phytase, as indicated by the up-regulated intestinal expressions of the cytokine genes (tnf-α and tgf-β) and hsp70. In addition, the gut microvilli height was significantly decreased in the phytase group. These results indicate that dietary microbial phytase may exert mixed effects on hybrid tilapia, and can guide our future selection of phytases as aquafeed additives - that is, eliminating those that can stimulate intestinal inflammation. PMID:27080419

  11. Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

    PubMed Central

    Sterngren, Anna E.; Rousk, Johannes

    2012-01-01

    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. PMID:22706045

  12. Low frequency electromagnetic waves as a supplemental energy source to sustain microbial growth?

    PubMed

    Gusev, Victor A; Schulze-Makuch, Dirk

    2005-03-01

    Microbial populations in tetra-distilled water collapsed when cultured in a permalloy chamber shielding the populations from the sun's and earth's electromagnetic field, but thrived when cultured in an ordinary thermostat open to the electromagnetic field. Theoretically, protons in liquid water can be excited at their natural resonance frequencies through Langmuir oscillations and obtain enough kinetic energy to charge the transmembrane potential of a cell. Microbes may be capable of converting this energy into chemical energy to supplement their energy needs. PMID:15700175

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

    PubMed

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

    2016-04-15

    The presence of pesticides in surface and groundwater has grown considerably in the last decades as a consequence of the intensive farming activity. Several studies have shown the benefits of using organic amendments to prevent losses of pesticides from runoff or leaching. A particular soil from the Guadalquivir valley was placed in open air ponds and amended at 1 or 2% (w/w) with alperujo compost (AC), a byproduct from the olive oil industry. Tricyclazole dissipation, rice growth and microbial diversity were monitored along an entire rice growing season. An increase in the net photosynthetic rate of Oryza sativa plants grown in the ponds with AC was observed. These plants produced between 1100 and 1300kgha(-1) more rice than plants from the unamended ponds. No significant differences were observed in tricyclazole dissipation, monitored for a month in soil, surface and drainage water, between the amended and unamended ponds. The structure and diversity of bacteria and fungi communities were also studied by the use of the polymerase chain reaction denaturing gel electrophoresis (PCR-DGGE) from DNA extracted directly from soil samples. The banding pattern was similar for all treatments, although the density of bands varied throughout the time. Apparently, tricyclazole did not affect the structure and diversity of bacteria and fungi communities, and this was attributed to its low bioavailability. Rice cultivation under paddy field conditions may be more efficient under the effects of this compost, due to its positive effects on soil properties, rice yield, and soil microbial diversity. PMID:26849328

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

    PubMed Central

    2010-01-01

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

  15. Effects of electron beam irradiation on the microbial growth and quality of beef jerky during storage

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

    Electron beam irradiation was applied to improve the microbial safety of beef jerky during storage. Beef jerky samples were irradiated at doses of 1, 3, 5, and 10 kGy and stored at 20 °C for 60 d. Microbiological data indicated that the populations of total aerobic bacteria significantly decreased with increasing irradiation dosage. In particular, the populations of total aerobic bacteria were significantly decreased by 1.76 log CFU/g at 10 kJ/m 2, compared to the control. Color measurements showed reduced Hunter L and a values of beef jerky for all the treatments during storage, and the Hunter L, a, and b values of beef jerky were not significantly different among the treatments. Sensory evaluation results also showed that electron beam irradiation did not affect sensory scores in overall during storage. Therefore, the results suggest that electron beam irradiation could be useful in improving the microbial safety without impairing the quality of beef jerky during storage.

  16. TatC-dependent translocation of pyoverdine is responsible for the microbial growth suppression.

    PubMed

    Lee, Yeji; Kim, Yong-Jae; Lee, Jung-Hoon; Yu, Hyung Eun; Lee, Kiho; Jin, Shouguang; Ha, Un-Hwan

    2016-02-01

    Infections are often not caused by a colonization of Pseudomonas aeruginosa alone but by a consortium of other bacteria. Little is known about the impact of P. aeruginosa on the growth of other bacteria upon coinfection. Here, cell-ree culture supernatants obtained from P. aeruginosa suppressed the growth of a number of bacterial strains such as Corynebacterium glutamicum, Bacillus subtilis, Staphylococcus aureus, and Agrobacterium tumefaciens, but had little effect on the growth of Escherichia coli and Salmonella Typhimurium. The growth suppression effect was obvious when P. aeruginosa was cultivated in M9 minimal media, and the suppression was not due to pyocyanin, a well-known antimicrobial toxin secreted by P. aeruginosa. By performing transposon mutagenesis, PA5070 encoding TatC was identified, and the culture supernatant of its mutant did not suppress the growth. HPLC analysis of supernatants showed that pyoverdine was a secondary metabolite present in culture supernatants of the wild-type strain, but not in those of the PA5070 mutant. Supplementation of FeCl2 as a source of iron compromised the growth suppression effect of supernatants and also recovered biofilm formation of S. aureus, indicating that pyoverdine-mediated iron acquisition is responsible for the growth suppression. Thus, this study provides the action of TatC-dependent pyoverdine translocation for the growth suppression of other bacteria, and it might aid understanding of the impact of P. aeruginosa in the complex community of bacterial species upon coinfection. PMID:26832668

  17. Microbial activity balance in size fractionated suspended growth biomass from full-scale sidestream combined nitritation-anammox reactors.

    PubMed

    Shi, Yijing; Wells, George; Morgenroth, Eberhard

    2016-10-01

    The purpose of this study was to determine the abundance, distribution and activity of aerobic ammonia-oxidizing bacteria (AOB) and anammox in size fractionated aggregates from full-scale suspended growth combined nitritation-anammox sidestream reactors. Plants with or without a cyclone device were also studied to assess a purported enrichment of anammox granules. Specific aerobic ammonium oxidation rates (p=0.01) and specific oxygen uptake rates (p=0.02) were significantly greater in flocs than in granules. AOB abundance measured using quantitative FISH was significantly higher in flocs than in granules (p=0.01). Conversely, anammox abundance was significantly greater in granules (p=0.03). The average ratio of anammox/AOB in systems employing hydrocyclone separation devices was 2.4, significantly higher (p=0.02) than the average ratio (0.5) in a system without a hydrocyclone. Our results demonstrate substantial functional and population-level segregation between floccular and granular fractions, and provide a key corroboration that cyclone separation devices can increase anammox levels in such systems. PMID:27347796

  18. Influence of Growth Phase, pH, and Temperature on the Abundance and Composition of Tetraether Lipids in the Thermoacidophile Picrophilus torridus.

    PubMed

    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

  19. 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

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

    DOE PAGESBeta

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

    2016-08-15

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

  1. rRNA Gene Expression of Abundant and Rare Activated-Sludge Microorganisms and Growth Rate Induced Micropollutant Removal.

    PubMed

    Vuono, David C; Regnery, Julia; Li, Dong; Jones, Zackary L; Holloway, Ryan W; Drewes, Jörg E

    2016-06-21

    The role of abundant and rare taxa in modulating the performance of wastewater-treatment systems is a critical component of making better predictions for enhanced functions such as micropollutant biotransformation. In this study, we compared 16S rRNA genes (rDNA) and rRNA gene expression of taxa in an activated-sludge-treatment plant (sequencing batch membrane bioreactor) at two solids retention times (SRTs): 20 and 5 days. These two SRTs were used to influence the rates of micropollutant biotransformation and nutrient removal. Our results show that rare taxa (<1%) have disproportionally high ratios of rRNA to rDNA, an indication of higher protein synthesis, compared to abundant taxa (≥1%) and suggests that rare taxa likely play an unrecognized role in bioreactor performance. There were also significant differences in community-wide rRNA expression signatures at 20-day SRT: anaerobic-oxic-anoxic periods were the primary driver of rRNA similarity. These results indicate differential expression of rRNA at high SRTs, which may further explain why high SRTs promote higher rates of micropollutant biotransformation. An analysis of micropollutant-associated degradation genes via metagenomics and direct measurements of a suite of micropollutants and nutrients further corroborates the loss of enhanced functions at 5-day SRT operation. This work advances our knowledge of the underlying ecosystem properties and dynamics of abundant and rare organisms associated with enhanced functions in engineered systems. PMID:27196630

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

    PubMed Central

    Ahmed, S. T.; Hossain, M. E.; Kim, G. M.; Hwang, J. A.; Ji, H.; Yang, C. J.

    2013-01-01

    A study was conducted to evaluate the effects of resveratrol and essential oils from medicinal plants on the growth performance, immunity, digestibility, and fecal microbial shedding of weaned piglets. A total of 48 weaned piglets (8 kg initial weight, 28-d-old) were randomly allotted to four dietary treatments with 3 replications of 4 piglets each. The dietary treatments were NC (negative control; basal diet), PC (positive control; basal diet+0.002% apramycin), T1 (basal diet+0.2% resveratrol), and T2 (basal diet+0.0125% essential oil blend). All piglets were orally challenged with 5 ml culture fluid containing 2.3×108 cfu/ml of Escherichia coli KCTC 2571 and 5.9×108 cfu/ml Salmonella enterica serover Typhimurium. The PC group (p<0.05) showed the highest average daily gain (ADG) and average daily feed intake (ADFI) throughout the experimental period, although feed conversion ratio (FCR) was improved in the T1 group (p>0.05). Serum IgG level was increased in the T1 group, whereas TNF-α levels was reduced in the supplemented groups compared to control (p<0.05). The PC diet improved the dry matter (DM) digestibility, whereas PC and T2 diets improved nitrogen (N) digestibility compared to NC and T1 diets (p<0.05). Fecal Salmonella and E. coli counts were reduced in all treatment groups compared to control (p<0.05). Fecal Lactobacillus spp. count was increased in the T2 group compared to others (p<0.05). Dietary treatments had no significant effect on fecal Bacillus spp. count throughout the entire experimental period. Based on these results, resveratrol showed strong potential as antibiotic alternatives for reversing the adverse effects of weaning stress on growth performance, immunity and microbial environment in E. coli and Salmonella-challenged piglets. PMID:25049839

  3. Effect of high oxygen modified atmosphere packaging on microbial growth and sensorial qualities of fresh-cut produce.

    PubMed

    Jacxsens, L; Devlieghere, F; Van der Steen, C; Debevere, J

    2001-12-30

    The application of High Oxygen Atmospheres (HOA) (i.e. > 70% O2) for packaging ready-to-eat vegetables was evaluated as an alternative technique for low O2 Equilibrium Modified Atmosphere (EMA) packaging (3% O2-5% CO2-balance N2) for respiring products. Comparative experiments between both techniques were performed in-vitro and in-vivo. Typical spoilage causing microorganisms (Pseudomonas fluorescens, Candida lambica), the moulds Botrytis cinerea, Aspergillus flavus and the opportunistic psychrotrophic human pathogenic microorganism associated with refrigerated minimally processed vegetables. Aeromonas caviae (HG4), showed a retarded growth during the conducted in-vitro studies at 4 degrees C in 70%, 80% and 95% O2 as examples of HOA compared to the in-vitro experiments in 5% O2 (as example of EMA packaging) and the effect was more pronounced in 95% O2. The effect of the high O2-concentrations on the human pathogen Listeria monocytogenes resulted in an extended lag phase (95% O2). The plant pathogen Erwinia carotovora was increasingly stimulated by increasing high O2-concentrations. During a storage experiment of three types of ready-to-eat vegetables (mushroom slices, grated celeriac and shredded chicory endive), which are sensitive to enzymatic browning and microbial spoilage, the effect of EMA and HOA (95% O2-5% N2) on their quality and shelf life was compared. High O2 atmospheres were found to be particularly effective in inhibiting enzymatic browning of the tested vegetables. Also, the microbial quality was better as a reduction in yeast growth was observed. The HOA can be applied as an alternative for low O2 modified atmospheres for some specific types of ready-to-eat vegetables, sensitive to enzymatic browning and spoilage by yeasts. PMID:11789938

  4. Microbial Growth and Air Pollutants in the Corrosion of Carbonate Rocks: Results from Laboratory and Outdoor Experimental Tests

    NASA Astrophysics Data System (ADS)

    Moroni, B.; Poli, G.; Pitzurra, L.

    2003-04-01

    Microorganisms and atmospheric pollution are primary causes of deterioration of materials exposed to open air. Due to the variety of chemical-mineralogical compositions and textures, stone represents a variegated substrate that interacts with environmental fluids and particulate, and is a selective environment for biological proliferation. Carbonate rocks, in particular, are highly exposed to environmental decay and extremely susceptible to acid attack caused by atmospheric pollutants and metabolic acid production. The aim of this work is to study the combined effect of microbial contamination and atmospheric pollutants in the weathering of carbonate rocks by means of laboratory and outdoor exposure tests. Laboratory experiments performed on carbonate rocks allowed evaluation of the influence of the gas mixture in the chemical modifications of the lithic substrate, and formulation of a kinetic model of sulphation. The obtained results suggest that nucleation alternates with growth as leading processes in the development of sulphation. In particular, nucleation of the reaction products is the leading process in the initial period of sulphation, which is characterized by a marked slowdown of the reaction progress, whereas growth of the products is the leading process in the subsequent period of resumption of sulphation. In situ experiments performed by exposing limestone specimens at two air monitoring stations in Perugia with different degrees of urban air pollution showed high levels of fungal colonization at early times and the presence of weathering products (i.e. gypsum) in the longer term. Results point to a combined effect of microbial colonization and atmospheric pollutants in promoting the weathering of stone through acid attack within the film of water present on the surface of the exposed material, and through the oxidation of metal sulphide particulate pollutant to sulphate. Laboratory tests assaying the extent of fungal colonization and/or chemical

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

    PubMed

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

    2003-04-01

    Glycol/seawater mixtures containing > 50% glycol inhibit corrosion of 316L stainless steel and do not support bacterial growth. The results indicate bacteria are able to use low concentrations of glycol (10%) as a growth medium, but bacterial growth decreased with increasing glycol concentration. Pitting potential, determined by anodic polarization, was used to evaluate susceptibility of 316L SS to corrosion in seawater-contaminated glycol. Mixture containing a minimum concentration of 50% propylene glycol-based coolant inhibited pitting corrosion. A slightly higher minimum concentration (55%) was needed for corrosion protection in ethylene glycol mixtures. PMID:14618716

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  7. 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., Jr.

    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.

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

    PubMed

    Herron, Patrick M; Gage, Daniel J; Arango Pinedo, Catalina; Haider, Zane K; Cardon, Zoe G

    2013-01-01

    The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to) environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constitutive promoter nptII and luxCDABE (coding for light-emitting proteins) from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L.), black poplar (Populus nigra L.), or tomato (Solanum lycopersicum L.) was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1-4 and 20-35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. PMID:24032034

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

    PubMed Central

    Herron, Patrick M.; Gage, Daniel J.; Arango Pinedo, Catalina; Haider, Zane K.; Cardon, Zoe G.

    2013-01-01

    The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to) environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constitutive promoter nptII and luxCDABE (coding for light-emitting proteins) from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L.), black poplar (Populus nigra L.), or tomato (Solanum lycopersicum L.) was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1–4 and 20–35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. PMID:24032034

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

    PubMed

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

    2015-11-01

    Wastewater treatment plant incorporates physical, chemical and biological processes to treat and remove the contaminants. The main drawback of conventional activated sludge process is the huge production of excess sludge, which is an unavoidable byproduct. The treatment and disposal of excess sludge costs about 60% of the total operating cost. The ideal way to reduce excess sludge production during wastewater treatment is by preventing biomass formation within the aerobic treatment train rather than post treatment of the generated sludge. In the present investigation two different mechanical devices namely, Ultrasonic and Shear Gap homogenizers have been employed to disintegrate the aerobic biomass. This study is intended to restrict the multiplication of microbial biomass and at the same time degrade the organics present in wastewater by increasing the oxidative capacity of microorganisms. The disintegrability on biomass was determined by biochemical methods. Degree of inactivation provides the information on inability of microorganisms to consume oxygen upon disruption. The soluble COD quantifies the extent of release of intra cellular compounds. The participation of disintegrated microorganism in wastewater treatment process was carried out in two identical respirometeric reactors. The results show that Ultrasonic homogenizer is very effective in the disruption of microorganisms leading to a maximum microbial growth reduction of 27%. On the other hand, Shear gap homogenizer does not favor the sludge growth reduction rather it facilitates the growth. This study also shows that for better microbial growth reduction, floc size reduction alone is not sufficient but also microbial disruption is essential. PMID:25866205

  11. Growth of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, and Pseudomonas fluorescens 2-79

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence of human illness associated with the consumption of fresh sprouts has increased very sharply during the past decade. The objective of this study was to investigate the growth dynamics of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, an...

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

    PubMed

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

    2001-01-01

    Soil inoculation with liquid cultures of Bacillus megaterium 501 and Exophiala nigrum A-29 capable of degrading several organophosphorus pesticides accelerated growth and development of experimental plants, formation of their generative organs, and improved their productivity. This was particularly observed under stress plant growth conditions on phytotoxic peach substrates. The microorganisms inoculated can probably degrade phytotoxins present in soils, thereby favoring the plant development. PMID:11443911

  13. Prediction of competitive microbial growth in mixed culture at dynamic temperature patterns.

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

    A novel competition model developed with the new logistic model and the Lotka-Volterra model successfully predicted the growth of bacteria in mixed culture using the mesophiles Staphylococcus aureus, Escherichia coli, and Salmonella at a constant temperature in our previous studies. In this study, we further studied the prediction of the growth of those bacteria in mixed culture at dynamic temperatures with various initial populations with the competition model. First, we studied the growth kinetics of the species in a monoculture at various constant temperatures ranging from 16℃ to 32℃. With the analyzed data in the monoculture, we then examined the prediction of bacterial growth in mixed culture with two and three species. The growth of the bacteria in the mixed culture at dynamic temperatures was successfully predicted with the model. The residuals between the observed and predicted populations at the data points were <0.5 log at most points, being 83.3% and 84.2% for the two-species mixture and the three-species mixture, respectively. The present study showed that the model could be applied to the competitive growth in mixed culture at dynamic temperature patterns. PMID:25252643

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  15. Relative abundance, age, growth, and fecundity of grubby Myoxocephalus aenaeus in Niantic River and Niantic Bay, Long Island Sound

    NASA Astrophysics Data System (ADS)

    Roseman, Edward F.; Tomichek, Christine A.; Maynard, Tracy; Burton, Jennifer A.

    2005-04-01

    Grubby ( Myoxocephalus aenaeus, Cottidae) is a common benthic fish of inshore waters and estuaries of eastern Long Island Sound; however, little information exists on their life history or population demographics. This study utilised a long-term data series (1976-2002) to assess grubby life history and population demographics and explores trends in the Niantic River and Niantic Bay populations. In addition, we examined the age, size, and fecundity of adult grubby in 2001-02 to determine the population characteristics in the region. Mean grubby catch per unit effort (CPUE) in Niantic Bay ranged from 0.4 per trawl in 1976 to 2.9 per trawl in 1984 while river CPUE ranged from 0.4 per trawl in 1977 to 7.6 per trawl in 1989. Catch of grubby in bottom trawls varied seasonally with highest CPUE occurring in winter. Highest entrainment of grubby larvae occurred in 2001 while the lowest entrainment observed was in 1991. Four age classes, 0+ through III+, were derived from otolith analysis (N = 51) although length frequency analysis suggested the possibility of older fish in the population. The total number of eggs in ovaries ranged from 286 to 16 451 for grubby (N = 64) between 52 mm and 155 mm TL. Results of this study indicated a decline in abundance of adult grubby over the 26-year period, possibly related to concurrent declines in eelgrass ( Zostera marina) abundance and/or increased water temperature.

  16. Microbial growth inhibition by alternating electric fields in mice with Pseudomonas aeruginosa lung infection.

    PubMed

    Giladi, Moshe; Porat, Yaara; Blatt, Alexandra; Shmueli, Esther; Wasserman, Yoram; Kirson, Eilon D; Palti, Yoram

    2010-08-01

    High-frequency, low-intensity electric fields generated by insulated electrodes have previously been shown to inhibit bacterial growth in vitro. In the present study, we tested the effect of these antimicrobial fields (AMFields) on the development of lung infection caused by Pseudomonas aeruginosa in mice. We demonstrate that AMFields (10 MHz) significantly inhibit bacterial growth in vivo, both as a stand-alone treatment and in combination with ceftazidime. In addition, we show that peripheral (skin) heating of about 2 degrees C can contribute to bacterial growth inhibition in the lungs of mice. We suggest that the combination of alternating electric fields, together with the heat produced during their application, may serve as a novel antibacterial treatment modality. PMID:20547811

  17. Assessing the use of delta(13)C natural abundance in separation of root and microbial respiration in a Danish beech (Fagus sylvatica L.) forest.

    PubMed

    Formánek, Pavel; Ambus, Per

    2004-01-01

    Our understanding of forest biosphere-atmosphere interactions is fundamental for predicting forest ecosystem responses to climatic changes. Currently, however, our knowledge is incomplete partly due to inability to separate the major components of soil CO(2) effluxes, viz. root respiration, microbial decomposition of soil organic matter and microbial decomposition of litter material. In this study we examined whether the delta(13)C characteristics of solid organic matter and respired CO(2) from different soil-C components and root respiration in a Danish beech forest were useful to provide information on the root respiration contribution to total CO(2) effluxes. The delta(13)C isotopic analyses of CO(2) were performed using a FinniganMAT Delta(PLUS) isotope-ratio mass spectrometer coupled in continuous flow mode to a trace gas preparation-concentration unit (PreCon). Gas samples in 2-mL crimp seal vials were analysed in a fully automatic mode with an experimental standard error +/-0.11 per thousand. We observed that the CO(2) derived from root-free mineral soil horizons (A, B(W)) was more enriched in (13)C (delta(13)C range -21.6 to -21.2 per thousand ) compared with CO(2) derived from root-free humus layers (delta(13)C range -23.6 to -23.4 per thousand ). The CO(2) evolved from root respiration in isolated young beech plants revealed a value intermediate between those for the soil humus and mineral horizons, delta(13)C(root) = -22.2 per thousand, but was associated with great variability (SE +/- 1.0 per thousand ) due to plant-specific differences. delta(13)C of CO(2) from in situ below-ground respiration averaged -22.8 per thousand, intermediate between the values for the humus layer and root respiration, but variability was great (SE +/- 0.4 per thousand ) due to pronounced spatial patterns. Overall, we were unable to statistically separate the CO(2) of root respiration vs. soil organic matter decomposition based solely on delta(13)C signatures, yet the trend in

  18. Kinetics of microbial growth and biodegradation of methanol and toluene in biofilters and an analysis of the energetic indicators.

    PubMed

    Avalos Ramirez, Antonio; Bénard, Sandrine; Giroir-Fendler, Anne; Jones, J Peter; Heitz, Michèle

    2008-11-25

    The kinetics of microbial growth and the biodegradation of methanol and toluene in (a) biofilters (BFs), and (b) biotrickling filters (BTFs), packed with inert materials, has been studied and analyzed. The specific growth rate, mu, for the treatment of methanol was 0.037h(-1) for a wide range of operating conditions. In the BF, mu was found to be a function of the methanol and toluene concentrations in the biofilm. In the BF used for treating methanol, mu was found to be affected by (1) the nitrogen concentration present in the nutrient solution, and (2) the kind of packing material employed. The kinetics of the methanol and toluene biodegradations were also analyzed using "mixed order" models. A Michaelis-Menten model type provided a good fit for the elimination capacity (EC) of the BTF treating methanol, while a Haldane model type provided a good fit to the EC of the BF treating methanol and toluene. The carbon dioxide production rate was related to the packed bed temperature and the content of the volatile solids within the biofilm. For the BF, the ratio of temperature/carbon dioxide production rate (PCO(2)) was 0.024 degrees C per unit of PCO(2), and for the BTF it was 0.15 degrees C per unit of PCO(2). PMID:18778740

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

    PubMed Central

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

    2013-01-01

    Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications. PMID:24367356

  20. Evolution of cooperation in microbial biofilms - A stochastic model for the growth and survival of bacterial mats

    NASA Astrophysics Data System (ADS)

    Knebel, Johannes; Cremer, Jonas; Melbinger, Anna; Frey, Erwin

    2012-02-01

    Cooperative behavior is essential for microbial biofilms. The structure and composition of a biofilm change over time and thereby influence the evolution of cooperation within the system. In turn, the level of cooperation affects the growth dynamics of the biofilm. Here, we investigate this coupling for an experimentally well-defined situation in which mutants of the Pseudomonas fluorescens strain form a mat at the liquid-air interface by the production of an extra-cellular matrix [1]. We model the occurrence of cooperation in this bacterial population by taking into account the formation of the mat. The presence of cooperators enhances the growth of the mat, but at the same time cheaters can infiltrate the population and put the viability of the mat at risk. We find that the survival time of the mat crucially depends on its initial dynamics which is subject to demographic fluctuations [2]. More generally, our work provides conceptual insights into the requirements and mechanisms for the evolution of cooperation.[1] P. Rainey et al., Nature 425, 72 (2003).[2] A. Melbinger et al., PRL 105, 178101 (2010).

  1. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

    PubMed Central

    Jaeger, Philipp A.; McElfresh, Cameron; Wong, Lily R.

    2015-01-01

    Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. PMID:26070672

  2. Heavy metals and TPH effects on microbial abundance and diversity in two estuarine areas of the southern-central coast of São Paulo State, Brazil.

    PubMed

    Pinto, Aline Bartelochi; Pagnocca, Fernando Carlos; Pinheiro, Marcelo Antonio Amaro; Fontes, Roberto Fioravanti Carelli; de Oliveira, Ana Júlia Fernandes Cardoso

    2015-07-15

    Coastal areas may be impacted by human and industrial activities, including contamination by wastewater, heavy metals and hydrocarbons. This study aimed to evaluate the impact of hydrocarbons (TPH) and metals on the microbiota composition and abundance in two estuarine systems in the coast of São Paulo: the Santos (SE) and Itanhaém (IE) estuaries. The SE was found to be chronically contaminated by heavy metals and highly contaminated by hydrocarbons. This finding was correlated with the increased density of cyanobacteria in sediments and suggests the possible use of cyanobacteria for bioremediation. These contaminants influence the density and composition of estuarine microbiota that respond to stress caused by human activity. The results are troubling because quantitative and qualitative changes in the microbiota of estuarine sediments may alter microbiological processes such as decomposition of organic matter. Moreover, this pollution can result in damage to the environment, biota and human health. PMID:26021289

  3. Effects of random motility on microbial growth and competition in a flow reactor

    SciTech Connect

    Ballyk, M.; Dung, L.; Jones, D.A.; Smith, H.L.

    1998-11-01

    The authors investigate the effects of random motility on the ability of a microbial population to survive in pure culture and to be a good competitor for scarce nutrient in mixed culture in a flow reactor model consisting of a nonlinear parabolic system of partial differential equations. For pure culture (*a single population), a sharp condition is derived which distinguishes between the two outcomes: (1) washout of the population from the reactor or (2) persistence of the population and the existence of a unique single-population steady state. The simulations suggest that this steady state is globally attracting. For the case of two populations competing for scarce nutrient, they obtain sufficient conditions for the uniform persistence of the two populations, for the existence of a coexistence steady state, and for the ability of one population to competitively exclude a rival. Extensive simulations are reported which suggest that (1) all solutions approach some steady state solution, (2) all possible outcomes exhibited by the classical competitive Lotka-Volterra ODE model can occur in the model, and (3) the outcome of competition between two bacterial strains can depend rather subtly on their respective random motility coefficients.

  4. Statistical support for the ATL program. [microbial growth in zero gravity

    NASA Technical Reports Server (NTRS)

    Hinkelmann, K.; Myers, R. H.

    1976-01-01

    Statistical experimental designs are presented for various numbers of organisms and agar solutions pertinent to the experiment, ""colony growth in zero gravity''. Missions lasting 7 and 30 days are considered. For the designs listed, the statistical analysis of the observations obtained on the space shuttle are outlined.

  5. Influence of Partial Denitrification and Mixotrophic Growth of NOB on Microbial Distribution in Aerobic Granular Sludge.

    PubMed

    Winkler, Mari-K H; Le, Quan H; Volcke, Eveline I P

    2015-09-15

    In aerobic granular sludge (AGS), the growth of nitrite oxidizing bacteria (NOB) can be uncoupled from the nitrite supply of ammonia oxidizing bacteria (AOB). Besides, unlike for conventional activated sludge, Nitrobacter was found to be the dominant NOB and not Nitrospira. To explain these experimental observations, two possible pathways have been put forward in literature. The first one involves the availability of additional nitrite from partial denitrification (nitrite-loop) and the second one consists of mixotrophic growth of Nitrobacter in the presence of acetate (ping-pong). In this contribution, mathematical models were set up to assess the possibility of these pathways to explain the reported observations. Simulation results revealed that both pathways influenced the nitrifier distribution in the granules. The nitrite-loop pathway led to an elevated NOB/AOB ratio, while mixotrophic growth of Nitrobacter guaranteed their predominance among the NOB population. Besides, mixotrophic growth of Nitrobacter could lead to NO emission from AGS. An increasing temperature and/or a decreasing oxygen concentration led to an elevated NOB/AOB ratio and increased NO emissions. PMID:26248168

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Microbial Inoculation Improves Growth of Oil Palm Plants (Elaeis guineensis Jacq.)

    PubMed Central

    Om, Azlin Che; Ghazali, Amir Hamzah Ahmad; Keng, Chan Lai; Ishak, Zamzuri

    2009-01-01

    Introduction of diazotrophic rhizobacteria to oil palm tissues during the in vitro micropropagation process establishes an early associative interaction between the plant cells and bacteria. In the association, the diazotrophs provide the host plants with phytohormones and fixed nitrogen. This study was conducted to observe growth of bacterised tissue cultured oil palm plants under ex vitro conditions after 280 days of growth. Root dry weight, shoot dry weight, root volume, bacterial colonisation, leaf protein and chlorophyll content of the host plants were observed. The results revealed that the inocula successfully colonised roots of the host plants. Plants inoculated with Acetobacter diazotrophicus (R12) had more root dry weight and volume than plants inoculated with Azospirillum brasilense (Sp7). Leaf protein and chlorophyll content were higher in the bacterised plants compared to Control 2 plants (inoculated with killed Sp7). These results suggest that the diazotrophs successfully improved the growth of the host plant (oil palm) and minimised the amount of N fertiliser necessary for growth. PMID:24575180

  8. The mechanism of ethanol treatment on inhibiting lettuce enzymatic browning and microbial growth

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tissue browning of fresh-cut lettuce greatly affects its quality and consumers’ appreciation. This study investigated the effects of ethanol treatment on enzymatic browning and natural microflora growth of lettuce stem discs. After treated with 20% ethanol for 2 min and then drained by a spinner, le...

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

    PubMed

    Voychuk, S I; Gromozova, E N

    2012-01-01

    Populations of microorganisms display fluctuations in the variable physiological and biochemical properties during cultivation under constant laboratory conditions. A series of explanations were proposed for this phenomenon, and different factors were studied as possible regulators. It was found that such fluctuations possess cosmic rhythms, but no factor(s) were proposed that could sufficiently explain and predict the magnitude of changes that happened on a daily basis in the long-term experiments. In this study we investigated specific growth rate fluctuations of Saccharomyces cerevisiae yeasts that were marked daily during cultivation under constant conditions. The effects of different solar and terrestrial factors were then analysed. The significant correlation indices were found for growth rate fluctuations against solar wind speed and the number of flares M on the Sun. These two factors determined the cyclic nature of the growth rate fluctuations, and thus its general course of increase or decrease. The effects of several other factors (Flares C number, planetary A index variation, and changes in the atmospheric factors such as temperature and humidity) and their two-way interactions were significant in producing an equation to describe the magnitude of changes of the yeast's growth parameters. The R2 of the equation achieved 91% and adjusted R2 was 78%. It is obvious that temperature and humidity are the factors that cannot directly influence the yeast populations under laboratory conditions and thus we suppose that they only reflect modifications of the really important factor(s) that take place in the Earth's atmosphere. We have concluded that different solar and terrestrial factors are responsible for the fluctuations in the daily kinetic parameters of the yeast growth. PMID:22830199

  10. Use of spectral distance, spectral angle, and plant abundance derived from hyperspectral imagery to characterize crop growth variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vegetation indices (VIs) derived from remote sensing imagery are commonly used to quantify crop growth and yield variations. As hyperspectral imagery is becoming more available, the number of possible VIs that can be calculated is overwhelmingly large. The objectives of this study were to examine sp...

  11. Arctic microbial and next-generation sequencing approach for bacteria in snow and frost flowers: selected identification, abundance and freezing nucleation

    NASA Astrophysics Data System (ADS)

    Mortazavi, R.; Attiya, S.; Ariya, P. A.

    2015-06-01

    During the spring of 2009, as part of the Ocean-Atmosphere-Sea Ice-Snowpack (OASIS) campaign in Barrow, Alaska, USA, we examined the identity, population diversity, freezing nucleation ability of the microbial communities of five different snow types and frost flowers. In addition to the culturing and gene-sequence-based identification approach, we utilized a state-of-the-art genomic next-generation sequencing (NGS) technique to examine the diversity of bacterial communities in Arctic samples. Known phyla or candidate divisions were detected (11-18) with the majority of sequences (12.3-83.1%) belonging to one of the five major phyla: Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria. The number of genera detected ranged from, 101-245. The highest number of cultivable bacteria was observed in frost flowers (FFs) and accumulated snow (AS) with 325 ± 35 and 314 ± 142 CFU m L-1, respectively; and for cultivable fungi 5 ± 1 CFU m L-1 in windpack (WP) and blowing snow (BS). Morphology/elemental composition and ice-nucleating abilities of the identified taxa were obtained using high resolution electron microscopy with energy-dispersive X-ray spectroscopy and ice nucleation cold-plate, respectively. Freezing point temperatures for bacterial isolates ranged from -20.3 ± 1.5 to -15.7 ± 5.6 °C, and for melted snow samples from -9.5 ± 1.0 to -18.4 ± 0.1 °C. An isolate belonging to the genus Bacillus (96% similarity) had ice nucleation activity of -6.8 ± 0.2 °C. Comparison with Montreal urban snow, revealed that a seemingly diverse community of bacteria exists in the Arctic with some taxa possibly originating from distinct ecological environments. We discuss the potential impact of snow microorganisms in the freezing and melting process of the snowpack in the Arctic.

  12. The pro-oxidant buthionine sulfoximine (BSO) reduces tumor growth of implanted Lewis lung carcinoma in mice associated with increased protein carbonyl, tubulin abundance, and aminopeptidase activity.

    PubMed

    Rodríguez-Gómez, Isabel; Carmona-Cortés, Javier; Wangensteen, Rosemary; Vargas-Tendero, Pablo; Banegas, Inmaculada; Quesada, Andrés; García-Lora, Angel M; Vargas, Félix

    2014-08-01

    This study evaluated the effects of the pro-oxidant buthionine sulfoximine (BSO) and of the interaction between BSO and TETRAC, an antagonist of αvß3 integrin, on tumor development and aminopeptidase (AP) activity in a murine model of implanted Lewis's carcinoma. Male CBA-C57 mice were untreated (controls) or treated with BSO (222 mg/100 mL in drinking water), TETRAC (10 mg/kg/day, i.p.), or BSO + TETRAC. BSO for 28 days and TETRAC were given for the last 20 days. Mice were subcutaneously inoculated with 1 × 10(6) Lewis carcinoma 3LL cells into the dorsum. Study variables were tumor weight (TW); Hb, as index of tumor-mediated angiogenesis; vascular endothelial growth factor (VEGF) protein abundance; protein carbonyl content; α-tubulin abundance; and GluAp, AlaAp, and AspAp activities. BSO produced a major decrease in TW (203 ± 18 mg) with respect to controls (365 ± 26) and a reduction in Hb content. The TETRAC group also showed marked reductions in TW (129 ± 15) and Hb concentration associated with a reduced VEGF content. The BSO + TETRAC group showed a major TW reduction (125 ± 13); although, the difference with the TETRAC group was not significant. BSO treatment increased protein carbonyl and tubulin abundance in comparison to controls. The activity of all APs was increased in the three experimental groups and was strongly and negatively correlated with TW. In conclusion, administration of BSO reduced the TW, which inversely correlated with protein carbonyl content, suggesting a loss of microtubule polymerization. The finding of a negative correlation between TW and AP activity opens up new perspectives for the study of APs as tumor growth modulators. PMID:24816945

  13. Effects of chestnut tannins and coconut oil on growth performance, methane emission, ruminal fermentation, and microbial populations in sheep.

    PubMed

    Liu, H; Vaddella, V; Zhou, D

    2011-12-01

    This study was conducted to evaluate the effects of chestnut tannins (CT) and coconut oil (CO) on growth performance, methane (CH₄) emission, ruminal fermentation, and microbial populations in sheep. A total of 48 Rideau Arcott sheep (average body weight 31.5±1.97 kg, 16 wk old) were randomly assigned into 6 treatment groups in a 3 × 2 factorial design, with CT and CO as the main effects (8 sheep per group). The treatments were control diet (CTR), 10 or 30 g of CT/kg of diet (CT10 and CT30), 25 g of CO/kg of concentrate (CO25), and 10 or 30 g of CT/kg of diet+25 g of CO/kg of concentrate (CT10CO25 and CT30CO25). After the feeding trial (60 d), all sheep were moved to respiratory chambers to measure CH₄ emission. After CH₄ emission measurements, all sheep were slaughtered to obtain rumen fluid samples. Results showed that the addition of CT, CO, and CT+CO had no significant effects on growth performance of sheep but reduced CH₄ emission. Addition of CT reduced the NH₃-N concentration in rumen fluid in CT30. Addition of CO decreased the concentration of total volatile fatty acids in rumen fluid. No significant differences were observed in pH and molar proportion of volatile fatty acids among treatments. Addition of CT, CO, and CT+CO significantly decreased methanogen and protozoa populations. Moreover, CO decreased counts of Fibrobacter succinogenes. No significant differences were observed in populations of fungi, Ruminococcus flavefaciens, or Ruminococcus albus among treatments. In conclusion, supplementation of CT and CO seemed to be a feasible means of decreasing emissions of CH₄ from sheep by reduction of methanogen and protozoa populations with no negative effect on growth performance. PMID:22118094

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

    PubMed

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

    2013-10-01

    The background microbiota of 5 Norwegian small-scale cheese production sites was examined and the effect of the isolated strains on the growth and survival of Listeria monocytogenes was investigated. Samples were taken from the air, food contact surfaces (storage surfaces, cheese molds, and brine) and noncontact surfaces (floor, drains, and doors) and all isolates were identified by sequencing and morphology (mold). A total of 1,314 isolates were identified and found to belong to 55 bacterial genera, 1 species of yeast, and 6 species of mold. Lactococcus spp. (all of which were Lactococcus lactis), Staphylococcus spp., Microbacterium spp., and Psychrobacter sp. were isolated from all 5 sites and Rhodococcus spp. and Chryseobacterium spp. from 4 sites. Thirty-two genera were only found in 1 out of 5 facilities each. Great variations were observed in the microbial background flora both between the 5 producers, and also within the various production sites. The greatest diversity of bacteria was found in drains and on rubber seals of doors. The flora on cheese storage shelves and in salt brines was less varied. A total of 62 bacterial isolates and 1 yeast isolate were tested for antilisterial activity in an overlay assay and a spot-on-lawn assay, but none showed significant inhibitory effects. Listeria monocytogenes was also co-cultured on ceramic tiles with bacteria dominating in the cheese production plants: Lactococcus lactis, Pseudomonas putida, Staphylococcus equorum, Rhodococcus spp., or Psychrobacter spp. None of the tested isolates altered the survival of L. monocytogenes on ceramic tiles. The conclusion of the study was that no common background flora exists in cheese production environments. None of the tested isolates inhibited the growth of L. monocytogenes. Hence, this study does not support the hypothesis that the natural background flora in cheese production environments inhibits the growth or survival of L. monocytogenes. PMID:23891302

  15. Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers.

    PubMed

    Chew, S C; Kundukad, B; Teh, W K; Doyle, P; Yang, L; Rice, S A; Kjelleberg, S

    2016-06-21

    Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix. PMID:27191395

  16. Effect of warming and drought on grassland microbial communities.

    PubMed

    Sheik, Cody S; Beasley, William Howard; Elshahed, Mostafa S; Zhou, Xuhui; Luo, Yiqi; Krumholz, Lee R

    2011-10-01

    The soil microbiome is responsible for mediating key ecological processes; however, little is known about its sensitivity to climate change. Observed increases in global temperatures and alteration to rainfall patterns, due to anthropogenic release of greenhouse gases, will likely have a strong influence on soil microbial communities and ultimately the ecosystem services they provide. Therefore, it is vital to understand how soil microbial communities will respond to future climate change scenarios. To this end, we surveyed the abundance, diversity and structure of microbial communities over a 2-year period from a long-term in situ warming experiment that experienced a moderate natural drought. We found the warming treatment and soil water budgets strongly influence bacterial population size and diversity. In normal precipitation years, the warming treatment significantly increased microbial population size 40-150% but decreased diversity and significantly changed the composition of the community when compared with the unwarmed controls. However during drought conditions, the warming treatment significantly reduced soil moisture thereby creating unfavorable growth conditions that led to a 50-80% reduction in the microbial population size when compared with the control. Warmed plots also saw an increase in species richness, diversity and evenness; however, community composition was unaffected suggesting that few phylotypes may be active under these stressful conditions. Our results indicate that under warmed conditions, ecosystem water budget regulates the abundance and diversity of microbial populations and that rainfall timing is critical at the onset of drought for sustaining microbial populations. PMID:21451582

  17. Influence of chromium compounds on microbial growth and nucleic acid synthesis

    SciTech Connect

    Ogawa, Toshihiko; Usui, Masauji; Yatome, Chizuko; Idaka, Eiichi )

    1989-08-01

    The wastewaters of the dyeing and the tanning industry contain often various chromium compounds, e.g. K{sub 2}Cr{sub 2}O{sub 7} and CrCl{sub 3}, with a large quantity of organic substances. Biological treatments have generally been employed in these industrial factories for the biodegradation of organic substances. The toxicity of the chromium compounds have been studied regarding mutagenicity and carcinogenicity from the medical view point. This is also of interest from the view point of wastewater biological treatments. The inhibitory effects of the compounds on the cell growth and the respiration in activated sludge have been reported in detail, but mechanisms have not been sufficiently elucidated. Therefore, the influence of K{sub 2}Cr{sub 2}O{sub 7} and CrCl{sub 3} on the cell growth and on the nucleic acid content was measured. Both compounds were the inhibitors of DNA synthesis. These action resulted in increased generation time a decrease in cell division. Chromium compounds and dyes coexist often in the wastewaters of the dyeing industries. The growth inhibitions of the mixed solution were measured.

  18. Gibberellin Regulates PIN-FORMED Abundance and Is Required for Auxin Transport–Dependent Growth and Development in Arabidopsis thaliana[C][W

    PubMed Central

    Willige, Björn C.; Isono, Erika; Richter, René; Zourelidou, Melina; Schwechheimer, Claus

    2011-01-01

    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. PMID:21642547

  19. Algal growth and species composition under experimental control of herbivory, phosphorus and coral abundance in Glovers Reef, Belize.

    PubMed

    McClanahan, T R; Cokos, B A; Sala, E

    2002-06-01

    The proliferation of algae on disturbed coral reefs has often been attributed to (1) a loss of large-bodied herbivorous fishes, (2) increases in sea water nutrient concentrations, particularly phosphorus, and (3) a loss of hard coral cover or a combination of these and other factors. We performed replicated small-scale caging experiments in the offshore lagoon of Glovers Reef atoll, Belize where three treatments had closed-top (no large-bodied herbivores) and one treatment had open-top cages (grazing by large-bodied herbivores). Closed-top treatments simulated a reduced-herbivory situation, excluding large fishes but including small herbivorous fishes such as damselfishes and small parrotfishes. Treatments in the closed-top cages included the addition of high phosphorus fertilizer, live branches of Acropora cervicornis and a third unmanipulated control treatment. Colonization, algal biomass and species composition on dead A. palmata "plates" were studied weekly for 50 days in each of the four treatments. Fertilization doubled the concentration of phosphorus from 0.35 to 0.77 microM. Closed-top cages, particularly the fertilizer and A. cervicornis additions, attracted more small-bodied parrotfish and damselfish than the open-top cages such that there was moderate levels of herbivory in closed-top cages. The open-top cages did, however, have a higher abundance of the chemically and morphologically defended erect algal species including Caulerpa cupressoides, Laurencia obtusa, Dictyota menstrualis and Lobophora variegata. The most herbivore-resistant calcareous green algae (i.e. Halimeda) were, however, uncommon in all treatments. Algal biomass increased and fluctuated simultaneously in all treatments over time, but algal biomass, as measured by wet, dry and decalcified weight, did not differ greatly between the treatments with only marginally higher biomass (p < 0.06) in the fertilized compared to open-top cages. Algal species composition was influenced by all

  20. Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time

    PubMed Central

    Crump, Byron C.; Hopkinson, Charles S.; Sogin, Mitchell L.; Hobbie, John E.

    2004-01-01

    Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([14C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and Actinobacteria. Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil. PMID:15006771

  1. Cultivation and quantitative proteomic analyses of acidophilic microbial communities

    SciTech Connect

    Belnap, Christopher P.; Pan, Chongle; Verberkmoes, Nathan C; Power, Mary E.; Samatova, Nagiza F; Carver, Rudolf L.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

  2. Impact of flue gas desulfurization-calcium sulfite and gypsum on soil microbial activity and wheat growth

    SciTech Connect

    Lee, Y.B.; Bigham, J.M.; Dick, W.A.; Kim, P.J.

    2008-08-15

    We conducted greenhouse tests to evaluate the effects of FGD-CaSO{sub 3} applied at rates of 0, 2.2, 4.4, and 8.8 Mg ha(-1) on wheat growth, soil enzyme activities, and the chemical properties of two soils with differing pH (4.0 vs. 6.2). A gypsum treatment applied at the rate of 2.2 Mg ha{sup -1} was used as a positive control. Exchangeable Ca{sup 2+} and water-extractable Ca{sup 2+} and SO{sub 4}{sup 2-} increased significantly with increasing FGD-CaSO{sub 3} application. SO{sub 4}{sup 2-} increased in both soils, indicating rapid oxidation of SO{sub 3}{sup 2-} to SO{sub 4}{sup 2-} when neither water nor oxygen was limiting. No changes in soil pH were measured. Applications of 2.2, 4.4, or 8.8 Mg CaSO{sub 3} ha{sup -1} to the pH 6.2 soil produced no effect on wheat growth or the uptake of N, P, Ca{sup 2+}, and Mg{sup 2+}. The uptake of SO{sub 4}{sup 2-} -S increased, whereas K uptake decreased. No significant differences in the activities of urease, {beta}-glucosidase, alkaline phosphatase, or arylsulfatase were observed relative to a control. In the acid soil, an application of 2.2 Mg ha{sup -1} FGD-CaSO{sub 3} increased wheat root growth and dry matter yield compared with an untreated control. The uptake of N, P, Ca{sup 2+}, and K{sup +} also increased presumably because of enhanced root development resulting from decreases in exchangeable Al{sup 3+} and increases in soluble Ca{sup 2+}. Wheat growth and alkaline phosphatase and arylsulfatase activities were significantly inhibited by addition of 8.8 Mg ha{sup -1} of FGD-CaSO{sub 3} compared with the untreated control or the same soil receiving 2.2 Mg ha{sup -1} gypsum. We conclude that surface applications of FGD-CaSO{sub 3} may be as effective as gypsum for inhibiting soil crusting, improving water infiltration, and promoting the movement of Ca{sup 2+} into acid subsoils. Moreover, application rates of equal to or less than 4.4 Mg ha-1 should have no negative impact on soil microbial activities or plant growth.

  3. Red light-regulated growth. I. Changes in the abundance of indoleacetic acid and a 22-kilodalton auxin-binding protein in the maize mesocotyl

    NASA Technical Reports Server (NTRS)

    Jones, A. M.; Cochran, D. S.; Lamerson, P. M.; Evans, M. L.; Cohen, J. D.

    1991-01-01

    We examined the changes in the levels of indoleacetic acid (IAA), IAA esters, and a 22-kilodalton subunit auxin-binding protein (ABP1) in apical mesocotyl tissue of maize (Zea mays L.) during continuous red light (R) irradiation. These changes were compared with the kinetics of R-induced growth inhibition in the same tissue. Upon the onset of continuous irradiation, growth decreased in a continuous manner following a brief lag period. The decrease in growth continued for 5 hours, then remained constant at 25% of the dark rate. The abundance of ABP1 and the level of free IAA both decreased in the mesocotyl. Only the kinetics of the decrease in IAA within the apical mesocotyl correlated with the initial change in growth, although growth continued to decrease even after IAA content reached its final level, 50% of the dark control. This decrease in IAA within the mesocotyl probably occurs primarily by a change in its transport within the shoot since auxin applied as a pulse move basipetally in R-irradiated tissue at the same rate but with half the area as dark control tissue. In situ localization of auxin in etiolated maize shoots revealed that R-irradiated shoots contained less auxin in the epidermis than the dark controls. Irradiated mesocotyl grew 50% less than the dark controls even when incubated in an optimal level of auxin. However, irradiated and dark tissue contained essentially the same amount of radioactivity after incubation in [14C]IAA indicating that the light treatment does not affect the uptake into the tissue through the cut end, although it is possible that a small subset of cells within the mesocotyl is affected. These observations support the hypothesis that R causes a decrease in the level of auxin in epidermal cells of the mesocotyl, consequently constraining the growth of the entire mesocotyl.

  4. Effects of irradiance on growth and winter bud production by Vallisneria americana and consequences to its abundance and distribution

    USGS Publications Warehouse

    Korschgen, Carl E.; Green, W.L.; Kenow, Kevin P.

    1997-01-01

    Number, total biomass, and individual mass of winter buds of Vallisneria americana was significantly related to the depth of the 1% of surface irradiance (Z) and the photosynthetic photon irradiance calculated for each shading treatment imposed during this study. Between the range of 23.8 and 111.2 cm depth for the 1% Z, total biomass of winterbuds produced ranged from 0.63 to 0.01 g, counts ranged from 3.5 to 0.1, and mass of individual winterbuds ranged from 0.18 to 0.04 g. Total biomass of winter buds produced was reduced when plants were exposed to a 14-day period without irradiance during the middle of the growing season. Applying the results of the culture experiments to conditions found in Navigation Pool 8 of the Upper Mississippi River suggests that irradiance may indeed limit the distribution and abundance of Vallisneria americana by reducing the number and size of winter buds. (C) 1997 Elsevier Science B.V.

  5. Universality of human microbial dynamics.

    PubMed

    Bashan, Amir; Gibson, Travis E; Friedman, Jonathan; Carey, Vincent J; Weiss, Scott T; Hohmann, Elizabeth L; Liu, Yang-Yu

    2016-06-01

    Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and the Student Microbiome Project--we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies. PMID:27279224

  6. Universality of human microbial dynamics

    NASA Astrophysics Data System (ADS)

    Bashan, Amir; Gibson, Travis E.; Friedman, Jonathan; Carey, Vincent J.; Weiss, Scott T.; Hohmann, Elizabeth L.; Liu, Yang-Yu

    2016-06-01

    Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.

  7. Effects of earthworms and plants on the soil structure, the physical stabilization of soil organic matter and the microbial abundance and diversity in soil aggregates in a long term study

    NASA Astrophysics Data System (ADS)

    Zangerlé, Anne; Hissler, Christophe; Lavelle, Patrick

    2014-05-01

    Earthworms and plant roots, as ecosystem engineers, have large effects on biotic and abiotic properties of the soil system. They create biogenic soil macroaggregates (i.e. earthworm casts and root macroaggregates) with specific physical, chemical and microbiological properties. Research to date has mainly considered their impacts in isolation thereby ignoring potential interactions between these organisms. On the other hand, most of the existing studies focused on short to midterm time scale. We propose in this study to consider effect of earthworms and plants on aggregate dynamics at long time scale. A 24 months macrocosm experiment, under semi-controlled conditions, was conducted to assess the impacts of corn and endogeic plus anecic earthworms (Apporectodea caliginosa and Lumbricus terrestris) on soil structure, C stabilization and microbial abundance and biodiversity. Aggregate stability was assessed by wet-sieving. Macroaggregates (>2 mm) were also visually separated according to their biological origin (e.g., earthworms, roots). Total C and N contents were measured in aggregates of all size classes and origins. Natural abundances of 13C of corn, a C4 plant, were used as a supplemental marker of OM incorporation in aggregates. The genetic structure and the abundance of the bacterial and fungal communities were characterized by using respectively the B- and F-ARISA fingerprinting approach and quantitative PCR bacteria (341F/515R) and fungi (FF330/FR1). They significantly impacted the soil physical properties in comparison to the other treatments: lower bulk density in the first 10cm of the soil with 0.95 g/cm3 in absence of corn plants and 0.88 g/cm3 in presence of corn plants compared to control soil (1.21g/cm3). The presence of earthworms increased aggregate stability (mean weight diameter) by 7.6 %, while plants alone had no simple impacts on aggregation. A significant interaction revealed that earthworms increased aggregate stability in the presence of

  8. Impact of fenoxycarb, a carbamate insect growth regulator, on some aquatic invertebrates abundant in mosquito breeding habitats.

    PubMed

    Miura, T; Takahashi, R M

    1987-09-01

    The insect growth regulator, Fenoxycarb, induced various morphogenetic aberrations in Notonecta unifasciata, Anax junius and Pantala hymenaea after treatment of late nymphal stages. Most affected nymphs died while molting from nymphs to adults. Fenoxycarb is also ovicidal to young eggs of N. unifasciata. The treatment rate of 0.034 kg AI/ha fenoxycarb induced some reduction in N. unifasciata population densities and produced a few morphogenetic abnormalities in some Odonata. However, planktonic organisms and aquatic beetles regularly found in the mosquito breeding habitats showed no deleterious effect. PMID:3504932

  9. Effect of androgens and glucocorticoids on microbial growth and antimicrobial susceptibility.

    PubMed

    Plotkin, Balbina J; Roose, Robert J; Erikson, Quenby; Viselli, Susan M

    2003-12-01

    The effects of androgens, testosterone and dihydrotestosterone (DHT), of an environmental anti-androgen, 2,2-bis(4-chlorophenyl)-1,1-dichloroethylene (DDE), and of glucocorticoids, hydrocortisone and dexamethasone, on growth kinetics and antibiotic susceptibility of E. faecalis, E. coli, P. aeurginosa, and S. aureus were measured. For P. aeurginosa, the presence of either DHT or DDE caused at least a fourfold shift in the minimum inhibitory concentration (MIC) of cefepime and tobramycin. DHT and DDE also affected the response of E. faecalis to meropenem and norfloxacin, resulting in a shift from sensitive to intermediate resistance (four-fold increase in MIC). Hydrocortisone (2 microM) induced an increase in the sensitivity of S. aureus to erythromycin, as compared to hormone-free control (from 0.5 to 0.06 microg/mL). The susceptibility pattern of E. coli was unaffected by the hormones tested. These changes in susceptibility to antibiotics were unrelated to alterations in growth kinetics. For all organisms tested, the alterations in MICs occurred only in the presence of hormone, indicative of changes in the phenotype of these stable quality control strains. PMID:14756537

  10. Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities

    PubMed Central

    Lara, Lidia Susana; Rodriguez, Alia; Uribe-Vélez, Daniel; Sanders, Ian R.

    2016-01-01

    Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities. PMID:27253975

  11. Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities.

    PubMed

    Ordoñez, Yuli Marcela; Fernandez, Belen Rocio; Lara, Lidia Susana; Rodriguez, Alia; Uribe-Vélez, Daniel; Sanders, Ian R

    2016-01-01

    Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities. PMID:27253975

  12. Fighting fish (Betta splendens) bubble nests do not inhibit microbial growth.

    PubMed

    Brown, Alexandria C; Clotfelter, Ethan D

    2012-12-01

    Some organisms produce antimicrobial substances in nesting foam to favorably manipulate the environment to which their developing offspring are exposed. We tested if fighting fish Betta splendens foamy nest material, which is comprised of bubbles produced in the oral cavity of nesting males, has antimicrobial properties against a pathogenic bacteria (Edwardsiella tarda), a nonpathogenic bacteria (Escherichia coli), or a pathogenic oomycete (Saprolegnia parasitica). We also tested if exposure to nest material increases larval survival by performing in vitro fertilizations and individually incubating eggs in bubble nest extract or tank water (control). Our results show no evidence of antimicrobial properties of bubble nests. On the contrary, bubble nests provided favorable microenvironments for the growth of Saprolegnia parasitica. Our results confirm earlier work citing the importance of male nest attendance, and suggest that the mechanism responsible for decreased survival in the absence of attending males is pathogenic microbes. PMID:22753365

  13. Optimization of marine waste based-growth media for microbial lipase production using mixture design methodology.

    PubMed

    Sellami, Mohamed; Kedachi, Samiha; Frikha, Fakher; Miled, Nabil; Ben Rebah, Faouzi

    2013-01-01

    Lipase production by Staphylococcus xylosus and Rhizopus oryzae was investigated using a culture medium based on a mixture of synthetic medium and supernatants generated from tuna by-products and Ulva rigida biomass. The proportion of the three medium components was optimized using the simplex-centroid mixture design method (SCMD). Results indicated that the experimental data were in good agreement with predicted values, indicating that SCMD was a reliable method for determining the optimum mixture proportion of the growth medium. Maximal lipase activities of 12.5 and 23.5 IU/mL were obtained with a 50:50 (v:v) mixture of synthetic medium and tuna by-product supernatant for Staphylococcus xylosus and Rhizopus oryzae, respectively. The predicted responses from these mixture proportions were also validated experimentally. PMID:24350480

  14. Accuracy of microbial growth predictions with square root and polynomial models.

    PubMed

    Delignette-Muller, M L; Rosso, L; Flandrois, J P

    1995-10-01

    The results of growth predictions using square root and polynomial models published in 14 papers were studied. Errors on quantities of practical interest such as lag time, generation time or the time required to reach a given increase in number of cells, are analyzed. The distribution of these errors was examined with the perspective of the practical use of predictive models in food industry. Highly unsafe predictions and significant average errors were observed in some cases. A good knowledge of predictive models accuracy seems essential for their efficient and safe use, for example to predict the shelf life of a product. Yet, authors generally gave no pragmatic information on such things as the average relative error or the range of errors on predicted variables. Problems of robustness of models when tested in different conditions were noticed, which corroborates the necessity of a systematic validation of models on new data. PMID:8579985

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  16. Linking microbial carbon utilization with microbially-derived soil organic matter

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

    Soil microbial communities are fundamental to plant C turnover, as all C inputs eventually pass through the microbial biomass. In turn, there is increasing evidence that this biomass accumulates as a significant portion of stable soil organic matter (SOM) via physiochemical interactions with the soil matrix. However, when exploring SOM dynamics, these two processes are often regarded as discrete from one another, despite potentially important linkages between microbial C utilization and the fate of that biomass C as SOM. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil C inputs that influence microbial biomass production and microbial C allocation. Microbial physiology, such as microbial growth efficiency (MGE), growth rate and turnover have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM accumulation may not necessarily be a function of resistance to decay but the degree to which it optimizes microbial biomass production. To examine the relationship between microbial C utilization and microbial contributions to SOM, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine 1) if, in absence of plant-derived C, chemically complex SOM similar to natural soils can accumulate through the production of microbial residues and 2) how differences in C utilization of simple substrates, varying in energy yields, influence the quantity and chemistry of newly formed SOM. Over the course of the incubation, MGE

  17. THE LOCAL EXPRESSION AND ABUNDANCE OF INSULIN-LIKE GROWTH FACTOR (IGF) BINDING PROTEINS IN SKELETAL MUSCLE ARE REGULATED BY AGE AND GENDER BUT NOT LOCAL IGF-I "IN VIVO"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We wished to determine whether sustained IGF-I production in skeletal muscle increases local IGF binding protein (IGFBP) abundance, thereby mitigating the long-term stimulation of muscle growth by IGF-I. Muscle growth of transgenic mice that overexpress IGF-I in muscle (SIS2) and of wild-type (Wt) m...

  18. One-pot enzymatic conversion of carbon dioxide and utilization for improved microbial growth.

    PubMed

    Hong, Sung-Gil; Jeon, Hancheol; Kim, Han Sol; Jun, Seung-Hyun; Jin, EonSeon; Kim, Jungbae

    2015-04-01

    We developed a process for one-pot CO2 conversion and utilization based on simple conversion of CO2 to bicarbonate at ambient temperature with no energy input, by using the cross-linking-based composites of carboxylated polyaniline nanofibers (cPANFs) and carbonic anhydrase. Carbonic anhydrase was immobilized on cPANFs via the approach of magnetically separable enzyme precipitate coatings (Mag-EPC), which consists of covalent enzyme attachment, enzyme precipitation, and cross-linking with amine-functionalized magnetic nanoparticles. Mag-EPC showed a half-life of 236 days under shaking, even resistance to 70% ethanol sterilization, and recyclability via facile magnetic separation. For one-pot CO2 conversion and utilization, Mag-EPC was used to accelerate the growth of microalga by supplying bicarbonate from CO2, representing 1.8-fold increase of cell concentration when compared to the control sample. After two repeated uses via simple magnetic separation, the cell concentration with Mag-EPC was maintained as high as the first cycle. This one-pot CO2 conversion and utilization is an alternative as well as complementary process to adsorption-based CO2 capture and storage as an environmentally friendly approach, demanding no energy input based on the effective action of the stabilized enzyme system. PMID:25815899

  19. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  20. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    SciTech Connect

    Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Fang, Yilin; Mahadevan, Radhakrishnan; Lovley, Derek R.

    2013-09-07

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under

  1. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

    2012-12-01

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model

  2. Identification of an AAA ATPase VPS4B-Dependent Pathway That Modulates Epidermal Growth Factor Receptor Abundance and Signaling during Hypoxia

    PubMed Central

    Lin, H. Helen; Li, Xu; Chen, Jo-Lin; Sun, Xiuzhu; Cooper, Fariba Norouziyan; Chen, Yun-Ru; Zhang, Wenyu; Chung, Yiyin; Li, Angela; Cheng, Chun-Ting; Yang, Lixin; Deng, XuTao; Liu, Xiyong; Yen, Yun; Johnson, Deborah L.; Shih, Hsiu-Ming; Yang, Austin

    2012-01-01

    VPS4B, an AAA ATPase (ATPase associated with various cellular activities), participates in vesicular trafficking and autophagosome maturation in mammalian cells. In solid tumors, hypoxia is a common feature and an indicator of poor treatment outcome. Our studies demonstrate that exogenous or endogenous (assessed with anchorage-independent three-dimensional multicellular spheroid culture) hypoxia induces VPS4B downregulation by the ubiquitin-proteasome system. Inhibition of VPS4B function by short hairpin VPS4B (sh-VPS4B) or expression of dominant negative VPS4B(E235Q) promotes anchorage-independent breast cancer cell growth and resistance to gefitinib, U0126, and genotoxicity. Biochemically, hyperactivation of epidermal growth factor receptor (EGFR), a receptor tyrosine kinase essential for cell proliferation and survival, accompanied by increased EGFR accumulation and altered intracellular compartmentalization, is observed in cells with compromised VPS4B. Furthermore, enhanced FOS/JUN induction and AP-1 promoter activation are noted in EGF-treated cells with VPS4B knockdown. However, VPS4B depletion does not affect EGFRvIII stability or its associated signaling. An inverse correlation between VPS4B expression and EGFR abundance is observed in breast tumors, and high-grade or recurrent breast carcinomas exhibit lower VPS4B expression. Together, our findings highlight a potentially critical role of VPS4B downregulation or chronic-hypoxia-induced VPS4B degradation in promoting tumor progression, unveiling a nongenomic mechanism for EGFR overproduction in human breast cancer. PMID:22252323

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

    PubMed Central

    Oloyede, Ganiyat K.; Oyelola, Martha S.

    2013-01-01

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

  4. Microbial Ecophysiology is a Missing Link in Emerging Microbial-based Soil Organic Matter Frameworks

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.; Frey, S. D.

    2012-12-01

    Recently, our epistemology of soil C dynamics has been undergoing a major transformation; where in the past soil organic matter (SOM) formation was attributed to the biochemical recalcitrance of plant litter, we now know that microbially transformed plant residues and microbial necromass are key precursors of SOM formation. SOM formation is thus a result of complex ecological interactions between substrate availability, the soil biological community, and the decomposing environment, and is a function of multiple ecosystem processes related to climate, soil type and their interactions with resident decomposer communities. Under this emerging new view, microbial biomass is treated generally, without consideration of the ecophysiological processes that regulate the chemistry and abundance of biomass production. In reality, biomass inputs are far more complex in terms of their input rates and potential to serve as a precursor to SOM formation. We explore microbial growth efficiencies (MGE) and growth rates and how their expression across different soil environments can be incorporated into our emerging conceptual models of microbial-mediated SOM formation. MGE and growth rates are both poorly understood despite their direct impact on SOM formation. Specifically, the physiological trade-offs associated with growth rates and MGE need to be assessed in terms of their relative influence on microbial inputs to SOM. Additionally, we need a better understanding of the variation in chemistry of cellular biomass, metabolites and exocellular excretions across species. At a broad level, we know that fungal and bacterial cell walls differ in their chemical recalcitrance and organo-mineral interactions but the degree to which this variation results in long-term differences in SOM dynamics remains unknown. To explore these uncertainties, we use a model-based approach to examine how potential tradeoffs between MGE and growth rates, and their responses to varying environmental

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

    PubMed

    Jiao, Hai-hua; Cui, Bing-jian; Wu, Shang-hua; Bai, Zhi-hui; Huang, Zhan-bin

    2015-09-01

    In order to explore the effect of Mirabilis jalapa Linn. growth on the structure characteristics of the microbial community and the degradation of petroleum hydrocarbon (TPH) in the petroleum-contaminated saline-alkali soil, Microbial biomass and species in the rhizosphere soils of Mirabilis jalapa Linn. in the contaminated saline soil were studied with the technology of phospholipid fatty acids (PLFAs) analysis. The results showed that comparing to CK soils without Mirabilis jalapa Linn., the ratio of PLFAs species varied were 71. 4%, 69. 2% and 33. 3% in the spring, summer and autumn season, respectively. In addition, there was distinct difference of the biomasses of the microbial community between the CK and rhizosphere soils and among the difference seasons of growth of Mirabilis jalapa Linn.. Compare to CK soil, the degradation rates of total petroleum hydrocarbon (TPH) was increased by 47. 6%, 28. 3%, and 18. 9% in spring, summer, and autumn rhizosphere soils, respectively. Correlation analysis was used to determine the correlation between TPH degradation and the soil microbial community. 77. 8% of the total soil microbial PLFAs species showed positive correlation to the TPH degradation (the correlation coefficient r > 0), among which, 55. 6% of PLFAs species showed high positive correlation(the correlation coefficient was r≥0. 8). In addition, the relative content of SAT and MONO had high correlation with TPH degradation in the CK sample soils, the corelation coefficient were 0. 92 and 0. 60 respectively; However, the percent of positive correlation was 42. 1% in the rhizosphere soils with 21. 1% of them had high positive correlation. The relative content of TBSAT, MONO and CYCLO had moderate or low correlation in rhizosphere soils, and the correlation coefficient were 0. 56, 0. 50, and 0. 07 respectively. Our study showed that the growth of mirabilis Mirabilis jalapa Linn. had a higher influence on the species and biomass of microbial community in the

  6. The activated sludge ecosystem contains a core community of abundant organisms

    PubMed Central

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

  7. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  8. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    PubMed Central

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  9. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  10. Potential roles for autophosphorylation, kinase activity, and abundance of a CDK-activating kinase (Ee;CDKF;1) during growth in leafy spurge.

    PubMed

    Chao, Wun S; Serpe, Marcelo D; Jia, Ying; Shelver, Weilin L; Anderson, James V; Umeda, Masaaki

    2007-02-01

    Leafy spurge (Euphorbia esula L.) is a deep-rooted perennial weed that propagates both by seeds and underground adventitious buds located on the crown and roots. To enhance our understanding of growth and development during seed germination and vegetative propagation, a leafy spurge gene (Accession No. AF230740) encoding a CDK-activating kinase (Ee;CDKF;1) involved in cell-cycle progression was identified, and its function was confirmed based on its ability to rescue a yeast temperature-sensitive CAK mutant (GF2351) and through in vitro kinase assays. Site-directed mutagenesis of Ee;CDKF;1 indicated that two threonine residues (Thr291 and Thr296) were mutually responsible for intra-molecular autophosphorylation and for phosphorylating its substrate protein, cyclin-dependent kinase (CDK). Polyclonal antibodies generated against the Ee;CDKF;1 protein or against a phosphorylated Ee;CDKF;1 peptide [NERYGSL(pT)SC] were used to examine abundance and phosphorylation of CDKF;1 during seed germination and bud growth. The levels of CDKF;1 were lower in dry or imbibed seeds than in germinating seeds or seedlings. Differences in CDKF;1 were also observed during adventitious bud development; small buds appeared to have greater levels of CDKF;1 than large buds. Similar patterns of CDKF;1 expression were detected with either the polyclonal antibody developed using the CDKF;1 protein or the phosphorylated peptide. These results indicated that Thr291 is constitutively phosphorylated in vivo and associated with Ee;CDKF;1 activity. Our results further suggest that a certain level of CDKF;1 activity is maintained in most tissues and may be an important phenomenon for enzymes that regulate early steps in cell-cycle signaling pathways. PMID:17063377

  11. A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty.

    PubMed

    Chen, Yi-Shih; Lo, Shuen-Fang; Sun, Peng-Kai; Lu, Chung-An; Ho, Tuan-Hua D; Yu, Su-May

    2015-01-01

    Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water-use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin-dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress-suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty. PMID:25200982

  12. Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

    SciTech Connect

    Li, Zhou; Wang, Yingfeng; Yao, Qiuming; Justice, Nicholas B.; Ahn, Tae-Hyuk; Xu, Dong; Hettich, Robert {Bob} L; Banfield, Jillian F.; Pan, Chongle

    2014-01-01

    Detailed characterization of posttranslational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.

  13. Indirect microbial detection

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R. (Inventor)

    1981-01-01

    The growth of microorganisms in a sample is detected and monitored by culturing microorganisms in a growth medium and detecting a change in potential between two electrodes, separated from the microbial growth by a barrier which is permeable to charged paticles but microorganism impermeable.

  14. Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth

    PubMed Central

    Oikonomou, Georgios; Teixeira, Andre Gustavo Vieira; Foditsch, Carla; Bicalho, Marcela Lucas; Machado, Vinicius Silva; Bicalho, Rodrigo Carvalho

    2013-01-01

    In this study, we use barcoded pyrosequencing of the 16S rRNA gene to characterize the fecal microbiota of neonatal calves and identify possible relationships of certain microbiota profiles with health and weight gain. Fecal samples were obtained weekly from 61 calves from birth until weaning (seventh week of the calves' life). Firmicutes was the most prevalent phylum, with a prevalence ranging from 63.84% to 81.90%, followed by Bacteroidetes (8.36% to 23.93%), Proteobacteria (3.72% to 9.75%), Fusobacteria (0.76% to 5.67%), and Actinobacteria (1.02% to 2.35%). Chao1 index gradually increased from the first to the seventh postnatal week. Chao1 index was lower during the third, fourth, and fifth week of life in calves that suffered from pneumonia and were treated with antibiotics. Diarrhea incidence during the first four weeks of the calves' life was also associated with a reduction of microbial diversity during the third week of life. Increased fecal microbial diversity after the second week of life was associated with higher weight gain. Using discriminant analysis we were able to show differences in the microbiota profiles between different weeks of life, between high and low weight gain groups of calves, and between calves affected and not affected with diarrhea during the first four weeks life. The prevalence of Faecalibacterium spp. in the first week of life was associated with weight gain and the incidence of diarrhea, with higher prevalence being associated with higher weight gain and less diarrhea. Representative sequences from Faecalibacterium spp. were closely affiliated to Faecalibacterium prausnitzii. Results presented here provide new information regarding the intestinal microbiota of neonatal calves and its association with health and growth. Fecal microbial diversity was associated with calf age, disease status and growth rates. Results suggesting a possible beneficial effect of Faecalibacterium spp. on health and growth are promising. PMID:23646192

  15. Increased microbial activity in a warmer and wetter climate enhances the risk of coastal hypoxia.

    PubMed

    Nydahl, Anna; Panigrahi, Satya; Wikner, Johan

    2013-08-01

    The coastal zone is the most productive area of the marine environment and the area that is most exposed to environmental drivers associated with human pressures in a watershed. In dark bottle incubation experiments, we investigated the short-term interactive effects of changes in salinity, temperature and riverine dissolved organic matter (rDOM) on microbial respiration, growth and abundance in an estuarine community. An interaction effect was found for bacterial growth, where the assimilation of rDOM increased at higher salinities. A 3 °C rise in the temperature had a positive effect on microbial respiration. A higher concentration of DOM consistently enhanced respiration and bacterial abundance, while an increase in temperature reduced bacterial abundance. The latter result was most likely caused by a positive interaction effect of temperature, salinity and rDOM on the abundance of bacterivorous flagellates. Elevated temperature and precipitation, causing increased discharges of rDOM and an associated lowered salinity, will therefore primarily promote bacterial respiration, growth and bacterivore abundance. Our results suggest a positive net outcome for microbial activity under the projected climate change, driven by different, partially interacting environmental factors. Thus, hypoxia in coastal zones may increase due to enhanced respiration caused by higher temperatures and rDOM discharge acting synergistically. PMID:23551052

  16. Quantifying remobilization of pre-existing nitrogen from cuttings to new growth of woody plants using 15N at natural abundance

    PubMed Central

    2013-01-01

    Background For measurements of nitrogen isotope composition at natural abundance, carry-over of pre-existing nitrogen remobilized to new plant growth can cause deviation of measured isotope composition (δ15N) from the δ15Nof newly acquired nitrogen. To account for this problem, a two-step approach was proposed to quantify and correct for remobilized nitrogen from vegetative cuttings of Populus balsamifera L. grown with either nitrate (δ15N = 58.5‰) or ammonium (δ15N = −0.96‰). First, the fraction of carry-over nitrogen remaining in the cutting was estimated by isotope mass balance. Then measured δ15N values were adjusted for the fraction of pre-existing nitrogen remobilized to the plant. Results Mean plant δ15N prior to correction was 49‰ and −5.8‰ under nitrate and ammonium, respectively. Plant δ15N was non-linearly correlated to biomass (r2 = 0.331 and 0.249 for nitrate and ammonium, respectively; P < 0.05) where the δ15N of plants with low biomass approached the δ15N of the pre-existing nitrogen. Approximately 50% of cutting nitrogen was not remobilized, irrespective of size. The proportion of carry-over nitrogen in new growth was not different between sources but ranged from less than 1% to 21% and was dependent on plant biomass and, to a lesser degree, the size of the cutting. The δ15N of newly acquired nitrogen averaged 52.7‰ and −6.4‰ for nitrate and ammonium-grown plants, respectively; both lower than their source values, as expected. Since there was a greater difference in δ15N between the carried-over pre-existing and newly assimilated nitrogen where nitrate was the source, the difference between measured δ15N and adjusted δ15N was also greater. There was no significant relationship between biomass and plant δ15N with either ammonium or nitrate after adjusting for carry-over nitrogen. Conclusion Here, we provide evidence of remobilized pre-existing nitrogen influencing δ15N of new growth of P. balsamifera L

  17. Microbial biotechnology.

    PubMed

    Demain, A L

    2000-01-01

    For thousands of years, microorganisms have been used to supply products such as bread, beer and wine. A second phase of traditional microbial biotechnology began during World War I and resulted in the development of the acetone-butanol and glycerol fermentations, followed by processes yielding, for example, citric acid, vitamins and antibiotics. In the early 1970s, traditional industrial microbiology was merged with molecular biology to yield more than 40 biopharmaceutical products, such as erythropoietin, human growth hormone and interferons. Today, microbiology is a major participant in global industry, especially in the pharmaceutical, food and chemical industries. PMID:10631778

  18. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.

    PubMed

    Yin, Jinbao; Zhang, Xu-Xiang; Wu, Bing; Xian, Qiming

    2015-12-01

    Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge. PMID:26423395

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate rate of passage and nutrient digestibility. Yet nothing is known relative to their potential impact on fecal microbial ecology and subsequent VFA generation. Two experiments utilizing a total o...

  20. Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures†

    PubMed Central

    Kucharzyk, Katarzyna H.; Deshusses, Marc A.; Porter, Kaitlyn A.; Hsu-Kim, Heileen

    2016-01-01

    Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHg using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production. PMID:26211614

  1. Abundance, composition and growth rate of coral recruits on dead corals following the 2010 bleaching event at Mu Ko Surin, the Andaman Sea

    NASA Astrophysics Data System (ADS)

    Yucharoen, Mathinee; Yeemin, Thamasak; Casareto, Beatriz E.; Suzuki, Yoshimi; Samsuvan, Watchara; Sangmanee, Kanwara; Klinthong, Wanlaya; Pengsakun, Sittiporn; Sutthacheep, Makamas

    2015-06-01

    Elevated seawater temperatures in the summer months of 2010 were associated with widespread coral mortality in Thailand. A large number of corals at Mu Ko Surin died following the bleaching event. Understanding of the recruitment of corals would improve our ability to predict the potential for coral recovery from the impacts of bleaching events, as well as the interpretation of spatio-temporal variability in coral community structure. This study aims to examine the composition, abundance and growth rate of juvenile corals and the potential of reef recovery at Mu Ko Surin in order to help to understand how reefs react to major disturbances. We found that the densities of coral recruits varied among years and study sites. In the year 2011, coral recruitments ranged between 0.18 ± 0.02 to 1.67 ± 0.07 recruits per m2 for 10 study sites. While in 2012, the monitoring revealed a range between 0.96 ± 0.16 and 2.19 ± 0.21 recruits per m2 from 5 study sites. Fungia, Acropora, Porites and Favites were the dominant groups of coral recruits. In terms substrate forms, they were significant differences between sampling years but the preferential dominant substrate forms did not differ. The Acropora recruits at Ko Torinla showed normal distributions of size class during the two periods. Their ranges in 2011 and 2012 were 4-30 and 13-54 mm, respectively. Six species of Acropora recruits, i.e. Acropora intermedia, A. nasuta, A. cerealis, A. subulata, A. muricata and A. lat