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Sample records for quantifying microbial utilization

  1. Quantifying electron fluxes in methanogenic microbial communities

    NARCIS (Netherlands)

    Junicke, H.

    2015-01-01

    Anaerobic digestion is a widely applied process in which close interactions between different microbial groups result in the formation of renewable energy in the form of biogas. Nevertheless, the regulatory mechanisms of the electron transfer between acetogenic bacteria and methanogenic archaea in t

  2. Microbial thiocyanate utilization under highly alkaline conditions.

    Science.gov (United States)

    Sorokin, D Y; Tourova, T P; Lysenko, A M; Kuenen, J G

    2001-02-01

    Three kinds of alkaliphilic bacteria able to utilize thiocyanate (CNS-) at pH 10 were found in highly alkaline soda lake sediments and soda soils. The first group included obligate heterotrophs that utilized thiocyanate as a nitrogen source while growing at pH 10 with acetate as carbon and energy sources. Most of the heterotrophic strains were able to oxidize sulfide and thiosulfate to tetrathionate. The second group included obligately autotrophic sulfur-oxidizing alkaliphiles which utilized thiocyanate nitrogen during growth with thiosulfate as the energy source. Genetic analysis demonstrated that both the heterotrophic and autotrophic alkaliphiles that utilized thiocyanate as a nitrogen source were related to the previously described sulfur-oxidizing alkaliphiles belonging to the gamma subdivision of the division Proteobacteria (the Halomonas group for the heterotrophs and the genus Thioalkalivibrio for autotrophs). The third group included obligately autotrophic sulfur-oxidizing alkaliphilic bacteria able to utilize thiocyanate as a sole source of energy. These bacteria could be enriched on mineral medium with thiocyanate at pH 10. Growth with thiocyanate was usually much slower than growth with thiosulfate, although the biomass yield on thiocyanate was higher. Of the four strains isolated, the three vibrio-shaped strains were genetically closely related to the previously described sulfur-oxidizing alkaliphiles belonging to the genus Thioalkalivibrio. The rod-shaped isolate differed from the other isolates by its ability to accumulate large amounts of elemental sulfur inside its cells and by its ability to oxidize carbon disulfide. Despite its low DNA homology with and substantial phenotypic differences from the vibrio-shaped strains, this isolate also belonged to the genus Thioalkalivibrio according to a phylogenetic analysis. The heterotrophic and autotrophic alkaliphiles that grew with thiocyanate as an N source possessed a relatively high level of cyanase

  3. Silicon Utilizing Microbial Bioactivities in the Biosphere

    Science.gov (United States)

    Sen, M. M.; Das, S.

    2012-12-01

    Diatoms are unicellular eukaryotic algae and an important member of the silicon utilizing organisms, that generate ~20% of the ~100 billion metric tons of organic carbon produced through photosynthesis on Earth each year. Fragilariopsis is a dominating psychrophilic diatom genus in polar sea ice. The two species Fragilariopsis cylindrus and Fragilariopsis curta are able to grow and divide below freezing temperature. Antifreeze proteins (AFPs), involved in cold adaptation in several psychrophilic organisms, are widespread in this two polar species. Achanthes minutissima isolated as dominant diatom has degradable effects involving petroleum hydocarbons. Phaeodactylum tricornutum, have antibacterial activity and the fatty acid, eicosapentaenoic acid (EPA), has been identified as one compound responsible for this activity. Other antibacterial compounds are monounsaturated fatty acid (9Z)-hexadecenoic acid (palmitoleic acid; C16:1 n-7) and the relatively unusual polyunsaturated fatty acid (6Z, 9Z, 12Z)-hexadecatrienoic acid (HTA; C16:3 n-4). Both are active against Gram-positive bacteria and many Gram-negative pathogen. Palmitoleic acid is active at micro-molar concentrations, kills bacteria rapidly, and is highly active against multidrug-resistant Staphylococcus aureus. Domoic acid -a neurotoxin produced by Pseudo-nitzschia accumulates in marine invertebrates. Evidences of sea lion (Zalophus californianus) and human poisoning following consumption of contaminated blue mussels (Mytilus edulis) is mainly due to this toxin. Among the most prominent features described in human beings was memory impairment which led to the name Amnesic Shellfish Poisoning [ASP]. Silicon utilizing organisms can act as a bioindicator of environmental contamination, thus a rapid change in phytochelatins to both the increase in and the withdrawal of environmental Cd stress was found in Thalassiosira nordenskioeldii. Some of them also can produce biofuels particularly diatoms have significant

  4. Microbial degradation and utilization of cassava peel.

    Science.gov (United States)

    Ofuya, C O; Nwajiuba, C J

    1990-06-01

    Cassava peel was readily degraded and utilized by a strain ofRhizopus growing in a solid-state fermentation. Growth was maximal at 45°C and was proportional to the degree of hydrolysis of the peel. The yield of biomass, as weight of dry mycellum from the reducing sugars of the peel, was 51%. After 72 h fermentation, the peel contained 76% moisture, 6% cellulose, 7% hemicellulose and 0.4% ash and the protein content had increased from 5.6% to 16%. These results suggest a possible economic value of cassava peel in the production of fungal biomass and feedstock.

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

    Science.gov (United States)

    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

  6. Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

    Science.gov (United States)

    Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

    2012-09-01

    Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

  7. Quantifying online visuomotor feedback utilization in the frequency domain.

    Science.gov (United States)

    de Grosbois, John; Tremblay, Luc

    2016-12-01

    The utilization of sensory information during activities of daily living is ubiquitous both prior to and during movements (i.e., related to planning and online control, respectively). Because of the overlapping nature of online corrective processes, the quantification of feedback utilization has proven difficult. In the present study, we primarily sought to evaluate the utility of a novel analysis in the frequency domain for identifying visuomotor feedback utilization (i.e., online control). A second goal was to compare the sensitivity of the frequency analysis to that of currently utilized measures of online control. Participants completed reaching movements to targets located 27, 30, and 33 cm from a start position. During these reaches, vision of the environment was either provided or withheld. Performance was assessed across contemporary measures of online control. For the novel frequency analysis presented in this study, the acceleration profiles of reaching movements were detrended with a 5th-order polynomial fit, and the proportional power spectra were computed from the residuals of these fits. The results indicated that the use of visual feedback during reaching movements increased the contribution of the 4.68-Hz frequency to the residuals of the acceleration profiles. Comparisons across all measures of online control showed that the most sensitive measure was the squared Fisher transform of the correlation between the positions at 75 % and 100 % of the movement time. However, because such correlational measures can be contaminated by offline control processes, the frequency-domain analysis proposed herein represents a viable and promising alternative to detect changes in online feedback utilization.

  8. Microbial Phytase and Phosphorus Utilization by Broiler Chickens

    Directory of Open Access Journals (Sweden)

    Martin Kliment

    2012-05-01

    Full Text Available The aim of study was to investigate the mathematical and statistical assesment of the micorbial 6-phytase efficacy on phosphorus utilization at broiler chickens Cobb 500. Broiler chickens fed commercial feed mixtures based on soyabean-maize meal. Each feed mixture was fed ad libitum to chickens in boxes in commercial poultry farm. The trial consited of three groups of broiler chickens, one control group (CG and two trial groups, in which were broiler chickens fed by feed mixtures with decreased phosphorus content (TG1 and with microbial 6-phytase (TG2. A body weight of chickens at the end of the trial (42 day was 1900.0 g compared with 1883,0 g (TG1 and 1827.0 g (CG with not statistically significant differences (P≥0.05. Phosphorus, calcium and magnesium content in blood serum of broiler chickens in every group was not staticstically significant (P≥0.05. Phosphorus content in broiler chickens excreta was most higher in in control group (4.2556 g/kg in comparison with trial group (2.0911 g/kg were was microbial 6-phytase added and in trial group (3.1851 g/kg were was phosphorus content in feed mixtures decreased. In addition we concluded that microbial 6-phytase. Phytase addition into feed mixtures has not negative effect on broiler chickens growth ability and health, and helped to better utilization of phytate phosphorus from feed mixtures in relation to excreted phosphorus.

  9. Passive methods for quantifying the In Situ Flux of Water, Uranium, and Microbial Biomass

    Science.gov (United States)

    Newman, M. A.; Peacock, A.; Hatfield, K.; Stucker, V.; Cho, J.; Klammler, H.; Ranville, J. F.; Cabaniss, S.; Annable, M. D.; Perminova, I.

    2011-12-01

    /d and 183 mg/d respectively. The uranium flux measured by the PFM sensor and Biomass fluxes estimated from BMLS data and PFM water fluxes will be used to characterize microbial community and active biomass at synonymous wells in order to quantify spatial changes in uranium flux and field-scale rates of uranium attenuation (ambient and stimulated).

  10. Quantifying the structure of the mesopelagic microbial loop from observed depth profiles of bacteria and protozoa

    Directory of Open Access Journals (Sweden)

    T. F. Thingstad

    2004-08-01

    Full Text Available t is widely recognized that organic carbon exported to the ocean aphotic layer is significantly consumed by heterotrophic organisms such as bacteria and zooplankton in the mesopelagic layer. However, very little is known for the trophic link between bacteria and zooplankton or the structure of the microbial loop in this layer. In the northwestern Mediterranean, recent studies have shown that viruses, bacteria, heterotrophic nanoflagellates, and ciliates distribute down to 2000 m with group-specific depth-dependent decreases, and that bacterial production decreases with depth down to 1000 m. Here we show that such data can be analyzed using a simple steady-state food chain model to quantify the carbon flow from bacteria to zooplankton over the mesopelagic layer. The model indicates that a similar amount of bacterial production is allocated to viruses and heterotrophic nanoflagellates, and that heterotrophic nanoflagellates are the important remineralizers.

  11. Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods

    Science.gov (United States)

    Keisam, Santosh; Romi, Wahengbam; Ahmed, Giasuddin; Jeyaram, Kumaraswamy

    2016-01-01

    Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9–52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods. PMID:27669673

  12. [Biomass energy utilization in microbial fuel cells: potentials and challenges].

    Science.gov (United States)

    Huang, Liping; Cheng, Shaoan

    2010-07-01

    Microbial fuel cells (MFCs) that can harvest biomass energy from organic wastes through microbial catalysis have garnered more and more attention within the past decade due to its potential benefits to ecological environment. In this article, the updated progress in MFCs is reviewed, with a focus on frontier technologies such as chamber configurations, feedstock varieties and the integration of MFCs with microbial electrolysis cells for hydrogen production. And on the other hand, the challenges like development of cost-effective electrode materials, improvement of biomass energy recovery and power output, design and optimization of commercial MFC devices are presented.

  13. Utilization of Alternate Chirality Enantiomers in Microbial Communities

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-01-01

    Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

  14. Radiation application for the utilization of microbial resources

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Keun; Kim, Jae Sung; Lee, Sang Jae (and others)

    2007-07-15

    Domestic microbes which had the antifungal, pesticide residue degradable, and heavy metal adsorbent activities were isolated individually. Mutants of their improved functions were induced by radiation. And finally microbial formulae of biocontroller were manufactured and respected to be industrialized promisingly. The effectiveness of the developed microbial formulae were confirmed in pepper, radish, and Chinese cabbage by field experiments for 5 kinds of fungal diseases. This technology is respected to be transferred to the agricultural companies. And a novel venture company could be established by the involved researchers using this technology. As a result, the productivity in environmentally-friendly farm could be improved gradually in the near future.

  15. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    Science.gov (United States)

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies

    Energy Technology Data Exchange (ETDEWEB)

    Rosnow, Joshua J. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Anderson, Lindsey N. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Nair, Reji N. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Baker, Erin S. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA; Wright, Aaron T. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

    2016-07-20

    The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emergent technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint to advance biofuel production.

  17. Microbial utilization of sugars in soil assessed by position-specific labeling and compound-specific 13C-PLFA-analysis

    Science.gov (United States)

    Apostel, Carolin; Dippold, Michaela; Glaser, Bruno; Kuzyakov, Yakov

    2014-05-01

    For the transformation of low molecular weight organic substances (LMWOS) in soil, which is an important process in the turnover of organic matter, microbial utilization is one of the most important processes. Position-specific labeling combined with compound-specific 13C-PLFA-analysis allows a closer look on the mechanisms of LMWOS transformation in soil. We assessed short- (3 and 10 days) and long-term (half year) transformations of monosaccharides by adding position-specifically 13C labeled glucose and ribose to soil in a field experiment conducted on an agriculturally used luvisol located in north-western Bavaria. We quantified the microbial utilization of the different functional groups by 13C-analysis of microbial biomass with the chloroform-fumigation-extraction method (CFE). 13C-PLFA analysis enabled us to distinguish individual microbial groups and compare their C-utilization. Preferential degradation of glucoses C-3 and C-4 respectively C-1 position enabled differentiation between the two main hexose metabolic pathways - glycolysis and the pentose phosphate pathway. Microbial groups revealed different incorporation of specific C positions into their PLFA. The highest incorporation was reached by the prokaryotic gram- negative groups. The application of position-specifically labeled substances, coupled with compound-specific 13C-PLFA analysis opens a new way to investigate the microbial transformations of LMWOS in soil. Observing single C atoms and their utilization by specific microbial groups allow conclusions about the mechanisms and kinetics of microbial utilization and interaction between these groups and therefore will improve our understanding of soil carbon fluxes.

  18. Microbial risk and removal--a utility perspective.

    Science.gov (United States)

    Stanger, M; Agutter, P A; Lake, R C; Ashbolt, N J; Roser, D J

    2006-01-01

    In this paper the results of a sampling programme, undertaken as part of the EU MicroRisk project, are described. This project was undertaken to ascertain the occurrence of pathogens and indicators in the River Thames and their subsequent removal through a treatment works. Appropriate physico-chemical surrogates, as determined by statistical correlation are proposed for the microorganisms identified in the raw water. This study shows that under normal raw water conditions the treatment works is able to remove microbial contamination with a significant margin of safety.

  19. Utilization of Practice Session Average Inertial Load to Quantify College Football Injury Risk.

    Science.gov (United States)

    Wilkerson, Gary B; Gupta, Ashish; Allen, Jeff R; Keith, Clay M; Colston, Marisa A

    2016-09-01

    Wilkerson, GB, Gupta, A, Allen, JR, Keith, CM, and Colston, MA. Utilization of practice session average inertial load to quantify college football injury risk. J Strength Cond Res 30(9): 2369-2374, 2016-Relatively few studies have investigated the potential injury prevention value of data derived from recently developed wearable technology for measurement of body mass accelerations during the performance of sport-related activities. The available evidence has been derived from studies focused on avoidance of overtraining syndrome, which is believed to induce a chronically fatigued state that can be identified through monitoring of inertial load accumulation. Reduced variability in movement patterns is also believed to be an important injury risk factor, but no evidence currently exists to guide interpretation of data derived from inertial measurement units (IMUs) in this regard. We retrospectively analyzed archived data for a cohort of 45 National Collegiate Athletic Association Division 1-football bowl subdivision football players who wore IMUs on the upper back during practice sessions to quantify any associations between average inertial load measured during practice sessions and occurrence of musculoskeletal sprains and strains. Both the coefficient of variation for average inertial load and frequent exposure to game conditions were found to be strongly associated with injury occurrence. Having either or both of the 2 risk factors provided strong discrimination between injured and noninjured players (χ = 9.048; p = 0.004; odds ratio = 8.04; 90% CI: 2.39, 27.03). Our findings may facilitate identification of individual football players who are likely to derive the greatest benefit from training activities designed to reduce injury risk through improved adaptability to rapidly changing environmental demands.

  20. Engineering sugar utilization and microbial tolerance toward lignocellulose conversion

    Directory of Open Access Journals (Sweden)

    Lizbeth M. Nieves

    2015-02-01

    Full Text Available Production of fuels and chemicals through a fermentation-based manufacturing process that uses renewable feedstock such as lignocellulosic biomass is a desirable alternative to petrochemicals. Although it is still in its infancy, synthetic biology offers great potential to overcome the challenges associated with lignocellulose conversion. In this review, we will summarize the identification and optimization of synthetic biological parts used to enhance the utilization of lignocellulose-derived sugars and to increase the biocatalyst tolerance for lignocellulose-derived fermentation inhibitors. We will also discuss the ongoing efforts and future applications of synthetic integrated biological systems used to improve lignocellulose conversion.

  1. Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

    Science.gov (United States)

    Musat, N.; Kuypers, M. M. M.

    2009-04-01

    Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

  2. Microbial network for waste activated sludge cascade utilization in an integrated system of microbial electrolysis and anaerobic fermentation

    DEFF Research Database (Denmark)

    Liu, Wenzong; He, Zhangwei; Yang, Chunxue

    2016-01-01

    and Parabacteroides, which showed a delayed contribution to the extracellular electron transport leading to a slow cascade utilization of WAS. Conclusions: Efficient pretreatment could supply more short-chain fatty acids and higher conductivities in the fermentative liquid, which facilitated mass transfer in anodic......Background: Bioelectrochemical systems have been considered a promising novel technology that shows an enhanced energy recovery, as well as generation of value-added products. A number of recent studies suggested that an enhancement of carbon conversion and biogas production can be achieved...... in an integrated system of microbial electrolysis cell (MEC) and anaerobic digestion (AD) for waste activated sludge (WAS). Microbial communities in integrated system would build a thorough energetic and metabolic interaction network regarding fermentation communities and electrode respiring communities...

  3. [Carbon Source Utilization Characteristics of Soil Microbial Community for Apple Orchard with Interplanting Herbage].

    Science.gov (United States)

    Du, Yi-fei; Fang, Kai-kai; Wang, Zhi-kang; Li, Hui-ke; Mao, Peng-juan; Zhang, Xiang-xu; Wang, Jing

    2015-11-01

    As soil fertility in apple orchard with clean tillage is declined continuously, interplanting herbage in orchard, which is a new orchard management model, plays an important role in improving orchard soil conditions. By using biolog micro-plate technique, this paper studied the functional diversity of soil microbial community under four species of management model in apple orchards, including clear tillage model, interplanting white clover model, interplanting small crown flower model and interplanting cocksfoot model, and the carbon source utilization characteristics of microbial community were explored, which could provide a reference for revealing driving mechanism of ecological process of orchard soil. The results showed that the functional diversity of microbial community had a significant difference among different treatments and in the order of white clover > small crown flower > cocksfoot > clear tillage. The correlation analysis showed that the average well color development (AWCD), Shannon index, Richness index and McIntosh index were all highly significantly positively correlated with soil organic carbon, total nitrogen, microbial biomass carbon, and Shannon index was significantly positively correlated with soil pH. The principal component analysis and the fingerprints of the physiological carbon metabolism of the microbial community demonstrated that grass treatments improved carbon source metabolic ability of soil microbial community, and the soil microbes with perennial legumes (White Clover and small crown flower) had a significantly higher utilization rate in carbohydrates (N-Acetyl-D-Glucosamine, D-Mannitol, β-Methyl-D-Glucoside), amino acids (Glycyl-L-Glutamic acid, L-Serine, L-Threonine) and polymers (Tween 40, Glycogen) than the soil microbes with clear tillage. It was considered that different treatments had the unique microbial community structure and peculiar carbon source utilization characteristics.

  4. Electrochemical Characterization of a Microbial Fuel Cell (MFC) that Utilizes cow Manure as Energy Source

    Energy Technology Data Exchange (ETDEWEB)

    Vinas, M.; Prenafeta, F.; Flotats, X.; Gerritse, J.

    2009-07-01

    Microbial fuel cells are new types of bioreactors that convert the chemical energy encountered in organic matter directly to electricity. The efficiency of this energy conversion is potentially higher than described in other environmental technologies focused on energy production from organic wastes, such as biogas utilization. A MFC reactor utilizes microorganisms as catalysts to transfer electrons from the biological oxidation of the organic matter to an electrode (anode) in anaerobic conditions. (Author)

  5. Changes in enzymes activity, substrate utilization pattern and diversity of soil microbial communities under cadmium pollution

    Institute of Scientific and Technical Information of China (English)

    Muhammad Akmal; WANG Hai-zhen; WU Jian-jun; XU Jian-ming; XU De-fu

    2005-01-01

    Heavy metal pollution has received increasing attention in recent years mainly because of the public awareness of environmental issues. In this study we have evaluated the effect of cadmium(Cd) on enzymes activity, substrate utilization pattern and diversity of microbial communities in soil spiked with 0, 20, 40, 60, 80, and 100 mg/kg Cd, during 60 d of incubation at 25℃. Enzyme activities determined at 0, 15, 30, 45, and 60 d after heavy metal application(DAA) showed marked declines for various Cd treatments, and up to 60 DAA, 100 mg/kg Cd resulted in 50.1%, 47.4%, and 39.8 % decreases in soil urease, acid phosphatase and dehydrogenase activities,respectively to control. At 60 DAA, substrate utilization pattern of soil microbial communities determined by inoculating Biolog ECO plates indicated that Cd addition had markedly inhibited the functional activity of soil microbial communities and multivariate analysis of sole carbon source utilization showed significantly different utilization patterns for 80 and 100 mg/kg Cd treatments. The structural diversity of soil microbial communities assessed by PCR-DGGE method at 60 DAA, illustrated that DGGE patterns in soil simplified with increasing Cd concentration, and clustering of DGGE profiles for various Cd treatments revealed that they had more than 50% difference with that of control.

  6. Quantifying and visualizing the transfer of exogenous plasmids to environmental microbial communities

    DEFF Research Database (Denmark)

    Dechesne, Arnaud

    2015-01-01

    of a community to take up exogenous plasmid should, however, be an important element affecting the fate of mobile genetic elements released in the environment. We have devised a method to evaluate the permissiveness of a bacterial community towards exogenous plasmids, both quantitatively (how many bacteria can......, our findings highlight the high potential for exogenous plasmids to be transferred to soil microbial communities and indicate that community permissiveness – as affected by environmental conditions- needs to be considered to predict the fate of plasmids in the environment....

  7. Amazon peatlands: quantifying ecosytem's stocks, GHG fluxes and their microbial connections

    Science.gov (United States)

    Cadillo-Quiroz, Hinsby; Lähteenoja, Outi; Buessecker, Steffen; van Haren, Joost

    2017-04-01

    Reports of hundreds of peatlands across basins in the West and Central Amazon suggest they play an important, previously not considered regional role in organic carbon (OC) and GHG dynamics. Amazon peatlands store ˜3-6 Gt of OC in their waterlogged soils with strong potential for conversion and release of GHG, in fact our recent, and others', efforts have confirmed variable levels of GHG emissions (CO2, N2O, CH4), as well as variable microbial communities across rich to poor soil peatlands. Here, we report early results of quantification of different components making up the aboveground C stocks, the rates and paths for GHG release, and microbial organisms occurring in three ecologically distinct peatland types in the Pastaza-Marañon region of the Peruvian Amazon. Evaluations were done in duplicated continuous monitoring plots established since 2015 at a "palm swamp" (PS), poor "pole forest" (pPF) and a rich "forested" (rF) peatlands. Although overall vegetation "structure" with a few dominant plus several low frequency species was common across the three sites, their botanical composition and tree density was highly contrasting. Aboveground C stocks content showed the following order among sites: rF>PS>pPF, and hence we tested whether this differences can have a direct effect on CH4 emissions rates. CH4 emissions rates from soils were observed in average at 11, 6, and 0.8 mg-C m-2 h-1for rF, PS, and pPF respectively. However, these estimated fluxes needed to be revised when we develop quantifications of CH4 emissions from tree stems. Tree stem fluxes were detected showing a broad variation with nearly nill emissions in some species all the way to maximum fluxes near to ˜90 mg-C m-2 h-1 in other species. Mauritia flexuosa, a highly dominant palm species in PS and ubiquitous to the region, showed the highest ranges of CH4 flux. In the PS site, overall CH4 flux estimate increased by ˜50% when including stem emission weighted by trees' species, density and heights

  8. Rapid and reagentless detection of microbial contamination within meat utilizing a smartphone-based biosensor

    Science.gov (United States)

    Liang, Pei-Shih; Park, Tu San; Yoon, Jeong-Yeol

    2014-08-01

    A smartphone-utilized biosensor was developed for detecting microbial spoilage on ground beef, without using antibodies, microbeads or any other reagents, towards a preliminary screening tool for microbial contamination on meat products, and potentially towards wound infection. Escherichia coli K12 solutions (101-108 CFU/mL) were added to ground beef products to simulate microbial spoilage. An 880 nm near infrared LED was irradiated perpendicular to the surface of ground beef, and the scatter signals at various angles were evaluated utilizing the gyro sensor and the digital camera of a smartphone. The angle that maximized the Mie scatter varied by the E. coli concentration: 15° for 108 CFU/mL, 30° for 104 CFU/mL, and 45° for 10 CFU/mL, etc. SEM and fluorescence microscopy experiments revealed that the antigens and cell fragments from E. coli bonded preferably to the fat particles within meat, and the size and morphologies of such aggregates varied by the E. coli concentration.

  9. Rice rhizodeposition and its utilization by microbial groups depends on nitrogen fertilization

    Science.gov (United States)

    Ge, Tida; Zhu, Zhenke; Wu, Jinshui

    2016-04-01

    Rhizodeposited carbon (C) has received considerable attention because it plays an important role in regulating soil C sequestration and global C cycling, and represents the main C source for rhizosphere microorganisms. However, limited information exists on the utilization of rhizodeposited C by different microbial groups, its role in the turnover of soil organic matter (SOM) pools in rice paddies and how this is influenced by nitrogen (N) fertilization. Rice (Oryza sativa L.) was grown in soil at one of five N fertilization rates (0, 10, 20, 40, or 60 mg N kg-1 soil) and then continuously labeled by exposure to a 13CO2 atmosphere for 18 days. The utilization of root-derived C by microbial groups within the rhizosphere was assessed by following the incorporation of 13C into phospholipid fatty acids (PLFAs). Rice shoot and root biomass strongly increased with N fertilization rate. Rhizodeposition was greater, but total 13C incorporation into microorganisms was lower, in N-fertilized soils than in unfertilized soil. The contribution of root-derived 13C to SOM formation increased with root biomass. The roots tended to grow into large aggregates (0.25-2.0 mm diameter), and N fertilization stimulated incorporation of 13C into these macroaggregates, presumably due to the relatively high root biomass. The ratio of 13C in soil pools (SOM, microbial biomass) to 13C in roots decreased as a result of N fertilization. N fertilization increased 13C incorporation into fungi (18:2ω6, 9c, 18:1ω9c), AM fungi (16:1ω5c), and actinomycetes (10Me 16:0, 10Me 18:0), but decreased 13C incorporation into Gram-positive (i14:0, i15:0, a15:0, i16:0, i17:0, a17:0) and Gram-negative (16:1ω7c, 18:1ω7c, cy17:0, cy19:0) bacteria. Thus, the uptake and processing of root-derived C by microbial groups depended on soil N status. Relative to the unfertilized controls, the contribution of rhizodeposited-C to SOM and microorganisms was increased by low to intermediate N fertilization rates, but

  10. Quantifying the Effect of Fast Charger Deployments on Electric Vehicle Utility and Travel Patterns via Advanced Simulation: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Wood, E.; Neubauer, J.; Burton, E.

    2015-02-01

    The disparate characteristics between conventional (CVs) and battery electric vehicles (BEVs) in terms of driving range, refill/recharge time, and availability of refuel/recharge infrastructure inherently limit the relative utility of BEVs when benchmarked against traditional driver travel patterns. However, given a high penetration of high-power public charging combined with driver tolerance for rerouting travel to facilitate charging on long-distance trips, the difference in utility between CVs and BEVs could be marginalized. We quantify the relationships between BEV utility, the deployment of fast chargers, and driver tolerance for rerouting travel and extending travel durations by simulating BEVs operated over real-world travel patterns using the National Renewable Energy Laboratory's Battery Lifetime Analysis and Simulation Tool for Vehicles (BLAST-V). With support from the U.S. Department of Energy's Vehicle Technologies Office, BLAST-V has been developed to include algorithms for estimating the available range of BEVs prior to the start of trips, for rerouting baseline travel to utilize public charging infrastructure when necessary, and for making driver travel decisions for those trips in the presence of available public charging infrastructure, all while conducting advanced vehicle simulations that account for battery electrical, thermal, and degradation response. Results from BLAST-V simulations on vehicle utility, frequency of inserted stops, duration of charging events, and additional time and distance necessary for rerouting travel are presented to illustrate how BEV utility and travel patterns can be affected by various fast charge deployments.

  11. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

    Science.gov (United States)

    Sharpton, Thomas J; Riesenfeld, Samantha J; Kembel, Steven W; Ladau, Joshua; O'Dwyer, James P; Green, Jessica L; Eisen, Jonathan A; Pollard, Katherine S

    2011-01-20

    Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?

  12. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

    Directory of Open Access Journals (Sweden)

    Thomas J Sharpton

    Full Text Available Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA sequences into operational taxonomic units (OTUs. Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?

  13. Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean

    Science.gov (United States)

    Arrieta, Jesús M.; Duarte, Carlos M.; Sala, M. Montserrat; Dachs, Jordi

    2016-01-01

    Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget. PMID:26834717

  14. Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean

    KAUST Repository

    Arrieta, Jesus

    2016-01-20

    Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget.

  15. Harvest and utilization of chemical energy in wastes by microbial fuel cells.

    Science.gov (United States)

    Sun, Min; Zhai, Lin-Feng; Li, Wen-Wei; Yu, Han-Qing

    2016-05-21

    Organic wastes are now increasingly viewed as a resource of energy that can be harvested by suitable biotechnologies. One promising technology is microbial fuel cells (MFC), which can generate electricity from the degradation of organic pollutants. While the environmental benefits of MFC in waste treatment have been recognized, their potential as an energy producer is not fully understood. Although progresses in material and engineering have greatly improved the power output from MFC, how to efficiently utilize the MFC's energy in real-world scenario remains a challenge. In this review, fundamental understandings on the energy-generating capacity of MFC from real waste treatment are provided and the challenges and opportunities are discussed. The limiting factors restricting the energy output and impairing the long-term reliability of MFC are also analyzed. Several energy storage and in situ utilization strategies for the management of MFC's energy are proposed, and future research needs for real-world application of this approach are explored.

  16. Phosphorus utilization and microbial community in response to lead/iron addition to a waterlogged soil

    Institute of Scientific and Technical Information of China (English)

    ZHONG Shunqing; WU Yuping; XU Jianming

    2009-01-01

    Constructed wetlands have emerged as a viable option for helping to solve a wide range of water quality problems. However, heavy metals adsorbed by substrates would decrease the growth of plants, impair the functions of wetlands and eventually result in failure of contaminant removal. Typha latifolia L., tolerant to heavy metals, has been widely used for phytoremediation of Pb/Zn mine tailings under waterlogged conditions. This study examined effects of iron as ferrous sulfate (100 and 500 mg/kg) and lead as lead nitrate (0, 100, 500 and 1000 mg/kg) on phosphorus utilization and microbial community structure in a constructed wetland. Wetland plants (T. latifolia) were grown for 8 weeks in rhizobags filled with a paddy soil under waterlogged conditions. The results showed that both the amount of iron plaque on the roots and phosphorus adsorbed on the plaque decreased with the amount of lead addition. When the ratio of added iron to lead was 1:1, phosphorus utilized by plants was the maximum. Total amount of phospholipids fatty acids (PLFAs) was 23%-59% higher in the rhizosphere soil than in bulk soil. The relative abundance of Gram-negative bacteria, aerobic bacteria, and methane oxidizing bacteria was also higher in the rhizosphere soil than in bulk soil, but opposite was observed for other bacteria and fungi. Based on cluster analysis, microbial communities were mostly controlled by the addition of ferrous sulfate and lead nitrate in rhizosphere and bulk soil, respectively.

  17. Quantifying the release of lactose from polymer matrix tablets with an amperometric biosensor utilizing cellobiose dehydrogenase.

    Science.gov (United States)

    Knöös, Patrik; Schulz, Christopher; Piculell, Lennart; Ludwig, Roland; Gorton, Lo; Wahlgren, Marie

    2014-07-01

    The release of lactose (hydrophilic) from polymer tablets made with hydrophobically modified poly(acrylic acid) (HMPAA) have been studied and compared to the release of ibuprofen, a hydrophobic active substance. Lactose is one of the most used excipients for tablets, but lactose release has not been widely studied. One reason could be a lack of good analytical tools. A novel biosensor with cellobiose dehydrogenase (CDH) was used to detect the lactose release, which has a polydiallyldimethylammonium chloride (PDADMAC) layer that increases the response. A sample treatment using polyethylenimine (PEI) was developed to eliminate possible denaturants. The developed methodology provided a good approach to detect and quantify the released lactose. The release was studied with or without the presence of a model amphiphilic substance, sodium dodecyl sulphate (SDS), in the release medium. Ibuprofen showed very different release rates in the different media, which was attributed to hydrophobic interactions between the drug, the HMPAA and the SDS in the release medium. The release of hydrophilic lactose, which did not associate to any of the other components, was rapid and showed only minor differences. The new methodology provides a useful tool to further evaluate tablet formulations by a relatively simple set of experiments.

  18. Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides

    Directory of Open Access Journals (Sweden)

    Magnus Liljenberg

    2013-04-01

    Full Text Available A computational approach using density functional theory to compute the energies of the possible σ-complex reaction intermediates, the “σ-complex approach”, has been shown to be very useful in predicting regioselectivity, in electrophilic as well as nucleophilic aromatic substitution. In this article we give a short overview of the background for these investigations and the general requirements for predictive reactivity models for the pharmaceutical industry. We also present new results regarding the reaction rates and regioselectivities in nucleophilic substitution of fluorinated aromatics. They were rationalized by investigating linear correlations between experimental rate constants (k from the literature with a theoretical quantity, which we call the sigma stability (SS. The SS is the energy change associated with formation of the intermediate σ-complex by attachment of the nucleophile to the aromatic ring. The correlations, which include both neutral (NH3 and anionic (MeO− nucleophiles are quite satisfactory (r = 0.93 to r = 0.99, and SS is thus useful for quantifying both global (substrate and local (positional reactivity in SNAr reactions of fluorinated aromatic substrates. A mechanistic analysis shows that the geometric structure of the σ-complex resembles the rate-limiting transition state and that this provides a rationale for the observed correlations between the SS and the reaction rate.

  19. Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides.

    Science.gov (United States)

    Liljenberg, Magnus; Brinck, Tore; Rein, Tobias; Svensson, Mats

    2013-01-01

    A computational approach using density functional theory to compute the energies of the possible σ-complex reaction intermediates, the "σ-complex approach", has been shown to be very useful in predicting regioselectivity, in electrophilic as well as nucleophilic aromatic substitution. In this article we give a short overview of the background for these investigations and the general requirements for predictive reactivity models for the pharmaceutical industry. We also present new results regarding the reaction rates and regioselectivities in nucleophilic substitution of fluorinated aromatics. They were rationalized by investigating linear correlations between experimental rate constants (k) from the literature with a theoretical quantity, which we call the sigma stability (SS). The SS is the energy change associated with formation of the intermediate σ-complex by attachment of the nucleophile to the aromatic ring. The correlations, which include both neutral (NH3) and anionic (MeO(-)) nucleophiles are quite satisfactory (r = 0.93 to r = 0.99), and SS is thus useful for quantifying both global (substrate) and local (positional) reactivity in SNAr reactions of fluorinated aromatic substrates. A mechanistic analysis shows that the geometric structure of the σ-complex resembles the rate-limiting transition state and that this provides a rationale for the observed correlations between the SS and the reaction rate.

  20. Novel method utilizing microbial treatment for cleaner production of diosgenin from Dioscorea zingiberensis C.H. Wright (DZW).

    Science.gov (United States)

    Wei, Mi; Bai, Yun; Ao, Mingzhang; Jin, Wenwen; Yu, Panpan; Zhu, Min; Yu, Longjiang

    2013-10-01

    A novel method utilizing microbial treatment for cleaner production of diosgenin from Dioscorea zingiberensis C.H. Wright (DZW) was presented. A new Bacillus pumilus HR19, which has the great ability to secrete pectinase, was screened and applied in the microbial treatment. Low-pressure steam expansion pretreatment (LSEP) was employed in advance to assist microbial treatment efficiently in releasing saponins, which are the precursors of diosgenin. Compared with the traditional process of acid hydrolysis, this novel process reduced the consumptions of water, acid and organic solvent by more than 92.5%, 97.0%, 97.0%, respectively, while simultaneously increasing the diosgenin yield by 6.21%. In addition, the microbial treatment was more efficient than enzymatic treatment, which arised from that microorganisms could be induced to secrete related enzymes by the compositions of DZW and relieve product inhibition by utilizing enzyme hydrolysates.

  1. Microbial utilization of low molecular weight organics in soil depends on the substances properties

    Science.gov (United States)

    Gunina, Anna

    2016-04-01

    Utilization of low molecular weight organic substances (LMWOS) in soil is regulated by microbial uptake from solution and following incorporation of into specific cell cycles. Various chemical properties of LMWOS, namely oxidation state, number of carbon (C) atoms, number of carboxylic (-COOH) groups, can affect their uptake from soil solution and further microbial utilization. The aim of the study was to trace the initial fate (including the uptake from soil solution and utilization by microorganisms) of three main classes of LMWOS, having contrast properties - sugars, carboxylic and amino acids. Top 10 cm of mineral soil were collected under Silver birch stands within the Bangor DIVERSE experiment, UK. Soil solution was extracted by centrifugation at 4000 rpm during 15 min. Soil was spiked with 14C glucose or fructose; malic, succinic or formic acids; alanine or glycine. No additional non-labeled LMWOS were added. 14C was traced in the dissolved organic matter (DOM), CO2, cytosol and soil organic matter (SOM) during one day. To estimate half-life times (T1 /2)of LMWOS in soil solution and in SOM pools, the single and double first order kinetic equations were fitted to the uptake and mineralization dynamics, respectively. The LMWOS T1 /2in DOM pool varied between 0.6-5 min, with the highest T1 /2for sugars (3.7 min) and the lowest for carboxylic acids (0.6-1.4 min). Thus, initial uptake of LMWOS is not a limiting step of microbial utilization. The T1 /2 of carboxylic and amino acids in DOM were closely related with oxidation state, showing that reduced substances remain in soil solution longer, than oxidized. The initial T1 /2 of LMWOS in SOM ranged between 30-80 min, with the longest T1 /2 for amino acids (50-80 min) and the shortest for carboxylic acids (30-48 min). These T1 /2values were in one-two orders of magnitude higher than LMWOS T1 /2 in soil solution, pointing that LMWOS mineralization occur with a delay after the uptake. Absence of correlations between

  2. Utilizing dynamic tensiometry to quantify contact angle hysteresis and wetting state transitions on nonwetting surfaces.

    Science.gov (United States)

    Kleingartner, Justin A; Srinivasan, Siddarth; Mabry, Joseph M; Cohen, Robert E; McKinley, Gareth H

    2013-11-05

    Goniometric techniques traditionally quantify two parameters, the advancing and receding contact angles, that are useful for characterizing the wetting properties of a solid surface; however, dynamic tensiometry, which measures changes in the net force on a surface during the repeated immersion and emersion of a solid into a probe liquid, can provide further insight into the wetting properties of a surface. We detail a framework for analyzing tensiometric results that allows for the determination of wetting hysteresis, wetting state transitions, and characteristic topographical length scales on textured, nonwetting surfaces, in addition to the more traditional measurement of apparent advancing and receding contact angles. Fluorodecyl POSS, a low-surface-energy material, was blended with commercially available poly(methyl methacrylate) (PMMA) and then dip- or spray-coated onto glass substrates. These surfaces were probed with a variety of liquids to illustrate the effects of probe liquid surface tension, solid surface chemistry, and surface texture on the apparent contact angles and wetting hysteresis of nonwetting surfaces. Woven meshes were then used as model structured substrates to add a second, larger length scale for the surface texture. When immersed into a probe liquid, these spray-coated mesh surfaces can form a metastable, solid-liquid-air interface on the largest length scale of surface texture. The increasing hydrostatic pressure associated with progressively greater immersion depths disrupts this metastable, composite interface and forces penetration of the probe liquid into the mesh structure. This transition is marked by a sudden change in the wetting hysteresis, which can be systematically probed using spray-coated, woven meshes of varying wire radius and spacing. We also show that dynamic tensiometry can accurately and quantitatively characterize topographical length scales that are present on microtextured surfaces.

  3. Microbial utilization of rice straw and its derived biochar in a paddy soil

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Fuxia [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yaying [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China); Chapman, Stephen James [The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH (United Kingdom); Khan, Sardar [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Department of Environmental Science, University of Peshawar (Pakistan); Yao, Huaiying, E-mail: hyyao@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 (China); Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo 315800 (China)

    2016-07-15

    that the function, size and structure of the microbial community were strongly influenced by the substrate composition and availability. - Highlights: • The influence of straw/biochar on CO{sub 2} emission and microbial community was tested. • Straw significantly increased respiration and PLFAs than biochar and the control. • {sup 13}C-PLFA profile in straw amendment was significantly different from biochar. • Soil microorganisms utilized more straw-C than biochar-C • The substrate composition/availability influenced the microbes and their function.

  4. Performance and Nutrient Utilization of Layers Fed Diet Supplemented with Microbial Phytase and Cellulase

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A 31-week feeding trial was conducted to investigated the effects of dietary supplementation of microbial phytase and cellulase on performance,nutrients utilization and tibia quality of laying hens fed maize and soybean meal diets.192 18-week-old Hisex layers were used in the trial A 2×2×2 factorial design was used in the experiment with three factors of two levels each:0.38% and 0.16% of dietary non-phytate P(nP).0 and 300 U*kg-1 of phytase (Ph),and 0 and 0.10% of cellulase (Ce).The results showed that supplementation of 300 U*kg-1 phytase significantly improved utilization of dietary crude ash,CP,Ca,total P and copper (P<0.05),and improved tibia breaking strength (P<0.05).No effect of phytase on performance was observed.Addition of 0.10% cellulase decreased feed intake (P<0.05),increased utilization of CF (P<0.05) and Ca(P<0.01),and decreased total tibia ash weight (P<0.05).300 U*kg-1 phytase and 0.10% cellulase exhibited obvious positive interactions to enhance utilization of dietary phytic P and copper (P<0.05).0.16% nP did not reduce performance of the layers,but improved egg shell quality at 20 wks,increased utilization of dietary total P,phytic P and Copper (P<0.01),decreased utilization of dietary CP,increased tibia breaking strength and Ca,Mn contents of tibia(P<0.01)

  5. Functional diversity of the microbial community in healthy subjects and periodontitis patients based on sole carbon source utilization.

    Directory of Open Access Journals (Sweden)

    Yifei Zhang

    Full Text Available Chronic periodontitis is one of the most common forms of biofilm-induced diseases. Most of the recent studies were focus on the dental plaque microbial diversity and microbiomes. However, analyzing bacterial diversity at the taxonomic level alone limits deeper comprehension of the ecological relevance of the community. In this study, we compared the metabolic functional diversity of the microbial community in healthy subjects and periodontitis patients in a creative way--to assess the sole carbon source utilization using Biolog assay, which was first applied on oral micro-ecology assessment. Pattern analyses of 95-sole carbon sources catabolism provide a community-level phenotypic profile of the microbial community from different habitats. We found that the microbial community in the periodontitis group had greater metabolic activity compared to the microbial community in the healthy group. Differences in the metabolism of specific carbohydrates (e.g. β-methyl-D-glucoside, stachyose, maltose, D-mannose, β-methyl-D-glucoside and pyruvic acid were observed between the healthy and periodontitis groups. Subjects from the healthy and periodontitis groups could be well distinguished by cluster and principle component analyses according to the utilization of discriminate carbon sources. Our results indicate significant difference in microbial functional diversity between healthy subjects and periodontitis patients. We also found Biolog technology is effective to further our understanding of community structure as a composite of functional abilities, and it enables the identification of ecologically relevant functional differences among oral microbial communities.

  6. Energy utilization, nitrogen balance and microbial protein supply in cattle fed Pennisetum purpureum and condensed tannins.

    Science.gov (United States)

    Piñeiro-Vázquez, A T; Canul-Solis, J R; Alayón-Gamboa, J A; Chay-Canul, A J; Ayala-Burgos, A J; Solorio-Sánchez, F J; Aguilar-Pérez, C F; Ku-Vera, J C

    2017-02-01

    The aim of the experiment was to assess the effect of condensed tannins (CT) on feed intake, dry matter digestibility, nitrogen balance, supply of microbial protein to the small intestine and energy utilization in cattle fed a basal ration of Pennisetum purpureum grass. Five heifers (Bos taurus × Bos indicus) with an average live weight of 295 ± 19 kg were allotted to five treatments consisting of increasing levels of CT (0, 1, 2, 3 and 4% CT/kg DM) in a 5 × 5 Latin square design. Dry matter intake (DMI) was similar (p > 0.05) between treatments containing 0, 1, 2 and 3% of CT/kg DM and it was reduced (p balance, purine derivatives excretion in urine, microbial protein synthesis and efficiency of synthesis of microbial nitrogen in the rumen were not affected (p ≥ 0.05) by the increase in the levels of condensed tannins in the ration. Energy loss as CH4 was on average 2.7% of the gross energy consumed daily. Metabolizable energy intake was 49.06 MJ/day in cattle fed low-quality tropical grass with a DMI of 6.27 kg/day. It is concluded that concentrations of CT between 2 and 3% of DM of ration reduced energy loss as CH4 by 31.3% and 47.6%, respectively, without affecting intakes of dry and organic matter; however, digestibilities of dry and organic matter are negatively affected.

  7. Combined Effect of Nutrient and Pest Managements on Substrate Utilization Pattern of Soil Microbial Population in Hybrid Rice Cropping System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A field experiment was conducted to study the combined effect of nutrient and pest managements on soil biomass phospholipid contents, functional biodiversity and substrate utilization patterns of soil microbial populations in hybrid rice cropping system. The mineral N, P and K fertilizers (as urea, calcium superphosphate and KCl respectively) were incorporated at 100, 25, and 100 kg ha-1, respectively, and the various pesticides were applied at the recommended rates. The results of the experiment demonstrated a decline in the microbial abundance and soil microbial biomass phospholipid contents with the advancement of crop growth, and significant changes in substrate utilization pattern of soil microbial population studied were observed with different management practices and at different growth stages. The principal component analysis (PGA) using all 95-carbon sources (BIOLOG plates) gave good differentiation among the treatments, indicating that they have different patterns of carbon utilization under different habitats. The data showed that diversity in microbial community continuously changed with the progression in crop stage, particularly at physiological maturity (PM) stage that was evident from the utilization of different carbon sources at various crop stages.

  8. Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia

    Directory of Open Access Journals (Sweden)

    Semen A. Leyn

    2017-07-01

    Full Text Available Two nearly identical unicyanobacterial consortia (UCC were previously isolated from benthic microbial mats that occur in a heliothermal saline lake in northern Washington State. Carbohydrates are a primary source of carbon and energy for most heterotrophic bacteria. Since CO2 is the only carbon source provided, the cyanobacterium must provide a source of carbon to the heterotrophs. Available genomic sequences for all members of the UCC provide opportunity to investigate the metabolic routes of carbon transfer between autotroph and heterotrophs. Here, we applied a subsystem-based comparative genomics approach to reconstruct carbohydrate utilization pathways and identify glycohydrolytic enzymes, carbohydrate transporters and pathway-specific transcriptional regulators in 17 heterotrophic members of the UCC. The reconstructed metabolic pathways include 800 genes, near a one-fourth of which encode enzymes, transporters and regulators with newly assigned metabolic functions resulting in discovery of novel functional variants of carbohydrate utilization pathways. The in silico analysis revealed the utilization capabilities for 40 carbohydrates and their derivatives. Two Halomonas species demonstrated the largest number of sugar catabolic pathways. Trehalose, sucrose, maltose, glucose, and beta-glucosides are the most commonly utilized saccharides in this community. Reconstructed regulons for global regulators HexR and CceR include central carbohydrate metabolism genes in the members of Gammaproteobacteria and Alphaproteobacteria, respectively. Genomics analyses were supplemented by experimental characterization of metabolic phenotypes in four isolates derived from the consortia. Measurements of isolate growth on the defined medium supplied with individual carbohydrates confirmed most of the predicted catabolic phenotypes. Not all consortia members use carbohydrates and only a few use complex polysaccharides suggesting a hierarchical carbon flow from

  9. Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia

    Science.gov (United States)

    Leyn, Semen A.; Maezato, Yukari; Romine, Margaret F.; Rodionov, Dmitry A.

    2017-01-01

    Two nearly identical unicyanobacterial consortia (UCC) were previously isolated from benthic microbial mats that occur in a heliothermal saline lake in northern Washington State. Carbohydrates are a primary source of carbon and energy for most heterotrophic bacteria. Since CO2 is the only carbon source provided, the cyanobacterium must provide a source of carbon to the heterotrophs. Available genomic sequences for all members of the UCC provide opportunity to investigate the metabolic routes of carbon transfer between autotroph and heterotrophs. Here, we applied a subsystem-based comparative genomics approach to reconstruct carbohydrate utilization pathways and identify glycohydrolytic enzymes, carbohydrate transporters and pathway-specific transcriptional regulators in 17 heterotrophic members of the UCC. The reconstructed metabolic pathways include 800 genes, near a one-fourth of which encode enzymes, transporters and regulators with newly assigned metabolic functions resulting in discovery of novel functional variants of carbohydrate utilization pathways. The in silico analysis revealed the utilization capabilities for 40 carbohydrates and their derivatives. Two Halomonas species demonstrated the largest number of sugar catabolic pathways. Trehalose, sucrose, maltose, glucose, and beta-glucosides are the most commonly utilized saccharides in this community. Reconstructed regulons for global regulators HexR and CceR include central carbohydrate metabolism genes in the members of Gammaproteobacteria and Alphaproteobacteria, respectively. Genomics analyses were supplemented by experimental characterization of metabolic phenotypes in four isolates derived from the consortia. Measurements of isolate growth on the defined medium supplied with individual carbohydrates confirmed most of the predicted catabolic phenotypes. Not all consortia members use carbohydrates and only a few use complex polysaccharides suggesting a hierarchical carbon flow from cyanobacteria to

  10. Copper catalysis for enhancement of cobalt leaching and acid utilization efficiency in microbial fuel cells.

    Science.gov (United States)

    Liu, Yaxuan; Shen, Jingya; Huang, Liping; Wu, Dan

    2013-11-15

    Enhancement of both cobalt leaching from LiCoO2 and acid utilization efficiency (AUE) in microbial fuel cells (MFCs) was successfully achieved by the addition of Cu(II). A dosage of 10mg/L Cu(II) improved both cobalt leaching up to 308% and AUE of 171% compared to the controls with no presence of Cu(II). The apparent activation energy of cobalt leaching catalyzed by Cu(II) in MFCs was only 11.8 kJ/mol. These results demonstrate cobalt leaching in MFCs using Cu(II) as a catalyst may be an effective strategy for cobalt recovery and recycle of spent Li-ion batteries, and the evidence of influence factors including solid/liquid ratio, temperature, and pH and solution conductivity can contribute to improving understanding of and optimizing cobalt leaching catalyzed by Cu(II) in MFCs.

  11. Microbial synthesis gas utilization and ways to resolve kinetic and mass-transfer limitations.

    Science.gov (United States)

    Yasin, Muhammad; Jeong, Yeseul; Park, Shinyoung; Jeong, Jiyeong; Lee, Eun Yeol; Lovitt, Robert W; Kim, Byung Hong; Lee, Jinwon; Chang, In Seop

    2015-02-01

    Microbial conversion of syngas to energy-dense biofuels and valuable chemicals is a potential technology for the efficient utilization of fossils (e.g., coal) and renewable resources (e.g., lignocellulosic biomass) in an environmentally friendly manner. However, gas-liquid mass transfer and kinetic limitations are still major constraints that limit the widespread adoption and successful commercialization of the technology. This review paper provides rationales for syngas bioconversion and summarizes the reaction limited conditions along with the possible strategies to overcome these challenges. Mass transfer and economic performances of various reactor configurations are compared, and an ideal case for optimum bioreactor operation is presented. Overall, the challenges with the bioprocessing steps are highlighted, and potential solutions are suggested. Future research directions are provided and a conceptual design for a membrane-based syngas biorefinery is proposed.

  12. Cathode Assessment for Maximizing Current Generation in Microbial Fuel Cells Utilizing Bioethanol Effluent as Substrate

    Directory of Open Access Journals (Sweden)

    Guotao Sun

    2016-05-01

    Full Text Available Implementation of microbial fuel cells (MFCs for electricity production requires effective current generation from waste products via robust cathode reduction. Three cathode types using dissolved oxygen cathodes (DOCs, ferricyanide cathodes (FeCs and air cathodes (AiCs were therefore assessed using bioethanol effluent, containing 20.5 g/L xylose, 1.8 g/L arabinose and 2.5 g/L propionic acid. In each set-up the anode and cathode had an electrode surface area of 88 cm2, which was used for calculation of the current density. Electricity generation was evaluated by quantifying current responses to substrate loading rates and external resistance. At the lowest external resistance of 27 Ω and highest substrate loading rate of 2 g chemical oxygen demand (COD per L·day, FeC-MFC generated highest average current density (1630 mA/m2 followed by AiC-MFC (802 mA/m2 and DOC-MFC (184 mA/m2. Electrochemical impedance spectroscopy (EIS was used to determine the impedance of the cathodes. It was thereby confirmed that the FeC-MFC produced the highest current density with the lowest internal resistance for the cathode. However, in a setup using bioethanol effluent, the AiC-MFC was concluded to be the most sustainable option since it does not require ferricyanide. The data offer a new add-on option to the straw biorefinery by using bioethanol effluent for microbial electricity production.

  13. Utilization of subsurface microbial electrochemical systems to elucidate the mechanisms of competition between methanogenesis and microbial iron(III)/humic acid reduction in Arctic peat soils

    Science.gov (United States)

    Friedman, E. S.; Miller, K.; Lipson, D.; Angenent, L. T.

    2012-12-01

    High-latitude peat soils are a major carbon reservoir, and there is growing concern that previously dormant carbon from this reservoir could be released to the atmosphere as a result of continued climate change. Microbial processes, such as methanogenesis and carbon dioxide production via iron(III) or humic acid reduction, are at the heart of the carbon cycle in Arctic peat soils [1]. A deeper understanding of the factors governing microbial dominance in these soils is crucial for predicting the effects of continued climate change. In previous years, we have demonstrated the viability of a potentiostatically-controlled subsurface microbial electrochemical system-based biosensor that measures microbial respiration via exocellular electron transfer [2]. This system utilizes a graphite working electrode poised at 0.1 V NHE to mimic ferric iron and humic acid compounds. Microbes that would normally utilize these compounds as electron acceptors donate electrons to the electrode instead. The resulting current is a measure of microbial respiration with the electrode and is recorded with respect to time. Here, we examine the mechanistic relationship between methanogenesis and iron(III)- or humic acid-reduction by using these same microbial-three electrode systems to provide an inexhaustible source of alternate electron acceptor to microbes in these soils. Chamber-based carbon dioxide and methane fluxes were measured from soil collars with and without microbial three-electrode systems over a period of four weeks. In addition, in some collars we simulated increased fermentation by applying acetate treatments to understand possible effects of continued climate change on microbial processes in these carbon-rich soils. The results from this work aim to increase our fundamental understanding of competition between electron acceptors, and will provide valuable data for climate modeling scenarios. 1. Lipson, D.A., et al., Reduction of iron (III) and humic substances plays a major

  14. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

    DEFF Research Database (Denmark)

    Wigneswaran, Vinoth; Amador Hierro, Cristina Isabel; Jelsbak, Lotte;

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial co...

  15. Short-term utilization of carbon by the soil microbial community under future climatic conditions in a temperate heathland

    DEFF Research Database (Denmark)

    Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa

    2014-01-01

    was observed in rhizosphere associated gram-negative bacteria followed by gram-positive bacteria. Utilization of recently assimilated C by rhizosphere associated actinomycetes and fungi was relatively low, but much more pronounced in the soil. The utilization of recently assimilated C by the microbial...... (PLFA) biomarker profiles. Climate treatments did not affect microbial abundance in soil or rhizosphere fractions in terms of total PLFA-C concentration. Elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy), but did not affect the abundance of decomposers (fungi...... and actinomycetes) in rhizosphere fractions. Drought favored the bacterial community in rhizosphere fractions whereas increased temperature reduced the abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). Fastest and highest utilization of recently assimilated C...

  16. Microbial utilization of low molecular weight organic substrates in soil depends on their carbon oxidation state

    Science.gov (United States)

    Gunina, Anna; Smith, Andrew; Jones, Davey; Kuzyakov, Yakov

    2017-04-01

    Removal of low molecular weight organic substances (LMWOS), originating from plants and microorganisms, from soil solution is regulated by microbial uptake. In addition to the concentration of LMWOS in soil solution, the chemical properties of each substance (e.g. C oxidation state, number of C atoms, number of -COOH groups) can affect their uptake and subsequent partitioning of C within the soil microbial community. The aim of this study was to trace the initial fate of three dominant classes of LMWOS in soil (sugars, carboxylic and amino acids), including their removal from solution and utilization by microorganisms, and to reveal the effect of substance chemical properties on these processes. Soil solution, spiked at natural abundance levels with 14C-labelled glucose, fructose, malate, succinate, formate, alanine or glycine, was added to the soil and 14C was traced in the dissolved organic carbon (DOC), CO2, cytosol and soil organic carbon (SOC) over 24 hours. The half-life time of all LMWOS in the DOC (T1 /2-solution) varied between 0.6-5.0 min showing extremely fast initial uptake of LMWOS. The T1 /2-solution of substances was dependent on C oxidation state, indicating that less oxidized organic substances (with C oxidation state "0") were retained longer in soil solution than oxidized substances. The LMWOS-C T1 /2-fast, characterizing the half-life time of 14C in the fast mineralization pool, ranged between 30 and 80 min, with the T1 /2-fast of carboxylic acids (malic acid) being the fastest and the T1 /2-fast of amino acids (glycine) being the slowest. An absence of correlation between T1 /2-fast and either C oxidation state, number of C atoms, or number of -COOH groups suggests that intercellular metabolic pathways are more important for LMWOS transformation in soil than their basic chemical properties. The CO2 release during LMWOS mineralization accounted for 20-90% of 14C applied. Mineralization of LMWOS was the least for sugars and the greatest for

  17. Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions.

    Science.gov (United States)

    Johnson, Jamie M; Wawrik, Boris; Isom, Catherine; Boling, Wilford B; Callaghan, Amy V

    2015-02-01

    Based on the transient exposure of Chesapeake Bay sediments to hydrocarbons and the metabolic versatility of known anaerobic alkane-degrading microorganisms, it was hypothesized that distinct Bay sediment communities, governed by geochemical gradients, would have intrinsic alkane-utilizing potential under sulfate-reducing and/or methanogenic conditions. Sediment cores were collected along a transect of the Bay. Community DNA was interrogated via pyrosequencing of 16S rRNA genes, PCR of anaerobic hydrocarbon activation genes, and qPCR of 16S rRNA genes and genes involved in sulfate reduction/methanogenesis. Site sediments were used to establish microcosms amended with n-hexadecane under sulfate-reducing and methanogenic conditions. Sequencing of 16S rRNA genes indicated that sediments associated with hypoxic water columns contained significantly greater proportions of Bacteria and Archaea consistent with syntrophic degradation of organic matter and methanogenesis compared to less reduced sediments. Microbial taxa frequently associated with hydrocarbon-degrading communities were found throughout the Bay, and the genetic potential for hydrocarbon metabolism was demonstrated via the detection of benzyl-(bssA) and alkylsuccinate synthase (assA) genes. Although microcosm studies did not indicate sulfidogenic alkane degradation, the data suggested that methanogenic conversion of alkanes was occurring. These findings highlight the potential role that anaerobic microorganisms could play in the bioremediation of hydrocarbons in the Bay.

  18. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

    Science.gov (United States)

    Wang, Yuanqi; Hatt, Janet K; Tsementzi, Despina; Rodriguez-R, Luis M; Ruiz-Pérez, Carlos A; Weigand, Michael R; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C; Konstantinidis, Konstantinos T

    2017-04-15

    A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The

  19. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    2014-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyze important biogeochemical reactions. In anoxic methane- and sulfide-rich environments, microbes may have unique adaptations for metal acquisition and utilization due to decreased bioavailability as a result of metal sulfide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulfidic (>1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5,600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalyzing anaerobic oxidation of methane utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrotolerant microorganisms. Finally, our data suggest that chemical speciation of metals in highly sulfidic porewaters may exert a stronger influence on microbial bioavailability than total concentration

  20. Assessing the utility of trace and rare earth elements as biosignatures in microbial iron oxyhydroxides

    Directory of Open Access Journals (Sweden)

    Christine eHeim

    2015-02-01

    Full Text Available Microbial iron oxyhydroxides are common deposits in natural waters, recent sediments and mine drainage systems and often contain significant accumulations of trace and rare earth elements (TREE. TREE patterns are widely used to characterize minerals and rocks, and to elucidate their evolution and origin. Whether and which characteristic TREE signatures distinguish between a biological and an abiological origin of iron minerals is still not well understood. Long-term flow reactor studies were performed in the Äspö Hard Rock Laboratory to investigate the development of microbial mats dominated by iron-oxidizing bacteria, namely Mariprofundus sp. and Gallionella sp. The experiments investigated the accumulation and fractionation of TREE under controlled conditions and enabled us to assess potential biosignatures evolving within the microbial iron oxyhydroxides. Concentrations of Be, Y, Zn, Zr, Hf, W, Th, Pb, and U in the microbial mats were 1e3- to 1e5-fold higher than in the feeder fluids whereas the rare earth elements and Y (REE+Y contents were 1e4 and 1e6 fold enriched. Except for a hydrothermally induced Eu anomaly, the normalized REE+Y patterns of the microbial iron oxyhydroxides were very similar to published REE+Y distributions of Archaean Banded Iron Formations. The microbial iron oxyhydroxides from the flow reactors were compared to iron oxyhydroxides that were artificially precipitated from the same feeder fluid. These abiotic and inorganic iron oxyhydroxides show the same REE+Y distribution patterns. Our results indicate that the REE+Y mirror quite exactly the water chemistry, but they do not allow to distinguish microbially mediated from inorganic iron precipitates. All TREE studied showed an overall similar fractionation behavior in biogenic, abiotic and inorganic iron oxyhydroxides. Exceptions are Ni and Tl, which were only accumulated in the microbial iron oxyhydroxides and may point to a potential usage of these elements as

  1. Acetate is a superior substrate for microbial fuel cell initiation preceding bioethanol effluent utilization

    DEFF Research Database (Denmark)

    Sun, Guotao; Thygesen, Anders; Meyer, Anne S.

    2015-01-01

    This study assessed cell voltage development, electricity recovery, and microbial community composition in response to initial substrate including acetate, xylose, acetate/xylose 1:1 mixture (ace/xyl), and bioethanol effluent (BE)during microbial fuel cell (MFC) operation at 1000Ω external......), maximum current density (709±27 mA/m2), and coulombic efficiency (25±0.5 %) in the acetate-initiated MFCs. The microbial community inacetate-initiated MFCs was less diverse and contained more electrogenic bacteria (13.9±0.4 %) including Geobactersulfurreducens and Desulfuromonas acetexigen than the...

  2. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments.

    Science.gov (United States)

    Glass, Jennifer B; Yu, Hang; Steele, Joshua A; Dawson, Katherine S; Sun, Shulei; Chourey, Karuna; Pan, Chongle; Hettich, Robert L; Orphan, Victoria J

    2014-06-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  3. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Pan, Chongle [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    2013-01-01

    Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.

  4. Teaching the Methodology of Science: The Utilization of Microbial Model Systems for Biometric Analysis.

    Science.gov (United States)

    Adamo, Joseph A.

    Students set in their ways are usually reluctant, as a general rule, to deal with open-ended investigative scenarios. In order to acquaint the student with the physical method and philosophical thought process of the discipline, the tone of the course must be set early on. The present study was conducted to develop scenarios and microbial model…

  5. Microbial utilization of rice straw and its derived biochar in a paddy soil.

    Science.gov (United States)

    Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Khan, Sardar; Yao, Huaiying

    2016-07-15

    The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using (13)C-labeled rice straw and its derived biochar ((13)C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96mgCkg(-1)soilh(-1)) at 1d and 3d after incubation, respectively. Straw amendment significantly (pstraw amended soil than the (13)C-labeled biochar amended soil. According to the (13)C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of (13)C-PLFAs derived from straw amendment was significantly (pstraw amendments. Our results suggest that the function, size and structure of the microbial community were strongly influenced by the substrate composition and availability.

  6. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes.

    Science.gov (United States)

    Weitz, Joshua S; Stock, Charles A; Wilhelm, Steven W; Bourouiba, Lydia; Coleman, Maureen L; Buchan, Alison; Follows, Michael J; Fuhrman, Jed A; Jover, Luis F; Lennon, Jay T; Middelboe, Mathias; Sonderegger, Derek L; Suttle, Curtis A; Taylor, Bradford P; Frede Thingstad, T; Wilson, William H; Eric Wommack, K

    2015-06-01

    Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.

  7. Quantifying Resistant Starch Using Novel, In Vivo Methodology and the Energetic Utilization of Fermented Starch in Pigs

    NARCIS (Netherlands)

    Gerrits, W.J.J.; Bosch, M.W.; Borne, van den J.J.G.C.

    2012-01-01

    To quantify the energy value of fermentable starch, 10 groups of 14 pigs were assigned to one of two dietary treatments comprising diets containing 45% of either pregelatinized (P) or retrograded (R) corn starch. In both diets, a contrast in natural 13C enrichment between the starch and nonstarch

  8. Quantifying Resistant Starch Using Novel, In Vivo Methodology and the Energetic Utilization of Fermented Starch in Pigs

    NARCIS (Netherlands)

    Gerrits, W.J.J.; Bosch, M.W.; Borne, van den J.J.G.C.

    2012-01-01

    To quantify the energy value of fermentable starch, 10 groups of 14 pigs were assigned to one of two dietary treatments comprising diets containing 45% of either pregelatinized (P) or retrograded (R) corn starch. In both diets, a contrast in natural 13C enrichment between the starch and nonstarch co

  9. Utility of Microbial Source-Tracking Markers for Assessing Fecal Contamination in the Portage River Watershed, Northwestern Ohio, 2008

    Science.gov (United States)

    Kephart, Christopher M.; Bushon, Rebecca N.

    2010-01-01

    An influx of concentrated animal feeding operations in northwest Ohio has prompted local agencies to examine the effects of these industrial farms on water quality in the upper Portage River watershed. The utility of microbial source-tracking (MST) tools as a means of characterizing sources of fecal contamination in the watershed was evaluated. From 2007 to 2008, scientists with the U.S. Geological Survey, Bowling Green State University, and the Wood County Health Department collected and analyzed 17 environmental samples and 13 fecal source samples for Bacteroides-based host-associated DNA markers. At many of the environmental sites tested, MST marker results corroborated the presumptive fecal contamination sources. Results from this demonstration study support the utility of using MST with host-specific molecular markers to characterize the sources of fecal contamination in the Portage River watershed.

  10. Utilization of multiple "omics" studies in microbial pathogeny for microbiology insights.

    Science.gov (United States)

    Wiwanitkit, Viroj

    2013-04-01

    In the present day, bioinformatics becomes the modern science with several advantages. Several new "omics" sciences have been introduced for a few years and those sciences can be applied in biomedical work. Here, the author will summarize and discuss on important applications of omics studies in microbiology focusing on microbial pathogeny. It can be seen that genomics and proteinomics can be well used in this area of biomedical studies.

  11. Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon.

    Science.gov (United States)

    Alonso, Cecilia; Piccini, Claudia; Unrein, Fernando; Bertoglio, Florencia; Conde, Daniel; Pernthaler, Jakob

    2013-01-01

    Laguna de Rocha belongs to a series of shallow coastal lagoons located along South America. It is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. Its most frequent state is the separation of a Northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a Southern zone with higher salinity and light penetration, and low nutrient content and macrophyte biomass. This zonation is reflected in microbial assemblages with contrasting abundance, activity, and community composition. The physicochemical conditions exerted a strong influence on community composition, and transplanted assemblages rapidly transformed to resembling the community of the recipient environment. Moreover, the major bacterial groups responded differently to their passage between the zones, being either stimulated or inhibited by the environmental changes, and exhibiting contrasting sensitivities to gradients. Addition of allochthonous carbon sources induced pronounced shifts in the bacterial communities, which in turn affected the microbial trophic web by stimulating heterotrophic flagellates and virus production. By contrast, addition of organic and inorganic nutrient sources (P or N) did not have significant effects. Altogether, our results suggest that (i) the planktonic microbial assemblage of this lagoon is predominantly carbon-limited, (ii) different bacterial groups cope differently with this constraint, and (iii) the hydrological cycle of the lagoon plays a key role for the alleviation or aggravation of bacterial carbon limitation. Based on these findings we propose a model of how hydrology affects the composition of bacterioplankton and of carbon processing in Laguna de Rocha. This might serve as a starting hypothesis for further studies about the microbial ecology of this lagoon, and of comparable transitional systems.

  12. Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon

    Directory of Open Access Journals (Sweden)

    Cecilia eAlonso

    2013-02-01

    Full Text Available Laguna de Rocha belongs to a series of shallow coastal lagoons located along South America. It is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. Its most frequent state is the separation of a Northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a Southern zone with higher salinity and light penetration, and low nutrient content and macrophyte biomass. This zonation is reflected in microbial assemblages with contrasting abundance, activity and community composition. The physicochemical conditions exerted a strong influence on community composition, and transplanted assemblages rapidly transformed to resembling the community of the recipient environment. Moreover, the major bacterial groups responded differently to their passage between the zones, being either stimulated or inhibited by the environmental changes, and exhibiting contrasting sensitivities to gradients. Addition of allochthonous carbon sources induced pronounced shifts in the bacterial communities, which in turn affected the microbial trophic web by stimulating heterotrophic flagellates and virus production. By contrast, addition of organic and inorganic nutrient sources (P or N did not have significant effects. Altogether, our results suggest that i the planktonic microbial assemblage of this lagoon is predominantly carbon limited, ii different bacterial groups cope differently with this constraint, and iii the hydrological cycle of the lagoon plays a key role for the alleviation or aggravation of bacterial carbon limitation. Based on these findings we propose a model of how hydrology affects the composition of bacterioplankton and of carbon processing in Laguna de Rocha. This might serve as a starting hypothesis for further studies about the microbial ecology of this lagoon, and of comparable transitional

  13. World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide.

    Science.gov (United States)

    Wu, Linhuan; Sun, Qinglan; Desmeth, Philippe; Sugawara, Hideaki; Xu, Zhenghong; McCluskey, Kevin; Smith, David; Alexander, Vasilenko; Lima, Nelson; Ohkuma, Moriya; Robert, Vincent; Zhou, Yuguang; Li, Jianhui; Fan, Guomei; Ingsriswang, Supawadee; Ozerskaya, Svetlana; Ma, Juncai

    2017-01-04

    The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes >368 000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.

  14. Recent advances in the development and utilization of modern anode materials for high performance microbial fuel cells.

    Science.gov (United States)

    Sonawane, Jayesh M; Yadav, Abhishek; Ghosh, Prakash C; Adeloju, Samuel B

    2017-04-15

    Microbial fuel cells (MFCs) are novel bio-electrochemical device for spontaneous or single step conversion of biomass into electricity, based on the use of metabolic activity of bacteria. The design and use of MFCs has attracted considerable interests because of the potential new opportunities they offer for sustainable production of energy from biodegradable and reused waste materials. However, the associated slow microbial kinetics and costly construction materials has limited a much wider commercial use of the technology. In the past ten years, there has been significant new developments in MFCs which has resulted in several-fold increase in achievable power density. Yet, there is still considerable possibility for further improvement in performance and development of new cost effective materials. This paper comprehensively reviews recent advances in the construction and utilization of novel anodes for MFCs. In particular, it highlights some of the critical roles and functions of anodes in MFCs, strategies available for improving surface areas of anodes, dominant performance of stainless-steel based anode materials, and the emerging benefits of inclusion of nanomaterials. The review also demonstrates that some of the materials are very promising for large scale MFC applications and are likely to replace conventional anodes for the development of next generation MFC systems. The hurdles to the development of commercial MFC technology are also discussed. Furthermore, the future directions in the design and selection of materials for construction and utilization of MFC anodes are highlighted. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Universal quantifier derived from AFM analysis links cellular mechanical properties and cell-surface integration forces with microbial deposition and transport behavior.

    Science.gov (United States)

    Li, Yueyun; Wang, Xin; Onnis-Hayden, Annalisa; Wan, Kai-tak; Gu, April Z

    2014-01-01

    In this study, we employed AFM analysis combined with mathematical modeling for quantifying cell-surface contact mechanics and magnitude and range of cell-surface interaction forces for seven bacterial strains with a wide range of cell morphology, dimension, and surface characteristics. Comprehensive cell-surface characterization including surface charge, extracellular polymeric substance content, hydrophobicity, and cell-cell aggregation analyses were performed. Flow-through column tests were employed to determine the attachment efficiency and deposition-transport behavior of these bacterial strains. No statistically significant correlation between attachment efficiency and any single-cell surface property was identified. Single-cell characterization by atomic force microscopy (AFM) yielded the mechanical deformation and elastic modulus, penetration resistance to AFM probe penetration by cellular surface substances (CSS), range and magnitude of the repulsive-attractive intersurface forces, and geometry of each strain. We proposed and derived a universal dimensionless modified Tabor's parameter to integrate all these properties that account for their collective behavior. Results showed that the Tabor parameter derived from AFM analysis correlated well with experimentally determined attachment efficiency (α), which therefore is able to link microscale cell-surface properties with macroscale bacterial transport behavior. Results suggested that the AFM tests performed between a single cell and a surface captured the key quantities of the interactions between the cell and the surface that dictate overall cell attachment behavior. Tabor's parameter therefore can be potentially incorporated into the microbial transport model.

  16. Quantifying the statistical importance of utilizing regression over classic energy intensity calculations for tracking efficiency improvements in industry

    Energy Technology Data Exchange (ETDEWEB)

    Nimbalkar, Sachin U. [ORNL; Wenning, Thomas J. [ORNL; Guo, Wei [ORNL

    2017-08-01

    In the United States, manufacturing facilities account for about 32% of total domestic energy consumption in 2014. Robust energy tracking methodologies are critical to understanding energy performance in manufacturing facilities. Due to its simplicity and intuitiveness, the classic energy intensity method (i.e. the ratio of total energy use over total production) is the most widely adopted. However, the classic energy intensity method does not take into account the variation of other relevant parameters (i.e. product type, feed stock type, weather, etc.). Furthermore, the energy intensity method assumes that the facilities’ base energy consumption (energy use at zero production) is zero, which rarely holds true. Therefore, it is commonly recommended to utilize regression models rather than the energy intensity approach for tracking improvements at the facility level. Unfortunately, many energy managers have difficulties understanding why regression models are statistically better than utilizing the classic energy intensity method. While anecdotes and qualitative information may convince some, many have major reservations about the accuracy of regression models and whether it is worth the time and effort to gather data and build quality regression models. This paper will explain why regression models are theoretically and quantitatively more accurate for tracking energy performance improvements. Based on the analysis of data from 114 manufacturing plants over 12 years, this paper will present quantitative results on the importance of utilizing regression models over the energy intensity methodology. This paper will also document scenarios where regression models do not have significant relevance over the energy intensity method.

  17. Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Anderton, Christopher R.; Chu, Rosalie K.; Tolic, Nikola; Creissen, Alain V.; Pasa-Tolic, Ljiljana

    2016-01-07

    The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it had many limitations that include uneven matrix coverage and limitation in the types of matrices one could employ in their studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus Subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.

  18. Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

    Science.gov (United States)

    Anderton, Christopher R.; Chu, Rosalie K.; Tolić, Nikola; Creissen, Alain; Paša-Tolić, Ljiljana

    2016-03-01

    The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it has many limitations that include uneven matrix coverage and limitation in the types of matrices that could be employed in studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied, and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.

  19. Utilization of A New Microbial Transglutaminase from Streptomyces for The Formation of Edible Soybean Protein Films

    Institute of Scientific and Technical Information of China (English)

    Wang Zhang

    2002-01-01

    Soybean protein isolate (SPI) wasused to investigate the formation of edibleprotein films through an enzymatic cross-linkingmethod with a purified microbial transglutaminse(MTG) produced and purified from a neweffective strain Streptomyces sp. WZFF.L-M1preserved in my laboratory, followed by theaddition of glycerol and suitable heating anddrying treatments. Cheaper partially-purifiedskimmed soybean protein powder (SSP) andwhey protein isolates (WPI) were used as thesubstitutes partially replacing the expensive SPIproducts, and purified β-lactoglobulin was takenas the positive control of WPI. The effects ofthe concentrations of the three substitutes andtheir relative ratios have been compared withSPI as a control, and the methodologies ofMTG treatment were examined. Attempts havealso been approached for the films formation-enhancing substances such as glycerol. As theresults, the three alternatives could also formhigh efficient edible films in the optimaloperation conditions experimented. Those filmsmade with SPI alternatives, thin around 50 μm,had the microscopic homogenous networkstructures, without any holes by naked eye. Thetests for the properties of these films showedthat they had high water-keeping capacity andstrong elasticity, that the ultimate tensile strength(TS) and the elongation at break (Eb) had beenremarkably increased (TS>5 MPa, Eb>50%,respectively), and that the prevention ratesagainst the permeability of water vapor andoxygen in air were also upgraded more than85% and 70%, respectively.

  20. Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals.

    Science.gov (United States)

    Lang, Jennifer M; Erb, Racheal; Pechal, Jennifer L; Wallace, John R; McEwan, Ryan W; Benbow, Mark Eric

    2016-01-04

    Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.

  1. Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals

    Directory of Open Access Journals (Sweden)

    Jennifer M. Lang

    2016-01-01

    Full Text Available Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses and epilithic (biofilms on unglazed ceramic tiles communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.

  2. Importance and utility of microbial elements in evaluating soil quality: case studies in silvopastoral systems

    Directory of Open Access Journals (Sweden)

    Victoria Eugenia Vallejo Quintero

    2013-07-01

    Full Text Available Environmental sustainability is achieved by main-taining and improving soil quality. This quality is defined as “the ability of soil to function” and is evaluated through measuring a minimum set of data corresponding to different soil properties (physical, chemical and biological. However, assessment of these properties does not meet all the conditions necessary to be ideal indicators such as: clearly discriminating between the systems use and / or management evaluation, sensitivity to stress conditions associated with anthropogenic actions, easy measurement, accessibility to many users and short response time. Because loss in quality is associated with the alteration of many processes performed by soil microorganisms they meet the above conditions and have been proposed as valid indicators for diagnosing the impact of changes in land-use and ecosystem restoration. Thus, through the evaluation of the density, activity and /or structure-composition of microorganisms we can determine whether current management systems maintain, improve or degrade the soil. In this article we review the main concepts related to soil quality and its indicators. We discuss the effect of the implementation of silvopastoral systems on soil quality, with an emphasis on the use of microbial indicators.

  3. Utilization of A New Microbial Transglutaminase from Streptomyces for The Formation of Edible Soybean Protein Films

    Institute of Scientific and Technical Information of China (English)

    WangZhang

    2002-01-01

    Soybean protein isolate(SPI) was used to investigate the formation of edible protein films through an enzymatic cross-linking method with a purified microbial transglutaminse(MTG) produced and purified from a new effective strain Streptomyces sp.WZFF.L-M1 preserved in my laboratory,followed by the addition of glycerol and suitable heating and drying treatments.Cheaper partially-purified skimmed soybean protein powder(SSP) and whey protein isolates(WPI) were used as the substitutes partially replacing the expensive SPI products,and purified β-lactoglobulin was taken as the positive control of WPI.The effects of the concentrations of the three substitutes and their relative ratios have been compared with SPI as a control,and the methodologies of MTG treatment were examined.Attempts have also been approached for the films formation-enhancing substances such as glycerol.As the results,the three alternatives could also form high efficient edible films in the optimal operation conditions experimented.Those films made with SPI alternatives,thin around 50 μm,had the microscopic homogenous network structures,without any holes by naked eye.The tests for the properties of these films showed that they had high water-keeping capacity and strong elasticity,that the ultimate tensile sterength(TS)and the elongation at break(Eb) had been remarkably increased(TS>5 MPa,Eb>50%,respectively),and that the prevention rates against the permeability of water vapor and oxygen in air were also upgraded more than 85% and 70%,respectively.

  4. Effect of Wheat Middlings, Microbial Phytase, and Citric Acid on Phytate-Phosphorus, Calcium, and Protein Utilization of Broilers

    Institute of Scientific and Technical Information of China (English)

    GONG Yi-feng; LIAO He-rong; WANG Jin-fu; LI Hong-yan

    2006-01-01

    A corn-soybean meal diet (CSB) (or Diet 1) containing 23% crude protein (CP) was used as the positive control, and another corn-soybean meal diet containing 21% CP and 15% wheat middlings (WM) (or Diet 2) was used as the basal diet, which was treated with four different treatments. Digestibility experiment was employed to discuss the collective effect of citric acid, and intrinsic and microbial phytase. By comparing and analyzing effects of them in the low-nutrient broiler diets, the results showed five treatments had similar effects on Tibia ash (%) (mg) (P > 0.05). Under the supplementation of bacterial phytase or citric acid, the daily body weight gain (ADG), gain:feed (G:F) ratio, and calcium (Ca) utilization were similar to that of standard-nutrient CSB diet (Diet 1) (P > 0.05). And, fecal phosphorus (P) and CP utilization were lower than (P < 0.05) that of Diet 1. But P utilization was significantly higher than (P < 0.01) that of Diet 1.However, the ADG, G:F, and CP utilization produced by supplementation of intrinsic phytase were lower than those of Diet 1, but other aspects were similar to those produced by Diet 1 (P > 0.05). In Diet 5, citric acid, intrinsic and bacterial phytase were added to the diet, which produced a 1.4% decrease on fecal P, a 7.2% increase on Ca utilization, which was significantly higher than (P < 0.01) those of the other four Diets, a 3.9% increase on G:F, which was similar to that of Diet 1, and a 2.3% increase on CP utilization, which was higher than (P < 0.05) that of the other three diets. In summary, the results of this study indicated that citric acid, intrinsic and bacterial phytase might have some additive or synergistic effects, and low-nutrient CSB diets with 15% wheat middlings, 750 U kg-1 phytase, and 3% citric acid might substitute completely for standard CSB in broilers.

  5. Microbial utilization of crude glycerol for the production of value-added products.

    Science.gov (United States)

    Dobson, Rosemary; Gray, Vincent; Rumbold, Karl

    2012-02-01

    Energy fuels for transportation and electricity generation are mainly derived from finite and declining reserves of fossil hydrocarbons. Fossil hydrocarbons are also used to produce a wide range of organic carbon-based chemical products. The current global dependency on fossil hydrocarbons will not be environmentally or economically sustainable in the long term. Given the future pessimistic prospects regarding the complete dependency on fossil fuels, political and economic incentives to develop carbon neutral and sustainable alternatives to fossil fuels have been increasing throughout the world. For example, interest in biodiesel has undergone a revival in recent times. However, the disposal of crude glycerol contaminated with methanol, salts, and free fatty acids as a by-product of biodiesel production presents an environmental and economic challenge. Although pure glycerol can be utilized in the cosmetics, tobacco, pharmaceutical, and food industries (among others), the industrial purification of crude glycerol is not economically viable. However, crude glycerol could be used as an organic carbon substrate for the production of high-value chemicals such as 1,3-propanediol, organic acids, or polyols. Microorganisms have been employed to produce such high-value chemicals and the objective of this article is to provide an overview of studies on the utilization of crude glycerol by microorganisms for the production of economically valuable products. Glycerol as a by-product of biodiesel production could be used a feedstock for the manufacture of many products that are currently produced by the petroleum-based chemical industry.

  6. Effect of -based Direct-fed Microbial on Performance, Nutrient Utilization, Intestinal Morphology and Cecal Microflora in Broiler Chickens

    Directory of Open Access Journals (Sweden)

    Xinjian Lei

    2015-02-01

    Full Text Available The present study was conducted to evaluate the effect of the dietary supplementation of Bacillus amyloliquefaciens-based direct-fed microbial (DFM on growth performance, nutrient utilization, intestinal morphology and cecal microflora in broiler chickens. A total of two hundred and eighty eight 1-d-old Arbor Acres male broilers were randomly allocated to one of four experimental treatments in a completely randomized design. Each treatment was fed to eight replicate cages, with nine birds per cage. Dietary treatments were composed of an antibiotic-free basal diet (control, and the basal diet supplemented with either 15 mg/kg of virginiamycin as antibiotic growth promoter (AGP, 30 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 30 or 60 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 60. Experimental diets were fed in two phases: starter (d 1 to 21 and finisher (d 22 to 42. Growth performance, nutrient utilization, morphological parameters of the small intestine and cecal microbial populations were measured at the end of the starter (d 21 and finisher (d 42 phases. During the starter phase, DFM and virginiamycin supplementation improved the feed conversion ratio (FCR; p<0.01 compared with the control group. For the finisher phase and the overall experiment (d 1 to 42 broilers fed diets with the DFM had better body weight gain (BWG and FCR than that of control (p<0.05. Supplementation of virginiamycin and DFM significantly increased the total tract apparent digestibility of crude protein (CP, dry matter (DM and gross energy during both starter and finisher phases (p<0.05 compared with the control group. On d 21, villus height, crypt depth and villus height to crypt depth ratio of duodenum, jejunum, and ileum were significantly increased for the birds fed with the DFM diets as compared with the control group (p<0.05. The DFM 30, DFM 60, and AGP groups decreased the Escherichia coli population in cecum at d 21 and d 42 compared with control

  7. A flexible microbial co-culture platform for simultaneous utilization of methane and carbon dioxide from gas feedstocks

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Eric A.; Chrisler, William B.; Beliaev, Alex S.; Bernstein, Hans C.

    2017-03-01

    A new co-cultivation technology is presented that converts greenhouse gasses, CH4 and CO2, into microbial biomass. The methanotrophic bacterium, Methylomicrobium alcaliphilum 20z, was coupled to a cyanobacterium, Synechococcus PCC 7002 via oxygenic photosynthesis. The system exhibited robust growth on diverse gas mixtures ranging from biogas to those representative of a natural gas feedstock. A continuous processes was developed on a synthetic natural gas feed that achieved steady-state by imposing coupled light and O2 limitations on the cyanobacterium and methanotroph, respectively. Continuous co-cultivation resulted in an O2 depleted reactor and does not require CH4/O2 mixtures to be fed into the system, thereby enhancing process safety considerations over traditional methanotroph mono-culture platforms. This co-culture technology is scalable with respect to its ability to utilize different gas streams and its biological components constructed from model bacteria that can be metabolically customized to produce a range of biofuels and bioproducts.

  8. Fermentation of a Malaysian Bacillus thuringiensis serotype H-14 isolate, a mosquito microbial control agent utilizing local wastes.

    Science.gov (United States)

    Lee, H L; Seleena, P

    1991-03-01

    A screening program searching for indigenous microbial control agents of mosquitos in Malaysia is initiated since 1987 and to date at least 20 isolates of mosquitocidal Bacillus thuringiensis serotypes have been obtained. Preliminary field evaluation of several isolates indicated that they are highly effective in the control of medically important mosquito species. For operational purposes, there is an urgent need to produce this agent utilizing cheap and locally available wastes through fermentation biotechnology. Fermentation studies in shake-flasks containing standard nutrient broth and soya bean waste, respectively, indicate that it takes about 37 hours for a Malaysian isolate of B. thuringiensis serotype H-14 to mature. In the grated coconut waste, fishmeal and rice bran, the bacteria took 28 hours, 26 hours and 126 hours respectively to mature. The endotoxin was harvested from the standard nutrient broth at 55 hours and at 50 hours from soybean, grated coconut waste and fishmeal. The endotoxin could only be harvested 150 hours after inoculation from rice bran medium. However, no bacterial growth was detected in palm oil effluent. In terms of endotoxin and biomass production, fishmeal appears to be a suitable medium. Variations in the pH of the fermenting media were also noted.

  9. Enhanced hydrogen production from waste activated sludge by cascade utilization of organic matter in microbial electrolysis cells.

    Science.gov (United States)

    Lu, Lu; Xing, Defeng; Liu, Bingfeng; Ren, Nanqi

    2012-03-15

    Fermentative hydrogen production from waste activated sludge (WAS) has low H2 yield because WAS contains limited amounts of carbohydrate suitable for use by hydrogen-producing bacteria. Here, augmentation of hydrogen production from WAS by microbial electrolysis cells (MECs) was implemented. H2 yields of 3.89±0.39 mg-H2/g-DS (5.67±0.61 mg-H2/g-VSS) from raw WAS and 6.78±0.94 mg-H2/g-DS (15.08±1.41 mg-H2/g-VSS) from alkaline-pretreated WAS were obtained in the two-chamber MECs (TMECs). This was several times higher than yields obtained previously by fermentation. Single-chamber MECs (SMECs) with low internal resistance showed a H2 production rate that 13 times that of TMECs with similar H2 yield when alkaline-pretreated WAS was used. However, methanogenesis was detected after several batch cycles. A yield balance calculation revealed that carbohydrates were not the only substrates for electrohydrogenesis. Protein and its acidification products, such as volatile fatty acids are also responsible for a portion of H2 generation in MEC. Characterization of WAS in TMECs by three-dimensional excitation-emission matrix (EEM) fluorescence spectroscopy with parallel factor analysis indicated that electrohydrogenesis reacted on the extracellular polymeric substances and intracellular substances of WAS. Cascade utilization of organic matter in MECs increased hydrogen production from WAS. MECs showed high hydrogen yield from WAS, fewer H2 sinks, and insensitivity to temperature. Optimizing MEC configurations and operation conditions and improving the pretreatment processes of WAS are necessary before practical application can take place on a large scale.

  10. [Effects of long-term fertilization on microbial biomass carbon and nitrogen and on carbon source utilization of microbes in a red soil].

    Science.gov (United States)

    Sun, Feng-xia; Zhang, Wei-hua; Xu, Ming-gang; Zhang, Wen-ju; Li, Zhao-qiang; Zhang, Jing-ye

    2010-11-01

    In order to explore the effects of long-term fertilization on the microbiological characters of red soil, soil samples were collected from a 19-year long-term experimental field in Qiyang of Hunan, with their microbial biomass carbon (MBC) and nitrogen (MBN) and microbial utilization ratio of carbon sources analyzed. The results showed that after 19-year fertilization, the soil MBC and MBN under the application of organic manure and of organic manure plus inorganic fertilizers were 231 and 81 mg x kg(-1) soil, and 148 and 73 mg x kg(-1) soil, respectively, being significantly higher than those under non-fertilization, inorganic fertilization, and inorganic fertilization plus straw incorporation. The ratio of soil MBN to total N under the application of organic manure and of organic manure plus inorganic fertilizers was averagely 6.0%, significantly higher than that under non-fertilization and inorganic fertilization. Biolog-ECO analysis showed that the average well color development (AWCD) value was in the order of applying organic manure plus inorganic fertilizers = applying organic manure > non-fertilization > inorganic fertilization = inorganic fertilization plus straw incorporation. Under the application of organic manure or of organic manure plus inorganic fertilizers, the microbial utilization rate of carbon sources, including carbohydrates, carboxylic acids, amino acids, polymers, phenols, and amines increased; while under inorganic fertilization plus straw incorporation, the utilization rate of polymers was the highest, and that of carbohydrates was the lowest. Our results suggested that long-term application of organic manure could increase the red soil MBC, MBN, and microbial utilization rate of carbon sources, improve soil fertility, and maintain a better crop productivity.

  11. Evaluating the utility of the medium-spatial resolution Landsat 8 multispectral sensor in quantifying aboveground biomass in uMgeni catchment, South Africa

    Science.gov (United States)

    Dube, Timothy; Mutanga, Onisimo

    2015-03-01

    Aboveground biomass estimation is critical in understanding forest contribution to regional carbon cycles. Despite the successful application of high spatial and spectral resolution sensors in aboveground biomass (AGB) estimation, there are challenges related to high acquisition costs, small area coverage, multicollinearity and limited availability. These challenges hamper the successful regional scale AGB quantification. The aim of this study was to assess the utility of the newly-launched medium-resolution multispectral Landsat 8 Operational Land Imager (OLI) dataset with a large swath width, in quantifying AGB in a forest plantation. We applied different sets of spectral analysis (test I: spectral bands; test II: spectral vegetation indices and test III: spectral bands + spectral vegetation indices) in testing the utility of Landsat 8 OLI using two non-parametric algorithms: stochastic gradient boosting and the random forest ensembles. The results of the study show that the medium-resolution multispectral Landsat 8 OLI dataset provides better AGB estimates for Eucalyptus dunii, Eucalyptus grandis and Pinus taeda especially when using the extracted spectral information together with the derived spectral vegetation indices. We also noted that incorporating the optimal subset of the most important selected medium-resolution multispectral Landsat 8 OLI bands improved AGB accuracies. We compared medium-resolution multispectral Landsat 8 OLI AGB estimates with Landsat 7 ETM + estimates and the latter yielded lower estimation accuracies. Overall, this study demonstrates the invaluable potential and strength of applying the relatively affordable and readily available newly-launched medium-resolution Landsat 8 OLI dataset, with a large swath width (185-km) in precisely estimating AGB. This strength of the Landsat OLI dataset is crucial especially in sub-Saharan Africa where high-resolution remote sensing data availability remains a challenge.

  12. Microbial Characteristics of Nosocomial Infections and Their Association with the Utilization of Hand Hygiene Products: A Hospital-Wide Analysis of 78,344 Cases.

    Science.gov (United States)

    Liu, Song; Wang, Meng; Wang, Gefei; Wu, Xiuwen; Guan, Wenxian; Ren, Jianan

    Nosocomial infections are the main adverse events during health care delivery. Hand hygiene is the fundamental strategy for the prevention of nosocomial infections. Microbial characteristics of nosocomial infections in the Asia-Pacific region have not been investigated fully. Correlation between the use of hand hygiene products and the incidence of nosocomial infections is still unknown. This study investigates the microbial characteristics of nosocomial infections in the Asia-Pacific region and analyzes the association between the utilization of hand hygiene products and the incidence of nosocomial infections. A total of 78,344 patients were recruited from a major tertiary hospital in China. Microbial characteristics of major types of nosocomial infections were described. The association between the utilization of hand hygiene products and the incidence of nosocomial infections was analyzed using correlation and regression models. The overall incidence of nosocomial infections was 3.04%, in which the incidence of surgical site infection was 1%. Multi-drug resistance was found in 22.8% of all pathogens, in which multi-drug-resistant Acinetobacter baumannii and methicillin-resistant Staphylococcus aureus were 56.6% and 54.9%, respectively. The utilization of hand hygiene products (including hand sanitizer, soap and paper towel) was associated negatively with the incidence of surgical site infection in surgical departments and the incidence of nosocomial infections in non-intensive care unit (ICU) departments (especially in surgical departments). Regression analysis further identified that higher utilization of hand hygiene products correlated with decreased incidence of major types of nosocomial infections. Multi-drug-resistant organisms are emerging in Asia-Pacific health care facilities. Utilization of hand hygiene products is associated with the incidence of nosocomial infections.

  13. Assessing microbial utilization of free versus sorbed Alanine by using position-specific 13C labeling and 13C-PLFA analysis

    Science.gov (United States)

    Herschbach, Jennifer; Apostel, Carolin; Spielvogel, Sandra; Kuzyakov, Yakov; Dippold, Michaela

    2016-04-01

    Microbial utilization is a key transformation process of soil organic matter (SOM). Sorption of low molecular weight organic substances (LMWOS) to soil mineral surfaces blocks or delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil science, combined with 13C-phospholipid fatty acid (PLFA) analysis, to assess microbial utilization of sorbed and non-sorbed Alanine in soil. Alanine has various functional groups enabling different sorption mechanisms via its positive charge (e.g. to clay minerals by cation exchange), as well as via its negative charge (e.g. to iron oxides by ligand exchange). To assess changes in the transformation pathways caused by sorption, we added uniformly and position-specifically 13C and 14C labeled Alanine to the Ap of a loamy Luvisol in a short-term (10 days) incubation experiment. To allow for sorption of the tracer solution to an aliquot of this soil, microbial activity was minimized in this subsample by sterilizing the soil by γ-radiation. After shaking, the remaining solutions were filtered and the non-sorbed Alanine was removed with Millipore water and then added to non-sterilized soil. For the free Alanine treatment, solutions with Alanine of similar amount and isotopic composition were prepared, added to the soil and incubated as well. The respired CO2 was trapped in NaOH and its 14C-activity was determined at increasing times intervals. Microbial utilization of Alanine's individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Sorption to soil minerals delayed respiration to CO2 and reduced initial respiration rate by 80%. Irrespective of sorption, the highest amount was respired from the carboxylic position (C-1), whereas the amino-bound (C-2) and the methylic position (C-3) were preferentially incorporated into PLFA of microorganisms due to the

  14. Utilization of microbial oil obtained from crude glycerol for the production of polyol and its subsequent conversion to polyurethane foams.

    Science.gov (United States)

    Uprety, Bijaya K; Reddy, Jayanth Venkatarama; Dalli, Sai Swaroop; Rakshit, Sudip K

    2017-07-01

    We have demonstrated possible use of microbial oil in biopolymer industries. Microbial oil was produced from biodiesel based crude glycerol and subsequently converted into polyol. Fermentation of crude glycerol in a batch bioreactor using Rhodosporidium toruloides ATCC 10788 produced 18.69g/L of lipid at the end of 7days. The microbial oil was then chemically converted to polyol and characterized using FT-IR and (1)H NMR. For comparison, canola oil and palm oil were also converted into their respective polyols. The hydroxyl numbers of polyols from canola, palm and microbial oil were found to be 266.86, 222.32 and 230.30 (mgKOH/g of sample) respectively. All the polyols were further converted into rigid and semi-rigid polyurethanes (maintaining the molar -NCO/-OH ratio of 1.1) to examine their suitability in polymer applications. Conversion of microbial lipid to polyurethane foam also provides a new route for the production of polymers using biodiesel based crude glycerol. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Yongzhuo Liu

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

  16. Effects of rumen fluid collection site on microbial population structure during in vitro fermentation of the different substrates quantified by 16S rRNA hybridisation.

    Science.gov (United States)

    Muetzel, S; Krishnamoorthy, U; Becker, K

    2001-01-01

    Rumen fluid samples from a cow were withdrawn manually from the feed mat (solid phase) or the liquid phase below this mat and incubated in vitro with wheat straw, sorghum hay and a concentrate mixture. From the inoculum and several samples collected during in vitro incubation RNA was extracted to assess microbial population size and structure. RNA content recovered from the solid phase rumen fluid was significantly higher than from the liquid phase. The composition of the microbial population in the solid phase material was characterised by a high proportion of Ruminococci. Neither the proportion of other cell wall degrading organisms (Fibrobacter and Chytridiomycetes) nor the Eukarya and Archaea populations differed between the two sampling sites. Gas production was higher when substrates were incubated with solid phase than with liquid phase rumen fluid regardless of sampling time. However, the higher level of gas production was not accompanied by a corresponding increase in true digestibility. The RNA probes showed that during in vitro incubation with liquid phase rumen fluid, the eukaryotic population was inactive no matter which substrate was used and the activity of methanogens (Archaea) was lower than with solid phase rumen fluid. The population pattern of the cell wall degrading organisms was influenced mainly by the substrate fermented, and to a smaller extent by the inoculum used for in vitro fermentation.

  17. Decimal place slope, a fast and precise method for quantifying 13C incorporation levels for detecting the metabolic activity of microbial species.

    Science.gov (United States)

    Jehmlich, Nico; Fetzer, Ingo; Seifert, Jana; Mattow, Jens; Vogt, Carsten; Harms, Hauke; Thiede, Bernd; Richnow, Hans-Hermann; von Bergen, Martin; Schmidt, Frank

    2010-06-01

    The metabolic incorporation of stable isotopes such as (13)C or (15)N into proteins has become a powerful tool for qualitative and quantitative proteome studies. We recently introduced a method that monitors heavy isotope incorporation into proteins and presented data revealing the metabolic activity of various species in a microbial consortium using this technique. To further develop our method using an liquid chromatography (LC)-mass spectrometry (MS)-based approach, we present here a novel approach for calculating the incorporation level of (13)C into peptides by using the information given in the decimal places of peptide masses obtained by modern high-resolution MS. In the present study, the applicability of this approach is demonstrated using Pseudomonas putida ML2 proteins uniformly labeled via the consumption of [(13)C(6)]benzene present in the medium at concentrations of 0, 10, 25, 50, and 100 atom %. The incorporation of (13)C was calculated on the basis of several labeled peptides derived from one band on an SDS-PAGE gel. The accuracy of the calculated incorporation level depended upon the number of peptide masses included in the analysis, and it was observed that at least 100 peptide masses were required to reduce the deviation below 4 atom %. This accuracy was comparable with calculations of incorporation based on the isotope envelope. Furthermore, this method can be extended to the calculation of the labeling efficiency for a wide range of biomolecules, including RNA and DNA. The technique will therefore allow a highly accurate determination of the carbon flux in microbial consortia with a direct approach based solely on LC-MS.

  18. Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination

    OpenAIRE

    Guey-Horng Wang; Chiu-Yu Cheng; Man-Hai Liu; Tzu-Yu Chen; Min-Chi Hsieh; Ying-Chien Chung

    2016-01-01

    Fast hexavalent chromium (Cr(VI)) determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI)-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI) concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of t...

  19. Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

    Directory of Open Access Journals (Sweden)

    M. E. Nowak

    2017-08-01

    Full Text Available Isotopes of dissolved inorganic carbon (DIC are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria and biotic factors influence the δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in the δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE, a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less, DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL. Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells. Changes in 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water–rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings

  20. Feasibility of utilizing bioindicators for testing microbial inactivation in sweetpotato purees processed with a continuous-flow microwave system.

    Science.gov (United States)

    Brinley, T A; Dock, C N; Truong, V-D; Coronel, P; Kumar, P; Simunovic, J; Sandeep, K P; Cartwright, G D; Swartzel, K R; Jaykus, L-A

    2007-06-01

    Continuous-flow microwave heating has potential in aseptic processing of various food products, including purees from sweetpotatoes and other vegetables. Establishing the feasibility of a new processing technology for achieving commercial sterility requires evaluating microbial inactivation. This study aimed to assess the feasibility of using commercially available plastic pouches of bioindicators containing spores of Geobacillius stearothermophilus ATCC 7953 and Bacillus subtilis ATCC 35021 for evaluating the degree of microbial inactivation achieved in vegetable purees processed in a continuous-flow microwave heating unit. Sweetpotato puree seeded with the bioindicators was subjected to 3 levels of processing based on the fastest particles: undertarget process (F(0) approximately 0.65), target process (F(0) approximately 2.8), and overtarget process (F(0) approximately 10.10). After initial experiments, we found it was necessary to engineer a setup with 2 removable tubes connected to the continuous-flow microwave system to facilitate the injection of indicators into the unit without interrupting the puree flow. Using this approach, 60% of the indicators injected into the system could be recovered postprocess. Spore survival after processing, as evaluated by use of growth indicator dyes and standard plating methods, verified inactivation of the spores in sweetpotato puree. The log reduction results for B. subtilis were equivalent to the predesigned degrees of sterilization (F(0)). This study presents the first report suggesting that bioindicators such as the flexible, food-grade plastic pouches can be used for microbial validation of commercial sterilization in aseptic processing of foods using a continuous-flow microwave system.

  1. Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination

    Directory of Open Access Journals (Sweden)

    Guey-Horng Wang

    2016-08-01

    Full Text Available Fast hexavalent chromium (Cr(VI determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of the microbial fuel cell (MFC-based biosensor indicated its potential as a reliable biosensor system. The MFC voltage decreased as the Cr(VI concentration in the MFC increased. Two satisfactory linear relationships were observed between the Cr(VI concentration and voltage output for various Cr(VI concentration ranges (0.0125–0.3 mg/L and 0.3–5 mg/L. The MFC biosensor is a simple device that can accurately measure Cr(VI concentrations in drinking water, groundwater, and electroplating wastewater in 45 min with low deviations (<10%. The use of the biosensor can help in preventing the violation of effluent regulations and the maximum allowable concentration of Cr(VI in water. Thus, the developed MFC biosensor has potential as an early warning detection device for Cr(VI determination even if O. anthropi YC152 is a possible opportunistic pathogen.

  2. Utility of Ochrobactrum anthropi YC152 in a Microbial Fuel Cell as an Early Warning Device for Hexavalent Chromium Determination.

    Science.gov (United States)

    Wang, Guey-Horng; Cheng, Chiu-Yu; Liu, Man-Hai; Chen, Tzu-Yu; Hsieh, Min-Chi; Chung, Ying-Chien

    2016-08-16

    Fast hexavalent chromium (Cr(VI)) determination is important for environmental risk and health-related considerations. We used a microbial fuel cell-based biosensor inoculated with a facultatively anaerobic, Cr(VI)-reducing, and exoelectrogenic Ochrobactrum anthropi YC152 to determine the Cr(VI) concentration in water. The results indicated that O. anthropi YC152 exhibited high adaptability to pH, temperature, salinity, and water quality under anaerobic conditions. The stable performance of the microbial fuel cell (MFC)-based biosensor indicated its potential as a reliable biosensor system. The MFC voltage decreased as the Cr(VI) concentration in the MFC increased. Two satisfactory linear relationships were observed between the Cr(VI) concentration and voltage output for various Cr(VI) concentration ranges (0.0125-0.3 mg/L and 0.3-5 mg/L). The MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in drinking water, groundwater, and electroplating wastewater in 45 min with low deviations (<10%). The use of the biosensor can help in preventing the violation of effluent regulations and the maximum allowable concentration of Cr(VI) in water. Thus, the developed MFC biosensor has potential as an early warning detection device for Cr(VI) determination even if O. anthropi YC152 is a possible opportunistic pathogen.

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

    Science.gov (United States)

    Saravanan, Pichiah; Pakshirajan, K; Saha, Prabirkumar

    2009-02-15

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

  4. Enhancing the power generation in microbial fuel cells with effective utilization of goethite recovered from mining mud as anodic catalyst.

    Science.gov (United States)

    Jadhav, Dipak A; Ghadge, Anil N; Ghangrekar, Makarand M

    2015-09-01

    Catalytic effect of goethite recovered from iron-ore mining mud was studied in microbial fuel cells (MFCs). Characterization of material recovered from mining mud confirms the recovery of iron oxide as goethite. Heat treated goethite (550 °C) and untreated raw goethite were coated on stainless-steel anode of MFC-1 and MFC-2, respectively; whereas, unmodified stainless-steel anode was used in MFC-3 (control). Fivefold increment in power was obtained in MFC-1 (17.1 W/m(3) at 20 Ω) than MFC-3 (3.5 W/m(3)). MFC with raw goethite coated anode also showed enhanced power (11 W/m(3)). Higher Coulombic efficiency (34%) was achieved in MFC-1 than control MFC-3 (13%). Decrease in mass-transport losses and higher redox current during electrochemical analyses support improved electron transfer with the use of goethite on anode. Cheaper goethite coating kinetically accelerates the electron transfer between bacteria and anode, proving to be a novel approach for enhancing the electricity generation along with organic matter removal in MFC.

  5. Nutrient utilization and manure P excretion in growing pigs fed corn-barley-soybean based diets supplemented with microbial phytase.

    Science.gov (United States)

    Emiola, Adewale; Akinremi, Oluwole; Slominski, Bogdan; Nyachoti, C Martin

    2009-02-01

    The effect of high levels of microbial phytase supplementation in diets for growing pigs was studied in a 2-week performance and nutrient digestibility trial involving 28 growing pigs weighing 16.4 +/- 1.06 (mean +/- SD) kg. Seven corn-barley-soybean meal-based diets consisting of a positive control (PC) formulated to meet or exceed NRC nutrient requirements; a negative control (NC) with non-phytate P reduced by 0.1% unit from NRC requirement and fed without or with 500 or 1000 U/kg; a doubled negative control (DNC) with no added inorganic P and fed without or with 2000 or 4000 U/kg. Chromic oxide was added as an indigestible marker and all diets were fed as mash. Pigs fed the PC diet had a higher P digestibility compared with those fed the NC (P DNC (P DNC diet resulted in linear (P DNC diets. Apparent total tract digestibility of N, OM and DM were higher (P DNC diet, but not the NC diet (P DNC diet resulted in a linear increase (P DNC diets linearly decreased fecal P (P DNC diets (P < 0.05). The results of this study show that complete removal of inorganic P from growing pig diets coupled with phytase supplementation improves digestibility and retention of P and N, thus reducing manure P excretion without any negative effect on pig performance.

  6. Controls on the microbial utilization of carbon monoxide and formic acid in Acidic Hydrothermal Springs in Yellowstone National Park

    Science.gov (United States)

    Urschel, M.; Kubo, M. W.; Hoehler, T. M.; Boyd, E. S.; Peters, J.

    2012-12-01

    In hydrothermal systems, dissolved carbon dioxide (CO2) in the presence of reduced iron-bearing minerals, such as those found in basalt, can be reduced to form formic acid (HCOOH). HCOOH can then be dehydrated in a side reaction, resulting in the generation of carbon monoxide (CO), which forms an equilibrium with HCOOH. HCOOH can also be further reduced to methane, and longer chain hydrocarbons. Geochemical measurements have demonstrated the presence of elevated concentrations of HCOOH, dissolved CO, and dissolved inorganic carbon (CO2, H2CO3), in high temperature, low pH springs in Yellowstone National Park (YNP). Likewise, a number of compounds that could potentially serve as electron acceptors (e.g. S0, SO42-, NO3-, Fe3+) in the oxidation of CO or formic acid have been detected in many of these systems. We hypothesized that the utilization of CO and HCOOH as carbon and/or energy sources is a broadly-distributed metabolic strategy in high temperature, low pH springs in YNP. To test this hypothesis, radiolabeled CO (14CO) and HCOOH (H14COOH) were used to determine rates of CO and formate oxidation activity in three hot springs in YNP ranging in temperature from 53 °C to 89 °C and pH from 2.5 to 5.3. In parallel, 16S rRNA gene sequencing and enrichment isolation techniques were employed to identify the microorganisms responsible for these activities. Our results indicate that CO and HCOOH are important sources of carbon and/or energy in high temperature, low pH hydrothermal springs in Yellowstone National Park. Rates of CO oxidation appear to be orders of magnitude lower than those of HCOOH oxidation. One possible explanation for this result is that HCOOH is preferentially utilized, consistent with thermodynamic calculations indicating that HCOOH liberates approximately 215 kJ/mol more Gibbs energy (under standard conditions) than CO when oxidized with oxygen (O2) as the electron acceptor. Redox couples of HCOOH oxidation with other electron acceptors (e.g. SO4

  7. The dynamic process of atmospheric water sorption in [BMIM][Ac]: quantifying bulk versus surface sorption and utilizing atmospheric water as a structure probe.

    Science.gov (United States)

    Chen, Yu; Cao, Yuanyuan; Yan, Chuanyu; Zhang, Yuwei; Mu, Tiancheng

    2014-06-19

    The dynamic process of the atmospheric water absorbed in acetate-based ionic liquid 1-butyl-3-methyl-imidazolium acetate ([BMIM][Ac]) within 360 min could be described with three steps by using two-dimensional correlation infrared (IR) spectroscopy technique. In Step 1 (0-120 min), only bulk sorption via hydrogen bonding interaction occurs. In Step 2 (120-320 min), bulk and surface sorption takes place simultaneously via both hydrogen bonding interaction and van der Waals force. In Step 3, from 320 min to steady state, only surface sorption via van der Waals force occurs. Specifically, Step 2 could be divided into three substeps. Most bulk sorption with little surface sorption takes place in Step 2a (120-180 min), comparative bulk and surface sorption happens in Step 2b (180-260 min), and most surface sorption while little bulk sorption occurs in Step 2c (260-320 min). Interestingly, atmospheric water is found for the first time to be able to be used as a probe to detect the chemical structure of [BMIM][Ac]. Results show that one anion is surrounded by three C4,5H molecules and two anions are surrounded by five C2H molecules via hydrogen bonds, which are very susceptible to moisture water especially for the former one. The remaining five anions form a multimer (equilibrating with one dimer and one trimer) via a strong hydrogen bonding interaction, which is not easily affected by the introduction of atmospheric water. The alkyl of the [BMIM][Ac] cation aggregates to some extent by van der Walls force, which is moderately susceptible to the water attack. Furthermore, the proportion of bulk sorption vs surface sorption is quantified as about 70% and 30% within 320 min, 63% and 37% within 360 min, and 11% and 89% until steady-state, respectively.

  8. Effect of Bacillus amyloliquefaciens-based Direct-fed Microbial on Performance, Nutrient Utilization, Intestinal Morphology and Cecal Microflora in Broiler Chickens

    Science.gov (United States)

    Lei, Xinjian; Piao, Xiangshu; Ru, Yingjun; Zhang, Hongyu; Péron, Alexandre; Zhang, Huifang

    2015-01-01

    The present study was conducted to evaluate the effect of the dietary supplementation of Bacillus amyloliquefaciens-based direct-fed microbial (DFM) on growth performance, nutrient utilization, intestinal morphology and cecal microflora in broiler chickens. A total of two hundred and eighty eight 1-d-old Arbor Acres male broilers were randomly allocated to one of four experimental treatments in a completely randomized design. Each treatment was fed to eight replicate cages, with nine birds per cage. Dietary treatments were composed of an antibiotic-free basal diet (control), and the basal diet supplemented with either 15 mg/kg of virginiamycin as antibiotic growth promoter (AGP), 30 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 30) or 60 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 60). Experimental diets were fed in two phases: starter (d 1 to 21) and finisher (d 22 to 42). Growth performance, nutrient utilization, morphological parameters of the small intestine and cecal microbial populations were measured at the end of the starter (d 21) and finisher (d 42) phases. During the starter phase, DFM and virginiamycin supplementation improved the feed conversion ratio (FCR; pvirginiamycin and DFM significantly increased the total tract apparent digestibility of crude protein (CP), dry matter (DM) and gross energy during both starter and finisher phases (p<0.05) compared with the control group. On d 21, villus height, crypt depth and villus height to crypt depth ratio of duodenum, jejunum, and ileum were significantly increased for the birds fed with the DFM diets as compared with the control group (p<0.05). The DFM 30, DFM 60, and AGP groups decreased the Escherichia coli population in cecum at d 21 and d 42 compared with control group (p<0.01). In addition, the population of Lactobacillus was increased in DFM 30 and DFM 60 groups as compared with control and AGP groups (p<0.01). It can be concluded that Bacillus amyloliquefaciens-based DFM could be an

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

    Science.gov (United States)

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

    2012-10-01

    The effects of replacing 35% of cereals-based concentrate with feed blocks (FB) containing waste fruits of tomato, cucumber, or barley grain in diets for lactating goats on nutrient utilization, ruminal fermentation, microbial N flow to the duodenum, milk yield and quality, methane emissions, and abundances of total bacteria and methanogens were studied. Eight Murciano-Granadina goats (39.4 ± 5.39 kg of body weight, mean ± SD) in the middle of the third lactation were used and 4 diets were studied in a replicated 4×4 Latin square experimental design. Diets consisted of alfalfa hay (A) plus concentrate (C) in a 1:1 ratio (diet AC) or diets in which 35% of the concentrate was replaced with FB including wastes of tomato fruit, cucumber, or barley. In each period, 2 goats were randomly assigned to 1 of the dietary treatments. Intakes of FB including tomato, cucumber, and barley were 208 ± 65, 222 ± 52, and 209 ± 83 g of dry matter per animal and day, respectively. The replacement of 35% of concentrate with FB did not compromise nutrient apparent digestibility, total purine derivative urinary excretion, milk yield and composition, and total bacteria and methanogen abundances. Digestible energy and that in methane and urine were higher for AC than for FB-containing diets, whereas the metabolizable energy value was not affected by diet. The inclusion of tomato and cucumber fruits in FB decreased N in urine and CH(4) emissions compared with AC, which is environmentally relevant. However, tomato-based FB decreased microbial N flow in the rumen, whereas goats fed cucumber-based FB had the highest values for this measurement. Moreover, FB containing barley or tomato and cucumber led to lower rumen volatile fatty acid and NH(3)-N concentrations, respectively. Milk from goats fed diets including tomato and cucumber-based FB had higher linoleic, linolenic, and total polyunsaturated fatty acid concentrations than that from goats fed AC. Overall, our study suggests that

  10. Quantifying Concordance

    CERN Document Server

    Seehars, Sebastian; Amara, Adam; Refregier, Alexandre

    2015-01-01

    Quantifying the concordance between different cosmological experiments is important for testing the validity of theoretical models and systematics in the observations. In earlier work, we thus proposed the Surprise, a concordance measure derived from the relative entropy between posterior distributions. We revisit the properties of the Surprise and describe how it provides a general, versatile, and robust measure for the agreement between datasets. We also compare it to other measures of concordance that have been proposed for cosmology. As an application, we extend our earlier analysis and use the Surprise to quantify the agreement between WMAP 9, Planck 13 and Planck 15 constraints on the $\\Lambda$CDM model. Using a principle component analysis in parameter space, we find that the large Surprise between WMAP 9 and Planck 13 (S = 17.6 bits, implying a deviation from consistency at 99.8% confidence) is due to a shift along a direction that is dominated by the amplitude of the power spectrum. The Surprise disa...

  11. Utility of SNP arrays in detecting, quantifying, and determining meiotic origin of tetrasomy 12p in blood from individuals with Pallister-Killian syndrome.

    Science.gov (United States)

    Conlin, Laura K; Kaur, Maninder; Izumi, Kosuke; Campbell, Lindsey; Wilkens, Alisha; Clark, Dinah; Deardorff, Matthew A; Zackai, Elaine H; Pallister, Phillip; Hakonarson, Hakon; Spinner, Nancy B; Krantz, Ian D

    2012-12-01

    Identification of the isochromosome 12p (i(12p)) associated with Pallister-Killian syndrome is complicated by the low frequency of this supernumerary chromosome in PHA stimulated peripheral blood lymphocytes, and frequently requires cytogenetic analysis of fibroblast cells. Recently, it has been shown that array CGH techniques are able to detect tetrasomy 12p in peripheral blood, even when not identified by traditional cytogenetic techniques. We studied 15 patients with a previous cytogenetic and clinical diagnosis of Pallister-Killian syndrome using genome-wide SNP arrays to investigate the ability of this platform to identify the i(12p) in blood and tissue. Array analysis verified tetrasomy 12p in all samples from fibroblasts, but was only able to detect it in 46% of blood samples. The genotyping information available from the SNP arrays allowed for the detection of as low as 5% mosaicism, as well as suggesting a Meiosis II origin for the isochromosome in the majority of patients. Analysis of the percentage of abnormal cells with patient age at time of study suggests that the frequency of the i(12p) decreased with age in blood, but not in fibroblasts. These highlight the power of SNP arrays in detecting and characterizing the isochromosome 12p in Pallister-Killian syndrome as well as underscoring the important utility of traditional cytogenetic techniques.

  12. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Vinoth Wigneswaran

    2016-03-01

    Full Text Available Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.

  13. The Utilization of Microbial Inoculants Based on Irradiated Compost in Dryland Remediation to Increase the Growth of King Grass and Maize

    Directory of Open Access Journals (Sweden)

    T.R.D. Larasati

    2016-04-01

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

  14. Improvement of Carbon Dioxide Sweep Efficiency by Utilization of Microbial Permeability Profile Modification to Reduce the Amount of Oil Bypassed During Carbon Dioxide Flood

    Energy Technology Data Exchange (ETDEWEB)

    Schmitz, Darrel [Mississippi State Univ., Mississippi State, MS (United States); Brown, Lewis [Mississippi State Univ., Mississippi State, MS (United States); Lynch, F. Leo [Mississippi State Univ., Mississippi State, MS (United States); Kirkland, Brenda L. [Mississippi State Univ., Mississippi State, MS (United States); Collins, Krystal M. [Mississippi State Univ., Mississippi State, MS (United States); Funderburk, William K. [Mississippi State Univ., Mississippi State, MS (United States)

    2010-12-31

    The objective of this project was to couple microbial permeability profile modification (MPPM), with carbon dioxide flooding to improve oil recovery from the Upper Cretaceous Little Creek Oil Field situated in Lincoln and Pike counties, MS. This study determined that MPPM technology, which improves production by utilizing environmentally friendly nutrient solutions to simulate the growth of the indigenous microflora in the most permeable zones of the reservoir thus diverting production to less permeable, previously unswept zones, increased oil production without interfering with the carbon dioxide flooding operation. Laboratory tests determined that no microorganisms were produced in formation waters, but were present in cores. Perhaps the single most significant contribution of this study is the demonstration that microorganisms are active at a formation temperature of 115°C (239°F) by using a specially designed culturing device. Laboratory tests were employed to simulate the MPPM process by demonstrating that microorganisms could be activated with the resulting production of oil in coreflood tests performed in the presence of carbon dioxide at 66°C (the highest temperature that could be employed in the coreflood facility). Geological assessment determined significant heterogeneity in the Eutaw Formation, and documented relatively thin, variably-lithified, well-laminated sandstone interbedded with heavily-bioturbated, clay-rich sandstone and shale. Live core samples of the Upper Cretaceous Eutaw Formation from the Heidelberg Field, MS were quantitatively assessed using SEM, and showed that during MPPM permeability modification occurs ubiquitously within pore and throat spaces of 10-20 μm diameter. Testing of the MPPM procedure in the Little Creek Field showed a significant increase in production occurred in two of the five production test wells; furthermore, the decline curve in each of the production wells became noticeably less steep. This project greatly

  15. Supplemental macronutrients and microbial fermentation products improve the uptake and transport of foliar applied zinc in sunflower (Helianthus annuus L.) plants. Studies utilizing micro X-ray florescence.

    Science.gov (United States)

    Tian, Shengke; Lu, Lingli; Xie, Ruohan; Zhang, Minzhe; Jernstedt, Judith A; Hou, Dandi; Ramsier, Cliff; Brown, Patrick H

    2014-01-01

    Enhancing nutrient uptake and the subsequent elemental transport from the sites of application to sites of utilization is of great importance to the science and practical field application of foliar fertilizers. The aim of this study was to investigate the mobility of various foliar applied zinc (Zn) formulations in sunflower (Helianthus annuus L.) and to evaluate the effects of the addition of an organic biostimulant on phloem loading and elemental mobility. This was achieved by application of foliar formulations to the blade of sunflower (H. annuus L.) and high-resolution elemental imaging with micro X-ray fluorescence (μ-XRF) to visualize Zn within the vascular system of the leaf petiole. Although no significant increase of total Zn in petioles was determined by inductively-coupled plasma mass-spectrometer, μ-XRF elemental imaging showed a clear enrichment of Zn in the vascular tissues within the sunflower petioles treated with foliar fertilizers containing Zn. The concentration of Zn in the vascular of sunflower petioles was increased when Zn was applied with other microelements with EDTA (commercial product Kick-Off) as compared with an equimolar concentration of ZnSO4 alone. The addition of macronutrients N, P, K (commercial product CleanStart) to the Kick-Off Zn fertilizer, further increased vascular system Zn concentrations while the addition of the microbially derived organic biostimulant "GroZyme" resulted in a remarkable enhancement of Zn concentrations in the petiole vascular system. The study provides direct visualized evidence for phloem transport of foliar applied Zn out of sites of application in plants by using μ-XRF technique, and suggests that the formulation of the foliar applied Zn and the addition of the organic biostimulant GroZyme increases the mobility of Zn following its absorption by the leaf of sunflower.

  16. Supplemental macronutrients and microbial fermentation products improve the uptake and transport of foliar applied zinc in sunflower (Helianthus annuus L. plants. Studies utilizing micro X-ray florescence

    Directory of Open Access Journals (Sweden)

    Shengke eTian

    2015-01-01

    Full Text Available Enhancing nutrient uptake and the subsequent elemental transport from the sites of application to sites of utilization is of great importance to the science and practical field application of foliar fertilizers. The aim of this study was to investigate the mobility of various foliar applied Zn formulations in sunflower (Helianthus annuus L. and to evaluate the effects of the addition of an organic biostimulant on phloem loading and elemental mobility. This was achieved by application of foliar formulations to the blade of sunflower (Helianthus annuus L. and high-resolution elemental imaging with micro X-ray fluorescence (μ-XRF to visualize Zn within the vascular system of the leaf petiole. Although no significant increase of total Zn in petioles was determined by ICP-MS, μ-XRF elemental imaging showed a clear enrichment of Zn in the vascular tissues within the sunflower petioles treated with foliar fertilizers containing Zn. The concentration of Zn in the vascular of sunflower pertioles was increased when Zn was applied with other microelements with EDTA (commercial product Kick-Off as compared with an equimolar concentration of ZnSO4 alone. The addition of macronutrients N, P, K (commercial product CleanStart to the Kick-Off Zn fertilizer, further increased vascular system Zn concentrations while the addition of the microbially derived organic biostimulant GroZyme resulted in a remarkable enhancement of Zn concentrations in the petiole vascular system. The study provides direct visualized evidence for phloem transport of foliar applied Zn out of sites of application in plants by using µ-XRF technique, and suggests that the formulation of the foliar applied Zn and the addition of the organic biostimulant GroZyme increases the mobility of Zn following its absorption by the leaf of sunflower.

  17. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  18. Inferring Microbial Fitness Landscapes

    Science.gov (United States)

    2016-02-25

    experiments on evolving microbial populations. Although these experiments have produced examples of remarkable phenomena – e.g. the emergence of mutator...what specific mutations, avian influenza viruses will adapt to novel human hosts; or how readily infectious bacteria will escape antibiotics or the...infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND

  19. Microbial bioenergetics of coral-algal interactions

    Directory of Open Access Journals (Sweden)

    Ty N.F. Roach

    2017-06-01

    Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify

  20. Research progress of utilization of excess sludge with microbial fuel cell technology%以微生物燃料电池技术资源化利用剩余污泥的研究进展

    Institute of Scientific and Technical Information of China (English)

    沈春花; 曾庆玲; 郭义海

    2011-01-01

    介绍了剩余污泥存在的问题与剩余污泥资源化利用方法,重点介绍以微生物燃料电池技术资源化利用剩余污泥的研究进展,包括直接利用剩余污泥与间接利用剩余污泥为燃料的微生物燃料电池技术方面的最新研究进展。直接利用剩余污泥作为微生物燃料电池的燃料,介绍了该方法的产电输出功率密度、污泥中总化学需氧量(TCOD)等的去除情况、污泥的减量效果等;间接利用剩余污泥作为燃料,包括剩余污泥微波预处理上清液作为燃料与剩余污泥发酵产生的挥发性脂肪酸(VFA)作为燃料,这些微生物燃料电池技术都能有效地资源化利用剩余污泥,同时达到污泥减量%Excess sludge and sludge utilization methods are described.Excess sludge utilized with microbial fuel cell technology is introduced,including utilization of excess sludge as the fuel for microbial fuel cell directly and indirectly.In the case of excess sludge utilized as the fuel for microbial fuel cell directly,the output power density,removal efficiencies of TCOD and SS are described.In the case of excess sludge was utilized as the fuel for microbial fuel cell indirectly,the supernatant fluid of microwave pretreated sludge or the volatile fatty acids(VFA)produced by sludge fermentation is used as the fuel.These methods can utilize excess sludge effectively and have broad application prospects.

  1. Development of synthetic chromosomes and improved microbial strains to utilize cellulosic feedstocks and express valuable coproducts for sustainable production of biofuels from corn

    Science.gov (United States)

    A sustainable biorefinery must convert a broad range of renewable feedstocks into a variety of product streams, including fuels, power, and value-added bioproducts. To accomplish this, microbial-based technologies that enable new commercially viable coproducts from corn-to-ethanol biofuel fermentati...

  2. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    Science.gov (United States)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  3. Uncertainty quantified trait predictions

    Science.gov (United States)

    Fazayeli, Farideh; Kattge, Jens; Banerjee, Arindam; Schrodt, Franziska; Reich, Peter

    2015-04-01

    Functional traits of organisms are key to understanding and predicting biodiversity and ecological change, which motivates continuous collection of traits and their integration into global databases. Such composite trait matrices are inherently sparse, severely limiting their usefulness for further analyses. On the other hand, traits are characterized by the phylogenetic trait signal, trait-trait correlations and environmental constraints, all of which provide information that could be used to statistically fill gaps. We propose the application of probabilistic models which, for the first time, utilize all three characteristics to fill gaps in trait databases and predict trait values at larger spatial scales. For this purpose we introduce BHPMF, a hierarchical Bayesian extension of Probabilistic Matrix Factorization (PMF). PMF is a machine learning technique which exploits the correlation structure of sparse matrices to impute missing entries. BHPMF additionally utilizes the taxonomic hierarchy for trait prediction. Implemented in the context of a Gibbs Sampler MCMC approach BHPMF provides uncertainty estimates for each trait prediction. We present comprehensive experimental results on the problem of plant trait prediction using the largest database of plant traits, where BHPMF shows strong empirical performance in uncertainty quantified trait prediction, outperforming the state-of-the-art based on point estimates. Further, we show that BHPMF is more accurate when it is confident, whereas the error is high when the uncertainty is high.

  4. Quantifying innovation in surgery.

    Science.gov (United States)

    Hughes-Hallett, Archie; Mayer, Erik K; Marcus, Hani J; Cundy, Thomas P; Pratt, Philip J; Parston, Greg; Vale, Justin A; Darzi, Ara W

    2014-08-01

    The objectives of this study were to assess the applicability of patents and publications as metrics of surgical technology and innovation; evaluate the historical relationship between patents and publications; develop a methodology that can be used to determine the rate of innovation growth in any given health care technology. The study of health care innovation represents an emerging academic field, yet it is limited by a lack of valid scientific methods for quantitative analysis. This article explores and cross-validates 2 innovation metrics using surgical technology as an exemplar. Electronic patenting databases and the MEDLINE database were searched between 1980 and 2010 for "surgeon" OR "surgical" OR "surgery." Resulting patent codes were grouped into technology clusters. Growth curves were plotted for these technology clusters to establish the rate and characteristics of growth. The initial search retrieved 52,046 patents and 1,801,075 publications. The top performing technology cluster of the last 30 years was minimally invasive surgery. Robotic surgery, surgical staplers, and image guidance were the most emergent technology clusters. When examining the growth curves for these clusters they were found to follow an S-shaped pattern of growth, with the emergent technologies lying on the exponential phases of their respective growth curves. In addition, publication and patent counts were closely correlated in areas of technology expansion. This article demonstrates the utility of publically available patent and publication data to quantify innovations within surgical technology and proposes a novel methodology for assessing and forecasting areas of technological innovation.

  5. Quantifiers, Anaphora and Intensionality

    CERN Document Server

    Dalrymple, M; Pereira, F C N; Saraswat, V; Dalrymple, Mary; Lamping, John; Pereira, Fernando; Saraswat, Vijay

    1995-01-01

    The relationship between Lexical-Functional Grammar (LFG) {\\em functional structures} (f-structures) for sentences and their semantic interpretations can be expressed directly in a fragment of linear logic in a way that correctly explains the constrained interactions between quantifier scope ambiguity, bound anaphora and intensionality. This deductive approach to semantic interpretaion obviates the need for additional mechanisms, such as Cooper storage, to represent the possible scopes of a quantified NP, and explains the interactions between quantified NPs, anaphora and intensional verbs such as `seek'. A single specification in linear logic of the argument requirements of intensional verbs is sufficient to derive the correct reading predictions for intensional-verb clauses both with nonquantified and with quantified direct objects. In particular, both de dicto and de re readings are derived for quantified objects. The effects of type-raising or quantifying-in rules in other frameworks here just follow as li...

  6. Decomposing generalized quantifiers

    NARCIS (Netherlands)

    Westerståhl, D.

    2008-01-01

    This note explains the circumstances under which a type <1> quantifier can be decomposed into a type <1, 1> quantifier and a set, by fixing the first argument of the former to the latter. The motivation comes from the semantics of Noun Phrases (also called Determiner Phrases) in natural languages, b

  7. Decomposing generalized quantifiers

    NARCIS (Netherlands)

    Westerståhl, D.

    2008-01-01

    This note explains the circumstances under which a type <1> quantifier can be decomposed into a type <1, 1> quantifier and a set, by fixing the first argument of the former to the latter. The motivation comes from the semantics of Noun Phrases (also called Determiner Phrases) in natural languages,

  8. Understanding quantifiers in language

    NARCIS (Netherlands)

    Szymanik, J.; Zajenkowski, M.; Taatgen, N.; van Rijn, H.

    2009-01-01

    We compare time needed for understanding different types of quantifiers. We show that the computational distinction between quantifiers recognized by finite-automata and push-down automata is psychologically relevant. Our research improves upon hypothesis and explanatory power of recent neuroimaging

  9. Microbial utilization of the industrial wastewater pollutants 2-ethylhexylthioglycolic acid and iso-octylthioglycolic acid by aerobic gram-negative bacteria.

    Science.gov (United States)

    Toups, Mario; Wübbeler, Jan Hendrik; Steinbüchel, Alexander

    2010-04-01

    Industrial wastewater from the production of sulfur containing esters and the resulting products of this synthesis, 2-ethylhexylthioglycolic acid (EHTG) and iso-octylthioglycolic acid (IOTG), were deployed in this study to enrich novel bacterial strains, since no wastewater and EHTG or IOTG degrading microorganisms were hitherto described or available. In addition, nothing is known about the biodegradation of these thiochemicals. The effect of this specific wastewater on the growth behaviour of microorganisms was investigated using three well-known Gram-negative bacteria (Escherichia coli, Pseudomonas putida, and Ralstonia eutropha). Concentrations of 5% (v/v) wastewater in complex media completely inhibited growth of these three bacterial strains. Six bacterial strains were successfully isolated, characterized and identified by sequencing their 16S rRNA genes. Two isolates referred to as Achromobacter sp. strain MT-E3 and Pseudomonas sp. strain MT-I1 used EHTG or IOTG, respectively, as well as the wastewater as sole source of carbon and energy for weak growth. More notably, both isolates removed these sulfur containing esters in remarkable amounts from the cultures supernatant. One further isolate was referred to as Klebsiella sp. strain 58 and exhibited an unusual high tolerance against the wastewater's toxicity without utilizing the contaminative compounds. If cultivated with gluconic acid as additional carbon source, the strain grew even in presence of more than 40% (v/v) wastewater. Three other isolates belonging to the genera Bordetella and Pseudomonas tolerated these organic sulfur compounds but showed no degradation abilities.

  10. Utilization of wastewater originated from naturally fermented virgin coconut oil manufacturing process for bioextract production: physico-chemical and microbial evolution.

    Science.gov (United States)

    Tripetchkul, Sudarut; Kusuwanwichid, Sasithorn; Koonsrisuk, Songpon; Akeprathumchai, Saengchai

    2010-08-01

    Production of virgin coconut oil via natural fermentation has led to large amount of wastes being generated, i.e., coconut pulp and wastewater containing coconut crème. Objective of this study is to gain more insight into the feasibility of utilization of such wastes as raw materials together with several types of wastes such as fish waste and/or pineapple peel for bioextract production. Chemical, physico-chemical and biological changes including phytotoxicity of the fermented mixture were closely monitored. Physical observation suggested that fermentation of bioextract obtained with fish waste appeared to be complete within the first month of fermentation while bioextract obtained using pineapple waste seemed to be complete after 8 months post-fermentation. Fermentation broth is of blackish color with alcoholic as well as acidic odour with no gas bubble and/or yeast film present on top of the surface. During the whole fermentation interval, several attributes of both bioextracts, e.g., pH, chemical oxygen demand (COD) and organic acids, were statistically different. Further, the total bacteria and lactic acid bacteria present in pineapple bioextract were statistically higher than those of the fish bioextract (pbiofertilizer after 1 month fermentation. Results further showed that wastewater derived from virgin coconut oil manufacturing process could effectively be employed together with other types of wastes such as fish waste and pineapple peel for bioextract production. However, for the best bioextract quality, fermentation should be carefully planned since over fermentation led to bioextract of low qualities.

  11. Connected Car: Quantified Self becomes Quantified Car

    Directory of Open Access Journals (Sweden)

    Melanie Swan

    2015-02-01

    Full Text Available The automotive industry could be facing a situation of profound change and opportunity in the coming decades. There are a number of influencing factors such as increasing urban and aging populations, self-driving cars, 3D parts printing, energy innovation, and new models of transportation service delivery (Zipcar, Uber. The connected car means that vehicles are now part of the connected world, continuously Internet-connected, generating and transmitting data, which on the one hand can be helpfully integrated into applications, like real-time traffic alerts broadcast to smartwatches, but also raises security and privacy concerns. This paper explores the automotive connected world, and describes five killer QS (Quantified Self-auto sensor applications that link quantified-self sensors (sensors that measure the personal biometrics of individuals like heart rate and automotive sensors (sensors that measure driver and passenger biometrics or quantitative automotive performance metrics like speed and braking activity. The applications are fatigue detection, real-time assistance for parking and accidents, anger management and stress reduction, keyless authentication and digital identity verification, and DIY diagnostics. These kinds of applications help to demonstrate the benefit of connected world data streams in the automotive industry and beyond where, more fundamentally for human progress, the automation of both physical and now cognitive tasks is underway.

  12. 磷供应对玉米根际微生物碳源利用和功能多样性的影响%Effects of phosphorus supply on microbial carbon source utilization and functional diversity of maize rhizosphere

    Institute of Scientific and Technical Information of China (English)

    唐宏亮; 郭秋换; 张春潮; 段霄霄

    2015-01-01

    磷有效性能够改变根分泌物的组成和数量, 调节土壤微生物的群落结构和多样性, 但磷添加如何影响土壤微生物碳源利用和功能多样性尚不清楚.本研究通过盆栽土培试验,设置2个磷处理[低磷5.7 mg(P).kg-1和高磷200 mg(P).kg-1],以生长35 d的玉米根际土壤为研究对象,采用Biolog微平板法,分别在培养后240 h内每隔24 h检测具有31种不同碳源的微孔溶液颜色变化,揭示磷供应对玉米根际微生物碳源利用模式和功能多样性的影响.结果表明: 随着培养时间的延长, 土壤微生物对土壤碳源的利用呈现增加的趋势, 直至碳源消耗殆尽;高磷供应显著增加了玉米根际土壤微生物群落平均颜色变化率(average well color development, AWCD),提高了对糖类及其衍生物、氨基酸和代谢产物的利用,但没有显著提高对脂肪酸和脂类的利用;在培养前72 h内,高磷供应显著增加了玉米根际微生物多样性指数、优势度指数和均匀度指数,但培养72 h后,磷供应对其没有显著的影响.主成分分析结果表明, 提取的前 3 个主成分解释了 75.15%的碳源利用, 高磷和低磷处理具有显著不同的土壤微生物碳源利用模式.总之, 糖类及其衍生物、氨基酸和代谢产物是玉米根际土壤微生物利用的主要碳源, 短期磷添加能够显著增加土壤微生物对碳源的利用, 在一定程度上能够提高土壤微生物群落功能多样性.%Phosphorus (P) is a key nutrient which influences the growth, development and yield of crops. P availability can regulate soil microbial community structure and diversity by altering the quantity and components of root exudates. Whether P addition increases carbon resources utilization and functional diversity of soil microorganisms remains highly debatable. Also how P addition affects carbon resources utilization and functional diversity of soil microorganisms is not fully understood. In this

  13. Effects of grass forage species and long-term period of low quality forage diet feeding on growth performance, nutrient utilization and microbial nitrogen yield in growing wether lambs.

    Science.gov (United States)

    Kim, Da-Hye; Choi, Ki-Choon; Song, Sang-Houn; Ichinohe, Toshiyoshi

    2016-02-01

    Six growing lambs were used to evaluate the feeding value of two forage-based diets in a long-term feeding period by measuring body weight (BW) gain, digestibility, nitrogen (N) retention and microbial N (MBN) yield. The animals were fed imported low-quality timothy hay (TH) with concentrate diet (THD) or imported low-quality Italian ryegrass straw (IR) with concentrate diet (IRD) for 9 months. The forages were offered at 2% BW, and concentrate was fed at 40% of forage intake. The BW gain averaged 82.6 and 66.2 g/day for THD and IRD, respectively, without showing significant difference. Average forage intake (% BW) was significantly greater for IR than for TH, although it was not affected by feeding periods. The digestibility did not differ between diets or periods. The numerically greater (P = 0.06) ratio of retained N to absorbed N for IRD than that for THD was prominent. Neither diet nor period had significant effect on MBN supply and efficiency of MBN synthesis. The results suggest that the IR-based diet can be also used for long-term periods of feeding to growing ruminant animals as a grass hay-based diet without any detrimental effects on nutrient utilization and growth performance.

  14. The Wind Forecast Improvement Project (WFIP). A Public/Private Partnership for Improving Short Term Wind Energy Forecasts and Quantifying the Benefits of Utility Operations -- the Northern Study Area

    Energy Technology Data Exchange (ETDEWEB)

    Finley, Cathy [WindLogics, St. Paul, MN (United States)

    2014-04-30

    This report contains the results from research aimed at improving short-range (0-6 hour) hub-height wind forecasts in the NOAA weather forecast models through additional data assimilation and model physics improvements for use in wind energy forecasting. Additional meteorological observing platforms including wind profilers, sodars, and surface stations were deployed for this study by NOAA and DOE, and additional meteorological data at or near wind turbine hub height were provided by South Dakota State University and WindLogics/NextEra Energy Resources over a large geographical area in the U.S. Northern Plains for assimilation into NOAA research weather forecast models. The resulting improvements in wind energy forecasts based on the research weather forecast models (with the additional data assimilation and model physics improvements) were examined in many different ways and compared with wind energy forecasts based on the current operational weather forecast models to quantify the forecast improvements important to power grid system operators and wind plant owners/operators participating in energy markets. Two operational weather forecast models (OP_RUC, OP_RAP) and two research weather forecast models (ESRL_RAP, HRRR) were used as the base wind forecasts for generating several different wind power forecasts for the NextEra Energy wind plants in the study area. Power forecasts were generated from the wind forecasts in a variety of ways, from very simple to quite sophisticated, as they might be used by a wide range of both general users and commercial wind energy forecast vendors. The error characteristics of each of these types of forecasts were examined and quantified using bulk error statistics for both the local wind plant and the system aggregate forecasts. The wind power forecast accuracy was also evaluated separately for high-impact wind energy ramp events. The overall bulk error statistics calculated over the first six hours of the forecasts at both the

  15. A bottom-up geostatistical approach for quantifying landcover in Asian desert ecosystems and implications for global and climate models: a case study in Afghanistan utilizing a unique hyperspectral dataset

    Science.gov (United States)

    Shreve, C. M.; Okin, G. S.; Bowles, J.; Gardner, J.

    2007-12-01

    Political tensions, rough terrain, and remoteness have lead to a gap in the ecological understanding cold, mountainous deserts of Asia. Remote sensing is a time- and cost-efficient way to understand the spatial distribution and temporal dynamics of plant and snow cover in these regions. Here, a unique high-resolution hyperspectral dataset from Afghanistan is employed to classify ground cover at high resolution. The hyperspectral data was taken using a CASI-1500 Visible Near InfraRed (VNIR) spectrometer. The instrument was run in a mode with 1518 crosstrack pixels and 72 spectral bands between 380 and 1050 nm. The GSD was controlled by the altitude above ground level and aircraft speed, which varied resulting in GSD between 4 and 6 meters. Geolocation was provided by a CMIGITS II and the resulting accuracy will be better than 40 m. Atmospheric conditions were challenging and proper atmospheric compensation of the data remains a challenge. A bottom- up geostatistical approach for quantifying the coverage of vegetation and snow will be applied to establish the practical limits of coarse resolution MODIS data for classifying vegetation and snow cover, a scale suitable for monitoring large regions and for modeling. A Multiple Endmember Linear Spectral Mixture Algorithm (MESMA) will be applied to classify land cover. Semivariograms at the multispectral (30 m) and coarse resolution scale (1 km) will be compared with simulated variograms using hysperspectral data. Patches of vegetation and snow cover used for spatial comparison will be identified in the image and characterized using object-oriented image analysis software. The relative amount of cover will be determined using block-kriging and compared between scenes with statistical tests. Insight gained from this analysis can be applied to improve existing data products and can be applied for carbon budget and climate change models.

  16. Quantifying linguistic coordination

    DEFF Research Database (Denmark)

    Fusaroli, Riccardo; Tylén, Kristian

    ). We employ nominal recurrence analysis (Orsucci et al 2005, Dale et al 2011) on the decision-making conversations between the participants. We report strong correlations between various indexes of recurrence and collective performance. We argue this method allows us to quantify the qualities......Language has been defined as a social coordination device (Clark 1996) enabling innovative modalities of joint action. However, the exact coordinative dynamics over time and their effects are still insufficiently investigated and quantified. Relying on the data produced in a collective decision...

  17. Quantifying synergistic mutual information

    CERN Document Server

    Griffith, Virgil

    2012-01-01

    Quantifying cooperation among random variables in predicting a single target random variable is an important problem in many biological systems with 10s to 1000s of co-dependent variables. We review the prior literature of information theoretical measures of synergy and introduce a novel synergy measure, entitled *synergistic mutual information* and compare it against the three existing measures of cooperation. We apply all four measures against a suite of binary circuits to demonstrate our measure alone quantifies the intuitive concept of synergy across all examples.

  18. Is Time Predictability Quantifiable?

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2012-01-01

    -case execution time. To compare different approaches we would like to quantify time predictability. That means we need to measure time predictability. In this paper we discuss the different approaches for these measurements and conclude that time predictability is practically not quantifiable. We can only......Computer architects and researchers in the realtime domain start to investigate processors and architectures optimized for real-time systems. Optimized for real-time systems means time predictable, i.e., architectures where it is possible to statically derive a tight bound of the worst...... compare the worst-case execution time bounds of different architectures....

  19. Microbial enhanced oil recovery and wettability research program

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, C.P.; Bala, G.A.; Duvall, M.L.

    1991-07-01

    This report covers research results for the microbial enhanced oil recovery (MEOR) and wettability research program conducted by EG G Idaho, Inc. at the Idaho National Engineering Laboratory (INEL). The isolation and characterization of microbial species collected from various locations including target oil field environments is underway to develop more effective oil recovery systems for specific applications. The wettability research is a multi-year collaborative effort with the New Mexico Petroleum Recovery Research Center (NMPRRC), to evaluate reservoir wettability and its effects on oil recovery. Results from the wettability research will be applied to determine if alteration of wettability is a significant contributing mechanism for MEOR systems. Eight facultatively anaerobic surfactant producing isolates able to function in the reservoir conditions of the Minnelusa A Sands of the Powder River Basin in Wyoming were isolated from naturally occurring oil-laden environments. Isolates were characterized according to morphology, thermostability, halotolerance, growth substrates, affinity to crude oil/brine interfaces, degradative effects on crude oils, and biochemical profiles. Research at the INEL has focused on the elucidation of microbial mechanisms by which crude oil may be recovered from a reservoir and the chemical and physical properties of the reservoir that may impact the effectiveness of MEOR. Bacillus licheniformis JF-2 (ATCC 39307) has been used as a benchmark organism to quantify MEOR of medium weight crude oils (17.5 to 38.1{degrees}API) the capacity for oil recovery of Bacillus licheniformis JF-2 utilizing a sucrose-based nutrient has been elucidated using Berea sandstone cores. Spacial distribution of cells after microbial flooding has been analyzed with scanning electron microscopy. Also the effect of microbial surfactants on the interfacial tensions (IFT) of aqueous/crude oil systems has been measured. 87 refs., 60 figs., 15 tabs.

  20. Molecular Biomarkers for Detecting, Monitoring and Quantifying Reductive Microbial Processes

    Science.gov (United States)

    2013-07-01

    chlorinated   ethylenes   in...investigations   of   the   anaerobic   reductive   dechlorination   of   chlorinated   ethylenes   using   single   and   binary...dechlorination  of   chlorinated   ethylenes  by  two  different  mixed  cultures.  Environ.  Sci.  Technol.,

  1. Connecting Taxon-Specific Microbial Activities to Carbon Cycling in the Rhizosphere

    Science.gov (United States)

    Hungate, B. A.; Morrissey, E.; Schwartz, E.; Dijkstra, P.; Blazewicz, S.; Pett-Ridge, J.; Koch, G. W.; Marks, J.; Koch, B.; McHugh, T. A.; Mau, R. L.; Hayer, M.

    2016-12-01

    Plant carbon inputs influence microbial growth in the rhizosphere, but the quantitative details of these effects are not well understood, nor are their consequences for carbon cycling in the rhizosphere. With a new pulse of carbon input to soil, which microbial taxa increase their growth rates, and by how much? Do any microbial taxa respond negatively? And how does the extra carbon addition alter the utilization of other resources, including other carbon sources, as well as inorganic nitrogen? This talk will present new research using quantitative stable isotope probing that reveals the distribution of growth responses among microbial taxa, from positive to neutral to negative, and how these growth responses are associated with various substrates. For example, decomposition of soil C in response to added labile carbon occurred as a phylogenetically-diverse majority of taxa shifted toward soil C use for growth. In contrast, bacteria with suppressed growth or that relied directly on glucose for growth clustered strongly by phylogeny. These results suggest that priming is a prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the priming effect in nature. These results also illustrate the potential power of molecular tools and models that seek to estimate metrics directly relevant to quantitative ecology and biogeochemistry, moreso than is the standard currently in microbial ecology. Tools that estimate growth rate, mortality rate, and rates of substrate use - all quantified with the taxonomic precision afforded by modern sequencing - provide a foundation for quantifying the biogeochemical significance of microbial biodiversity, and a more complete understanding of the rich ecosystem of the rhizosphere.

  2. Performance of the FilmArray® blood culture identification panel utilized by non-expert staff compared with conventional microbial identification and antimicrobial resistance gene detection from positive blood cultures.

    Science.gov (United States)

    McCoy, Morgan H; Relich, Ryan F; Davis, Thomas E; Schmitt, Bryan H

    2016-07-01

    Utilization of commercially available rapid platforms for microbial identification from positive blood cultures is useful during periods of, or in laboratories with, limited expert staffing. We compared the results of the FilmArray® BCID Panel performed by non-expert technologists to those of conventional methods for organism identification performed by skilled microbiologists. Within 8 h of signalling positive by a continuous monitoring blood culture system, positive bottles were analysed by the FilmArray BCID Panel. Data from these analyses were compared to standard-of-care testing, which included conventional and automated methods. To gauge the ease of use of the BCID Panel by non-expert staff, technologists unfamiliar with diagnostic bacteriology performed the testing without prior knowledge of the Gram stain results, or even whether organisms were detected. Identifications of 172/200 (86 %) positive blood cultures using the BCID Panel were consistent with identifications provided by standard-of-care methods. Standard-of-care testing identified organisms in 20 positive blood cultures, which were not represented on the BCID Panel. Seven (3.5 %) blood cultures demonstrated a discrepancy between the methods, which could not be attributed to either a lack of representation on the panel or unclear separate detection of organisms in a mixed blood culture of a shared genus or grouping of organisms, e.g. Staphylococcus or Enterobacteriaceae . One (0.5 %) blood culture yielded invalid results on two separate panels, so it was eliminated from the study. The easy-to-use FilmArray® technology shows good correlation with blood culture identification and antibiotic resistance detection performed by conventional methods. This technology may be particularly useful in laboratories with limited staffing or limited technical expertise.

  3. Quantifying strain variability in modeling growth of Listeria monocytogenes

    NARCIS (Netherlands)

    Aryani, D.; Besten, den H.M.W.; Hazeleger, W.C.; Zwietering, M.H.

    2015-01-01

    Prediction of microbial growth kinetics can differ from the actual behavior of the target microorganisms. In the present study, the impact of strain variability on maximum specific growth rate (µmax) (h- 1) was quantified using twenty Listeria monocytogenes strains. The µmax was determined as functi

  4. Nitrogen amendments have predictable effects on soil microbial communities and processes

    Science.gov (United States)

    Ramirez, K. S.; Craine, J. M.; Fierer, N.

    2011-12-01

    Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. While there has been much effort devoted to quantifying aboveground impacts of anthropogenic N effects, less work has focused on identifying belowground impacts. Bacteria play critical roles in ecosystem processes and identifying how anthropogenic N impacts bacterial communities may elucidate how critical microbially-mediated ecosystem functions are altered by N additions. In order to connect changes in soil processes to changes in the microbial community, we need to first determine if the changes are consistent across different soil types and ecosystems. We assessed the patterns of N effects across a variety of ecosystems in two ways. First, utilizing long-term experimental N gradients at Cedar Creek LTER, MN and Kellogg Biological Station LTER, MI, we examined the response of microbial communities to anthropogenic N additions. Using high-throughput pyrosequencing techniques we quantified changes in soil microbial communities across the nitrogen gradients. We observed strong directional shifts in community composition at both sites; N fertilization consistently impacted both the phylogenetic and taxonomic structure of soil bacterial community structure in a predictable manner regardless of ecosystem type. For example, at both sites Acidobacteria experienced significant declines as nitrogen increased, while other groups such as Actinobacteria and Bacteroidetes increased in relative abundance. Our results suggest that bacterial communities across these N fertility gradients are structured by either nitrogen and/or soil carbon availability, rather than by shifts in the plant community or soil pH indirectly associated with the elevated nitrogen inputs. Still, this field-work does not incorporate changes in soil processes (e.g. soil respiration) or microbial activity (e.g. microbial biomass and extracellular enzyme activity), or separate N from C effects. To

  5. On Quantifying Semantic Information

    Directory of Open Access Journals (Sweden)

    Simon D’Alfonso

    2011-01-01

    Full Text Available The purpose of this paper is to look at some existing methods of semantic information quantification and suggest some alternatives. It begins with an outline of Bar-Hillel and Carnap’s theory of semantic information before going on to look at Floridi’s theory of strongly semantic information. The latter then serves to initiate an in-depth investigation into the idea of utilising the notion of truthlikeness to quantify semantic information. Firstly, a couple of approaches to measure truthlikeness are drawn from the literature and explored, with a focus on their applicability to semantic information quantification. Secondly, a similar but new approach to measure truthlikeness/information is presented and some supplementary points are made.

  6. Quantifying economic fluctuations

    Science.gov (United States)

    Stanley, H. Eugene; Nunes Amaral, Luis A.; Gabaix, Xavier; Gopikrishnan, Parameswaran; Plerou, Vasiliki

    2001-12-01

    This manuscript is a brief summary of a talk designed to address the question of whether two of the pillars of the field of phase transitions and critical phenomena-scale invariance and universality-can be useful in guiding research on interpreting empirical data on economic fluctuations. Using this conceptual framework as a guide, we empirically quantify the relation between trading activity-measured by the number of transactions N-and the price change G( t) for a given stock, over a time interval [ t, t+Δ t]. We relate the time-dependent standard deviation of price changes-volatility-to two microscopic quantities: the number of transactions N( t) in Δ t and the variance W2( t) of the price changes for all transactions in Δ t. We find that the long-ranged volatility correlations are largely due to those of N. We then argue that the tail-exponent of the distribution of N is insufficient to account for the tail-exponent of P{ G> x}. Since N and W display only weak inter-dependency, our results show that the fat tails of the distribution P{ G> x} arises from W. Finally, we review recent work on quantifying collective behavior among stocks by applying the conceptual framework of random matrix theory (RMT). RMT makes predictions for “universal” properties that do not depend on the interactions between the elements comprising the system, and deviations from RMT provide clues regarding system-specific properties. We compare the statistics of the cross-correlation matrix C-whose elements Cij are the correlation coefficients of price fluctuations of stock i and j-against a random matrix having the same symmetry properties. It is found that RMT methods can distinguish random and non-random parts of C. The non-random part of C which deviates from RMT results, provides information regarding genuine collective behavior among stocks. We also discuss results that are reminiscent of phase transitions in spin systems, where the divergent behavior of the response function at

  7. Microbial Metalloproteomics

    Directory of Open Access Journals (Sweden)

    Peter-Leon Hagedoorn

    2015-12-01

    Full Text Available Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.

  8. Quantifying Periodicity in Omics Data

    Directory of Open Access Journals (Sweden)

    Cornelia eAmariei

    2014-08-01

    Full Text Available Oscillations play a significant role in biological systems, with many examples in the fast, ultradian, circadian, circalunar and yearly time domains. However, determining periodicity in such data can be problematic. There are a number of computational methods to identify the periodic components in large datasets, such as signal-to-noise based Fourier decomposition, Fisher's g-test and autocorrelation. However, the available methods assume a sinusoidal model and do not attempt to quantify the waveform shape and the presence of multiple periodicities, which provide vital clues in determining the underlying dynamics. Here, we developed a Fourier based measure that generates a de-noised waveform from multiple significant frequencies. This waveform is then correlated with the raw data from the respiratory oscillation found in yeast, to provide oscillation statistics including waveform metrics and multi-periods. The method is compared and contrasted to commonly used statistics. Moreover we show the utility of the program in the analysis of noisy datasets and other high-throughput analyses, such as metabolomics and flow cytometry, respectively.

  9. Quantifying the vitamin D economy.

    Science.gov (United States)

    Heaney, Robert P; Armas, Laura A G

    2015-01-01

    Vitamin D enters the body through multiple routes and in a variety of chemical forms. Utilization varies with input, demand, and genetics. Vitamin D and its metabolites are carried in the blood on a Gc protein that has three principal alleles with differing binding affinities and ethnic prevalences. Three major metabolites are produced, which act via two routes, endocrine and autocrine/paracrine, and in two compartments, extracellular and intracellular. Metabolic consumption is influenced by physiological controls, noxious stimuli, and tissue demand. When administered as a supplement, varying dosing schedules produce major differences in serum metabolite profiles. To understand vitamin D's role in human physiology, it is necessary both to identify the foregoing entities, mechanisms, and pathways and, specifically, to quantify them. This review was performed to delineate the principal entities and transitions involved in the vitamin D economy, summarize the status of present knowledge of the applicable rates and masses, draw inferences about functions that are implicit in these quantifications, and point out implications for the determination of adequacy.

  10. Electricity generation and microbial community response to substrate changes in microbial fuel cell

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Min, Booki; Huang, L.;

    2011-01-01

    The effect of substrate changes on the performance and microbial community of two-chamber microbial fuel cells (MFCs) was investigated in this study. The MFCs enriched with a single substrate (e.g., acetate, glucose, or butyrate) had different acclimatization capability to substrate changes....... The MFC enriched with glucose showed rapid and higher power generation, when glucose was switched with acetate or butyrate. However, the MFC enriched with acetate needed a longer adaptation time for utilizing glucose. Microbial community was also changed when the substrate was changed. Clostridium...... of substrate fed to MFC is a very important parameter for reactor performance and microbial community, and significantly affects power generation in MFCs....

  11. Quantifying the adaptive cycle

    Science.gov (United States)

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

  12. Quantifying traffic exposure.

    Science.gov (United States)

    Pratt, Gregory C; Parson, Kris; Shinoda, Naomi; Lindgren, Paula; Dunlap, Sara; Yawn, Barbara; Wollan, Peter; Johnson, Jean

    2014-01-01

    Living near traffic adversely affects health outcomes. Traffic exposure metrics include distance to high-traffic roads, traffic volume on nearby roads, traffic within buffer distances, measured pollutant concentrations, land-use regression estimates of pollution concentrations, and others. We used Geographic Information System software to explore a new approach using traffic count data and a kernel density calculation to generate a traffic density surface with a resolution of 50 m. The density value in each cell reflects all the traffic on all the roads within the distance specified in the kernel density algorithm. The effect of a given roadway on the raster cell value depends on the amount of traffic on the road segment, its distance from the raster cell, and the form of the algorithm. We used a Gaussian algorithm in which traffic influence became insignificant beyond 300 m. This metric integrates the deleterious effects of traffic rather than focusing on one pollutant. The density surface can be used to impute exposure at any point, and it can be used to quantify integrated exposure along a global positioning system route. The traffic density calculation compares favorably with other metrics for assessing traffic exposure and can be used in a variety of applications.

  13. Quantifying loopy network architectures.

    Directory of Open Access Journals (Sweden)

    Eleni Katifori

    Full Text Available Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of approaches have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes from the metric topology (connectivity and edge weight and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

  14. Microbial Ecosystems, Protection of

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning.

  15. Microbial Ecosystems, Protection of

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning. Introdu

  16. Pareto utility

    NARCIS (Netherlands)

    Masako, I.; Laeven, R.J.A.; Magnus, J.R.; Muris, C.

    2013-01-01

    In searching for an appropriate utility function in the expected utility framework, we formulate four properties that we want the utility function to satisfy. We conduct a search for such a function, and we identify Pareto utility as a function satisfying all four desired properties. Pareto utility

  17. Microbial health hazard assessment associated with the utilization of source-separated human urine%源分离尿液收集、利用的病原性健康风险计算评估

    Institute of Scientific and Technical Information of China (English)

    仇付国; 高红伟; 卢文灏

    2013-01-01

    为了明确源分离生态卫生系统收集、利用尿液过程中所导致的人体健康风险,对尿液中病原体的含量进行了调查分析,采用蒙特卡洛方法对尿液收集、利用环节所导致的健康风险进行了模拟计算.结果表明,尿液中的病原体主要来自粪便的交叉污染,细菌和隐孢子虫等不会造成大的风险,风险主要来源于病毒,即使摄人剂量很低(1mL)的、没处理过的尿液,其中的病毒也会对人体健康产生很高的风险(0.02~0.87 a-,均值为0.08 a-1).尿液浇灌施肥时造成的感染风险和尿液的储存时间有关,经过30 d的储存后,细菌和原生动物的尿液对人体的感染风险都很低,然而对于在5℃下储存6个月的尿液或20℃下储存1个月的尿液,轮状病毒的感染风险概率为10-1 a-1的数量级.如果尿液喷洒前在20℃下储存6个月,平均风险会降低到10-5 a-1数量级.对食用尿液浇灌的农产品进行的风险计算表明,浇灌两周后采摘食用蔬菜造成的健康风险为10-9 a-数量级,可以忽略不计.%The paper is to introduce a microbial health hazard assessment associated with the utilization of source-separated human urine.The reason why we would like to pick up the research topic is to make benefits of the urine utilization as a natural fertilizer in agriculture in favor of reducing the nitrogen and phosphorus load in the domestic sewage and transmitting human excreta with less fresh water in comparison with the conventional gravitational flow drainage system.However,it is necessary to identify the infectious hazards of disease when handling and using the urine so as to protect people' s health and promote the development of ecological sanitation environment.In this study,we have collected data of human faecal sterols in the urine and worked out the faeces content in it based on the average sterol level in them.Then we have done the evaluation of the amount of pathogen in the isolated urine by

  18. Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

    Energy Technology Data Exchange (ETDEWEB)

    Firestone, Mary [Univ. of California, Berkeley, CA (United States)

    2015-03-31

    It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

  19. Microbial Risk Assessment

    Science.gov (United States)

    Ott, C. M.; Mena, K. D.; Nickerson, C.A.; Pierson, D. L.

    2009-01-01

    -response characteristics may be affected by a potentially dysfunctional crew immune system during a mission. In addition, microbial virulence has been shown to change under certain conditions during spaceflight, further complicating dose-response characterization. An initial study of the applicability of microbial risk assessment techniques was performed using Crew Health Care System (CHeCS) operational data from the International Space Station potable water systems. The risk of infection from potable water was selected as the flight systems and microbial ecology are well defined. This initial study confirmed the feasibility of using microbial risk assessment modeling for spaceflight systems. While no immediate threat was detected, the study identified several medically significant microorganisms that could pose a health risk if uncontrolled. The study also identified several specific knowledge gaps in making a risk assessment and noted that filling these knowledge gaps is essential as the risk estimates may change by orders of magnitude depending on the answers. The current phase of the microbial risk assessment studies focuses on the dose-response relationship of specific infectious agents, focusing on Salmonella enterica Typhimurium, Pseudomonas spp., and Escherichia coli, as their evaluation will provide a better baseline for determining the overall hazard characterization. The organisms were chosen as they either have been isolated on spacecraft or have an identified route of infection during a mission. The characterization will utilize dose-response models selected either from the peer-reviewed literature and/or by using statistical approaches. Development of these modeling and risk assessment techniques will help to optimize flight requirements and to protect the safety, health, and performance of the crew.

  20. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  1. Comparative Microbial Genomics and Forensics.

    Science.gov (United States)

    Massey, Steven E

    2016-08-01

    Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

  2. Quantifying Nitrogen Loss From Flooded Hawaiian Taro Fields

    Science.gov (United States)

    Deenik, J. L.; Penton, C. R.; Bruland, G. L.; Popp, B. N.; Engstrom, P.; Mueller, J. A.; Tiedje, J.

    2010-12-01

    In 2004 a field fertilization experiment showed that approximately 80% of the fertilizer nitrogen (N) added to flooded Hawaiian taro (Colocasia esculenta) fields could not be accounted for using classic N balance calculations. To quantify N loss through denitrification and anaerobic ammonium oxidation (anammox) pathways in these taro systems we utilized a slurry-based isotope pairing technique (IPT). Measured nitrification rates and porewater N profiles were also used to model ammonium and nitrate fluxes through the top 10 cm of soil. Quantitative PCR of nitrogen cycling functional genes was used to correlate porewater N dynamics with potential microbial activity. Rates of denitrification calculated using porewater profiles were compared to those obtained using the slurry method. Potential denitrification rates of surficial sediments obtained with the slurry method were found to drastically overestimate the calculated in-situ rates. The largest discrepancies were present in fields greater than one month after initial fertilization, reflecting a microbial community poised to denitrify the initial N pulse. Potential surficial nitrification rates varied between 1.3% of the slurry-measured denitrification potential in a heavily-fertilized site to 100% in an unfertilized site. Compared to the use of urea, fish bone meal fertilizer use resulted in decreased N loss through denitrification in the surface sediment, according to both porewater modeling and IPT measurements. In addition, sub-surface porewater profiles point to root-mediated coupled nitrification/denitrification as a potential N loss pathway that is not captured in surface-based incubations. Profile-based surface plus subsurface coupled nitrification/denitrification estimates were between 1.1 and 12.7 times denitrification estimates from the surface only. These results suggest that the use of a ‘classic’ isotope pairing technique that employs 15NO3- in fertilized agricultural systems can lead to a drastic

  3. Method for analyzing microbial communities

    Science.gov (United States)

    Zhou, Jizhong [Oak Ridge, TN; Wu, Liyou [Oak Ridge, TN

    2010-07-20

    The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

  4. Geophysical Monitoring of Microbial Activity within a Wetland Soil

    Science.gov (United States)

    O'Brien, M.; Zhang, C.; Ntarlagiannis, D.; Slater, L.; Yee, N.

    2007-05-01

    We performed Induced Polarization (IP) and Self Potential (SP) measurements to record the geoelectrical signatures of microbial activity within a wetland soil. The experiment was conducted in laboratory, utilizing an open flow column set up. Soil samples from Kearny Marsh (KM), a shallow water wetland, were collected and stored at 4o Celsius prior to the start of the experiment. Two columns were dry packed with a mix of KM soil and sterile Ottawa sand (50% by weight). One column was sterilized and used as a control while the other column retained the biologically active soil sample. Both columns were saturated with a minimal salts medium capable of supporting microbial life; after saturation, a steady flow rate of one pore volume per day was maintained throughout the experiment. Ambient temperature and pressure changes (at the inflow and outflow of each column) were continuously monitored throughout the experiment. Common geochemical parameters, such as Eh, pH, and fluid conductivity were measured at the inflow and outflow of each column at regular intervals. IP and SP responses were continuously recorded on both columns utilizing a series of electrodes along the column length; additionally for the SP measurements we used a reference electrode at the inflow tube. Strong SP anomalies were observed for all the locations along the active column. Black visible mineral precipitant also formed in the active column. The observed precipitation coincided with the times that SP anomalies developed at each electrode position. These responses are associated with microbial induced sulfide mineralization. We interpret the SP signal as the result of redox processes associated with this mineralization driven by gradients in ionic concentration and mobility within the column, similar to a galvanic cell mechanism. IP measurements show no correlation with these visual and SP responses. Destructive analysis of the samples followed the termination of the experiment. Scanning electron

  5. Recent advances in amino acid production by microbial cells.

    Science.gov (United States)

    Hirasawa, Takashi; Shimizu, Hiroshi

    2016-12-01

    Amino acids have been utilized for the production of foods, animal feeds and pharmaceuticals. After the discovery of the glutamic acid-producing bacterium Corynebacterium glutamicum by Japanese researchers, the production of amino acids, which are primary metabolites, has been achieved using various microbial cells as hosts. Recently, metabolic engineering studies on the rational design of amino acid-producing microbial cells have been successfully conducted. Moreover, the technology of systems biology has been applied to metabolic engineering for the creation of amino acid-producing microbial cells. Currently, new technologies including synthetic biology, single-cell analysis, and evolutionary engineering have been utilized to create amino acid-producing microbial cells. In addition, useful compounds from amino acids have been produced by microbial cells. Here, current researches into the metabolic engineering of microbial cells toward production of amino acids and amino acid-related compounds are reviewed.

  6. The Microbial Opsin Family of Optogenetic Tools

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Feng; Vierock, Johannes; Yizhar, Ofer; Fenno, Lief E.; Tsunoda, Satoshi; Kianianmomeni, Arash; Prigge, Matthias; Berndt, Andre; Cushman, John C.; Polle, Juergen E.; Magnuson, Jon K.; Hegemann, Peter; Deisseroth, Karl

    2011-12-23

    The capture and utilization of light is an exquisitely evolved process. The single-component microbial opsins, although more limited than multicomponent cascades in processing, display unparalleled compactness and speed. Recent advances in understanding microbial opsins have been driven by molecular engineering for optogenetics and by comparative genomics. Here we provide a Primer on these light-activated ion channels and pumps, describe a group of opsins bridging prior categories, and explore the convergence of molecular engineering and genomic discovery for the utilization and understanding of these remarkable molecular machines.

  7. [Application of FISH-NanoSIMS technique in environmental microbial ecology study].

    Science.gov (United States)

    Chen, Chen; Bai, Yao-hui; Liang, Jin-song; Yuan, Lin-jiang

    2015-01-01

    With the development of microbial ecology techniques, it is possible to analyze the distribution and function of microorganisms simultaneously in complex ecosystems. To explore the application of FISH-NanoSIMS in environmental microbial ecology study, our study used the stable isotope labeled compounds 13C-C6H12O6, and 15N-NH4Cl as C and N sources for cultivating the pure culture (manganese oxidizing bacteria, Pseudomonas sp. QJX-1) and environmental samples (the shallow soil and anaerobic sludge). FISH-NanoSIMS was used to detect the distribution of microorganisms and relatively quantify secondary ions (12C-, 13C-, 12C(14)N-, 12C15N-) in cultivated samples, in order to explore the utilization of C and N isotopes sources by the pure culture and microorganisms in environment samples. The results showed that the contents of 13C and 5N in the area of bacteria were significantly greater than the natural abundance in all samples. It indicated that Pseudomonas sp. QJX-1 and some specific bacteria in environmental samples could metabolize 13C-C6H12O6 and 15N-NH4C1. Furthermore, this study revealed that for Pseudomonas sp. QJX-1, the manganese oxidation only occurred when the carbon and nitrogen were consumed to a low level. For environmental samples, the bacterial nitrification and denitrification were both observed in the shallow soil and anaerobic sludge. In a word, our study demonstrated that the combination of FISH and NanoSIMS could simultaneously examine microbial distribution and microbial metabolic activity in environmental samples, which will help us to obtain the eco-physiology information of microbial community.

  8. Physicochemical properties influencing denitrification rate and microbial activity in denitrification bioreactors

    Science.gov (United States)

    Schmidt, C. A.

    2012-12-01

    The use of N-based fertilizer will need to increase to meet future demands, yet existing applications have been implicated as the main source of coastal eutrophication and hypoxic zones. Producing sufficient crops to feed a growing planet will require efficient production in combination with sustainable treatment solutions. The long-term success of denitrification bioreactors to effectively remove nitrate (NO¬3), indicates this technology is a feasible treatment option. Assessing and quantifying the media properties that affect NO¬3 removal rate and microbial activity can improve predictions on bioreactor performance. It was hypothesized that denitrification rates and microbial biomass would be correlated with total C, NO¬3 concentration, metrics of organic matter quality, media surface area and laboratory measures of potential denitrification rate. NO¬3 removal rates and microbial biomass were evaluated in mesocosms filled with different wood treatments and the unique influence of these predictor variables was determined using a multiple linear regression analysis. NO3 reduction rates were independent of NO¬3 concentration indicating zero order reaction kinetics. Temperature was strongly correlated with denitrification rate (r2=0.87; Q10=4.7), indicating the variability of bioreactor performance in differing climates. Fiber quality, and media surface area were strong (R>0.50), unique predictors of rates and microbial biomass, although C:N ratio and potential denitrification rate did not predict actual denitrification rate or microbial biomass. Utilizing a stepwise multiple linear regression, indicates that the denitrification rate can be effectively (r2=0.56;pbioreactors to achieve significant N load reductions in large watersheds. The nitrate reduction rate as a function of groundwater temperature for all treatments. Correlations between nitrate reduction rate and properties of carbon media;

  9. Microbial solar cells: applying photosynthetic and electrochemically active organisms

    NARCIS (Netherlands)

    Strik, D.P.B.T.B.; Timmers, R.A.; Helder, M.; Steinbusch, K.J.J.; Hamelers, H.V.M.; Buisman, C.J.N.

    2011-01-01

    Microbial solar cells (MSCs) are recently developed technologies that utilize solar energy to produce electricity or chemicals. MSCs use photoautotrophic microorganisms or higher plants to harvest solar energy, and use electrochemically active microorganisms in the bioelectrochemical system to gener

  10. Evaluation of soil microbial communities as influenced by crude oil ...

    African Journals Online (AJOL)

    Evaluation of soil microbial communities as influenced by crude oil pollution. ... Community-level approach for assessing patterns of sole carbon-source utilization ... impact of crude oil pollution, soil – biota interactions, ecosystem monitoring, ...

  11. Microbial conversions of terpenoids

    OpenAIRE

    Parshikov, Igor A

    2015-01-01

    The monograph describes examples of the application of microbial technology for obtaining of derivatives of terpenoids. Obtaining new derivatives of terpenoids, including artemisinin derivatives with increased antimalarial activity, is an important goal of research in microbial biotechnology and medicinal chemistry.

  12. Microbial degradation of petroleum hydrocarbons.

    Science.gov (United States)

    Varjani, Sunita J

    2017-01-01

    Petroleum hydrocarbon pollutants are recalcitrant compounds and are classified as priority pollutants. Cleaning up of these pollutants from environment is a real world problem. Bioremediation has become a major method employed in restoration of petroleum hydrocarbon polluted environments that makes use of natural microbial biodegradation activity. Petroleum hydrocarbons utilizing microorganisms are ubiquitously distributed in environment. They naturally biodegrade pollutants and thereby remove them from the environment. Removal of petroleum hydrocarbon pollutants from environment by applying oleophilic microorganisms (individual isolate/consortium of microorganisms) is ecofriendly and economic. Microbial biodegradation of petroleum hydrocarbon pollutants employs the enzyme catalytic activities of microorganisms to enhance the rate of pollutants degradation. This article provides an overview about bioremediation for petroleum hydrocarbon pollutants. It also includes explanation about hydrocarbon metabolism in microorganisms with a special focus on new insights obtained during past couple of years. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Priming in the microbial landscape: periphytic algal stimulation of litter-associated microbial decomposers.

    Science.gov (United States)

    Kuehn, Kevin A; Francoeur, Steven N; Findlay, Robert H; Neely, Robert K

    2014-03-01

    Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected and returned to the laboratory, where algal photosynthesis was manipulated (light/dark incubation), while rates of bacterial and fungal growth and productivity were simultaneously quantified. Bacteria and fungi were rapidly stimulated by exposure to light, thus establishing the potential for algal priming of microbial heterotrophic decay activities. Experimental incubations of decaying litter with 14C- and 13C-bicarbonate established that inorganic C fixed by algal photosynthesis was rapidly transferred to and assimilated by heterotrophic microbial decomposers. Periphytic algal stimulation of microbial heterotrophs, especially fungal decomposers, is an important and largely unrecognized interaction within the detrital microbial landscape, which may transform our current conceptual understanding of microbial secondary production and organic matter decomposition in aquatic ecosystems.

  14. Microbial Electrochemistry and its Application to Energy and Environmental Issues

    Science.gov (United States)

    Hastings, Jason Thomas

    Microbial electrochemistry forms the basis of a wide range of topics from microbial fuel cells to fermentation of carbon food sources. The ability to harness microbial electron transfer processes can lead to a greener and cleaner future. This study focuses on microbial electron transfer for liquid fuel production, novel electrode materials, subsurface environments and removal of unwanted byproducts. In the first chapter, exocellular electron transfer through direct contact utilizing passive electrodes for the enhancement of bio-fuel production was tested. Through the application of microbial growth in a 2-cell apparatus on an electrode surface ethanol production was enhanced by 22.7% over traditional fermentation. Ethanol production efficiencies of close to 95% were achieved in a fraction of the time required by traditional fermentation. Also, in this chapter, the effect of exogenous electron shuttles, electrode material selection and resistance was investigated. Power generation was observed using the 2-cell passive electrode system. An encapsulation method, which would also utilize exocellular transfer of electrons through direct contact, was hypothesized for the suspension of viable cells in a conductive polymer substrate. This conductive polymer substrate could have applications in bio-fuel production. Carbon black was added to a polymer solution to test electrospun polymer conductivity and cell viability. Polymer morphology and cell viability were imaged using electron and optical microscopy. Through proper encapsulation, higher fuel production efficiencies would be achievable. Electron transfer through endogenous exocellular protein shuttles was observed in this study. Secretion of a soluble redox active exocellular protein by Clostridium sp. have been shown utilizing a 2-cell apparatus. Cyclic voltammetry and gel electrophoresis were used to show the presence of the protein. The exocellular protein is capable of reducing ferrous iron in a membrane separated

  15. Microfluidics and microbial engineering.

    Science.gov (United States)

    Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

    2016-02-01

    The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

  16. Childhood microbial keratitis

    Directory of Open Access Journals (Sweden)

    Abdullah G Al Otaibi

    2012-01-01

    Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

  17. Microbial Biogeography of the Arctic Cryosphere

    DEFF Research Database (Denmark)

    Hauptmann, Aviaja Zenia Edna Lyberth

    communities. This has considerably improved our understanding that even harsh and seemingly barren environments such as the cryosphere, the frozen parts of our planet, is inhabited by diverse life. This thesis presents three studies in microbial biogeography of the Arctic cryosphere utilizing a range of NGS...

  18. Burr Utility

    NARCIS (Netherlands)

    Ikefuji, M.; Laeven, R.J.A.; Magnus, J.R.; Muris, C.H.M.

    2010-01-01

    This note proposes the Burr utility function. Burr utility is a flexible two-parameter family that behaves approximately power-like (CRRA) remote from the origin, while exhibiting exponential-like (CARA) features near the origin. It thus avoids the extreme behavior of the power family near the origi

  19. Estimating Utility

    DEFF Research Database (Denmark)

    Arndt, Channing; Simler, Kenneth R.

    2010-01-01

    an information-theoretic approach to estimating cost-of-basic-needs (CBN) poverty lines that are utility consistent. Applications to date illustrate that utility-consistent poverty measurements derived from the proposed approach and those derived from current CBN best practices often differ substantially......, with the current approach tending to systematically overestimate (underestimate) poverty in urban (rural) zones....

  20. Advances in industrial microbiome based on microbial consortium for biorefinery.

    Science.gov (United States)

    Jiang, Li-Li; Zhou, Jin-Jie; Quan, Chun-Shan; Xiu, Zhi-Long

    2017-01-01

    One of the important targets of industrial biotechnology is using cheap biomass resources. The traditional strategy is microbial fermentations with single strain. However, cheap biomass normally contains so complex compositions and impurities that it is very difficult for single microorganism to utilize availably. In order to completely utilize the substrates and produce multiple products in one process, industrial microbiome based on microbial consortium draws more and more attention. In this review, we first briefly described some examples of existing industrial bioprocesses involving microbial consortia. Comparison of 1,3-propanediol production by mixed and pure cultures were then introduced, and interaction relationships between cells in microbial consortium were summarized. Finally, the outlook on how to design and apply microbial consortium in the future was also proposed.

  1. Quantifying resource use in computations

    NARCIS (Netherlands)

    van Son, R.J.J.H.

    2009-01-01

    It is currently not possible to quantify the resources needed to perform a computation. As a consequence, it is not possible to reliably evaluate the hardware resources needed for the application of algorithms or the running of programs. This is apparent in both computer science, for in- stance, in

  2. Quantifying resource use in computations

    NARCIS (Netherlands)

    van Son, R.J.J.H.

    2009-01-01

    It is currently not possible to quantify the resources needed to perform a computation. As a consequence, it is not possible to reliably evaluate the hardware resources needed for the application of algorithms or the running of programs. This is apparent in both computer science, for in- stance, in

  3. Microbial source tracking: a forensic technique for microbial source identification?

    Science.gov (United States)

    Stapleton, Carl M; Wyer, Mark D; Kay, David; Crowther, John; McDonald, Adrian T; Walters, Martin; Gawler, Andrew; Hindle, Terry

    2007-05-01

    As the requirements of the Water Framework Directive (WFD) and the US Clean Water Act (USCWA) for the maintenance of microbiological water quality in 'protected areas' highlight, there is a growing recognition that integrated management of point and diffuse sources of microbial pollution is essential. New information on catchment microbial dynamics and, in particular, the sources of faecal indicator bacteria found in bathing and shellfish harvesting waters is a pre-requisite for the design of any 'programme of measures' at the drainage basin scale to secure and maintain compliance with existing and new health-based microbiological standards. This paper reports on a catchment-scale microbial source tracking (MST) study in the Leven Estuary drainage basin, northwest England, an area for which quantitative faecal indicator source apportionment empirical data and land use information were also collected. Since previous MST studies have been based on laboratory trials using 'manufactured' samples or analyses of spot environmental samples without the contextual microbial flux data (under high and low flow conditions) and source information, such background data are needed to evaluate the utility of MST in USCWA total maximum daily load (TMDL) assessments or WFD 'Programmes of Measures'. Thus, the operational utility of MST remains in some doubt. The results of this investigation, using genotyping of Bacteroidetes using polymerase chain reaction (PCR) and male-specific ribonucleic acid coliphage (F + RNA coliphage) using hybridisation, suggest some discrimination is possible between livestock- and human-derived faecal indicator concentrations but, in inter-grade areas, the degree to which the tracer picture reflected the land use pattern and probable faecal indicator loading were less distinct. Interestingly, the MST data was more reliable on high flow samples when much of the faecal indicator flux from catchment systems occurs. Whilst a useful supplementary tool, the MST

  4. Simplifying Microbial Electrosynthesis Reactor Design

    Directory of Open Access Journals (Sweden)

    Cloelle G.S. Giddings

    2015-05-01

    Full Text Available Microbial electrosynthesis, an artificial form of photosynthesis, can efficiently convert carbon dioxide into organic commodities; however, this process has only previously been demonstrated in reactors that have features likely to be a barrier to scale-up. Therefore, the possibility of simplifying reactor design by both eliminating potentiostatic control of the cathode and removing the membrane separating the anode and cathode was investigated with biofilms of Sporomusa ovata, which reduces carbon dioxide to acetate. In traditional ‘H-cell’ reactors, where the anode and cathode chambers were separated with a proton-selective membrane, the rates and columbic efficiencies of microbial electrosynthesis remained high when electron delivery at the cathode was powered with a direct current power source rather than with a poteniostat-poised cathode utilized in previous studies. A membrane-less reactor with a direct-current power source with the cathode and anode positioned to avoid oxygen exposure at the cathode, retained high rates of acetate production as well as high columbic and energetic efficiencies. The finding that microbial electrosynthesis is feasible without a membrane separating the anode from the cathode, coupled with a direct current power source supplying the energy for electron delivery, is expected to greatly simplify future reactor design and lower construction costs.

  5. Microbial Transformation of Arsenic

    Science.gov (United States)

    Stolz, J. F.

    2004-12-01

    Whether the source is natural or anthropogenic, it has become evident that arsenic is readily transformed by a great diversity of microbial species and has a robust biogeochemical cycle. Arsenic cycling primarily involves the oxidation of As(III) and the reduction of As(V). Over thirty arsenite oxidizing prokaryotes have been reported and include alpha, beta, and gamma Proteobacteria , Deinocci and Crenarchaeota. At least twenty species of arsenate-respiring prokaryotes are now known and include Crenarchaeota, thermophilic bacteria, low and high G+C gram positive bacteria, and gamma, delta, and epsilon Proteobacteria. These organisms are metabolically diverse, and depending on the species, capable of using other terminal electron acceptors (e.g., nitrate, selenate, fumarate, sulfate). In addition to inorganic forms (e.g., sodium arsenate) organoarsenicals can be utilized as a substrate. The feed additive roxarsone (3-nitro-4-hydroxyphenyl arsonic acid) has been shown to readily degrade leading to the release of inorganic arsenic (e.g., As(V)). Degradation proceeds via the cleavage of the arsenate functional group or the reduction of the nitro functional group and deamination. The rapid degradation (within 3 days) of roxarsone by Clostridium sp. strain OhILAs appears to follow the latter pathway and may involve Stickland reactions. The activities of these organisms affect the speciation and mobilization of arsenic, ultimately impacting water quality.

  6. Hydrogen utilization potential in subsurface sediments

    DEFF Research Database (Denmark)

    Adhikari, Rishi Ram; Glombitza, Clemens; Nickel, Julia

    2016-01-01

    Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen...... and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live...

  7. Exploring Subglacial Microbial Ecology (Invited)

    Science.gov (United States)

    Mikucki, J.; Mitchell, A. C.; Johnson, S. S.; Grzymski, J.

    2009-12-01

    Subglacial environments were long thought to be abiotic. We now know that microbial life exists below glaciers, but know relatively little about the in situ metabolic processes they mediate and how their activity transforms the geochemistry of subglacial efflux. It has been hypothesized that subglacial systems, driven to anoxia in the presence of sufficient organic matter, will follow a continuum of redox chemistries utilizing electron acceptors with decreasing reduction potential (i.e. Fe (III), sulfate, CO2). Indeed, sulfate reduction and methanogenesis have been detected in studies of polythermal glaciers. However, it is unclear whether there is sufficient organic matter to sustain highly reducing conditions below Antarctic ice. Here we present a broad overview of the microbial ecology of subglacial ecosystems and describe the links between microbial diversity and community function in these chemically complex environments. The subglacial environment below the Taylor Glacier, Antarctica provides an example where biogeochemical measurements made on subglacial efflux can inform specific mechanisms of microbial metabolism. We have tested the validity of these mechanisms using environmental genomic surveys and biogeochemical measurements of subglacial fluids to describe an active community that cycles iron and sulfur below Taylor Glacier. Examples include the incorporation of radiolabeled bicarbonate by cells in the outflow and detection of functional genes responsible for CO2-fixation (i.e. RuBisCO), and isotopic composition of sulfate sulfur and oxygen in the outflow indicative of sulfate reduction with the presence of functional genes of the sulfur cycle (i.e. APS reductase). Moving forward in our exploration of subglacial ecosystems, key questions regarding microbial energetics include: 1) How microorganisms cycle mineral substrates below glaciers to gain energy for growth 2) Whether subglacial microorganisms grow syntrophically in order to metabolize iron and

  8. Microbial Life in a Liquid Asphalt Desert

    CERN Document Server

    Schulze-Makuch, Dirk; Antonio, Marina Resendes de Sousa; Ali, Denzil; Hosein, Riad; Song, Young C; Yang, Jinshu; Zaikova, Elena; Beckles, Denise M; Guinan, Edward; Lehto, Harry J; Hallam, Steven J

    2010-01-01

    An active microbiota, reaching up to 10 E+7 cells/g, was found to inhabit a naturally occurring asphalt lake characterized by low water activity and elevated temperature. Geochemical and molecular taxonomic approaches revealed novel and deeply branching microbial assemblages mediating anaerobic hydrocarbon degradation, metal respiration and C1 utilization pathways. These results open a window into the origin and adaptive evolution of microbial life within recalcitrant hydrocarbon matrices, and establish the site as a useful analog for the liquid hydrocarbon environments on Saturn's moon Titan.

  9. Meditations on Quantified Constraint Satisfaction

    CERN Document Server

    Chen, Hubie

    2012-01-01

    The quantified constraint satisfaction problem (QCSP) is the problem of deciding, given a structure and a first-order prenex sentence whose quantifier-free part is the conjunction of atoms, whether or not the sentence holds on the structure. One obtains a family of problems by defining, for each structure B, the problem QCSP(B) to be the QCSP where the structure is fixed to be B. In this article, we offer a viewpoint on the research program of understanding the complexity of the problems QCSP(B) on finite structures. In particular, we propose and discuss a group of conjectures; throughout, we attempt to place the conjectures in relation to existing results and to emphasize open issues and potential research directions.

  10. Quantifier Elimination by Dependency Sequents

    CERN Document Server

    Goldberg, Eugene

    2012-01-01

    We consider the problem of existential quantifier elimination for Boolean formulas in Conjunctive Normal Form (CNF). We present a new method for solving this problem called Derivation of Dependency-Sequents (DDS). A Dependency-sequent (D-sequent) is used to record that a set of quantified variables is redundant under a partial assignment. We show that D-sequents can be resolved to obtain new, non-trivial D-sequents. We also show that DDS is compositional, i.e. if our input formula is a conjunction of independent formulas, DDS automatically recognizes and exploits this information. We introduce an algorithm based on DDS and present experimental results demonstrating its potential.

  11. Quantifying and measuring cyber resiliency

    Science.gov (United States)

    Cybenko, George

    2016-05-01

    Cyber resliency has become an increasingly attractive research and operational concept in cyber security. While several metrics have been proposed for quantifying cyber resiliency, a considerable gap remains between those metrics and operationally measurable and meaningful concepts that can be empirically determined in a scientific manner. This paper describes a concrete notion of cyber resiliency that can be tailored to meet specific needs of organizations that seek to introduce resiliency into their assessment of their cyber security posture.

  12. Quantifying Heuristic Bias: Anchoring, Availability, and Representativeness.

    Science.gov (United States)

    Richie, Megan; Josephson, S Andrew

    2017-07-28

    significance for students (Version A, M = 7.28, SD = 3.46; Version B, M = 5.82, SD = 3.22), t(153) = 2.67, p = .008, and residents (Version A, M = 7.19, SD = 3.24; Version B, M = 5.56, SD = 2.72), t(77) = 2.32, p = .02, but not attendings. Authors developed an instrument to isolate and quantify bias produced by the availability and representativeness heuristics, and illustrated the utility of their instrument by demonstrating decreased heuristic bias within medical contexts at higher training levels.

  13. Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis).

    Science.gov (United States)

    VanderWaal, Kimberly L; Atwill, Edward R; Isbell, Lynne A; McCowan, Brenda

    2014-03-01

    Although network analysis has drawn considerable attention as a promising tool for disease ecology, empirical research has been hindered by limitations in detecting the occurrence of pathogen transmission (who transmitted to whom) within social networks. Using a novel approach, we utilize the genetics of a diverse microbe, Escherichia coli, to infer where direct or indirect transmission has occurred and use these data to construct transmission networks for a wild giraffe population (Giraffe camelopardalis). Individuals were considered to be a part of the same transmission chain and were interlinked in the transmission network if they shared genetic subtypes of E. coli. By using microbial genetics to quantify who transmits to whom independently from the behavioural data on who is in contact with whom, we were able to directly investigate how the structure of contact networks influences the structure of the transmission network. To distinguish between the effects of social and environmental contact on transmission dynamics, the transmission network was compared with two separate contact networks defined from the behavioural data: a social network based on association patterns, and a spatial network based on patterns of home-range overlap among individuals. We found that links in the transmission network were more likely to occur between individuals that were strongly linked in the social network. Furthermore, individuals that had more numerous connections or that occupied 'bottleneck' positions in the social network tended to occupy similar positions in the transmission network. No similar correlations were observed between the spatial and transmission networks. This indicates that an individual's social network position is predictive of transmission network position, which has implications for identifying individuals that function as super-spreaders or transmission bottlenecks in the population. These results emphasize the importance of association patterns in

  14. Multiattribute Utility Theory without Expected Utility Foundations

    NARCIS (Netherlands)

    A.M. Stiggelbout; P.P. Wakker

    1995-01-01

    Methods for determining the form of utilities are needed for the implementation of utility theory in specific decisions. An important step forward was achieved when utility theorists characterized useful parametric families of utilities, and simplifying decompositions of multiattribute utilities. Th

  15. Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

    Science.gov (United States)

    Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

    2014-11-01

    Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output.

  16. Carbon Source Utilization and Functional Diversity of Soil Microbial Communities in Natural Secondary Forests with Different Management Regimes in Northeastern China%东北天然次生林不同经营模式下土壤微生物碳源利用与功能多样性

    Institute of Scientific and Technical Information of China (English)

    范垚城; 覃林; 王雅菲; 邹慧; 谭玲; 何友均

    2016-01-01

    Objective]In order to provide a reasonable reference for the management regime of natural secondary forests,the carbon source utilization and functional diversity of soil microbial communities were investigated under different forest management regimes of natural secondary forests in northeastern China.[Method]Four forests representing management regimes,traditional forest management ( FM1 ) ,target tree-based forest management ( FM2 ) ,conversion to mixed broadleaved-based forest management ( FM3 ) and nonintervention forest management ( FM4 ) ,were selected in Danqinghe Forestry Farm located in Harbin,Heilongjiang Province. Among them,the traditional forest management (FM1) puts more emphasis on obtaining the woods. Target tree-based forest management (FM2) is mainly based on the crop tree management,the weak interference and natural regeneration of the target trees. Conversion to mixed broadleaved-based forest management ( FM3 ) is a management that new hardwoods are introduced into the original management regime while logging. The nonintervention forest management ( FM4 ) is based on the natural growth without any disturbance. Under each forest management regime,we had 3 sampling plots. Each 50 m × 50 m plot was divided into 10 m × 10 m quadrats,generating a total of 25 quadrats. The topsoil (0 -20 cm) was collected in each quadrate. Based on the Biolog-Eco method,we studied the different characteristics of carbon source utilization and functional diversity in the four forest management regimes,and further explored the effect of soil chemical properties on soil carbon source utilization types.[Result]The carbon source utilization of soil microbial communities in FM1 was significantly lower than those in other three regimes,and it was highest in FM4,while there was no significant difference in soil carbon source utilization between in FM2 and FM3. Soil chemical properties,especially available nitrogen(AN),available potassium(AK), available phosphorus( AP

  17. Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems.

    Science.gov (United States)

    Ghimire, Rajan; Norton, Jay B; Stahl, Peter D; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  18. Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems.

    Directory of Open Access Journals (Sweden)

    Rajan Ghimire

    Full Text Available Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs. Under crop production, dissolved organic C (DOC content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably

  19. MICROBIAL FUEL CELL

    DEFF Research Database (Denmark)

    2008-01-01

    A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

  20. Biofilms: A microbial home

    Science.gov (United States)

    Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

    2011-01-01

    Microbial biofilms are mainly implicated in etiopathogenesis of caries and periodontal disease. Owing to its properties, these pose great challenges. Continuous and regular disruption of these biofilms is imperative for prevention and management of oral diseases. This essay provides a detailed insight into properties, mechanisms of etiopathogenesis, detection and removal of these microbial biofilms. PMID:21976832

  1. Biofilms: A microbial home

    OpenAIRE

    Chandki, Rita; Banthia, Priyank; Banthia, Ruchi

    2011-01-01

    Microbial biofilms are mainly implicated in etiopathogenesis of caries and periodontal disease. Owing to its properties, these pose great challenges. Continuous and regular disruption of these biofilms is imperative for prevention and management of oral diseases. This essay provides a detailed insight into properties, mechanisms of etiopathogenesis, detection and removal of these microbial biofilms.

  2. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Dwayne; Schadt, Christopher; Miller, Lance; Phelps, Tommy; Brown, S. D.; Arkin, Adam; Hazen, Terry; Drake, Megin; Yang, Z.K.; Podar, Mircea

    2010-05-17

    One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for

  3. Microbial acetone oxidation in coastal seawater

    Directory of Open Access Journals (Sweden)

    Joanna Lee Dixon

    2014-05-01

    Full Text Available Acetone is an important oxygenated volatile organic compound in the troposphere where it influences the oxidising capacity of the atmosphere. However, the air-sea flux is not well quantified, in part due to a lack of knowledge regarding which processes control oceanic concentrations, and, specifically whether microbial oxidation to CO2 represents a significant loss process. We demonstrate that 14C labelled acetone can be used to determine microbial oxidation to 14CO2. Linear microbial rates of acetone oxidation to CO2 were observed for between 0.75-3.5 hours at a seasonally eutrophic coastal station located in the western English Channel (L4. A kinetic experiment in summer at station L4 gave a Vmax of 4.1 pmol L-1 h-1, with a Km constant of 54 pM. We then used this technique to obtain microbial acetone loss rates ranging between 1.2-42 pmol L-1 h-1 (monthly averages over an annual cycle at L4, with maximum rates observed during winter months. The biological turnover time of acetone (in situ concentration divided by microbial oxidation rate in surface waters varied from ~3 days in February 2011, when in situ concentrations were 3 ± 1 nM, to >240 days in June 2011, when concentrations were more than 2 fold higher at 7.5 ± 0.7 nM. These relatively low marine microbial acetone oxidation rates, when normalised to in situ concentrations, suggest that marine microbes preferentially utilise other oxygenated volatile organic compounds such as methanol and acetaldehyde.

  4. Quantifying mixing using equilibrium reactions

    Science.gov (United States)

    Wheat, Philip M.; Posner, Jonathan D.

    2009-03-01

    A method of quantifying equilibrium reactions in a microchannel using a fluorometric reaction of Fluo-4 and Ca2+ ions is presented. Under the proper conditions, equilibrium reactions can be used to quantify fluid mixing without the challenges associated with constituent mixing measures such as limited imaging spatial resolution and viewing angle coupled with three-dimensional structure. Quantitative measurements of CaCl and calcium-indicating fluorescent dye Fluo-4 mixing are measured in Y-shaped microchannels. Reactant and product concentration distributions are modeled using Green's function solutions and a numerical solution to the advection-diffusion equation. Equilibrium reactions provide for an unambiguous, quantitative measure of mixing when the reactant concentrations are greater than 100 times their dissociation constant and the diffusivities are equal. At lower concentrations and for dissimilar diffusivities, the area averaged fluorescence signal reaches a maximum before the species have interdiffused, suggesting that reactant concentrations and diffusivities must be carefully selected to provide unambiguous, quantitative mixing measures. Fluorometric equilibrium reactions work over a wide range of pH and background concentrations such that they can be used for a wide variety of fluid mixing measures including industrial or microscale flows.

  5. Lexical NP and VP quantifiers in Bulgarian

    Directory of Open Access Journals (Sweden)

    Kristina Kalpakchieva

    2015-11-01

    Full Text Available Lexical NP and VP quantifiers in Bulgarian The paper focuses on uniqueness, existential and universal quantification within the Bulgarian noun and verb phrase. Quantifiers scope is considered with respect to whether the quantifiers are used alone or in a group with other expressions. Another factor that affects the strength of quantifiers is the expression’s containing additional specifying functions or setting some circumstance or condition. Quantifiers within the verb phrase are particularly strongly affected by other conditions, while quantifiers within the subject NP have a broad scope and are not affected by the additional conditions of the situation described.

  6. Quantifying Resource Use in Computations

    CERN Document Server

    van Son, R J J H

    2009-01-01

    It is currently not possible to quantify the resources needed to perform a computation. As a consequence, it is not possible to reliably evaluate the hardware resources needed for the application of algorithms or the running of programs. This is apparent in both computer science, for instance, in cryptanalysis, and in neuroscience, for instance, comparative neuro-anatomy. A System versus Environment game formalism is proposed based on Computability Logic that allows to define a computational work function that describes the theoretical and physical resources needed to perform any purely algorithmic computation. Within this formalism, the cost of a computation is defined as the sum of information storage over the steps of the computation. The size of the computational device, eg, the action table of a Universal Turing Machine, the number of transistors in silicon, or the number and complexity of synapses in a neural net, is explicitly included in the computational cost. The proposed cost function leads in a na...

  7. Quantifying and simulating human sensation

    DEFF Research Database (Denmark)

    Quantifying and simulating human sensation – relating science and technology of indoor climate research Abstract In his doctoral thesis from 1970 civil engineer Povl Ole Fanger proposed that the understanding of indoor climate should focus on the comfort of the individual rather than averaged...... archival material related to Lund Madsen’s efforts are preserved at the Technical University of Denmark and I have used these artefacts as the point of departure for my investigation. In this paper I will examine which factors the researchers perceived as important for human indoor comfort and how...... this understanding of human sensation was adjusted to technology. I will look into the construction of the equipment, what it measures and the relationship between theory, equipment and tradition....

  8. Metagenomics meets time series analysis: unraveling microbial community dynamics.

    Science.gov (United States)

    Faust, Karoline; Lahti, Leo; Gonze, Didier; de Vos, Willem M; Raes, Jeroen

    2015-06-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.

  9. ANAEROBIC BIODEGRADATION OF ORGANIC COMPOUNDS IN MICROBIAL FUEL CELLS

    Directory of Open Access Journals (Sweden)

    Samkov A. A.

    2014-09-01

    Full Text Available МF-4SК membrane-based microbial fuel cell (MFC was used for an anaerobic utilization of organic com-pounds of various liquid wastes. During incubation in short circuit mode, decreasing of the COD value on range 30-87 % depending on the type of wastes was detected. The dependence of the microbial fuel cell output power on the value of the external load was determined by a number of structural characteristics of MFC

  10. Hydrodynamics of Microbial Filter-Feeding

    Science.gov (United States)

    Andersen, Anders; Nielsen, Lasse Tor; Dolger, Julia; Kiorboe, Thomas

    2016-11-01

    Microbial filter-feeders form an important group of plankton with significance to the aquatic food webs. While the concept of filter-feeding is straightforward, our quantitative understanding of microbial filter-feeding leaves a lot to be desired. As a model organism, we focus on the filter-feeding choanoflagellate Diaphanoeca grandis. We quantify the feeding flow using particle tracking, and demonstrate that hydrodynamic theory underestimates the observed clearance rate by an order of magnitude. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. To resolve the paradox we argue that D. grandis and other choanoflagellates must have so far unbeknownst morphological features. Specifically, we suggest a flagellar vane that connects the flagellum to the filter, as known in choanocytes of sponges, creating a radically different, and order of magnitude more capable, pumping mechanism. The Centre for Ocean Life is a VKR Centre of Excellence supported by the Villum Foundation.

  11. Engineering microbial factories for synthesis of value-added products.

    Science.gov (United States)

    Du, Jing; Shao, Zengyi; Zhao, Huimin

    2011-08-01

    Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed.

  12. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D

    2011-06-01

    Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

  13. Urea transformation of wetland microbial communities.

    Science.gov (United States)

    Thorén, Ann-Karin

    2007-02-01

    Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12 degrees C) with the use of the 14C-urea tracer method, which measures the release of 14CO2 as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12-22 mmol urea-N m(-2) day(-1)) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1-0.2 mmol urea-N m(-2) day(-1)). The epiphytic activity of leaves of Typha latifolia was lower (0.001-0.03 mmol urea-N m(-2) day(-1)), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity-in the range of 23-33 m2 of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2-7 mmol urea-N m(-2) day(-1) and was in the same magnitude as the urea transformation in the sediment.

  14. [Soil microbial functional diversity of different altitude Pinus koraiensis forests].

    Science.gov (United States)

    Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

    2015-12-01

    In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

  15. Quantifying Evaporation in a Permeable Pavement System

    Science.gov (United States)

    Studies quantifying evaporation from permeable pavement systems are limited to a few laboratory studies and one field application. This research quantifies evaporation for a larger-scale field application by measuring the water balance from lined permeable pavement sections. Th...

  16. MURMoT. Design and Application of Microbial Uranium Reduction Monitoring Tools

    Energy Technology Data Exchange (ETDEWEB)

    Loeffler, Frank E. [Univ. of Tennessee, Knoxville, TN (United States)

    2014-12-31

    Uranium (U) contamination in the subsurface is a major remediation challenge at many DOE sites. Traditional site remedies present enormous costs to DOE; hence, enhanced bioremediation technologies (i.e., biostimulation and bioaugmentation) combined with monitoring efforts are being considered as cost-effective corrective actions to address subsurface contamination. This research effort improved understanding of the microbial U reduction process and developed new tools for monitoring microbial activities. Application of these tools will promote science-based site management decisions that achieve contaminant detoxification, plume control, and long-term stewardship in the most efficient manner. The overarching hypothesis was that the design, validation and application of a suite of new molecular and biogeochemical tools advance process understanding, and improve environmental monitoring regimes to assess and predict in situ U immobilization. Accomplishments: This project (i) advanced nucleic acid-based approaches to elucidate the presence, abundance, dynamics, spatial distribution, and activity of metal- and radionuclide-detoxifying bacteria; (ii) developed proteomics workflows for detection of metal reduction biomarker proteins in laboratory cultures and contaminated site groundwater; (iii) developed and demonstrated the utility of U isotopic fractionation using high precision mass spectrometry to quantify U(VI) reduction for a range of reduction mechanisms and environmental conditions; and (iv) validated the new tools using field samples from U-contaminated IFRC sites, and demonstrated their prognostic and diagnostic capabilities in guiding decision making for environmental remediation and long-term site stewardship.

  17. MURMoT. Design and Application of Microbial Uranium Reduction Monitoring Tools

    Energy Technology Data Exchange (ETDEWEB)

    Loffler, Frank E. [Univ. of Tennessee, Knoxville, TN (United States); Ritalahti, Kirsti [Univ. of Tennessee, Knoxville, TN (United States); Sanford, Robert A. [Univ. of Illinois at Urbana-Champaign, IL (United States); Lundstrom, Craig C. [Univ. of Illinois at Urbana-Champaign, IL (United States); Johnson, Thomas M. [Univ. of Illinois at Urbana-Champaign, IL (United States); Kemner, Kenneth [Argonne National Lab. (ANL), Argonne, IL (United States); Boyanov, Maxim [Argonne National Lab. (ANL), Argonne, IL (United States)

    2009-07-01

    Uranium (U) contamination in the subsurface is a major remediation challenge at many DOE sites. Traditional site remedies present enormous costs to DOE; hence, enhanced bioremediation technologies (i.e., biostimulation and bioaugmentation) combined with monitoring efforts are being considered as cost-effective corrective actions to address subsurface contamination. This research effort improved understanding of the microbial U reduction process and developed new tools for monitoring microbial activities. Application of these tools will promote science-based site management decisions that achieve contaminant detoxification, plume control, and long-term stewardship in the most efficient manner. The overarching hypothesis was that the design, validation and application of a suite of new molecular and biogeochemical tools advance process understanding, and improve environmental monitoring regimes to assess and predict in situ U immobilization. Accomplishments: This project (i) advanced nucleic acid-based approaches to elucidate the presence, abundance, dynamics, spatial distribution, and activity of metal- and radionuclide-detoxifying bacteria; (ii) developed proteomics workflows for detection of metal reduction biomarker proteins in laboratory cultures and contaminated site groundwater; (iii) developed and demonstrated the utility of U isotopic fractionation using high precision mass spectrometry to quantify U(VI) reduction for a range of reduction mechanisms and environmental conditions; and (iv) validated the new tools using field samples from U-contaminated IFRC sites, and demonstrated their prognostic and diagnostic capabilities in guiding decision making for environmental remediation and long-term site stewardship.

  18. Quantifier Scope in Categorical Compositional Distributional Semantics

    Directory of Open Access Journals (Sweden)

    Mehrnoosh Sadrzadeh

    2016-08-01

    Full Text Available In previous work with J. Hedges, we formalised a generalised quantifiers theory of natural language in categorical compositional distributional semantics with the help of bialgebras. In this paper, we show how quantifier scope ambiguity can be represented in that setting and how this representation can be generalised to branching quantifiers.

  19. Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

    Science.gov (United States)

    Birmele, Michele; Caro, Janicce; Newsham, Gerard; Roberts, Michael; Morford, Megan; Wheeler, Ray

    2012-01-01

    Microbial detection, identification, and control are essential for the maintenance and preservation of spacecraft water systems. Requirements set by NASA put limitations on the energy, mass, materials, noise, cost, and crew time that can be devoted to microbial control. Efforts are being made to attain real-time detection and identification of microbial contamination in microgravity environments. Research for evaluating technologies for capability enhancement on-orbit is currently focused on the use of adenosine triphosphate (ATP) analysis for detection purposes and polymerase chain reaction (peR) for microbial identification. Additional research is being conducted on how to control for microbial contamination on a continual basis. Existing microbial control methods in spacecraft utilize iodine or ionic silver biocides, physical disinfection, and point-of-use sterilization filters. Although these methods are effective, they require re-dosing due to loss of efficacy, have low human toxicity thresholds, produce poor taste, and consume valuable mass and crew time. Thus, alternative methods for microbial control are needed. This project also explores ultraviolet light-emitting diodes (UV-LEDs), surface passivation methods for maintaining residual biocide levels, and several antimicrobial materials aimed at improving current microbial control techniques, as well as addressing other materials presently under analysis and future directions to be pursued.

  20. Ocean microbial metagenomics

    Science.gov (United States)

    Kerkhof, Lee J.; Goodman, Robert M.

    2009-09-01

    Technology for accessing the genomic DNA of microorganisms, directly from environmental samples without prior cultivation, has opened new vistas to understanding microbial diversity and functions. Especially as applied to soils and the oceans, environments on Earth where microbial diversity is vast, metagenomics and its emergent approaches have the power to transform rapidly our understanding of environmental microbiology. Here we explore select recent applications of the metagenomic suite to ocean microbiology.

  1. Development of microbial biosensors for food analysis

    DEFF Research Database (Denmark)

    Lukasiak, Justyna

    Microbial biosensors are analytical devices composed of a biological recognition element (microorganism) integrated to a signal transduction element (i.e. bioluminescence), converting a biochemical signal into quantifiable response. Due to their molecular properties they can be diversely designed...... grains. It is a dietary fiber, with potential as a functional food ingredient. In this study, reporter strains targeting specifically L-rhamnose, L-arabinose and Dxylose using three different signal transducers: bioluminescence (luxCDABE), fluorescence (gfp) and ice nucleation (inaZ) were developed...

  2. Quantifying Cricket Fast Bowling Skill.

    Science.gov (United States)

    Feros, Simon A; Young, Warren B; O'Brien, Brendan J

    2017-09-27

    To evaluate the current evidence regarding the quantification of cricket fast bowling skill. Studies that assessed fast bowling skill (bowling speed and accuracy) were identified from searches in SPORTDiscus (EBSCO) in June 2017. The reference lists of identified papers were also examined for relevant investigations. Sixteen papers matched the inclusion criteria, and discrepancies in assessment procedures were evident. Differences in: test environment, pitch and cricket ball characteristics, the warm-up prior to test, test familiarisation procedures, permitted run-up lengths, bowling spell length, delivery sequence, test instructions, collection of bowling speed data, collection and reportage of bowling accuracy data were apparent throughout the literature. The reliability and sensitivity of fast bowling skill measures has rarely been reported across the literature. Only one study has attempted to assess the construct validity of their skill measures. There are several discrepancies in how fast bowling skill has been assessed and subsequently quantified in the literature to date. This is a problem, as comparisons between studies are often difficult. Therefore, a strong rationale exists for the creation of match-specific standardised fast bowling assessments that offer greater ecological validity while maintaining acceptable reliability and sensitivity of the skill measures. If prospective research can act on the proposed recommendations from this review, then coaches will be able to make more informed decisions surrounding player selection, talent identification, return to skill following injury, and the efficacy of short- and long-term training interventions for fast bowlers.

  3. Substrate-induced changes in microbial community-level physiological profiles and their application to discriminate soil microbial communities

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; XIE Huijun; ZHUANG Xuliang; ZHUANG Guoqiang; BAI Zhihui; ZHANG Hongxun

    2008-01-01

    The addition of simple substrates could affect the microbial respiration in soils.This substrate-induced respiration is widely used to estimate the soil microbial biomass,but little attention has been paid to its influence on the changes of community-level physiological profiles.In this study,the process of microbial communities responding to the added substrate using sole-carbon-source utilization (BIOLOG) was investigated.BIOLOG is biased toward fast-growing bacteria;this advantage Was taken to detect the prompt response of the active microbial communities to the added substrate.Four soil samples from agricultural fields adjacent to heavy metal mines were amended with L-arginine,citric acid,or D-glucose.Substrate amendments could,generally,not only increase the metabolic activity of the microbial communities,but also change the metabolic diverse patterns compared with no-substrate contr01.By tracking the process,it was found that the variance between substrate-induced treatment and control fluctuated greatly during the incubation course,and the influences of these three substrates were difierent.In addition,the application of these induced changes to discriminate soil microbial communities was tested.T1le distance among all samples was greatly increased.which further showed the functional variance among microbial communities in soils.This Can be very useful in the discrimination of microbial communities eveB with high similarity.

  4. Microbial Repopulation Following In Situ STAR Remediation

    Science.gov (United States)

    Gerhard, J.; Overbeeke, G.; Edwards, E.; Lomheim, L.; Grant, G.

    2016-12-01

    STAR (Self-sustaining Treatment for Active Remediation) is an emerging remediation technology that employs a self-sustaining smouldering reaction to destroy nonaqueous phase liquids (NAPLs) in the subsurface. The reaction front travels outwards from an ignition well at approximately 0.5 per day and subjects the soil to temperatures of 400°C-1000°C. The objectives of this work were to monitor re-saturation of the soil over time and quantify the microbial repopulation of the treated zone. STAR is currently being applied as a full scale, in situ remedy for coal tar beneath a former creosol manufacturing facility in New Jersey, USA. This study analyzed soil cores taken at regular intervals following STAR treatment, allowing time for groundwater to re-infiltrate and for microbial populations to potentially reestablish. Soil and groundwater were analyzed for total number of microorganisms via quantitative Polymerase Chain Reaction (qPCR), as well as microbial diversity via amplicon sequencing. Results demonstrate that microbes rapidly repopulated over a 2 month period to 106 gene copies/g of soil. However, concentrations in the treated zone did not rise above this concentration over 6 months post-STAR, indicating a low carrying capacity of the treated soil. To examine the system in more detail and consider the effects of bio-stimulation, a bench top column study using site soil and artificial groundwater explored the rate at which STAR-treated soil is repopulated with naturally occurring microorganisms in the presence and absence of lactate and a terminal electron acceptor. Results demonstrated that biostimulation did not increase the carrying capacity of the STAR treated sol, but rather shifted the microbial community to reflect the TEA provided, in this case, promoting sulfate reducers. Overall, the work illustrates that microbial populations in STAR treated soil do recover via groundwater infiltration but robust communities will take time to naturally establish.

  5. Microbial community structure of different electrode materials in constructed wetland incorporating microbial fuel cell.

    Science.gov (United States)

    Wang, Junfeng; Song, Xinshan; Wang, Yuhui; Abayneh, Befkadu; Ding, Yi; Yan, Denghua; Bai, Junhong

    2016-12-01

    The microbial fuel cell coupled with constructed wetland (CW-MFC) microcosms were operated under fed-batch mode for evaluating the effect of electrode materials on bioelectricity generation and microbial community composition. Experimental results indicated that the bioenergy output in CW-MFC increased with the substrate concentration; maximum average voltage (177mV) was observed in CW-MFC with carbon fiber felt (CFF). In addition, the four different materials resulted in the formation of significantly different microbial community distribution around the anode electrode. The relative abundance of Proteobacteria in CFF and foamed nickel (FN) was significantly higher than that in stainless steel mesh (SSM) and graphite rod (GR) samples. Notably, the findings indicate that CW-MFC utilizing FN anode electrode could apparently improve relative abundance of Dechloromonas, which has been regarded as a denitrifying and phosphate accumulating microorganism.

  6. Quantifying the shape of aging

    DEFF Research Database (Denmark)

    Wrycza, Tomasz F; Missov, Trifon I; Baudisch, Annette

    2015-01-01

    In Biodemography, aging is typically measured and compared based on aging rates. We argue that this approach may be misleading, because it confounds the time aspect with the mere change aspect of aging. To disentangle these aspects, here we utilize a time-standardized framework and, instead...... of aging rates, suggest the shape of aging as a novel and valuable alternative concept for comparative aging research. The concept of shape captures the direction and degree of change in the force of mortality over age, which—on a demographic level—reflects aging. We 1) provide a list of shape properties...... suggested here aim to provide a general means to classify aging patterns independent of any particular mortality model and independent of any species-specific time-scale. Thereby they support systematic comparative aging research across different species or between populations of the same species under...

  7. Quantifying consumption rates of dissolved oxygen along bed forms

    Science.gov (United States)

    Boano, Fulvio; De Falco, Natalie; Arnon, Shai

    2016-04-01

    Streambed interfaces represent hotspots for nutrient transformations because they host different microbial species, and the evaluation of these reaction rates is important to assess the fate of nutrients in riverine environments. In this work we analyze a series of flume experiments on oxygen demand in dune-shaped hyporheic sediments under losing and gaining flow conditions. We employ a new modeling code to quantify oxygen consumption rates from observed vertical profiles of oxygen concentration. The code accounts for transport by molecular diffusion and water advection, and automatically determines the reaction rates that provide the best fit between observed and modeled concentration values. The results show that reaction rates are not uniformly distributed across the streambed, in agreement with the expected behavior predicted by hyporheic exchange theory. Oxygen consumption was found to be highly influenced by the presence of gaining or losing flow conditions, which controlled the delivery of labile DOC to streambed microorganisms.

  8. Quantifying uncertainty from material inhomogeneity.

    Energy Technology Data Exchange (ETDEWEB)

    Battaile, Corbett Chandler; Emery, John M.; Brewer, Luke N.; Boyce, Brad Lee

    2009-09-01

    Most engineering materials are inherently inhomogeneous in their processing, internal structure, properties, and performance. Their properties are therefore statistical rather than deterministic. These inhomogeneities manifest across multiple length and time scales, leading to variabilities, i.e. statistical distributions, that are necessary to accurately describe each stage in the process-structure-properties hierarchy, and are ultimately the primary source of uncertainty in performance of the material and component. When localized events are responsible for component failure, or when component dimensions are on the order of microstructural features, this uncertainty is particularly important. For ultra-high reliability applications, the uncertainty is compounded by a lack of data describing the extremely rare events. Hands-on testing alone cannot supply sufficient data for this purpose. To date, there is no robust or coherent method to quantify this uncertainty so that it can be used in a predictive manner at the component length scale. The research presented in this report begins to address this lack of capability through a systematic study of the effects of microstructure on the strain concentration at a hole. To achieve the strain concentration, small circular holes (approximately 100 {micro}m in diameter) were machined into brass tensile specimens using a femto-second laser. The brass was annealed at 450 C, 600 C, and 800 C to produce three hole-to-grain size ratios of approximately 7, 1, and 1/7. Electron backscatter diffraction experiments were used to guide the construction of digital microstructures for finite element simulations of uniaxial tension. Digital image correlation experiments were used to qualitatively validate the numerical simulations. The simulations were performed iteratively to generate statistics describing the distribution of plastic strain at the hole in varying microstructural environments. In both the experiments and simulations, the

  9. Characteristics of microbial volatile organic compound flux rates from soil and plant litter

    Science.gov (United States)

    Gray, C. M.; Fierer, N.

    2013-12-01

    Our knowledge of microbial production and consumption of volatile organic compounds (VOCs) from soil and litter, as well as which microorganisms are involved, is relatively limited compared to what we know about VOC emissions from terrestrial plants. With climate change expecting to alter plant community composition, nitrogen (N) deposition rates, mean annual temperatures, precipitation patterns, and atmospheric VOC concentrations, it is unknown how microbial production and consumption of VOCs from litter and soil will respond. We have spent the last 5 years quantifying VOC flux rates in decaying plant litter, mineral soils and from a subalpine field site using a proton transfer reaction mass spectrometer (PTR-MS). Microbial production, relative to abiotic sources, accounted for 78% to 99% of the total VOC emissions from decomposing litter, highlighting the importance of microbial metabolisms in these systems. Litter chemistry correlated with the types of VOCs emitted, of which, methanol was emitted at the highest rates from all studies. The net emissions of carbon as VOCs was found to be up to 88% of that emitted as CO2 suggesting that VOCs likely represent an important component of the carbon cycle in many terrestrial systems. Nitrogen additions drastically reduced VOC emissions from litter to near zero, though it is still not understood whether this was due to an increase in consumption or a decrease in production. In the field, the root system contributed to 53% of the carbon that was emitted as VOCs from the soil with increasing air temperatures correlating to an increase in VOC flux rates from the soil system. Finally, we are currently utilizing next generation sequencing techniques (Illumina MiSeq) along with varying concentrations of isoprene, the third most abundant VOC in the atmosphere behind methane and methanol, above soils in a laboratory incubation to determine consumption rates and the microorganisms (bacteria, archaea and fungi) associated with the

  10. Utilization of Waste Materials for Microbial Carrier in Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    H. T. Le

    2016-01-01

    Full Text Available This research focused on the ammonium-nitrogen (NH4-N removal from the domestic wastewater using the attached growth reactors. Two types of waste material of corncob (biodegradable material and concrete (nonbiodegradable material were used as the carrier for microorganisms’ attachment. During operation, both reactors achieved absolutely high performance of ammonium removal (up to 99% and total nitrogen removal (up to 95%. The significant advantage of corncob carrier was that the corncob was able to be a source of carbon for biological denitrification, leading to no external carbon requirement for operating the system. However, the corncob caused an increasing turbidity of the effluent. On the other hand, the concrete carrier required the minimal external carbon of 3.5 C/N ratio to reach the good performance. Moreover, a longer period for microorganisms’ adaptation was found in the concrete carrier rather than the corncob carrier. Further, the same physiological and biochemical characteristics of active bacteria were found at the two carriers, which were negative gram, cocci shape, and smooth and white-turbid colony. Due to the effluent quality, the concrete was more appropriate carrier than the corncob for wastewater treatment.

  11. Effect of organic nutrient on microbial utilization of hydrocarbons on ...

    African Journals Online (AJOL)

    Administrator

    2006-05-16

    May 16, 2006 ... African Journal of Biotechnology Vol. 5 (10), pp. ... Full Length Research Paper. Effect of organic ... incident of oil spills occur in the mangrove swamp zones ..... methods for a number of residual fuel spill in Lee County, Florida.

  12. Microbial renewable feedstock utilization: A substrate-oriented approach

    NARCIS (Netherlands)

    Rumbold, K.; Buijsen, H.J.J. van; Gray, V.M.; Groenestijn, J.W. van; Overkamp, K.M.; Slomp, R.S.; Werf, M.J. van der; Punt, P.J.

    2010-01-01

    Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates consist of complex mixtures of different fermentable sugars, but also contain inhibitors and salts that affect the performance of the productgenerating microbes. The p

  13. Modeling adaptation of carbon use efficiency in microbial communities

    Directory of Open Access Journals (Sweden)

    Steven D Allison

    2014-10-01

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

  14. Determining and quantifying specific sources of light alkane

    Science.gov (United States)

    Bill, M.; Conrad, M. E.

    2015-12-01

    Determining and quantifying specific sources of emission of methane (an important greenhouse gas) and light alkanes from abandoned gas and oil wells, hydraulic fracturing or associated with CO2 sequestration are a challenge in determining their contribution to the atmospheric greenhouse gas budget or to identify source of groundwater contamination. Here, we review organic biogeochemistry proprieties and isotopic fingerprinting of C1-C5 alkanes to address this problem. For instance, the concentration ratios of CH4 to C2-C5 alkanes can be used to distinguish between thermogenic and microbial generated CH4. Together C and H isotopes of CH4 are used to differentiate bacterial generated sources and thermogenic CH4 and may also identify processes such as alteration and source mixing. Carbon isotope ratios pattern of C1-C5 alkanes highlight sources and oxidation processes in the gas reservoirs. Stable carbon isotope measurements are a viable tool for monitoring the degradation progress of methane and light hydrocarbons. The carbon isotope ratios of the reactants and products are independent of the concentration and only depend on the relative progress of the particular reaction. Oxidation/degradation of light alkanes are typically associated with increasing ð13C values. Isotopic mass balances offer the possibility to independently determine the fractions coming from microbial versus thermogenic and would also permit differentiation of the isotope fractionations associated with degradation. Unlike conventional concentration measurements, this approach is constrained by the different isotopic signatures of various sources and sinks.

  15. Development and optimization of microbial fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Davila, D.; Vigues, N.; Sanchez, O.; Garrido, L.; Tomas, N.; Mas, J. [Univ. Autonoma de Barcelona, Barcelona (Spain). Dept. de Genetica y Microbiologia; Esquivel, J.P.; Sabate, N.; Del Campo, F.J.; Munoz, F.J. [Inst. de Microelectronica de Barcelona-CNM (CSIC), Barcelona (Spain)

    2008-04-15

    While global energy demand increases daily, fossil fuel sources are being depleted at an unsustainable pace. Fuel cells represent a solution as they are more efficient than other energy sources. A microbial fuel cell is an electrochemical device capable of continuously converting chemical energy into electrical energy for as long as adequate fuel and oxidant are available. A microbial fuel cell (MFC) adds the benefit of converting chemical energy from organic compounds, such as simple carbohydrates or organic waste matter, into electricity by using bacteria as biocatalysts. This article described the effect of several parameters that affect the operation of a microbial fuel cell (MFC). The study is based on a methodology utilized in previous studies which employed escherichia coli as biocatalyst and neutral red as the electron mediator in a mediated electron transfer (MET) microbial fuel cell. The study analysed the influence of the bacterial concentration, the effective area of electrode and the volume of the cell. It was concluded that there is a proportional energy production to the bacterial concentration present in the anode compartment. It was demonstrated that an increase in the volume of the cell negatively affects the power produced by the cells. 8 refs., 1 tab., 5 figs.

  16. Microbial Enzymatic Degradation of Biodegradable Plastics.

    Science.gov (United States)

    Roohi; Bano, Kulsoom; Kuddus, Mohammed; Zaheer, Mohammed R; Zia, Qamar; Khan, Mohammed F; Ashraf, Ghulam Md; Gupta, Anamika; Aliev, Gjumrakch

    2017-01-01

    The renewable feedstock derived biodegradable plastics are important in various industries such as packaging, agricultural, paper coating, garbage bags and biomedical implants. The increasing water and waste pollution due to the available decomposition methods of plastic degradation have led to the emergence of biodegradable plastics and biological degradation with microbial (bacteria and fungi) extracellular enzymes. The microbes utilize biodegradable polymers as the substrate under starvation and in unavailability of microbial nutrients. Microbial enzymatic degradation is suitable from bioremediation point of view as no waste accumulation occurs. It is important to understand the microbial interaction and mechanism involved in the enzymatic degradation of biodegradable plastics under the influence of several environmental factors such as applied pH, thermo-stability, substrate molecular weight and/or complexity. To study the surface erosion of polymer film is another approach for hydrolytic degradation characteristion. The degradation of biopolymer is associated with the production of low molecular weight monomer and generation of carbon dioxide, methane and water molecule. This review reported the degradation study of various existing biodegradable plastics along with the potent degrading microbes (bacteria and fungi). Patents available on plastic biodegradation with biotechnological significance is also summarized in this paper. This paper assesses that new disposal technique should be adopted for the degradation of polymers and further research is required for the economical production of biodegradable plastics along with their enzymatic degradation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Evaluation of Microalgae as Microbial Fertilizer

    Directory of Open Access Journals (Sweden)

    Onder Uysal

    2015-06-01

    Full Text Available Microalgal biomass is utilized in many fields such as food, agriculture, energy, and cosmetic sectors. It is very well known that chemical fertilizer adversely affect soil, plant, and environment. To reduce this effect in recent years, interest to organic farming has been increasing. In this study, microbial fertilizers obtained from microalgae was applied to maize and wheat plants. Microbial fertilizers at four different doses were applied, namely, S1 (control: 0,00 dose-non fertilizer, S2 (0.50 dose, S3 (1.00 dose, and S4 (1.50 dose. All measurements were made at the end of 30th days.  The best results were determined for S3 dose applications. During the experiment, the soil temperature between 15 and 30⁰C and soil pH values between 6.5 and 8.5 were maintained. The results showed that the amount of soil organic matter and the water holding capacity were improved. Finally, microbial fertilizers obtained from microalgae can be reported to have positive effects on soil, plants and therefore environment. Keywords: Microalgae, biomass, agriculture, fertilizer, microbial

  18. Microbial communities associated with stable fly (Diptera: Muscidae) larvae and their developmental substrates

    Science.gov (United States)

    Bacteria are essential for stable fly (Stomoxys calcitrans (L.)) larval survival and development, but little is known about the innate microbial communities of stable flies, and it is not known if their varied dietary substrates influence their gut microbial communities. This investigation utilized ...

  19. Expansion of Microbial Forensics.

    Science.gov (United States)

    Schmedes, Sarah E; Sajantila, Antti; Budowle, Bruce

    2016-08-01

    Microbial forensics has been defined as the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes. Over the past 15 years, technology, particularly massively parallel sequencing, and bioinformatics advances now allow the characterization of microorganisms for a variety of human forensic applications, such as human identification, body fluid characterization, postmortem interval estimation, and biocrimes involving tracking of infectious agents. Thus, microbial forensics should be more broadly described as the discipline of applying scientific methods to the analysis of microbial evidence in criminal and civil cases for investigative purposes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    microbial identifier (GMI) initiative, aims to build a database of whole microbial genome sequencing data linked to relevant metadata, which can be used to identify microorganisms, their communities and the diseases they cause. It would be a platform for storing whole genome sequencing (WGS) data......) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open......-source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global...

  1. The Microbial Olympics

    Science.gov (United States)

    Youle, Merry; Rohwer, Forest; Stacy, Apollo; Whiteley, Marvin; Steel, Bradley C.; Delalez, Nicolas J.; Nord, Ashley L.; Berry, Richard M.; Armitage, Judith P.; Kamoun, Sophien; Hogenhout, Saskia; Diggle, Stephen P.; Gurney, James; Pollitt, Eric J. G.; Boetius, Antje; Cary, S. Craig

    2014-01-01

    Every four years, the Olympic Games plays host to competitors who have built on their natural talent by training for many years to become the best in their chosen discipline. Similar spirit and endeavour can be found throughout the microbial world, in which every day is a competition to survive and thrive. Microorganisms are trained through evolution to become the fittest and the best adapted to a particular environmental niche or lifestyle, and to innovate when the ‘rules of the game’ are changed by alterations to their natural habitats. In this Essay, we honour the best competitors in the microbial world by inviting them to take part in the inaugural Microbial Olympics. PMID:22796885

  2. Culture Independent Geochemical Tools for Adressing Microbial Activity

    Science.gov (United States)

    Lomstein, B. A.; Langerhuus, A. T.; Jørgensen, B. B.; Alperin, M. J.

    2014-12-01

    Decades of ocean drilling have demonstrated wide-spread microbial life in deep sub-seafloor sediment, and surprisingly high numbers of microbial cells and endospores. Despite the ubiquity of life in the deep biosphere, the large community sizes are not yet understood given the extremely low energy fluxes. We have developed and applied new approaches to the deep sub-seafloor to quantify distributions and turnover times of living microbial biomass, endospores and microbial necromass. The approach combines sensitive analyses of unique bacterial marker molecules (muramic acid and d-amino acids) and the bacterial endospore marker (dipicolinic acid) with a series of models that link microscopic (e.g., racemization dynamics of stereo-isomeric amino acids) and macroscopic (e.g., porewater geochemistry) properties. Model output includes production rates and turnover times of microbial biomass and necromass, concentration profiles of reactive organic carbon, and rates of organic carbon decomposition. In combination, these results allow us to assess the role of microbial activity in the sub-seafloor carbon budget. One key result is that the turnover time of biomass is far longer than turnover times found in cultures and active surface sediments.

  3. A biophysical index for predicting hydration-mediated microbial diversity in soils

    Science.gov (United States)

    Wang, G.; Or, D.

    2012-04-01

    Exploring the origins of soil microbial diversity represents an immense and uncharted scientific frontier. Progress in resolving mechanisms that promote and sustain the unparalleled soil microbial diversity found in soil requires development of process-based predictive tools that consider dynamic biophysical interactions at highly resolved spatial and temporal scales. We report a novel biophysical metric for hydration-mediated microbial coexistence in soils by integrating key biophysical variables, such as aquatic habitat size and connectivity, nutrient diffusion affecting microbial growth, and aqueous films controlling motility and dispersal, into a predictive index. Results show a surprisingly narrow range of hydration conditions (a few kPa) that mark a sharp transition from suppression (wet) to promotion (dry) of microbial diversity in unsaturated soils in agreement with limited observations and with simulation results based on individual-based models of competing populations. The framework enables systematic hypothesis testing for key factors that regulate microbial populations and affect soil bio-geochemical functions, and represents a step towards deciphering key mechanisms that support soil microbial diversity. New insights into the different roles of biophysical mechanisms in promoting soil microbial diversity enable predictions concerning microbial consortia function and bioremediation activities in soils, and may shape how we quantify microbial diversity within the context of land resources and biogeochemical cycling.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. Pretreatment of Dioscorea zingiberensis for Microbial Transformation

    Directory of Open Access Journals (Sweden)

    Tianxiang Zheng

    2014-09-01

    Full Text Available The influences of five pretreatments on fungal growth and enzyme production during microbial transformation of Dioscorea zingiberensis (DZW were studied. The biomass, α-rhamnase and β-glucosidase activities in the fermentation system were employed in the study to determine how each method affected the efficiency of microbial transformation. The fungal strain grew better on the substrate which contained easily utilized carbon source. While lack of carbon source induced the strain produce more glucosidase. Among five pretreatment methods, complex enzymatic hydrolyzation can remove 84.3% starch and 76.5% fibre from DZW in form of sugar, which resulted in high α-rhamnase activity of 2.89 IU/mL and β-glucosidase activity of 8.17 IU/mL in fermentation broth.

  6. Microbial Transglutaminase in Noodle and Pasta Processing

    DEFF Research Database (Denmark)

    Gharibzahedi, Seyed Mohammad Taghi; Yousefi, Shima; Chronakis, Ioannis S.

    2017-01-01

    Nowadays, there is an aggressive rate in consumption of noodles and pasta products throughout the world. Consumer acceptability and preference of these functional products can be promoted by the discovery of novel knowledge to improve their formulation and quality. The development of fortified......-formulations for noodles and pasta products based on microbial transglutaminase (MTGase) can guarantee the shelf life extension with minimum quality losses. The current review focuses on recent trends and future prospects of MTGase utilization in the structural matrix of noodles and pasta products and represents...... from new microbial sources. The high potential of MTGase in developing commercial noodles and pasta products is successfully demonstrated. MTGase by modifying the crystallinity or molecular structure via covalent crosslinks between protein molecules strengthens the doughs stability and the textural...

  7. INNOVATIVE MIOR PROCESS UTILIZING INDIGENOUS RESERVOIR CONSTITUENTS

    Energy Technology Data Exchange (ETDEWEB)

    D.O. Hitzman; A.K. Stepp; D.M. Dennis; L.R. Graumann

    2003-09-01

    This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions and technologies for improving oil production. The goal was to identify and utilize indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. Experimental laboratory work in model sandpack cores was conducted using microbial cultures isolated from produced water samples. Comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents were conducted in sand packs with natural field waters using cultures and conditions representative of oil reservoirs. Increased oil recovery in multiple model sandpack systems was achieved and the technology and results were verified by successful field studies. Direct application of the research results has lead to the development of a feasible, practical, successful, and cost-effective technology which increases oil recovery. This technology is now being commercialized and applied in numerous field projects to increase oil recovery. Two field applications of the developed technology reported production increases of 21% and 24% in oil recovery.

  8. Multiattribute Utility Theory without Expected Utility Foundations

    NARCIS (Netherlands)

    J. Miyamoto (John); P.P. Wakker (Peter)

    1996-01-01

    textabstractMethods for determining the form of utilities are needed for the implementation of utility theory in specific decisions. An important step forward was achieved when utility theorists characterized useful parametric families of utilities and simplifying decompositions of multiattribute ut

  9. Geoelectrical Signatures Of Microbial Stimulated Mineralization

    Science.gov (United States)

    Personna, Y. R.; Ntarlagiannis, D.; Slater, L.; O Brien, M.; Hubbard, S.; Williams, K. H.

    2007-05-01

    Bioremediation techniques are commonly utilized to address soil and groundwater contamination due to acid- mine drainage, industrial sources, and government nuclear weapon programs. One critical component of these efforts is the real time, spatially accurate monitoring of the remediation processes. For this reason non-invasive high resolution geophysical methods have been employed in the recent years to elucidate system transformations occurring during bioremediation. In our study, we performed laboratory column experiments to investigate the geoelectrical response of microbe-mediated iron sulfide (FeS) precipitation accompanying stimulated sulfate-reduction; a bioremediation technique currently utilized for the sequestration of heavy metals in the subsurface. In order to monitor the biomineralization process, we used two geoelectrical methods - induced polarization (IP) and self-potential (SP) - in conjunction with conventional geochemical measurements. The IP data showed significant anomalies associated with ongoing FeS mineralization accompanying microbial activity. The magnitude of the IP response can be considered a proxy for the mass of minerals accumulating in the pore space and may provide insight into the aggregation state of the mineralization. Additionally, strong SP anomalies developed during the mineralization as a result of the continuous redox state changes following the microbial induced mineral formation. Visibly black precipitates accumulated with the column indicating FeS precipitation, and high H2S content confirmed the observed geochemical and geophysical data. Overall, the results suggest that the IP and SP methods can be used to monitor the progress of the microbial induced mineralization process associated with the precipitation of insoluble metal sulfides, and indirectly monitor the microbial activity within the subsurface. These methods can be valuable tools to increase the efficiency of bioremediation techniques.

  10. Molecular ecology of microbial mats

    NARCIS (Netherlands)

    H. Bolhuis; M.S. Cretoiu; L.J. Stal

    2014-01-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

  11. Microbial ecology of biotechnological processes

    OpenAIRE

    Fraraccio, Serena

    2015-01-01

    The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete...

  12. Formation of distinct soluble microbial products by activated sludge: kinetic analysis and quantitative determination.

    Science.gov (United States)

    Ni, Bing-Jie; Fang, Fang; Xie, Wen-Ming; Xu, Juan; Yu, Han-Qing

    2012-02-07

    Soluble microbial products (SMP) released by microorganisms in bioreactors are classified into two distinct groups according to their different chemical and degradation kinetics: utilization-associated products (UAP) and biomass-associated products (BAP). SMP are responsible for effluent chemical oxygen demand or for membrane fouling of membrane bioreactor. Here an effective and convenient approach, other than the complicated chemical methods or complex models, is developed to quantify the formation of UAP and BAP together with their kinetics in activated sludge process. In this approach, an integrated substrate utilization equation is developed and used to determine UAP and their production kinetics. On the basis of total SMP measurements, BAP formation is determined with an integrated BAP formation equation. The fraction of substrate electrons diverted to UAP, and the content of BAP derived from biomass can then be calculated. Dynamic quantification data are obtained for UAP and BAP separately and conveniently. The obtained kinetic parameters are found to be reasonable as they are generally bounded and comparable to the literature values. The validity of this approach is confirmed by independent SMP production tests in six different activated sludge systems, which demonstrates its applicability in a wide range of engineered system regarding SMP production. This work provides a widely applied approach to determine the formation of UAP and BAP conveniently, which may offer engineers with basis to optimize bioreactor operation to avoid a high effluent soluble organics from SMP or SMP-based membrane fouling in membrane bioreactors.

  13. Understanding microbial/DOM interactions using fluorescence and flow cytometry

    Science.gov (United States)

    Fox, Bethany; Rushworth, Cathy; Attridge, John; Anesio, Alexandre; Cox, Tim; Reynolds, Darren

    2015-04-01

    The transformation and movement of dissolved organic carbon (DOC) within freshwater aquatic systems is an important factor in the global cycling of carbon. DOC within aquatic systems is known to underpin the microbial food web and therefore plays an essential role in supporting and maintaining the aquatic ecosystem. Despite this the interactions between bacteria and dissolved organic matter (DOM) are not well understood, although the literature indicates that the microbial processing of bioavailable DOM is essential during the production of autochthonous, labile, DOM. DOM can be broadly characterised by its fluorescing properties and Coble et al. (2014) define terrestrially derived DOM as exhibiting "peak C" fluorescence, whilst labile microbially derived DOM is defined as showing "peak T" fluorescence. Our work explores the microbial/DOM interactions by analysing aquatic samples using fluorescence excitation and emission matrices (EEMs) in conjunction with microbial consumption of dissolved oxygen. Environmental and synthetic water samples were subjected to fluorescence characterisation using both fluorescence spectroscopy and in situ fluorescence sensors (Chelsea Technologies Group Ltd.). PARAFAC analysis and peak picking were performed on EEMs and compared with flow cytometry data, used to quantify bacterial numbers present within samples. Synthetic samples were created using glucose, glutamic acid, nutrient-rich water and a standard bacterial seed. Synthetic samples were provided with terrestrially derived DOM via the addition of an aliquot of environmental water. Using a closed system approach, samples were incubated over time (up to a maximum of 20 days) and analysed at pre-defined intervals. The main focus of our work is to improve our understanding of microbial/DOM interactions and how these interactions affect both the DOM characteristics and microbial food web in freshwater aquatic systems. The information gained, in relation to the origin, microbial

  14. Quantifying synergistic information remains an unsolved problem

    CERN Document Server

    Griffith, Virgil

    2011-01-01

    We review the prior literature of information theoretical measures of synergy or synergistic information. We draw the hereto unnamed conceptual distinction between synergistic and holistic information and analyze six prior measures based on whether they aim to quantify synergy or holism. We apply all measures against a suite of examples to demonstrate no existing measure correctly quantifies synergy under all circumstances.

  15. Microbial Weathering of Olivine

    Science.gov (United States)

    McKay, D. S.; Longazo, T. G.; Wentworth, S. J.; Southam, G.

    2002-01-01

    Controlled microbial weathering of olivine experiments displays a unique style of nanoetching caused by biofilm attachment to mineral surfaces. We are investigating whether the morphology of biotic nanoetching can be used as a biosignature. Additional information is contained in the original extended abstract.

  16. Diazotrophic microbial mats

    NARCIS (Netherlands)

    Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

    2010-01-01

    Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically stra

  17. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  18. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    Science.gov (United States)

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213). Seagrasses ...

  19. Microbial keratitis in children.

    Science.gov (United States)

    Kunimoto, D Y; Sharma, S; Reddy, M K; Gopinathan, U; Jyothi, J; Miller, D; Rao, G N

    1998-02-01

    Microbial keratitis is a major cause of corneal blindness worldwide. This problem is particularly relevant to children, because most of their visual life is ahead of them, and they are uniquely at risk for irreversible ocular deficits, such as those resulting from amblyopia. The objective of this study was to determine the etiologic agents and predisposing factors in childhood infectious keratitis and to examine the outcome of treatment in terms of structure and visual acuity. The study design was a retrospective cases series. The authors studied 113 eyes in 107 children 16 years of age and younger who were treated for (nonviral) microbial keratitis at the LV Prasad Eye Institute in Hyderabad, India, during the 4.5-year period between February 1, 1991, and June 30, 1995. The patients who met the following criteria were included in the study: (1) corneal stromal infiltrate was present on slit-lamp examination; and (2) a corneal scraping was taken at the time of examination for suspected microbial keratitis. Etiologic micro-organisms, predisposing factors, treatment method, structural treatment outcome, and visual acuity treatment outcome of the infectious keratitis episode were measured. The principal predisposing factors identified in this study were trauma (21.2%), ocular disease (17.7%), systemic disease (15.9%), and prior penetrating keratoplasty in the same eye (8.8%). Vitamin A deficiency was an important factor within the category of severe systemic disease, and contact lens wear was not involved in any of the cases. A total of 85 organisms were isolated in cultures of corneal scrapings from 64 (56.6%) of the 113 cases. Staphylococcus species (43.7%), Streptococcus pneumoniae (18.8%), and fungi (17.2%) were the most common isolates. Eighteen eyes (15.9%) required surgery, and 28 (36.4%) of the 77 patients on whom visual acuity was assessed at last follow-up achieved an unaided visual acuity of 20/60 or better at last follow-up. This work represents the

  20. Computer aided microbial safety design of food processes.

    Science.gov (United States)

    Schellekens, M; Martens, T; Roberts, T A; Mackey, B M; Nicolaï, B M; Van Impe, J F; De Baerdemaeker, J

    1994-12-01

    To reduce the time required for product development, to avoid expensive experimental tests, and to quantify safety risks for fresh products and the consequence of processing there is a growing interest in computer aided food process design. This paper discusses the application of hybrid object-oriented and rule-based expert system technology to represent the data and knowledge of microbial experts and food engineers. Finite element models for heat transfer calculation routines, microbial growth and inactivation models and texture kinetics are combined with food composition data, thermophysical properties, process steps and expert knowledge on type and quantity of microbial contamination. A prototype system has been developed to evaluate changes in food composition, process steps and process parameters on microbiological safety and textual quality of foods.

  1. Submersible microbial fuel cell for electricity production from sewage sludge

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Olias, Lola Gonzalez; Kongjan, Prawit

    2010-01-01

    A submersible microbial fuel cell (SMFC) was utilized to treatment of sewage sludge and simultaneous generate electricity. Stable power generation (145±5 mW/m2) was produced continuously from raw sewage sludge for 5.5 days. The corresponding total chemical oxygen demand (TCOD) removal efficiency...

  2. PERN : An EU-Russia initiative for rhizosphere microbial resources

    NARCIS (Netherlands)

    Declerck, Stéphane; Willems, Anne; van der Heijden, Marcel G A; Varese, Giovanna Cristina; Turkovskaya, Olga; Evtushenko, Lyudmila; Ivshina, Irena; Desmeth, Philippe

    2015-01-01

    Millions of microbial taxa inhabit the rhizosphere and could be used as biofertilizers, biopesticides, and/or for bioremediation. Only a fraction of these microbes have been described and/or are being utilized. Most are dispersed in collections, but coordination of their accessibility and availabili

  3. Submersible microbial fuel cell for electricity production from sewage sludge

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Olias, Lola Gonzalez; Kongjan, Prawit;

    2011-01-01

    A submersible microbial fuel cell (SMFC) was utilized to treat sewage sludge and simultaneously generate electricity. Stable power generation (145± 5 mW/m2, 470 Ω) was produced continuously from raw sewage sludge for 5.5 days. The maximum power density reached 190±5 mW/m2. The corresponding total...

  4. A Metagenomic Analysis of Microbial Contamination in Aviation Fuels

    Science.gov (United States)

    2009-03-01

    microbial growth at phase interfaces (liquid-liquid, liquid-solid, liquid-gas, and so forth) (ASTM, 1999). Biosurfactant , n. — A surface-active...toxic and biodegradable. Biosurfactants enhance the emulsification of hydrocarbons, have the potential to solubilize hydrocarbon contaminants and...utilize secreted biosurfactants to solubilize the alkanes prior to metabolizing them (Rauch, 2008). Unfortunately, the biosurfactants have deleterious

  5. Microbial transglutaminase displays broad acyl-acceptor substrate specificity

    DEFF Research Database (Denmark)

    T. Gundersen, Maria; Keillor, Jeffrey W.; Pelletier, Joelle N.

    2013-01-01

    The great importance of amide bonds in industrial synthesis has encouraged the search for efficient catalysts of amide bond formation. Microbial transglutaminase (MTG) is heavily utilized in crosslinking proteins in the food and textile industries, where the side chain of a glutamine reacts...

  6. A Bayesian approach to simultaneously quantify assignments and linguistic uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Chavez, Gregory M [Los Alamos National Laboratory; Booker, Jane M [BOOKER SCIENTIFIC FREDERICKSBURG; Ross, Timothy J [UNM

    2010-10-07

    Subject matter expert assessments can include both assignment and linguistic uncertainty. This paper examines assessments containing linguistic uncertainty associated with a qualitative description of a specific state of interest and the assignment uncertainty associated with assigning a qualitative value to that state. A Bayesian approach is examined to simultaneously quantify both assignment and linguistic uncertainty in the posterior probability. The approach is applied to a simplified damage assessment model involving both assignment and linguistic uncertainty. The utility of the approach and the conditions under which the approach is feasible are examined and identified.

  7. Microbial Life in Soil - Linking Biophysical Models with Observations

    Science.gov (United States)

    Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

    2015-04-01

    Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

  8. Hydrodynamics of microbial filter feeding

    DEFF Research Database (Denmark)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia

    2017-01-01

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequat...... predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling....

  9. Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities*

    Science.gov (United States)

    Pan, Chongle; Fischer, Curt R.; Hyatt, Doug; Bowen, Benjamin P.; Hettich, Robert L.; Banfield, Jillian F.

    2011-01-01

    Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, ∼50%, and ∼98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13C or 15N in microbial communities. PMID:21285414

  10. The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

    Science.gov (United States)

    Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

    2011-12-01

    Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

  11. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    Science.gov (United States)

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

  12. Responses of soil microbial community to experimental warming and precipitation manipulation

    Science.gov (United States)

    Li, G.; Kim, S.; Park, M. J.; Han, S. H.; Lee, J.; Son, Y.

    2015-12-01

    An experimental nursery was established with two-year-old Pinus densiflora seedlings at Korea University to study soil microbial community responses to air warming (+3°C) and precipitation manipulation (-30% and +30%). Soil samplings were collected monthly from July to November, 2014. Substrate utilization profile of microbial community was examined using BIOLOG EcoPlate. Microbial community composition was assessed by high-throughput sequencing technology. The results showed that warming significantly affected the substrate utilization profile of microbial community (P0.05). In contrast, compared with unwarmed and precipitation control treatment, the bacterial community richness in the others were increased, but community abundance and diversity in those treatments were decreased (all P>0.05). These changes in microbial community structure resulted in the changes in community functional composition, which microbial metabolic functions were higher in warming plots than unwarmed plots. Since microorganisms differ in their susceptibility to stressors, changes in the soil environment affect the microbial community. Therefore, the results indicated that effects of warming and precipitation manipulation on soil microbial community might be related to warming and precipitation manipulation-induced changes in soil moisture. We suggested that shifts in the microbial community may be important implications for soil carbon and nitrogen dynamics in a warmer world. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

  13. Palygorskite changes heavy metal bioavailability and microbial functional diversity in sewage sludge composting.

    Science.gov (United States)

    Liu, Siying; Liu, Jia; Zhao, Juanjuan; Xia, Dongsheng; Pan, Fei; Liu, Ci; Kyzas, George Z; Fu, Jie

    2015-01-01

    To investigate the effects of palygorskite on chemical forms of heavy metal and microbial functional diversity in the sewage sludge composting, a compost matrix of sewage sludge, wheat straw and varying contents of palygorskite were inoculated with the compound microbial preparation. The chemical speciation analysis by a Community Bureau of Reference-sequential extraction indicated the contribution of palygorskite to reduce the bioavailability of a model metal, Cu, during the composting process. The Biolog EcoPlate(TM) test revealed that the microbial community showed better capability of utilizing complex macro-molecules (such as miscellaneous and polymers) in the presence of palygorskite. Increasing the palygorskite contents from 1% to 5%, the microbial activity showed an increasing tendency. However, continuously increasing the palygorskite resulted in a decline of the microbial metabolism. Therefore, appropriate content of palygorskite is an ideal additive for composting, not only enhancing the microbial activity, but also reducing the metal toxicity.

  14. Soil microbial and physical properties and their relations along a steep copper gradient

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Møldrup, Per; Holmstrup, Martin

    2012-01-01

    years; from background concentrations up to 3837 mg Cu kg–1) on soil microbial enzyme activity, physical properties and resilience to compression. Soil samples and cores were taken from a fallow sandy loam field in Denmark. Microbial activity was quantified using fluorescein diacetate (FDA......) and dehydrogenase (DHA) assays. Water dispersible clay was measured on field moist and air dried samples. For the resilience assay, soil cores (drained to –100 hPa) were subjected to uniaxial confined compression (200 kPa) followed by wet–dry or freeze–thaw cycles. Microbial enzyme activity significantly decreased...

  15. Quantifying the tensile strength of microbial mats grown over noncohesive sediments.

    Science.gov (United States)

    Vignaga, E; Haynes, H; Sloan, W T

    2012-05-01

    Biofilms in marine and fluvial environments can comprise strong bacterial and diatom mats covering large areas of the bed and act to bind sediments. In this case the bed material becomes highly resistant to shear stresses applied by the overlying fluid motion and detachment, when it does occur, is manifest in patches of biofilm of the order cm(2) being entrained into the flow. This article is the first to report tensile test data specific to the centimeter scale using moist biofilm/sediment composite materials; the strain (ε)-stress (σ) relationships permit quantification of the elasticity (Young's modulus, E) and cohesive strength of each specimen. Specifically, we compare the mechanical strength of cyanobacterial biofilm-only samples to that of biofilm cultured over sediment samples (glass beads or natural sands of d ~ 1 mm) for up to 8 weeks. The range of tensile strength (1,288-3,283 Pa) for composite materials was up to three times higher than previous tensile tests conducted at smaller scale on mixed culture biofilm [Ohashi et al. (1999) Water Sci Technol 39:261-268], yet of similar range to cohesive strength values recorded on return activated sludge flocs [RAS; Poppele and Hozalski (2003) J Microbiol Methods 55:607-615]. Composite materials were 3-6 times weaker than biofilm-only samples, indicating that adhesion to sediment grains is weaker than cohesion within the biofilm. Furthermore, in order to relate the tensile test results to the more common in-situ failure of bio-mats due to shear flow, controlled erosion experiments were conducted in a hydraulic flume with live fluid flow. Here, the fluid shear stress causing erosion was 3 orders of magnitude lower than tensile stress; this highlights both the problem of interpreting material properties measured ex-situ and the need for a better mechanistic model of bio-mat detachment.

  16. Impact of microbial distributions on food safety II. Quantifying impacts on public health and sampling

    NARCIS (Netherlands)

    Jongenburger, I.; Bassett, J.; Jackson, T.; Gorris, L.G.M.; Jewell, K.; Zwietering, M.H.

    2012-01-01

    The distributions of microorganisms in foods impact the likelihood that a foodstuff will cause illness and therefore also impact the consequential public health burden. As part of food safety management systems, food is sampled and microbiologically tested. The effectiveness of the sampling programm

  17. Quantifying Enhanced Microbial Dehalogenation Impacting the Fate and Transport of Organohalide Mixtures in Contaminated Sediments

    Science.gov (United States)

    2012-02-01

    Marsh mesocosms also including 25 mm of bentonite clay beneath the sediment layer to aid in core sample recovery. Depending on the treatment...analysis (41% sand: 39% silt: 20% clay ) were determined by the Rutgers University Soils Testing Laboratory. Microcosms were prepared using 200 mL site...approximately 200 mm (final settled thickness) of 72 Dimensions in mm Site Water AquaBlok Sediment (treated) Sediment (untreated) Bentonite Rhizon pore water

  18. Degradation of microbial polyesters.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P

    2004-08-01

    Microbial polyhydroxyalkanoates (PHAs), one of the largest groups of thermoplastic polyesters are receiving much attention as biodegradable substitutes for non-degradable plastics. Poly(D-3-hydroxybutyrate) (PHB) is the most ubiquitous and most intensively studied PHA. Microorganisms degrading these polyesters are widely distributed in various environments. Although various PHB-degrading microorganisms and PHB depolymerases have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. Distributions of PHB-degrading microorganisms, factors affecting the biodegradability of PHB, and microbial and enzymatic degradation of PHB are discussed in this review. We also propose an application of a new isolated, thermophilic PHB-degrading microorganism, Streptomyces strain MG, for producing pure monomers of PHA and useful chemicals, including D-3-hydroxycarboxylic acids such as D-3-hydroxybutyric acid, by enzymatic degradation of PHB.

  19. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1992-03-01

    The objective of this project is to perform a microbial enhanced oil recovery field pilot in the Southeast Vassar Vertz Sand Unit (SEVVSU) in Payne County, Oklahoma. Indigenous, anaerobic, nitrate reducing bacteria will be stimulated to selectively plug flow paths which have been referentially swept by a prior waterflood. This will force future flood water to invade bypassed regions of the reservoir and increase sweep efficiency. This report covers progress made during the second year, January 1, 1990 to December 31, 1990, of the Microbial Field Pilot Study project. Information on reservoir ecology, surface facilities design, operation of the unit, core experiments, modeling of microbial processes, and reservoir characterization and simulation are presented in the report. To better understand the ecology of the target reservoir, additional analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. The results of the produced and injected water analysis show increasing sulfide concentrations with respect to time. In March of 1990 Mesa Limited Partnership sold their interest in the SEVVSU to Sullivan and Company. In April, Sullivan and Company assumed operation of the field. The facilities for the field operation of the pilot were refined and implementation was begun. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. The experiments were performed at SEVVSU temperature using fluids and inoculum from the unit. The model described in last year's report was further validated using results from a core flood experiment. The model was able to simulate the results of one of the core flood experiments with good quality.

  20. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1992-03-01

    The objective of this project is to perform a microbial enhanced oil recovery field pilot in the Southeast Vassar Vertz Sand Unit (SEVVSU) in Payne County, Oklahoma. Indigenous, anaerobic, nitrate reducing bacteria will be stimulated to selectively plug flow paths which have been referentially swept by a prior waterflood. This will force future flood water to invade bypassed regions of the reservoir and increase sweep efficiency. This report covers progress made during the second year, January 1, 1990 to December 31, 1990, of the Microbial Field Pilot Study project. Information on reservoir ecology, surface facilities design, operation of the unit, core experiments, modeling of microbial processes, and reservoir characterization and simulation are presented in the report. To better understand the ecology of the target reservoir, additional analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. The results of the produced and injected water analysis show increasing sulfide concentrations with respect to time. In March of 1990 Mesa Limited Partnership sold their interest in the SEVVSU to Sullivan and Company. In April, Sullivan and Company assumed operation of the field. The facilities for the field operation of the pilot were refined and implementation was begun. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. The experiments were performed at SEVVSU temperature using fluids and inoculum from the unit. The model described in last year`s report was further validated using results from a core flood experiment. The model was able to simulate the results of one of the core flood experiments with good quality.

  1. Forum of Microbial Threats

    Science.gov (United States)

    2011-06-01

    and ―disease‖. Studies on leafcutter ants have revealed a complex web of symbiotic interactions, among ants, bacteria , and fungi that are associated...strains of bacteria and viruses are treatable with only a single drug, and some no longer have effective treatments. The disease burden from multi...microbes have played in driving adaptation and evolution of organisms. To date, most microbiome or microbial ecology studies have focused on bacteria

  2. Microbial desulfurization of coal

    Energy Technology Data Exchange (ETDEWEB)

    Danzet, C.; Buonfiglio, V.; Polidoro, M.; Valenti, P. (Rome Univ. La Sapienza (Italy). Ist. di Microbiologia)

    This paper reviews the biochemical and economics aspects of coal desulfurization processes involving the use of thermophile microorganisms such as sulfolobus, currently believed to be the the only type of microorganism capable of degrading both inorganic (pyrite-containing) and organic sulfur compounds. Comments are also made on the feasibility of the development of an in-lab, microbial based method for the transformation of the lignin component, obtained in the processing, by anaerobic fermentation, of lignocellulosic biomass, into humic acid.

  3. Quantifying drug-protein binding in vivo.

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B; Bench, G; Keating III, G; Palmblad, M; Vogel, J; Grant, P G; Hillegonds, D

    2004-02-17

    Accelerator mass spectrometry (AMS) provides precise quantitation of isotope labeled compounds that are bound to biological macromolecules such as DNA or proteins. The sensitivity is high enough to allow for sub-pharmacological (''micro-'') dosing to determine macromolecular targets without inducing toxicities or altering the system under study, whether it is healthy or diseased. We demonstrated an application of AMS in quantifying the physiologic effects of one dosed chemical compound upon the binding level of another compound in vivo at sub-toxic doses [4].We are using tissues left from this study to develop protocols for quantifying specific binding to isolated and identified proteins. We also developed a new technique to quantify nanogram to milligram amounts of isolated protein at precisions that are comparable to those for quantifying the bound compound by AMS.

  4. Impact of diverse soil microbial communities on crop residues decomposition

    Science.gov (United States)

    Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

    2017-04-01

    Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N

  5. Microbial reduction of iodate

    Science.gov (United States)

    Councell, T.B.; Landa, E.R.; Lovley, D.R.

    1997-01-01

    The different oxidation species of iodine have markedly different sorption properties. Hence, changes in iodine redox states can greatly affect the mobility of iodine in the environment. Although a major microbial role has been suggested in the past to account for these redox changes, little has been done to elucidate the responsible microorganisms or the mechanisms involved. In the work presented here, direct microbial reduction of iodate was demonstrated with anaerobic cell suspensions of the sulfate reducing bacterium Desulfovibrio desulfuricans which reduced 96% of an initial 100 ??M iodate to iodide at pH 7 in 30 mM NaHCO3 buffer, whereas anaerobic cell suspensions of the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens were unable to reduce iodate in 30 mM NaHCO3 buffer (pH 7). Both D. desulfuricans and S. putrefaciens were able to reduce iodate at pH 7 in 10 mM HEPES buffer. Both soluble ferrous iron and sulfide, as well as iron monosulfide (FeS) were shown to abiologically reduce iodate to iodide. These results indicate that ferric iron and/or sulfate reducing bacteria are capable of mediating both direct, enzymatic, as well as abiotic reduction of iodate in natural anaerobic environments. These microbially mediated reactions may be important factors in the fate and transport of 129I in natural systems.

  6. Advances in microbial amylases.

    Science.gov (United States)

    Pandey, A; Nigam, P; Soccol, C R; Soccol, V T; Singh, D; Mohan, R

    2000-04-01

    This review makes a comprehensive survey of microbial amylases, i.e. alpha-amylase, beta-amylase and glucoamylase. Amylases are among the most important enzymes and are of great significance in present-day biotechnology. Although they can be derived from several sources, such as plants, animals and micro-organisms, the enzymes from microbial sources generally meet industrial demands. Microbial amylases could be potentially useful in the pharmaceutical and fine-chemical industries if enzymes with suitable properties could be prepared. With the advent of new frontiers in biotechnology, the spectrum of amylase application has widened in many other fields, such as clinical, medicinal and analytical chemistries, as well as their widespread application in starch saccharification and in the textile, food, brewing and distilling industries. In this review, after a brief description of the sources of amylases, we discuss the molecular biology of amylases, describing structures, cloning, sequences, and protoplast fusion and mutagenesis. This is followed by sections on their production and finally the properties of various amylases.

  7. Microbial biosurfactants and biodegradation.

    Science.gov (United States)

    Ward, Owen P

    2010-01-01

    Microbial biosurfactants are amphipathic molecules having typical molecular weights of 500-1500 Da, made up of peptides, saccharides or lipids or their combinations. In biodegradation processes they mediate solubilisation, mobilization and/or accession of hydrophobic substrates to microbes. They may be located on the cell surface or be secreted into the extracellular medium and they facilitate uptake of hydrophobic molecules through direct cellular contact with hydrophobic solids or droplets or through micellarisation. They are also involved in cell physiological processes such as biofilm formation and detachment, and in diverse biofilm associated processes such as wastewater treatment and microbial pathogenesis. The protection of contaminants in biosurfactants micelles may also inhibit uptake of contaminants by microbes. In bioremediation processes biosurfactants may facilitate release of contaminants from soil, but soils also tend to bind surfactants strongly which makes their role in contaminant desorption more complex. A greater understanding of the underlying roles played by biosurfactants in microbial physiology and in biodegradative processes is developing through advances in cell and molecular biology.

  8. Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH)

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2015-01-01

    Microautoradiography (MAR) in combination with fluorescence in situ hybridization (FISH) is a powerful method of obtaining information about the ecophysiology of probe-defined single cells in mixed microbial communities. The incorporation of radiolabelled substrates can be quantified by automated...

  9. Batteryless, wireless sensor powered by a sediment microbial fuel cell.

    Science.gov (United States)

    Donovan, Conrad; Dewan, Alim; Heo, Deukhyoun; Beyenal, Haluk

    2008-11-15

    Sediment microbial fuel cells (SMFCs) are considered to be an alternative renewable power source for remote monitoring. There are two main challenges to using SMFCs as power sources: 1) a SMFC produces a low potential at which most sensor electronics do not operate, and 2) a SMFC cannot provide continuous power, so energy from the SMFC must be stored and then used to repower sensor electronics intermittently. In this study, we developed a SMFC and a power management system (PMS) to power a batteryless, wireless sensor. A SMFC operating with a microbial anode and cathode, located in the Palouse River, Pullman, Washington, U.S.A., was used to demonstrate the utility of the developed system. The designed PMS stored microbial energy and then started powering the wireless sensor when the SMFC potential reached 320 mV. It continued powering until the SMFC potential dropped below 52 mV. The system was repowered when the SMFC potential increased to 320 mV, and this repowering continued as long as microbial reactions continued. We demonstrated that a microbial fuel cell with a microbial anode and cathode can be used as an effective renewable power source for remote monitoring using custom-designed electronics.

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

    Science.gov (United States)

    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 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.

  11. Allelopathy-mediated competition in microbial mats from Antarctic lakes.

    Science.gov (United States)

    Slattery, Marc; Lesser, Michael P

    2017-05-01

    Microbial mats are vertically stratified communities that host a complex consortium of microorganisms, dominated by cyanobacteria, which compete for available nutrients and environmental niches, within these extreme habitats. The Antarctic Dry Valleys near McMurdo Sound include a series of lakes within the drainage basin that are bisected by glacial traverses. These lakes are traditionally independent, but recent increases in glacial melting have allowed two lakes (Chad and Hoare) to become connected by a meltwater stream. Microbial mats were collected from these lakes, and cultured under identical conditions at the McMurdo Station laboratory. Replicate pairings of the microbial mats exhibited consistent patterns of growth inhibition indicative of competitive dominance. Natural products were extracted from the microbial mats, and a disk diffusion assay was utilized to show that allelochemical compounds mediate competitive interactions. Both microscopy and 16S rRNA sequencing show that these mats contain significant populations of cyanobacteria known to produce allelochemicals. Two compounds were isolated from these microbial mats that might be important in the chemical ecology of these psychrophiles. In other disk:mat pairings, including extract versus mat of origin, the allelochemicals exhibited no effect. Taken together, these results indicate that Antarctic lake microbial mats can compete via allelopathy. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Ecofunctional enzymes of microbial communities in ground water.

    Science.gov (United States)

    Fliermans, C B; Franck, M M; Hazen, T C; Gorden, R W

    1997-07-01

    Biolog technology was initially developed as a rapid, broad spectrum method for the biochemical identification of clinical microorganisms. Demand and creative application of this technology has resulted in the development of Biolog plates for Gram-negative and Gram-positive bacteria, for yeast and Lactobacillus sp. Microbial ecologists have extended the use of these plates from the identification of pure culture isolates to a tool for quantifying the metabolic patterns of mixed cultures, consortia and entire microbial communities. Patterns that develop on Biolog microplates are a result of the oxidation of the substrates by microorganisms in the inoculum and the subsequent reduction of the tetrazolium dye to form a color in response to detectable reactions. Depending upon the functional enzymes present in the isolate or community one of a possible 4 x 10(28) patterns can be expressed. The patterns were used to distinguish the physiological ecology of various microbial communities present in remediated groundwater. The data indicate that one can observe differences in the microbial community among treatments of bioventing, 1% and 4% methane injection, and pulse injection of air, methane and nutrients both between and among wells. The investigation indicates that Biolog technology is a useful parameter to measure the physiological response of the microbial community to perturbation and allows one to design enhancement techniques to further the degradation of selected recalcitrant and toxic chemicals. Further it allows one to evaluate the recovery of the microbial subsurface ecosystem after the perturbations have ceased. We propose the term 'ecofunctional enzymes' (EFE) as the most descriptive and useful term for the Biolog plate patterns generated by microbial communities. We offer this designation and provide ecological application in an attempt to standardize the terminology for this relatively new and unique technology.

  13. Investigating the role for adaptation of the microbial community to transform trace organic chemicals during managed aquifer recharge

    KAUST Repository

    Alidina, Mazahirali

    2014-06-01

    This study was undertaken to investigate whether adaptation by pre-exposure to trace organic chemicals (TOrCs) was necessary for microbial transformation during managed aquifer recharge (MAR). Two pairs of laboratory-scale soil columns, each receiving a different primary substrate, were utilized to simulate the dominant bulk organic carbon present in MAR systems receiving wastewater effluent of varying quality and having undergone different degrees of pre-treatment, as well as organic carbon prevalent at different stages of subsurface travel. Each pair of columns consisted of duplicate set-ups receiving the same feed solution with only one pre-exposed to a suite of eight TOrCs for approximately ten months. Following the pre-exposure period, a spiking experiment was conducted in which the non-exposed columns also received the same suite of TOrCs. TOrC attenuation was quantified for the pre- and non-exposed columns of each pair during the spiking experiment. The microbial community structure and function of these systems were characterized by pyrosequencing of 16S rRNA gene and metagenomics, respectively. Biotransformation rather than sorption was identified as the dominant removal mechanism for almost all the TOrCs (except triclocarban). Similar removal efficiencies were observed between pre-exposed and non-exposed columns for most TOrCs. No obvious differences in microbial community structure were revealed between pre- and non-exposed columns. Using metagenomics, biotransformation capacity potentials of the microbial community present were also similar between pre- and non-exposed columns of each pair. Overall, the pre-exposure of MAR systems to TOrCs at ng/L levels did not affect their attenuation and had no obvious influence on the resulting microbial community structure and function. Thus, other factors such as bioavailability of the primary substrate play a greater role regarding biotransformation of TOrCs. These results indicate that MAR systems adapted to a

  14. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  15. Hydrogen utilization potential in subsurface sediments

    Directory of Open Access Journals (Sweden)

    Rishi Ram Adhikari

    2016-01-01

    Full Text Available Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific and Gulf of Mexico with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material.We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i increasing importance of fermentation in successively deeper biogeochemical zones and (ii adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones.

  16. Quantifying renewable groundwater stress with GRACE

    Science.gov (United States)

    Richey, Alexandra S.; Thomas, Brian F.; Lo, Min‐Hui; Reager, John T.; Voss, Katalyn; Swenson, Sean; Rodell, Matthew

    2015-01-01

    Abstract Groundwater is an increasingly important water supply source globally. Understanding the amount of groundwater used versus the volume available is crucial to evaluate future water availability. We present a groundwater stress assessment to quantify the relationship between groundwater use and availability in the world's 37 largest aquifer systems. We quantify stress according to a ratio of groundwater use to availability, which we call the Renewable Groundwater Stress ratio. The impact of quantifying groundwater use based on nationally reported groundwater withdrawal statistics is compared to a novel approach to quantify use based on remote sensing observations from the Gravity Recovery and Climate Experiment (GRACE) satellite mission. Four characteristic stress regimes are defined: Overstressed, Variable Stress, Human‐dominated Stress, and Unstressed. The regimes are a function of the sign of use (positive or negative) and the sign of groundwater availability, defined as mean annual recharge. The ability to mitigate and adapt to stressed conditions, where use exceeds sustainable water availability, is a function of economic capacity and land use patterns. Therefore, we qualitatively explore the relationship between stress and anthropogenic biomes. We find that estimates of groundwater stress based on withdrawal statistics are unable to capture the range of characteristic stress regimes, especially in regions dominated by sparsely populated biome types with limited cropland. GRACE‐based estimates of use and stress can holistically quantify the impact of groundwater use on stress, resulting in both greater magnitudes of stress and more variability of stress between regions. PMID:26900185

  17. Statistical Considerations in Environmental Microbial Forensics.

    Science.gov (United States)

    McBride, Graham; Gilpin, Brent

    2016-08-01

    In environmental microbial forensics, as in other pursuits, statistical calculations are sometimes inappropriately applied, giving rise to the appearance of support for a particular conclusion or failing to support an innately obvious conclusion. This is a reflection of issues related to dealing with sample sizes, the methodologies involved, and the difficulty of communicating uncertainties. In this brief review, we attempt to illustrate ways to minimize such problems. In doing so, we consider one of the most common applications of environmental microbial forensics-the use of genotyping in food and water and disease investigations. We explore three important questions. (i) Do hypothesis tests' P values serve as adequate metrics of evidence? (ii) How can we quantify the value of the evidence? (iii) Can we turn a value-of-evidence metric into attribution probabilities? Our general conclusions are as follows. (i) P values have the unfortunate property of regularly detecting trivial effects when sample sizes are large. (ii) Likelihood ratios, rather than any kind of probability, are the better strength-of-evidence metric, addressing the question "what do these data say?" (iii) Attribution probabilities, addressing the question "what should I believe?," can be calculated using Bayesian methods, relying in part on likelihood ratios but also invoking prior beliefs which therefore can be quite subjective. In legal settings a Bayesian analysis may be required, but the choice and sensitivity of prior assumptions should be made clear.

  18. Applying landscape genetics to the microbial world.

    Science.gov (United States)

    Dudaniec, Rachael Y; Tesson, Sylvie V M

    2016-07-01

    Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro- and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro- and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.

  19. Microbial Activity and Silica Degradation in Rice Straw

    Science.gov (United States)

    Kim, Esther Jin-kyung

    Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

  20. Microbial field pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Coates, J.D.; Chisholm, J.L.

    1993-05-01

    A multi-well microbially enhanced oil recovery field pilot has been performed in the Southeast Vassar Vertz Sand Unit in Payne County, Oklahoma. The primary emphasis of the experiment was preferential plugging of high permeability zones for the purpose of improving waterflood sweep efficiency. Studies were performed to determine reservoir chemistry, ecology, and indigenous bacteria populations. Growth experiments were used to select a nutrient system compatible with the reservoir that encouraged growth of a group of indigenous nitrate-using bacteria and inhibit growth of sulfate-reducing bacteria. A specific field pilot area behind an active line drive waterflood was selected. Surface facilities were designed and installed. Injection protocols of bulk nutrient materials were prepared to facilitate uniform distribution of nutrients within the pilot area. By the end of December, 1991, 82.5 tons (75.0 tonnes) of nutrients had been injected in the field. A tracer test identified significant heterogeneity in the SEVVSU and made it necessary to monitor additional production wells in the field. The tracer tests and changes in production behavior indicate the additional production wells monitored during the field trial were also affected. Eighty two and one half barrels (13.1 m[sup 3]) of tertiary oil have been recovered. Microbial activity has increased CO[sub 2] content as indicated by increased alkalinity. A temporary rise in sulfide concentration was experienced. These indicate an active microbial community was generated in the field by the nutrient injection. Pilot area interwell pressure interference test results showed that significant permeability reduction occurred. The interwell permeabilities in the pilot area between the injector and the three pilot production wells were made more uniform which indicates a successful preferential plugging enhanced oil recovery project.

  1. Submersible microbial fuel cell sensor for monitoring microbial activity and BOD in groundwater: Focusing on impact of anodic biofilm on sensor applicability

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Angelidaki, Irini

    2011-01-01

    A sensor, based on a submersible microbial fuel cell (SUMFC), was developed for in situ monitoring of microbial activity and biochemical oxygen demand (BOD) in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Fresh anode...... was required for application of the sensor for microbial activity measurement, while biofilm‐colonized anode was needed for utilizing the sensor for BOD content measurement. The current density of SUMFC sensor equipped with a biofilm‐colonized anode showed linear relationship with BOD content, to up to 250 mg...

  2. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Directory of Open Access Journals (Sweden)

    Peter Larsen

    Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  3. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Science.gov (United States)

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  4. Quantifying robustness of biochemical network models

    Directory of Open Access Journals (Sweden)

    Iglesias Pablo A

    2002-12-01

    Full Text Available Abstract Background Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robustness are needed. Results Two techniques for describing quantitatively the robustness of an oscillatory model were presented and contrasted. Single-parameter bifurcation analysis was used to evaluate the stability robustness of the limit cycle oscillation as well as the frequency and amplitude of oscillations. A tool from control engineering – the structural singular value (SSV – was used to quantify robust stability of the limit cycle. Using SSV analysis, we find very poor robustness when the model's parameters are allowed to vary. Conclusion The results show the usefulness of incorporating SSV analysis to single parameter sensitivity analysis to quantify robustness.

  5. [Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

    Science.gov (United States)

    Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

    2011-04-01

    In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

  6. Adherence and viability of intestinal bacteria to differentiated Caco-2 cells quantified by flow cytometry.

    Science.gov (United States)

    Grootaert, Charlotte; Boon, Nico; Zeka, Fjoralba; Vanhoecke, Barbara; Bracke, Marc; Verstraete, Willy; Van de Wiele, Tom

    2011-07-01

    Recent developments in host-microbe research give rise to a growing demand for rapid and accurate methods to quantify bacterial adhesion to epithelial cells. Here, we describe a new flow cytometric method to determine the amount and viability of gut bacteria, adhered to a monolayer of differentiated cells. The latter is a more relevant epithelium model than the suspended eukaryotic cells currently used in flow cytometric protocols. During the development of the method, we monitored the adhesion potential of six bacterial species and an intestinal microbial community to Caco-2 cells. The combination of SYBR Green I/propidium iodide was more efficient than carboxyfluorescein diacetate to stain the bacterial cells. In addition, a better separation between the Caco-2 background signal and viable and dead bacteria was obtained. A precise amount of Triton X-100 was used to detach adhered bacteria from Caco-2 cells and cell debris. Yet, a limited decrease in viability was observed for the intestinal microbial community treated with Triton X-100. The flow cytometric lower detection limit for pure bacterial cultures was 3.0-4.0log/mL, whereas a 5.0-5.5log/mL detection limit was obtained in the presence of Caco-2 cell background. The latter was sufficient to quantify adhered bacteria. To the best of our knowledge, this is the first description of a flow cytometric protocol that quantifies adhesion of both pure and mixed gut microbial cultures to a differentiated monolayer of Caco-2 cells and that allows to distinguish between viable and dead adhered bacteria.

  7. Soil microbial biomass and function are altered by 12 years of crop rotation

    Science.gov (United States)

    McDaniel, Marshall D.; Grandy, A. Stuart

    2016-11-01

    Declines in plant diversity will likely reduce soil microbial biomass, alter microbial functions, and threaten the provisioning of soil ecosystem services. We examined whether increasing temporal plant biodiversity in agroecosystems (by rotating crops) can partially reverse these trends and enhance soil microbial biomass and function. We quantified seasonal patterns in soil microbial biomass, respiration rates, extracellular enzyme activity, and catabolic potential three times over one growing season in a 12-year crop rotation study at the W. K. Kellogg Biological Station LTER. Rotation treatments varied from one to five crops in a 3-year rotation cycle, but all soils were sampled under a corn year. We hypothesized that crop diversity would increase microbial biomass, activity, and catabolic evenness (a measure of functional diversity). Inorganic N, the stoichiometry of microbial biomass and dissolved organic C and N varied seasonally, likely reflecting fluctuations in soil resources during the growing season. Soils from biodiverse cropping systems increased microbial biomass C by 28-112 % and N by 18-58 % compared to low-diversity systems. Rotations increased potential C mineralization by as much as 53 %, and potential N mineralization by 72 %, and both were related to substantially higher hydrolase and lower oxidase enzyme activities. The catabolic potential of the soil microbial community showed no, or slightly lower, catabolic evenness in more diverse rotations. However, the catabolic potential indicated that soil microbial communities were functionally distinct, and microbes from monoculture corn preferentially used simple substrates like carboxylic acids, relative to more diverse cropping systems. By isolating plant biodiversity from differences in fertilization and tillage, our study illustrates that crop biodiversity has overarching effects on soil microbial biomass and function that last throughout the growing season. In simplified agricultural systems

  8. Microbial response to triepthylphosphate

    Energy Technology Data Exchange (ETDEWEB)

    Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

    1997-05-01

    The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior to the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.

  9. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-12-23

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

  10. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  11. Microbial interactions during carrion decomposition

    Science.gov (United States)

    This addresses the microbial ecology of carrion decomposition in the age of metagenomics. It describes what is known about the microbial communities on carrion, including a brief synopsis about the communities on other organic matter sources. It provides a description of studies using state-of-the...

  12. Web Resources for Microbial Data

    Institute of Scientific and Technical Information of China (English)

    Qinglan Sun; Li Liu; Linhuan Wu; Wei Li; Quanhe Liu; Jianyuan Zhang; Di Liug; Juncai Ma

    2015-01-01

    There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.

  13. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  14. Microbial conversions of nitrogenous heterocycles

    OpenAIRE

    Parshikov, Igor A

    2015-01-01

    The monography describes examples of the application of microbial technologies for obtaining of derivatives from a series of nitrogen heterocycles (saturated nitrogen heterocycles, azaarenes and quinolones). It is proposed alternative ways for synthesize substances that are difficult to obtain by the methods of organic chemistry. Microbial technologies of synthesis of organic compounds may find out a practical application in the production of various drugs.

  15. A microbial world within us

    NARCIS (Netherlands)

    Zoetendal, E.G.; Vaughan, E.E.; Vos, de W.M.

    2006-01-01

    The microbial world within us includes a vast array of gastrointestinal (GI) tract communities that play an important role in health and disease. Significant progress has been made in recent years in describing the intestinal microbial composition based on the application of 16S ribosomal RNA (rRNA)

  16. Links between pseudometallophytes and rhizosphere microbial communities in a metalliferous soil

    NARCIS (Netherlands)

    Epelde, L.; Becerril, J.M.; Blanco, F.; Kowalchuk, G.A.; Garbisu, C.

    2012-01-01

    Short-term improvements in soil health derived from pseudometallophytes growth and metal phytoremediation were quantified based upon specific microbial properties of potential value as bioindicators of soil functioning. To this aim, plant consortia, consisting of 1-3 pseudometallophytes with differe

  17. A quantitative microbial risk assessment for meatborne Toxoplasma gondii infection in The Netherlands

    NARCIS (Netherlands)

    Opsteegh, M.; Prickaerts, S.; Frankena, K.; Evers, E.G.

    2011-01-01

    Toxoplasma gondii is an important foodborne pathogen, and the cause of a high disease burden due to congenital toxoplasmosis in The Netherlands. The aim of this study was to quantify the relative contribution of sheep, beef and pork products to human T. gondii infections by Quantitative Microbial Ri

  18. Tracer experiment and model evidence for macrofaunal shaping of microbial nitrogen functions along rocky shores

    Science.gov (United States)

    Pfister, Catherine A.; Altabet, Mark A.; Pather, Santhiska; Dwyer, Greg

    2016-06-01

    Seawater microbes as well as those associated with macrobiota are increasingly recognized as a key feature affecting nutrient cycling. Tidepools are ideal natural mesocosms to test macrofauna and microbe interactions, and we quantified rates of microbial nitrogen processing using tracer enrichment of ammonium (15NNH4) or nitrate (15NNO3) when tidepools were isolated from the ocean during low intertidal periods. Experiments were conducted during both day and night as well as in control tidepools and those from which mussels had been removed, allowing us to determine the role of both mussels and daylight in microbial nitrogen processing. We paired time series observations of 15N enrichment in NH4+, NO2- and NO3- with a differential equation model to quantify multiple, simultaneous nitrogen transformations. Mussel presence and daylight increased remineralization and photosynthetic nitrogen uptake. When we compared ammonium gain or loss that was attributed to any tidepool microbes vs. photosynthetic uptake, microbes accounted for 32 % of this ammonium flux on average. Microbial transformations averaged 61 % of total nitrate use; thus, microbial activity was almost 3 times that of photosynthetic nitrate uptake. Because it accounted for processes that diluted our tracer, our differential equation model assigned higher rates of nitrogen processing compared to prior source-product models. Our in situ experiments showed that animals alone elevate microbial nitrogen transformations by 2 orders of magnitude, suggesting that coastal macrobiota are key players in complex microbial nitrogen transformations.

  19. Switchgrass ecotypes alter microbial contribution to deep-soil C

    Science.gov (United States)

    Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

    2016-05-01

    Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

  20. Quantifying brain microstructure with diffusion MRI

    DEFF Research Database (Denmark)

    Novikov, Dmitry S.; Jespersen, Sune N.; Kiselev, Valerij G.

    2016-01-01

    We review, systematize and discuss models of diffusion in neuronal tissue, by putting them into an overarching physical context of coarse-graining over an increasing diffusion length scale. From this perspective, we view research on quantifying brain microstructure as occurring along the three ma...

  1. Quantifying the Reuse of Learning Objects

    Science.gov (United States)

    Elliott, Kristine; Sweeney, Kevin

    2008-01-01

    This paper reports the findings of one case study from a larger project, which aims to quantify the claimed efficiencies of reusing learning objects to develop e-learning resources. The case study describes how an online inquiry project "Diabetes: A waste of energy" was developed by searching for, evaluating, modifying and then…

  2. QS Spiral: Visualizing Periodic Quantified Self Data

    DEFF Research Database (Denmark)

    Larsen, Jakob Eg; Cuttone, Andrea; Jørgensen, Sune Lehmann

    2013-01-01

    In this paper we propose an interactive visualization technique QS Spiral that aims to capture the periodic properties of quantified self data and let the user explore those recurring patterns. The approach is based on time-series data visualized as a spiral structure. The interactivity includes ...

  3. Periodontal inflamed surface area : quantifying inflammatory burden

    NARCIS (Netherlands)

    Nesse, Willem; Abbas, Frank; van der Ploeg, Ids; Spijkervet, Frederik Karst Lucien; Dijkstra, Pieter Ubele; Vissink, Arjan

    2008-01-01

    Background: Currently, a large variety of classifications is used for periodontitis as a risk factor for other diseases. None of these classifications quantifies the amount of inflamed periodontal tissue, while this information is needed to assess the inflammatory burden posed by periodontitis. Aim:

  4. Periodontal inflamed surface area : quantifying inflammatory burden

    NARCIS (Netherlands)

    Nesse, Willem; Abbas, Frank; van der Ploeg, Ids; Spijkervet, Frederik Karst Lucien; Dijkstra, Pieter Ubele; Vissink, Arjan

    2008-01-01

    Background: Currently, a large variety of classifications is used for periodontitis as a risk factor for other diseases. None of these classifications quantifies the amount of inflamed periodontal tissue, while this information is needed to assess the inflammatory burden posed by periodontitis. Aim:

  5. The Emergence of the Quantified Child

    Science.gov (United States)

    Smith, Rebecca

    2017-01-01

    Using document analysis, this paper examines the historical emergence of the quantified child, revealing how the collection and use of data has become normalized through legitimizing discourses. First, following in the traditions of Foucault's genealogy and studies examining the sociology of numbers, this paper traces the evolution of data…

  6. Utilization of Emergent Neuroimaging for Thrombolysis-Eligible Stroke Patients.

    Science.gov (United States)

    Sanossian, Nerses; Fu, Katherine A; Liebeskind, David S; Starkman, Sidney; Hamilton, Scott; Villablanca, J Pablo; Burgos, Adrian M; Conwit, Robin; Saver, Jeffrey L

    2017-01-01

    Advances in diagnostic imaging of stroke include multimodal techniques such as noninvasive angiography and perfusion imaging. We aimed to characterize trends in neuroimaging utilization among acute stroke patients. Utilization of multimodal imaging for acute stroke in the community has remained largely uncharacterized despite its increased adoption at academic medical centers. We quantified neuroimaging utilization in the emergency department (ED) for 1,700 hyperacute stroke patients presenting Neuroimaging.

  7. Information Utility: Quantifying the Total Psychometric Information Provided by a Measure

    Science.gov (United States)

    Markon, Kristian E.

    2013-01-01

    Although advances have improved our ability to describe the measurement precision of a test, it often remains challenging to summarize how well a test is performing overall. Reliability, for example, provides an overall summary of measurement precision, but it is sample-specific and might not reflect the potential usefulness of a test if the…

  8. METHODOLOGIES FOR QUANTIFYING POLLUTION PREVENTION BENEFITS FROM LANDFILL GAS CONTROL AND UTILIZATION

    Science.gov (United States)

    The report describes developing emission factors for controlled primary pollutants (e.g., nonmethane organic compounds) and secondary air pollutants (e.g., carbon monoxide). The report addresses the following criteria air pollutants and greenhouse gases: carbon dioxide, carbon mo...

  9. Reactive iron(III) in sediments: Chemical versus microbial extractions

    Science.gov (United States)

    Hyacinthe, C.; Bonneville, S.; Van Cappellen, P.

    2006-08-01

    The availability of particulate Fe(III) to iron reducing microbial communities in sediments and soils is generally inferred indirectly by performing chemical extractions. In this study, the bioavailability of mineral-bound Fe(III) in intertidal sediments of a eutrophic estuary is assessed directly by measuring the kinetics and extent of Fe(III) utilization by the iron reducing microorganism Shewanella putrefaciens, in the presence of excess electron donor. Microbial Fe(III) reduction is compared to chemical dissolution of iron from the same sediments in buffered ascorbate-citrate solution (pH 7.5), ascorbic acid (pH 2), and 1 M HCl. The results confirm that ascorbate at near-neutral pH selectively reduces the reactive Fe(III) pool, while the acid extractants mobilize additional Fe(II) and less reactive Fe(III) mineral phases. Furthermore, the maximum concentrations of Fe(III) reducible by S. putrefaciens correlate linearly with the iron concentrations extracted by buffered ascorbate-citrate solution, but not with those of the acid extractions. However, on average, only 65% of the Fe(III) reduced in buffered ascorbate-citrate solution can be utilized by S. putrefaciens, probably due to physical inaccessibility of the remaining fraction of reactive Fe(III) to the cells. While the microbial and abiotic reaction kinetics further indicate that reduction by ascorbate at near-neutral pH most closely resembles microbial reduction of the sediment Fe(III) pool by S. putrefaciens, the results also highlight fundamental differences between chemical reductive dissolution and microbial utilization of mineral-bound ferric iron.

  10. Soil Microbial Mineralization of Cellulose in Frozen Soils

    Science.gov (United States)

    Segura, J.; Haei, M.; Sparrman, T.; Nilsson, M. B.; Schleucher, J.; Oquist, M. G.

    2014-12-01

    Soils of high-latitude ecosystems store a large fraction of the global soil carbon pool. In boreal forests, the mineralization of soil organic matter (SOM) during winter by soil heterotrophic activity can affect the ecosystems net carbon balance. Recent research has shown that microorganisms in the organic surface layer of boreal forest soil can mineralize and grow on simple, monomeric substrates under frozen conditions. However, any substantial impacts of microbial activity in frozen soils on long-term soil carbon balances depend on whether soil microorganisms can utilize the more complex, polymeric substrates in SOM. In order to evaluate the potential for soil microorganisms to metabolize carbon polymers at low temperatures, we incubated boreal forest soil samples amended with [13C]-cellulose and studied the microbial catabolic and anabolic utilization of the substrate under frozen and unfrozen conditions (-4 and +4°C). The [13C]-CO2 production rate in the samples at +4°C were 0.524 mg CO2 SOM -1 day-1 while rates in the frozen samples (-4°C) were 0.008 mg CO2 SOM -1 day-1. Thus, freezing of the soil markedly reduced microbial utilization of the cellulose. However, newly synthetized [13C]-enriched cell membrane lipids, PLFAs, were detected in soil samples incubated both above and below freezing, confirming microbial growth also in the frozen soil matrix. The reduced metabolic rates induced by freezing indicate constraints on exoenzymatic activity, as well as substrate diffusion rates that we can attribute to reduced liquid water content of the frozen soil. We conclude that the microbial population in boreal forest soil has the capacity to metabolize, and grow, on polymeric substrates at temperatures below zero. This also involves maintaining exoenzymatic activity in frozen soils. This capacity manifests the importance of SOM mineralization during the winter season and its importance for the net carbon balance of soils of high-latitude ecosystems.

  11. Composition and physiological profiling of sprout-associated microbial communities

    Science.gov (United States)

    Matos, Anabelle; Garland, Jay L.; Fett, William F.

    2002-01-01

    The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of

  12. Microbial Metallomics: A Bioinorganic Perspective

    Science.gov (United States)

    Elliott, S. J.

    2004-12-01

    The term "metallome", as described by R.J.P. Williams is synonymous with the instantaneously determined concentration of all inorganic species within a cellular system [1]. Here, we refine this definition to specify that metallomics should reflect not only the overall content of inorganic species in cells, but the chemical identity of such species (i.e., in both ligated and unligated states) a well as their location. Of particular interest to the metallobiochemist are the roles inorganic species play in the up- and down-regulation of protein expression in cells. Thus, we consider that a fully realized "metallome" will reflect the biochemical pathways associated with metal ion speciation and localization within cells. Here we will describe currently proposed strategy and methodology that is used by the Elliott Lab of Boston University to capture snapshots of the proteomic and metallomic landscape of a variety of microbial systems. Two such systems will be described in some detail. The first is Methylococcus capsulatus (Bath), a methanotrophic organism that is known to undergo dramatic morphological changes upon the introduction of varying concentrations of Fe and Cu in the growth medium. In particular, the introduction of increasing concentrations of copper induces the expression of extensive intracytosolic membranes [2]. The Fe:Cu ratio also controls the expression of gene transcripts for soluble and particulate methane monooxygenase enzymes. This provides a unique opportunity to explore metal sensing, uptake, speciation and localization in methanotrophs. A developing model of protein expression and metal input will be discussed. Specific metallomic experiments regarding Shewanella oneidensis will also be discussed, in the context of an ongoing effort to understand how this organism can utilize a dazzling array of electron acceptors, including Fe(III), Mn(IV), nitrite, DMSO, TMAO, and fumarate. [1] R.J.P. Williams, Coord. Chem. Rev., 216:583-595 (2001). [2] C

  13. Soil-plant-microbial relations in hydrothermally altered soils of Northern California

    Science.gov (United States)

    Blecker, S.W.; Stillings, L.L.; DeCrappeo, N.M.; Ippolito, J.A.

    2014-01-01

    Soils developed on relict hydrothermally altered soils throughout the Western USA present unique opportunities to study the role of geology on above and belowground biotic activity and composition. Soil and vegetation samples were taken at three unaltered andesite and three hydrothermally altered (acid-sulfate) sites located in and around Lassen VolcanicNational Park in northeastern California. In addition, three different types of disturbed areas (clearcut, thinned, and pipeline) were sampled in acid-sulfate altered sites. Soils were sampled (0–15 cm) in mid-summer 2010 from both under-canopy and between-canopy areas within each of the sites. Soils were analyzed for numerous physical and chemical properties along with soil enzyme assays, C and N mineralization potential, microbial biomass-C and C-substrate utilization. Field vegetation measurements consisted of canopy cover by life form (tree, shrub, forb, and grass), tree and shrub density, and above-ground net primary productivity of the understory. Overall, parameters at the clearcut sites were more similar to the unaltered sites, while parameters at the thinned and pipeline sites were more similar to the altered sites. We employed principal components analysis (PCA) to develop two soil quality indices (SQI) to help quantify the differences among the sites: one based on the correlation between soil parameters and canopy cover, and the second based on six sub-indices. Soil quality indices developed in these systems could provide a means for monitoring and identifying key relations between the vegetation, soils, and microorganisms.

  14. Microbial Impact on Success of Human Exploration Missions

    Science.gov (United States)

    Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

    2000-01-01

    The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

  15. A Seafloor Microbial Biome Hosted within Incipient Ferromanganese Crusts

    Energy Technology Data Exchange (ETDEWEB)

    Templeton, Alexis S.; Knowles, A. S.; Eldridge, D. L.; Arey, Bruce W.; Dohnalkova, Alice; Webb, Samuel M.; Bailey, B. E.; Tebo, Bradley M.; Staudigel, Hubert

    2009-11-15

    Unsedimented volcanic rocks exposed on the seafloor at ridge systems and Seamounts host complex, abundant and diverse microbial communities that are relatively cosmopolitan in distribution (Lysnes, Thorseth et al. 2004; Mason, Stingl et al. 2007; Santelli, Orcutt et al. 2008). The most commonly held hypothesis is that the energy released by the hydration, dissolution and oxidative alteration of volcanic glasses in seawater drives the formation of an ocean crust biosphere (Thorseth, Furnes et al. 1992; Fisk, Giovannoni et al. 1998; Furnes and Staudigel 1999). The combined thermodynamically favorable weathering reactions could theoretically support anywhere from 105 to 109 cells/gram of rock depending upon the metabolisms utilized and cellular growth rates and turnover (Bach and Edwards 2003; Santelli, Orcutt et al. 2008). Yet microbially-mediated basalt alteration and energy conservation has not been directly demonstrated on the seafloor. By using synchrotron-based x-ray microprobe mapping, x-ray absorption spectroscopy and high-resolution scanning and transmission electron microscopy observations of young volcanic glasses recovered from the outer flanks of Loihi Seamount, we intended to identify the initial rates and mechanisms of microbial basalt colonization and bioalteration. Instead, here we show that microbial biofilms are intimately associated with ferromanganese crusts precipitating onto basalt surfaces from cold seawater. Thus we hypothesize that microbial communities colonizing seafloor rocks are established and sustained by external inputs of potential energy sources, such as dissolved and particulate Fe(II), Mn(II) and organic matter, rather than rock dissolution.

  16. Review: quantifying mitochondrial dysfunction in complex diseases of aging.

    Science.gov (United States)

    Horan, Martin P; Pichaud, Nicolas; Ballard, J William O

    2012-10-01

    There is accumulating evidence that mitochondrial respiratory malfunction is associated with aging-associated complex diseases. However, progress in our understanding of these diseases has been hampered by the sensitivity and throughput of systems employed to quantify dysfunction and inherent limitations of the biological systems studied. In this review, we describe and contrast two methodologies that have been developed for measuring mitochondrial function to address the need for improved sensitivity and increased throughput. We then consider the utility of each methodology in studying three biological systems: isolated mitochondria, cultured cells, and cell fibers and tissues. Finally, we discuss the application of each methodology in the study of mitochondrial dysfunction in Alzheimer's disease, type 2 diabetes mellitus, and aging-associated autophagy impairment and mitochondrial malfunction. We conclude that the methodologies are complementary, and researchers may need to examine multiple biological systems to unravel complex diseases of aging.

  17. Quantifying greenhouse gas emissions from waste treatment facilities

    DEFF Research Database (Denmark)

    Mønster, Jacob

    times and the emissions ranged from 2.6 to 60.8 kg methane per hour, with the lowest emissions from the oldest and smallest landfills and the highest emissions from the bigger landfills. It was not possible to correlate the measured emission with a single factor such a landfill age, size or mitigation...... gas, and that this error becomes smaller with increasing measurement distance. A measurement protocol was developed and the methane emission was quantified from a series of landfills with different size, age and gas recovery and mitigation conditions. The landfills were measured between one and four...... actions. As an example the highest emission was measured at a landfill with active methane recovery and utilization. Compared with national and European greenhouse gas reporting schemes the measurement showed a large difference, with reporting ranging a factor of 100 above to a factor of 10 below...

  18. Quantifying the Impact of Unavailability in Cyber-Physical Environments

    Energy Technology Data Exchange (ETDEWEB)

    Aissa, Anis Ben [Université de Tunis El Manar, Tunisia; Abercrombie, Robert K [ORNL; Sheldon, Federick T. [University of Memphis; Mili, Ali [New Jersey Insitute of Technology

    2014-01-01

    The Supervisory Control and Data Acquisition (SCADA) system discussed in this work manages a distributed control network for the Tunisian Electric & Gas Utility. The network is dispersed over a large geographic area that monitors and controls the flow of electricity/gas from both remote and centralized locations. The availability of the SCADA system in this context is critical to ensuring the uninterrupted delivery of energy, including safety, security, continuity of operations and revenue. Such SCADA systems are the backbone of national critical cyber-physical infrastructures. Herein, we propose adapting the Mean Failure Cost (MFC) metric for quantifying the cost of unavailability. This new metric combines the classic availability formulation with MFC. The resulting metric, so-called Econometric Availability (EA), offers a computational basis to evaluate a system in terms of the gain/loss ($/hour of operation) that affects each stakeholder due to unavailability.

  19. Quantifying habitat interactions: sediment transport and freshwater mussels

    Science.gov (United States)

    Kozarek, J. L.; MacGregor, K. R.; Hornbach, D.; Hove, M.

    2016-12-01

    Freshwater mussel abundance and distribution are integrally linked with their habitat through sediment transport processes in moving waters, including suspended sediment loads and bed mobility. This research seeks to quantify these complex interactions using a combination of field data collection in the intensively agricultural Minnesota River Basin, and laboratory experiments in the Outdoor StreamLab (OSL) and flumes at St. Anthony Falls Laboratory (SAFL) at the University of Minnesota. The OSL is a field-scale sand-bed meandering stream channel with independent control over sediment feed (recirculated) and water flow (diverted from the Mississippi River). Experiments in the OSL focused on the interactions between moving bedload and freshwater mussel behavior. Flooding experiments were used to quantify the movement during and post flood for three mussel species with different shell sculptures: threeridge (Amblema plicata), plain pockebook (Lampsilus cardium), and white heelsplitter (Lasmigona complanata). Flow fields, bed shear stress, bedform migration, and bar topography were measured during each flooding event with and without mussels present (density = 4/m2) to examine the influence of flooding on mussel movement, and to quantify the influence of mussels on channel morphology under steady state bedload transport. Additional experiments were conducted with threeridge at low flow (no bedload), under aggrading and degrading bed conditions, and doubled mussel density (8/m2). Mussel response to suspended sediment loads was examined in a complementary series of experiments in an indoor flume with Mississippi River water. Mussels outfitted with gape sensors were utilized in paired control/treatment experiments to examine the influence of moderate term (48 hours) exposure to elevated suspended sediment loads on mussel filtering activity. Together, these experiments provide multiple measures of mussel stress under high sediment loads and reveal how freshwater mussels

  20. Microbial desalination cells for improved performance in wastewater treatment, electricity production, and desalination.

    Science.gov (United States)

    Luo, Haiping; Xu, Pei; Roane, Timberley M; Jenkins, Peter E; Ren, Zhiyong

    2012-02-01

    The low conductivity and alkalinity in municipal wastewater significantly limit power production from microbial fuel cells (MFCs). This study integrated desalination with wastewater treatment and electricity production in a microbial desalination cell (MDC) by utilizing the mutual benefits among the above functions. When using wastewater as the sole substrate, the power output from the MDC (8.01 W/m(3)) was four times higher than a control MFC without desalination function. In addition, the MDC removed 66% of the salts and improved COD removal by 52% and Coulombic efficiency by 131%. Desalination in MDCs improved wastewater characteristics by increasing the conductivity by 2.5 times and stabilizing anolyte pH, which therefore reduced system resistance and maintained microbial activity. Microbial community analysis revealed a more diverse anode microbial structure in the MDC than in the MFC. The results demonstrated that MDC can serve as a viable option for integrated wastewater treatment, energy production, and desalination.

  1. A kernel plus method for quantifying wind turbine performance upgrades

    KAUST Repository

    Lee, Giwhyun

    2014-04-21

    Power curves are commonly estimated using the binning method recommended by the International Electrotechnical Commission, which primarily incorporates wind speed information. When such power curves are used to quantify a turbine\\'s upgrade, the results may not be accurate because many other environmental factors in addition to wind speed, such as temperature, air pressure, turbulence intensity, wind shear and humidity, all potentially affect the turbine\\'s power output. Wind industry practitioners are aware of the need to filter out effects from environmental conditions. Toward that objective, we developed a kernel plus method that allows incorporation of multivariate environmental factors in a power curve model, thereby controlling the effects from environmental factors while comparing power outputs. We demonstrate that the kernel plus method can serve as a useful tool for quantifying a turbine\\'s upgrade because it is sensitive to small and moderate changes caused by certain turbine upgrades. Although we demonstrate the utility of the kernel plus method in this specific application, the resulting method is a general, multivariate model that can connect other physical factors, as long as their measurements are available, with a turbine\\'s power output, which may allow us to explore new physical properties associated with wind turbine performance. © 2014 John Wiley & Sons, Ltd.

  2. Quantifying prosthetic gait deviation using simple outcome measures

    Science.gov (United States)

    Kark, Lauren; Odell, Ross; McIntosh, Andrew S; Simmons, Anne

    2016-01-01

    AIM: To develop a subset of simple outcome measures to quantify prosthetic gait deviation without needing three-dimensional gait analysis (3DGA). METHODS: Eight unilateral, transfemoral amputees and 12 unilateral, transtibial amputees were recruited. Twenty-eight able-bodied controls were recruited. All participants underwent 3DGA, the timed-up-and-go test and the six-minute walk test (6MWT). The lower-limb amputees also completed the Prosthesis Evaluation Questionnaire. Results from 3DGA were summarised using the gait deviation index (GDI), which was subsequently regressed, using stepwise regression, against the other measures. RESULTS: Step-length (SL), self-selected walking speed (SSWS) and the distance walked during the 6MWT (6MWD) were significantly correlated with GDI. The 6MWD was the strongest, single predictor of the GDI, followed by SL and SSWS. The predictive ability of the regression equations were improved following inclusion of self-report data related to mobility and prosthetic utility. CONCLUSION: This study offers a practicable alternative to quantifying kinematic deviation without the need to conduct complete 3DGA. PMID:27335814

  3. Microbial activity in the marine deep biosphere: progress and prospects.

    Science.gov (United States)

    Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

    2013-01-01

    The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

  4. Microbial activity in the marine deep biosphere: Progress and prospects

    Directory of Open Access Journals (Sweden)

    Beth N Orcutt

    2013-07-01

    Full Text Available The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists – all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive. Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI "theme team" on microbial activity (www.darkenergybiosphere.org.

  5. Assessing the Accuracy of Quantitative Molecular Microbial Profiling

    Directory of Open Access Journals (Sweden)

    Denise M. O'Sullivan

    2014-11-01

    Full Text Available The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene or whole (metagenome sequencing (WGS. Both methods have been used to catalog the microbial taxa present in a sample and quantify their respective abundances. However, a comparison of the inherent precision or bias of the different sequencing approaches has not been performed. We previously developed a metagenomic control material (MCM to investigate error when performing different sequencing strategies. Amplicon sequencing using four different primer strategies and two 16S rRNA regions was examined (Roche 454 Junior and compared to WGS (Illumina HiSeq. All sequencing methods generally performed comparably and in good agreement with organism specific digital PCR (dPCR; WGS notably demonstrated very high precision. Where discrepancies between relative abundances occurred they tended to differ by less than twofold. Our findings suggest that when alternative sequencing approaches are used for microbial molecular profiling they can perform with good reproducibility, but care should be taken when comparing small differences between distinct methods. This work provides a foundation for future work comparing relative differences between samples and the impact of extraction methods. We also highlight the value of control materials when conducting microbial profiling studies to benchmark methods and set appropriate thresholds.

  6. Monitoring Microbially Influenced Corrosion

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    Abstract Microbially influenced corrosion (MIC) of carbon steel may occur in media with microbiological activity of especially sulphate-reducing bacteria (SRB). The applicability and reliability of a number of corrosion monitoring techniques for monitoring MIC has been evaluated in experiments...... and diffusional effects and unreliable corrosion rates, when biofilm and ferrous sulphide corrosion products cover the steel surface. Corrosion rates can be overestimated by a factor of 10 to 100 by electrochemical techniques. Weight loss coupons and ER are recommended as necessary basic monitoring techniques....... EIS might be used for detection of MIC as the appearance of very large capacitances can be attributed to the combined ferrous sulphide and biofilm formation. Capacitance correlates directly with sulphide concentration in sterile sulphide media. Keywords: Corrosion monitoring, carbon steel, MIC, SRB...

  7. New microbial growth factor

    Science.gov (United States)

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

    1977-01-01

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

  8. Microbial Field Pilot Study

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, R.M.; McInerney, M.J.; Menzie, D.E.; Chisholm, J.L.

    1990-11-01

    This report covers progress made during the first year of the Microbial Field Pilot Study project. Information on reservoir ecology and characterization, facility and treatment design, core experiments, bacterial mobility, and mathematical modeling are addressed. To facilitate an understanding of the ecology of the target reservoir analyses of the fluids which support bacteriological growth and the microbiology of the reservoir were performed. A preliminary design of facilities for the operation of the field pilot test was prepared. In addition, procedures for facilities installation and for injection treatments are described. The Southeast Vassar Vertz Sand Unit (SEVVSU), the site of the proposed field pilot study, is described physically, historically, and geologically. The fields current status is presented and the ongoing reservoir simulation is discussed. Core flood experiments conducted during the last year were used to help define possible mechanisms involved in microbial enhanced oil recovery. Two possible mechanisms, relative permeability effects and changes in the capillary number, are discussed and related to four Berea core experiments' results. The experiments were conducted at reservoir temperature using SEVVSU oil, brine, and bacteria. The movement and activity of bacteria in porous media were investigated by monitoring the growth of bacteria in sandpack cores under no flow conditions. The rate of bacteria advancement through the cores was determined. A mathematical model of the MEOR process has been developed. The model is a three phase, seven species, one dimensional model. Finite difference methods are used for solution. Advection terms in balance equations are represented with a third- order upwind differencing scheme to reduce numerical dispersion and oscillations. The model is applied to a batch fermentation example. 52 refs., 26 figs., 21 tabs.

  9. Universally Utility-Maximizing Privacy Mechanisms

    CERN Document Server

    Ghosh, Arpita; Sundararajan, Mukund

    2008-01-01

    A mechanism for releasing information about a statistical database with sensitive data must resolve a trade-off between utility and privacy. Privacy can be rigorously quantified using the framework of {\\em differential privacy}, which requires that a mechanism's output distribution is nearly the same (in a strong sense) whether or not a given database row is included or excluded. In this paper, we pursue much strong and general utility guarantees. We seek a mechanism that guarantees near-optimal utility to every potential user, independent of its side information. Formally, we model the side information of a potential user as a prior distribution over query results. An interaction between a user and a mechanism induces a posterior distribution, and we define the utility of the mechanism for this user as the accuracy of this posterior, as quantified via a user-specific loss function. A differentially private mechanism $M$ is (near-)optimal for a given user $u$ if $u$ derives (almost) as much utility from $M$ a...

  10. Utility usage forecasting

    Energy Technology Data Exchange (ETDEWEB)

    Hosking, Jonathan R. M.; Natarajan, Ramesh

    2017-08-22

    The computer creates a utility demand forecast model for weather parameters by receiving a plurality of utility parameter values, wherein each received utility parameter value corresponds to a weather parameter value. Determining that a range of weather parameter values lacks a sufficient amount of corresponding received utility parameter values. Determining one or more utility parameter values that corresponds to the range of weather parameter values. Creating a model which correlates the received and the determined utility parameter values with the corresponding weather parameters values.

  11. Microbial biosensors for environmental monitoring

    Directory of Open Access Journals (Sweden)

    David VOGRINC

    2015-12-01

    Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

  12. Effect of continuous oleate addition on microbial communities involved in anaerobic digestion process

    DEFF Research Database (Denmark)

    Baserba, Manel Garrido; Angelidaki, Irini; Karakashev, Dimitar Borisov

    2012-01-01

    In the present study, the microbial diversity in anaerobic reactors, continuously exposed to oleate, added to a manure reactor influent, was investigated. Relative changes in archaeal community were less remarkable in comparison to changes in bacterial community indicating that dominant archaeal ...... a comprehensive picture on oleate degrading microbial communities in high organic strength wastewater. The findings might be utilized for development of strategies for biogas production from lipid-riched wastes....

  13. Microbial Gas Production Used to Achieve Autonomous Buoyancy Control

    Science.gov (United States)

    2010-09-01

    counter weight. The microbe used is cultured in the Erlenmeyer flask. Clostridium acetobutylicum for micro1bial ballast In order to utilize microbial...34 20 0 --100% 0 20 40 60 80 Time(hr) Figure 6. Gas production by different S()lid-phase agar cultures of C. acetobutvlicum. Clostridium ... acetobutylicum as our model microbe; a gram-positive anaerobic bacterium known for its ability to produce hydrogen gas 4,5 To determine if there

  14. ATP measurements for monitoring microbial drinking water quality

    DEFF Research Database (Denmark)

    Vang, Óluva Karin

    methods are vital for an improved surveillance and distribution of clean and safe drinking water. One of these rapid methods is the ATP assay. This thesis encompasses various methodological aspects of the ATP assay describing the principal and theory of the ATP assay measurement. ATP is the main energy...... carrying molecule in living cells, thus ATP can be used as a parameter for microbial activity. ATP is extracted from cells through cell lysis and subsequently assayed with the luciferase enzyme and its substrate luciferin, resulting in bioluminescence, i.e. light emission which can be quantified....... The overall aim of this PhD study was to investigate various methodological features of the ATP assay for a potential implementation on a sensor platform as a real-time parameter for continuous on-line monitoring of microbial drinking water quality. Commercial reagents are commonly used to determine ATP...

  15. Utilization of carbohydrates by radiation processing

    Energy Technology Data Exchange (ETDEWEB)

    Kume, T. E-mail: kume@taka.jaeri.go.jp; Nagasawa, N.; Yoshii, F

    2002-03-01

    Upgrading and utilization of carbohydrates such as chitosan, sodium alginate, carrageenan, cellulose, pectin have been investigated for recycling these bio-resources and reducing the environmental pollution. These carbohydrates were easily degraded by irradiation and various kinds of biological activities such as anti-microbial activity, promotion of plant growth, suppression of heavy metal stress, phytoalexins induction, etc. were induced. On the other hand, some carbohydrate derivatives, carboxymethylcellulose and carboxymethylstarch, could be crosslinked under certain radiation condition and produce the biodegradable hydrogel for medical and agricultural use.

  16. Quantifying Stock Return Distributions in Financial Markets.

    Science.gov (United States)

    Botta, Federico; Moat, Helen Susannah; Stanley, H Eugene; Preis, Tobias

    2015-01-01

    Being able to quantify the probability of large price changes in stock markets is of crucial importance in understanding financial crises that affect the lives of people worldwide. Large changes in stock market prices can arise abruptly, within a matter of minutes, or develop across much longer time scales. Here, we analyze a dataset comprising the stocks forming the Dow Jones Industrial Average at a second by second resolution in the period from January 2008 to July 2010 in order to quantify the distribution of changes in market prices at a range of time scales. We find that the tails of the distributions of logarithmic price changes, or returns, exhibit power law decays for time scales ranging from 300 seconds to 3600 seconds. For larger time scales, we find that the distributions tails exhibit exponential decay. Our findings may inform the development of models of market behavior across varying time scales.

  17. Power Curve Measurements, quantify the production increase

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Vesth, Allan

    The purpose of this report is to quantify the production increase on a given turbine with respect to another given turbine. The used methodology is the “side by side” comparison method, provided by the client. This method involves the use of two neighboring turbines and it is based on the assumpt......The purpose of this report is to quantify the production increase on a given turbine with respect to another given turbine. The used methodology is the “side by side” comparison method, provided by the client. This method involves the use of two neighboring turbines and it is based...... on the assumption that the wind field in front of the tested turbines is statistically the same (i.e. has in average the same mean wind speed conditions in front of both turbines). The method is only used for the evaluation of a relative change in the AEP, not the AEP itself....

  18. Quantifying the robustness of metro networks

    CERN Document Server

    Wang, Xiangrong; Derrible, Sybil; Ahmad, Sk Nasir; Kooij, Robert E

    2015-01-01

    Metros (heavy rail transit systems) are integral parts of urban transportation systems. Failures in their operations can have serious impacts on urban mobility, and measuring their robustness is therefore critical. Moreover, as physical networks, metros can be viewed as network topological entities, and as such they possess measurable network properties. In this paper, by using network science and graph theoretical concepts, we investigate both theoretical and experimental robustness metrics (i.e., the robustness indicator, the effective graph conductance, and the critical thresholds) and their performance in quantifying the robustness of metro networks under random failures or targeted attacks. We find that the theoretical metrics quantify different aspects of the robustness of metro networks. In particular, the robustness indicator captures the number of alternative paths and the effective graph conductance focuses on the length of each path. Moreover, the high positive correlation between the theoretical m...

  19. Quantifying Shannon's Work Function for Cryptanalytic Attacks

    CERN Document Server

    van Son, R J J H

    2010-01-01

    Attacks on cryptographic systems are limited by the available computational resources. A theoretical understanding of these resource limitations is needed to evaluate the security of cryptographic primitives and procedures. This study uses an Attacker versus Environment game formalism based on computability logic to quantify Shannon's work function and evaluate resource use in cryptanalysis. A simple cost function is defined which allows to quantify a wide range of theoretical and real computational resources. With this approach the use of custom hardware, e.g., FPGA boards, in cryptanalysis can be analyzed. Applied to real cryptanalytic problems, it raises, for instance, the expectation that the computer time needed to break some simple 90 bit strong cryptographic primitives might theoretically be less than two years.

  20. Quantifying reliability uncertainty : a proof of concept.

    Energy Technology Data Exchange (ETDEWEB)

    Diegert, Kathleen V.; Dvorack, Michael A.; Ringland, James T.; Mundt, Michael Joseph; Huzurbazar, Aparna (Los Alamos National Laboratory, Los Alamos, NM); Lorio, John F.; Fatherley, Quinn (Los Alamos National Laboratory, Los Alamos, NM); Anderson-Cook, Christine (Los Alamos National Laboratory, Los Alamos, NM); Wilson, Alyson G. (Los Alamos National Laboratory, Los Alamos, NM); Zurn, Rena M.

    2009-10-01

    This paper develops Classical and Bayesian methods for quantifying the uncertainty in reliability for a system of mixed series and parallel components for which both go/no-go and variables data are available. Classical methods focus on uncertainty due to sampling error. Bayesian methods can explore both sampling error and other knowledge-based uncertainties. To date, the reliability community has focused on qualitative statements about uncertainty because there was no consensus on how to quantify them. This paper provides a proof of concept that workable, meaningful quantification methods can be constructed. In addition, the application of the methods demonstrated that the results from the two fundamentally different approaches can be quite comparable. In both approaches, results are sensitive to the details of how one handles components for which no failures have been seen in relatively few tests.

  1. The microbial ecology of permafrost

    DEFF Research Database (Denmark)

    Jansson, Janet; Tas, Neslihan

    2014-01-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

  2. Quantifying energy condition violations in traversable wormholes

    Indian Academy of Sciences (India)

    Sayan Kar; Naresh Dadhich; Matt Visser

    2004-10-01

    The `theoretical' existence of traversable Lorentzian wormholes in the classical, macroscopic world is plagued by the violation of the well-known energy conditions of general relativity. In this brief article we show: (i) how the extent of violation can be quantified using certain volume integrals and (ii) whether this `amount of violation' can be minimised for some specific cut-and-paste geometric constructions. Examples and possibilities are also outlined.

  3. Quantifying sediment production in steepland environments

    OpenAIRE

    2009-01-01

    Five published contributions to our understanding of the impacts of erosion processes on sustainable land management are reviewed and discussed. These focus on rapid shallow landsliding and gully erosion which are among the most prevalent forms of environmental degradation in New Zealand's hill country. The over-arching goal of this research has been to quantify the on-site (e.g., soil erosion, land productivity) impacts of these processes. Rather than measure erosion rates over long periods ...

  4. The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

    Energy Technology Data Exchange (ETDEWEB)

    Boundy-Mills, K.; Hess, Matthias; Bennett, A. R.; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A.; Inderbitzin, Patrik; Sitepu, Irnayuli R.; Torok, Tamas; Brown, Daniel R; Cho, Juliana; Wertz, John E.; Mukherjee, Supratim; Cady, Sherry L.; McCluskey, Kevin

    2015-09-01

    The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

  5. Short-Term Responses of Nitrogen Mineralization and Microbial Community to Moisture Regimes in Greenhouse Vegetable Soils

    Institute of Scientific and Technical Information of China (English)

    CHEN Qiu-Hui; FENG Ying; ZHANG Yan-Ping; ZHANG Qi-Chun; I.H.SHAMSI; ZHANG Yong-Song; LIN Xian-Yong

    2012-01-01

    Soil drying and wetting impose significant influences on soil nitrogen (N) dynamics and microbial communities.However,effects of drying-wetting cycles,while common in vegetable soils,especially under greenhouse conditions,have not been well studied.In this study,two greenhouse vegetable soils,which were collected from Xinji (X J) and Hangzhou (HZ),China,were maintained at 30% and 75% water-holding capacity (WHC),or five cycles of 75% WHC followed by a 7-day dry-down to 30% WHC (DW).Soil inorganic N content increased during incubation.Net N mineralization (Nmin),microbial activity,and microbial biomass were significantly higher in the DW treatment than in the 30% and 75% WHC treatments.The higher water content (75% WHC) treatment had higher Nmin,microbial activity,and microbial biomass than the lower water content treatment (30% WHC).Multivariate analyses of community-level physiological profile (CLPP) and phospholipid fatty acid (PLFA) data indicated that soil moisture regime had a significant effect on soil microbial community substrate utilization pattern and microbial community composition.The significant positive correlation between Nmin and microbial substrate utilization or PLFAs suggested that soil N mineralization had a close relationship with microbial community.

  6. Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes.

    Science.gov (United States)

    Bartz, Faith E; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos; Leon, Juan S

    2017-06-01

    To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples (n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli, Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands.IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. Copyright © 2017 American Society for Microbiology.

  7. Quantifying the dynamic of OSA brain using multifractal formalism: A novel measure for sleep fragmentation.

    Science.gov (United States)

    Raiesdana, Somayeh

    2017-01-01

    It is thought that the critical brain dynamics in sleep is modulated during frequent periods of wakefulness. This paper utilizes the capacity of EEG based scaling analysis to quantify sleep fragmentation in patients with obstructive sleep apnea. The scale-free (fractal) behavior refers to a state where no characteristic scale dominates the dynamics of the underlying process which is evident as long range correlations in a time series. Here, Multiscaling (multifractal) spectrum is utilized to quantify the disturbed dynamic of an OSA brain with fragmented sleep. The whole night multichannel sleep EEG recordings of 18 subjects were employed to compute and quantify variable power-law long-range correlations and singularity spectra. Based on this characteristic, a new marker for sleep fragmentation named ``scaling based sleep fragmentation'' was introduced. This measure takes into account the sleep run length and stage transition quality within a fuzzy inference system to improve decisions made on sleep fragmentation. The proposed index was implemented, validated with sleepiness parameters and compared to some common indexes including sleep fragmentation index, arousal index, sleep diversity index, and sleep efficiency index. Correlations were almost significant suggesting that the sleep characterizing measure, based on singularity spectra range, could properly detect fragmentations and quantify their rate. This method can be an alternative for quantifying the sleep fragmentation in clinical practice after being approved experimentally. Control of sleep fragmentation and, subsequently, suppression of excessive daytime sleepiness will be a promising outlook of this kind of researches.

  8. Eco-friendly fly ash utilization: potential for land application

    Energy Technology Data Exchange (ETDEWEB)

    Malik, A.; Thapliyal, A. [Indian Institute of Technology Delhi, New Delhi (India)

    2009-07-01

    The increase in demand for power in domestic, agricultural, and industrial sectors has increased the pressure on coal combustion and aggravated the problem of fly ash generation/disposal. Consequently the research targeting effective utilization of fly ash has also gained momentum. Fly ash has proved to be an economical substitute for expensive adsorbents as well as a suitable raw material for brick manufacturing, zeolite synthesis, etc. Fly ash is a reservoir of essential minerals but is deficient in nitrogen and phosphorus. By amending fly ash with soil and/or various organic materials (sewage sludge, bioprocess materials) as well as microbial inoculants like mycorrhizae, enhanced plant growth can be realized. Based on the sound results of large scale studies, fly ash utilization has grown into prominent discipline supported by various internationally renowned organizations. This paper reviews attempts directed toward various utilization of fly ash, with an emphasis on land application of organic/microbial inoculants amended fly ash.

  9. Effect of heavy metals on soil microbial activity and diversity in a reclaimed mining wasteland of red soil area

    Institute of Scientific and Technical Information of China (English)

    LIAO Min; CHEN Cheng-li; HUANG Chang-yong

    2005-01-01

    The microbial biomass, basal respiration and substrate utilization pattern in copper mining wasteland of red soil area, southern China, were investigated. The results indicated that soil microflora were obviously different compared with that of the non-mine soil.Microbial biomass and basal respiration were negatively affected by the elevated heavy metal levels. Two important microbial ecophysiological parameters, namely, the ratio of microbial biomass C( Cmic )/organic C( Corg ) and metabolic quotient(qCO2 ) were closely correlated to heavy metal stress. There was a significant decrease in the Cmic/Corg ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters had great potential to become the early sensitive, effective and liable indicators of the stresses or perturbations in soils of mining ecosystems.

  10. Entrez Programming Utilities

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at...

  11. High Doses of Microbial Phytase Affect Nutrient Utilization in Broiler Chicks Fed Corn-soybean Meal Diets%玉米-豆粕型日粮中添加高剂量植酸酶对肉鸡养分利用率的影响

    Institute of Scientific and Technical Information of China (English)

    孙宏选; 高秀华; 杨禄良

    2011-01-01

    本试验研究了玉米-豆粕型日粮中添加高剂量不同水平的植酸酶对0~3和4~6周肉鸡养分利用率的影响.选用1日龄AA肉鸡公雏576只,随机分为6组,每组8个重复,每个重复12只.试验日粮分0~3和4~6周两个阶段,6个处理组:正对照组(前期为总磷0.69%,0.45%NPP;后期为总磷0.59%,0.35%NPP);负对照组(前期总磷0.60%,0.35%NPP;后期为总磷0.49%,0.25%NPP);4个试验组在负对照日粮中分别添加500、2000、8000和32000 FTU/kg 4种植酸酶水平.结果显示:①日粮添加高剂量不同水平的植酸酶显著影响生长前期(17~21日龄)肉鸡的钙、磷的消化利用率(P<0.05),随着植酸酶添加水平增加,钙的消化利用率显著增加(P<0.05).②日粮添加高剂量不同水平的植酸酶显著影响38~42日龄肉鸡磷的消化利用率(P<0.05).在负对照组日粮中随着植酸酶水平添加的提高,钙的消化利用率呈现先增加后降低的趋势,磷的养分利用率反而显著减少.③日粮添加高剂量不同水平植酸酶显著增加生长前期(17~21日龄)肉鸡的粗蛋白质的消化利用率和表观代谢能(P<0.05),在生长后期(38~42日龄)对肉鸡的粗蛋白质的消化利用率和表观代谢能提高达到显著水平(P<0.05).因此,高剂量不同水平的植酸酶显著提高肉鸡AME和粗蛋白质,钙、磷的消化利用率,添加高水平植酸酶可以适当调低日粮能量和蛋白质水平,日粮中总磷(tP)水平应低于NRC标准,减少无机磷和钙的添加量,以提高钙、磷在体内的存留量.%An experiment was conducted to determine the effect of high levels of microbial phytase supplementation in cornsoy-based diets on nutrient availability of broiler chickens. A totalof 576 one-day old male Arbor Acres broilers were assigned to 6 dietary treatments,consisting of 8 pens of 12 birds each,and were fed two periods experimental diets from 1 to 21 d and 22 to 42 d. The diets include a positive control

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

    Science.gov (United States)

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

    2012-03-18

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

  13. Mercury in water and biomass of microbial communities in hot springs of Yellowstone National Park, USA

    Science.gov (United States)

    King, S.A.; Behnke, S.; Slack, K.; Krabbenhoft, D.P.; Nordstrom, D.K.; Burr, M.D.; Striegl, R.G.

    2006-01-01

    Ultra-clean sampling methods and approaches typically used in pristine environments were applied to quantify concentrations of Hg species in water and microbial biomass from hot springs of Yellowstone National Park, features that are geologically enriched with Hg. Microbial populations of chemically-diverse hot springs were also characterized using modern methods in molecular biology as the initial step toward ongoing work linking Hg speciation with microbial processes. Molecular methods (amplification of environmental DNA using 16S rDNA primers, cloning, denatured gradient gel electrophoresis (DGGE) screening of clone libraries, and sequencing of representative clones) were used to examine the dominant members of microbial communities in hot springs. Total Hg (THg), monomethylated Hg (MeHg), pH, temperature, and other parameters influential to Hg speciation and microbial ecology are reported for hot springs water and associated microbial mats. Several hot springs indicate the presence of MeHg in microbial mats with concentrations ranging from 1 to 10 ng g-1 (dry weight). Concentrations of THg in mats ranged from 4.9 to 120,000 ng g-1 (dry weight). Combined data from surveys of geothermal water, lakes, and streams show that aqueous THg concentrations range from l to 600 ng L-1. Species and concentrations of THg in mats and water vary significantly between hot springs, as do the microorganisms found at each site. ?? 2006.

  14. How plant functional traits cascade to microbial function and ecosystem services in mountain grasslands

    Science.gov (United States)

    Lavorel, S.; Grigulis, K.; Krainer, U.; Legay, N.; Turner, C.; Dumont, M.; Kastl, E.; Arnoldi, C.; Bardgett, R.; Poly, F.; Pommier, T.; Schloter, M.; Tappeiner, U.; Bahn, M.; Clément, J.-C.

    2012-04-01

    1. There is growing evidence that plant functional diversity and microbial communities of soil are tightly coupled, and that this coupling influences a range of ecosystem functions. Moreover, it has been hypothesized that changes in the nature of interactions between plant functional diversity and microbial communities along environmental gradients contributes to variation in the delivery of ecosystem services. Although there is empirical support for such relationships using broad plant and microbial functional classifications, or from studies of plant monocultures, such relationships and their consequences for ecosystem services have not been quantified under complex field conditions with diverse plant communities. 2. We aimed to provide an explicit quantification of how plant and microbial functional properties interplay to determine key ecosystem functions underlying ecosystem services provided by grasslands. At three mountain grassland sites in the French Alps, Austrian Tyrol and northern England, we quantified, along gradients of management intensity, (i) plant functional diversity, (ii) soil microbial community composition and parameters associated with nitrogen cycling, and (iii) key ecosystem processes related to the carbon and nitrogen cycles including aboveground biomass production, standing litter, litter decomposition, soil organic matter and nitrate and ammonium leaching . Considering that plants strongly determine microbial communities, we used a hierarchical approach that considered first direct effects of plant traits and then effects of soil microorganisms on processes, to determine the relative effects of plant and microbial functional parameters on key ecosystem properties. 3. We identified a gradient of relative effects of plant and microbial traits from properties controlled mostly by aboveground processes, such as plant biomass production and standing litter, to properties controlled mostly by microbial processes, such as soil leaching of

  15. Nonexpected utility and coherence

    NARCIS (Netherlands)

    Diecidue, E.

    2001-01-01

    The descriptive power of expected utility has been challenged by behavioral evidence showing that people deviate systematically from the expected utility paradigm. Since the end of the 70's several alternatives to the classical expected utility paradigm have been proposed in order to accommodate the

  16. Information, evolution and utility

    Directory of Open Access Journals (Sweden)

    Larry Samuelson

    2006-03-01

    Full Text Available Human utility embodies a number of seemingly irrational aspects. The leading example in this paper is that utilities often depend on the presence of salient unchosen alternatives. Our focus is to understand why an evolutionary process might optimally lead to such seemingly dysfunctional features in our motivations and to derive implications for the nature of our utility functions.

  17. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  18. Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China

    DEFF Research Database (Denmark)

    Liu, Lei; Gundersen, Per; Zhang, Tao;

    2012-01-01

    Elevated nitrogen (N) deposition in humid tropical regions may aggravate phosphorus (P) deficiency in forest on old weathered soil found in these regions. From January 2007 to August 2009, we studied the responses of soil microbial biomass and community composition to P addition (in two monthly...... portions at level of 15 g P m-2 yr-1) in three tropical forests in southern China. The forests were an old-growth forest and two disturbed forests (mixed species and pine dominated). The objective was to test the hypothesis that P addition would increase microbial biomass and change the composition...... of the microbial community, and that the old-growth forests would be more sensitive to P addition due to its higher soil N availability. Microbial biomass C (MBC) was estimated twice a year and the microbial community structure was quantified by phospholipid fatty acid (PLFA) analysis at the end of the experiment...

  19. Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

    Science.gov (United States)

    Unno, Yusuke; Shinano, Takuro

    2013-01-01

    While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.

  20. Teaching Microbial Growth by Simulation.

    Science.gov (United States)

    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)

  1. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    1993-01-01

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and sulfid

  2. Microbial production of gaseous hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Hideo

    1987-10-20

    Microbial production of ethylene, isobutane and a saturated gaseous hydrocarbon mixture was described. Microbial ethylene production was studied with Penicillium digitatum IFO 9372 and a novel pathway of the ethylene biosynthesis through alpha-ketoglutarate was proposed. Rhodotorula minuta IFO 1102 was selected for the microbial production of isobutane and the interesting actions of L-leucine and L-phenylalanine for the isobutane production were found. It was finally presented about the microbial production of a saturated gaseous hydrocarbon mixture with Rhizopus japonicus IFO 4758 was described. A gas mixture was produced through a chemical reaction of SH compounds and some cellular component such as squalene under aerobic conditions. (4 figs, 7 tabs, 41 refs)

  3. The microbial ecology of permafrost.

    Science.gov (United States)

    Jansson, Janet K; Taş, Neslihan

    2014-06-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.

  4. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  5. Microbial hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, P.F.; Maness, P.C.; Martin, S. [National Renewable Energy Lab., Golden, CO (United States)] [and others

    1995-09-01

    Photosynthetic bacteria inhabit an anaerobic or microaerophilic world where H{sub 2} is produced and consumed as a shared intermediary metabolite. Within a given bacterial isolate there are as many as 4 to 6 distinct enzymes that function to evolve or consume H{sub 2}. Three of the H{sub 2}-evolving physiologies involving three different enzymes from photosynthetic bacteria have been examined in detail for commercial viability. Nitrogenase-mediated H{sub 2} production completely dissimilates many soluble organic compounds to H{sub 2} and CO{sub 2} at rates up to 131 {mu}mol H{sub 2}{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} and can remain active for up to 20 days. This metabolism is very energy intensive, however, which limits solar conversion efficiencies. Fermentative hydrogenase can produce H{sub 2} at rates of 440 {mu}mol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1} at low levels of irradiation over indefinite periods. The equilibrium for this activity is low (<0.15 atmospheres), thereby requiring gas sparging, vacuuming, or microbial scavenging to retain prolonged activity. Microbial H{sub 2} production from the CO component of synthesis or producer gases maximally reaches activities of 1.5 mmol{sm_bullet}min{sup -1}{sm_bullet}g cdw{sup -1}. Mass transport of gaseous CO into an aqueous bacterial suspension is the rate-limiting step. Increased gas pressure strongly accelerates these rates. Immobilized bacteria on solid supports at ambient pressures also show enhanced shift activity when the bulk water is drained away. Scaled-up bioreactors with 100-200 cc bed volume have been constructed and tested. The near-term goal of this portion of the project is to engineer and economically evaluate a prototype system for the biological production of H{sub 2} from biomass. The CO shift enables a positive selection technique for O{sub 2}-resistant, H{sub 2}-evolving bacterial enzymes from nature.

  6. A graph-theoretic method to quantify the airline route authority

    Science.gov (United States)

    Chan, Y.

    1979-01-01

    The paper introduces a graph-theoretic method to quantify the legal statements in route certificate which specifies the airline routing restrictions. All the authorized nonstop and multistop routes, including the shortest time routes, can be obtained, and the method suggests profitable route structure alternatives to airline analysts. This method to quantify the C.A.B. route authority was programmed in a software package, Route Improvement Synthesis and Evaluation, and demonstrated in a case study with a commercial airline. The study showed the utility of this technique in suggesting route alternatives and the possibility of improvements in the U.S. route system.

  7. Microbial fuel cell as new technol

    Directory of Open Access Journals (Sweden)

    Mostafa Rahimnejad

    2015-09-01

    Full Text Available Recently, great attentions have been paid to microbial fuel cells (MFCs due to their mild operating conditions and using variety of biodegradable substrates as fuel. The traditional MFC consisted of anode and cathode compartments but there are single chamber MFCs. Microorganisms actively catabolize substrate, and bioelectricities are generated. MFCs could be utilized as power generator in small devices such as biosensor. Besides the advantages of this technology, it still faces practical barriers such as low power and current density. In the present article different parts of MFC such as anode, cathode and membrane have been reviewed and to overcome the practical challenges in this field some practical options have been suggested. Also, this research review demonstrates the improvement of MFCs with summarization of their advantageous and possible applications in future application. Also, Different key factors affecting bioelectricity generation on MFCs were investigated and these key parameters are fully discussed.

  8. Gains and Pitfalls of Quantifier Elimination as a Teaching Tool

    Science.gov (United States)

    Oldenburg, Reinhard

    2015-01-01

    Quantifier Elimination is a procedure that allows simplification of logical formulas that contain quantifiers. Many mathematical concepts are defined in terms of quantifiers and especially in calculus their use has been identified as an obstacle in the learning process. The automatic deduction provided by quantifier elimination thus allows…

  9. Issues in the study of floating universal numeric quantifiers

    NARCIS (Netherlands)

    R. Cirillo

    2010-01-01

    In the Germanic and Romance languages (among others) a universal quantifier can combine with a numeral and form a floating quantifier. I refer to these quantifiers as universal numeric quantifiers or simply ∀NumQ. The following examples from Dutch and Romanian demonstrate this phenomenon: The aim of

  10. Microbial genomes: Blueprints for life

    Energy Technology Data Exchange (ETDEWEB)

    Relman, David A.; Strauss, Evelyn

    2000-12-31

    Complete microbial genome sequences hold the promise of profound new insights into microbial pathogenesis, evolution, diagnostics, and therapeutics. From these insights will come a new foundation for understanding the evolution of single-celled life, as well as the evolution of more complex life forms. This report is an in-depth analysis of scientific issues that provides recommendations and will be widely disseminated to the scientific community, federal agencies, industry and the public.

  11. Microbial dynamics in natural aquifers

    OpenAIRE

    Bajracharya, Bijendra Man

    2016-01-01

    Microorganisms in groundwater form ecosystems that can transform chemical compounds. Quantitatively understanding microbial dynamics in soils and groundwater is thus essential for pollutant dynamics and biogeochemistry in the subsurface. This dissertation addresses three factors influencing microbial dynamics in aquifers and soils, namely: (1) the influence of grazing on bacteria in eutrophic aquifers, posing the question whether the carrying capacity of bacteria, which has been observed i...

  12. Olive ridley sea turtle hatching success as a function of the microbial abundance in nest sand at Ostional, Costa Rica.

    Directory of Open Access Journals (Sweden)

    Vanessa S Bézy

    Full Text Available 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.

  13. A method for quantifying bioavailable organic carbon in aquifer sediments

    Science.gov (United States)

    Rectanus, H.V.; Widdowson, M.; Novak, J.; Chapelle, F.

    2005-01-01

    The fact that naturally occurring microorganisms can biodegrade PCE and TCE allows the use of monitored natural attenuation (MNA) as a remediation strategy at chlorinated solvent-contaminated sites. Research at numerous chlorinated solvent sites indicates an active dechlorinating microbial population coupled with an ample supply of organic carbon are conditions needed to sustain reductive dechlorination. A series of extraction experiments was used to compare the ability of the different extractants to remove organic carbon from aquifer sediments. The different extractants included pyrophosphate, sodium hydroxide, and polished water. Pyrophosphate served as a mild extractant that minimally alters the organic structure of the extracted material. Three concentrations (0.1, 0.5, and 1%) of pyrophosphate extracted 18.8, 24.9, and 30.8% of sediment organic carbon, respectively. Under alkali conditions (0.5 N NaOH), which provided the harshest extractant, 30.7% of the sediment organic carbon was recovered. Amorphous organic carbon, measured by potassium persulfate oxidization, consisted of 44.6% of the sediment organic carbon and served as a baseline control for maximum carbon removal. Conversely, highly purified water provided a minimal extraction control and extracted 5.7% of the sediment organic carbon. The removal of organic carbon was quantified by aqueous TOC in the extract and residual sediment organic carbon content. Characterization of the organic carbon extracts by compositional analysis prior and after exposure to the mixed culture might indicate the type organic carbon and functional groups used and/or generated by the organisms. This is an abstract of a paper presented at the 8th International In Situ and On-Site Bioremediation Symposium (Baltimore, MD 6/6-9/2005).

  14. Prediction of Competitive Microbial Growth.

    Science.gov (United States)

    Fujikawa, Hiroshi

    2016-01-01

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

  15. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  16. Molecular ecology of microbial mats.

    Science.gov (United States)

    Bolhuis, Henk; Cretoiu, Mariana Silvia; Stal, Lucas J

    2014-11-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep and fluctuating physicochemical microgradients, that are the result of the ever changing environmental conditions and of the microorganisms' own activities, give rise to a plethora of potential niches resulting in the formation of one of the most diverse microbial ecosystems known to date. For several decades, microbial mats have been studied extensively and more recently molecular biological techniques have been introduced that allowed assessing and investigating the diversity and functioning of these systems. These investigations also involved metagenomics analyses using high-throughput DNA and RNA sequencing. Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring, and hypersaline). We also present a comparison of the available metagenomic data sets from mats emphasizing the major differences between them as well as elucidating the overlap in overall community composition.

  17. Chaos and microbial systems

    Energy Technology Data Exchange (ETDEWEB)

    Kot, M.

    1990-07-01

    A recurrent theme of much recent research is that seemingly random fluctuations often occur as the result of simple deterministic mechanisms. Hence, much of the recent work in nonlinear dynamics has centered on new techniques for identifying order in seemingly chaotic systems. To determine the robustness of these techniques, chaos must, to some extent, be brought into the laboratory. Preliminary investigations of the forced double-Monod equations, a model for a predator and a prey in a chemostat with periodic variation in inflowing substrate concentration, suggest that simple microbial systems may provide the perfect framework for determining the efficacy and relevance of the new nonlinear dynamics in dealing with complex population dynamics. This research has two main goals, that is the mathematical analysis and computer simulation of the periodically forced double-Monod equations and of related models; and experimental (chemostat) population studies that evaluate the accuracy and generality of the models, and that judge the usefulness of various new techniques of nonlinear dynamics to the study of populations.

  18. Microbial production of biovanillin

    Directory of Open Access Journals (Sweden)

    A. Converti

    2010-10-01

    Full Text Available This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  19. Quantifying metabolic rates in submarine hydrothermal vent chimneys: A reaction transport model

    Science.gov (United States)

    LaRowe, D.; Dale, A.; Aguilera, D.; Amend, J. P.; Regnier, P.

    2012-12-01

    The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rate of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation-reduction reactions associated with fluid mixing as a function of temperature. Methanogenesis, hydrogen oxidation by oxygen and sulfate, sulfide oxidation by oxygen and methane oxidation by oxygen and sulfate are the metabolisms included in the reaction network. Model results indicate that microbial catalysis is fastest in the hottest habitable portion of the vent chimney except for methane oxidation by oxygen, which peaks near the seawater-side of the chimney at 20 nmol /cm^3 yr. The dominant metabolisms in the chimney are hydrogen oxidation by sulfate and oxygen and sulfide oxidation at peak rates 3200 , 300 and 900 nmol /cm^3 yr, respectively. The maximum rate of hydrogenotrophic methanogensis is just under 0.07 nmol /cm^3 yr, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). The model developed here provides a quantitative approach to understanding the rates of biogeochemical transformations in hydrothermal systems and can be used to better understand the role of microbial activity in the deep subsurface.

  20. Quantifier spreading: children misled by ostensive cues

    Directory of Open Access Journals (Sweden)

    Katalin É. Kiss

    2017-04-01

    Full Text Available This paper calls attention to a methodological problem of acquisition experiments. It shows that the economy of the stimulus employed in child language experiments may lend an increased ostensive effect to the message communicated to the child. Thus, when the visual stimulus in a sentence-picture matching task is a minimal model abstracting away from the details of the situation, children often regard all the elements of the stimulus as ostensive clues to be represented in the corresponding sentence. The use of such minimal stimuli is mistaken when the experiment aims to test whether or not a certain element of the stimulus is relevant for the linguistic representation or interpretation. The paper illustrates this point by an experiment involving quantifier spreading. It is claimed that children find a universally quantified sentence like 'Every girl is riding a bicycle 'to be a false description of a picture showing three girls riding bicycles and a solo bicycle because they are misled to believe that all the elements in the visual stimulus are relevant, hence all of them are to be represented by the corresponding linguistic description. When the iconic drawings were replaced by photos taken in a natural environment rich in accidental details, the occurrence of quantifier spreading was radically reduced. It is shown that an extra object in the visual stimulus can lead to the rejection of the sentence also in the case of sentences involving no quantification, which gives further support to the claim that the source of the problem is not (or not only the grammatical or cognitive difficulty of quantification but the unintended ostensive effect of the extra object.  This article is part of the special collection: Acquisition of Quantification

  1. Production Strategies and Applications of Microbial Single Cell Oils

    Science.gov (United States)

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  2. Production Strategies and Applications of Microbial Single Cell Oils.

    Science.gov (United States)

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  3. Production strategies and applications of microbial single cell oils

    Directory of Open Access Journals (Sweden)

    Katrin Ochsenreither

    2016-10-01

    Full Text Available Polyunsaturated fatty acids (PUFAs of the -3 and -6 class (e.g. -linolenic acid, linoleic acid are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF or solid state fermentation (SSF. The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g. medium, pH-value, temperature, aeration, nitrogen source. From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids

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

    Directory of Open Access Journals (Sweden)

    Marek eStibal

    2015-03-01

    Full Text Available 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, 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 (10^2 – 10^7 cells ml-1 and mineral particle (0.1 – 100 mg/ml 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 ca 2 x 10^3 to ca 2 x 10^6 cells/ml while dust concentrations ranged from 0.01 to 2 mg/ml. 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 Greenland Ice Sheet.

  5. Temperature-mediated changes in microbial carbon use efficiency and 13C discrimination

    Science.gov (United States)

    Lehmeier, Christoph A.; Ballantyne, Ford, IV; Min, Kyungjin; Billings, Sharon A.

    2016-06-01

    Understanding how carbon dioxide (CO2) flux from ecosystems feeds back to climate warming depends in part on our ability to quantify the efficiency with which microorganisms convert organic carbon (C) into either biomass or CO2. Quantifying ecosystem-level respiratory CO2 losses often also requires assumptions about stable C isotope fractionations associated with the microbial transformation of organic substrates. However, the diversity of organic substrates' δ13C and the challenges of measuring microbial C use efficiency (CUE) in their natural environment fundamentally limit our ability to project ecosystem C budgets in a warming climate. Here, we quantify the effect of temperature on C fluxes during metabolic transformations of cellobiose, a common microbial substrate, by a cosmopolitan microorganism growing at a constant rate. Biomass C specific respiration rate increased by 250 % between 13 and 26.5 °C, decreasing CUE from 77 to 56 %. Biomass C specific respiration rate was positively correlated with an increase in respiratory 13C discrimination from 4.4 to 6.7 ‰ across the same temperature range. This first demonstration of a direct link between temperature, microbial CUE, and associated isotope fluxes provides a critical step towards understanding δ13C of respired CO2 at multiple scales, and towards a framework for predicting future ecosystem C fluxes.

  6. Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

    Science.gov (United States)

    Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

  7. Quantifying graininess of glossy food products

    DEFF Research Database (Denmark)

    Møller, Flemming; Carstensen, Jens Michael

    The sensory quality of yoghurt can be altered when changing the milk composition or processing conditions. Part of the sensory quality may be assessed visually. It is described how a non-contact method for quantifying surface gloss and grains in yoghurt can be made. It was found that the standard...... deviation of the entire image evaluated at different scales in a Gaussian Image Pyramid was a measure for graininess of yoghurt. This methodology is used to predict graininess (or grittiness) and to evaluate effect of yoghurt composition and processing....

  8. Quantifying information leakage of randomized protocols

    DEFF Research Database (Denmark)

    Biondi, Fabrizio; Legay, Axel; Malacaria, Pasquale;

    2015-01-01

    capable to observe the internal behavior of the system, and quantify the information leakage of such systems. We also use our method to obtain an algorithm for the computation of channel capacity from our Markovian models. Finally, we show how to use the method to analyze timed and non-timed attacks......The quantification of information leakage provides a quantitative evaluation of the security of a system. We propose the usage of Markovian processes to model deterministic and probabilistic systems. By using a methodology generalizing the lattice of information approach we model refined attackers...

  9. Quantifying information leakage of randomized protocols

    DEFF Research Database (Denmark)

    Biondi, Fabrizio; Legay, Axel; Malacaria, Pasquale

    2015-01-01

    The quantification of information leakage provides a quantitative evaluation of the security of a system. We propose the usage of Markovian processes to model deterministic and probabilistic systems. By using a methodology generalizing the lattice of information approach we model refined attackers...... capable to observe the internal behavior of the system, and quantify the information leakage of such systems. We also use our method to obtain an algorithm for the computation of channel capacity from our Markovian models. Finally, we show how to use the method to analyze timed and non-timed attacks...

  10. Microbial Effects on Nuclear Waste Packaging Materials

    Energy Technology Data Exchange (ETDEWEB)

    Horn, J; Martin, S; Carrillo, C; Lian, T

    2005-07-22

    Microorganisms may enhance corrosion of components of planned engineered barriers within the proposed nuclear waste repository at Yucca Mountain (YM). Corrosion could occur either directly, through processes collectively known as Microbiologically Influenced Corrosion (MIC), or indirectly, by adversely affecting the composition of water or brines that come into direct contact with engineered barrier surfaces. Microorganisms of potential concern (bacteria, archea, and fungi) include both those indigenous to Yucca Mountain and those that infiltrate during repository construction and after waste emplacement. Specific aims of the experimental program to evaluate the potential of microorganisms to affect damage to engineered barrier materials include the following: Indirect Effects--(1) Determine the limiting factors to microbial growth and activity presently in the YM environment. (2) Assess these limiting factors to aid in determining the conditions and time during repository evolution when MIC might become operant. (3) Evaluate present bacterial densities, the composition of the YM microbial community, and determining bacterial densities if limiting factors are overcome. During a major portion of the regulatory period, environmental conditions that are presently extant become reestablished. Therefore, these studies ascertain whether biomass is sufficient to cause MIC during this period and provide a baseline for determining the types of bacterial activities that may be expected. (4) Assess biogenic environmental effects, including pH, alterations to nitrate concentration in groundwater, the generation of organic acids, and metal dissolution. These factors have been shown to be those most relevant to corrosion of engineered barriers. Direct Effects--(1) Characterize and quantify microbiological effects on candidate containment materials. These studies were carried out in a number of different approaches, using whole YM microbiological communities, a subset of YM

  11. A Statistical Framework for Microbial Source Attribution

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P; Allen, J E; Cunningham, C T

    2009-04-28

    This report presents a general approach to inferring transmission and source relationships among microbial isolates from their genetic sequences. The outbreak transmission graph (also called the transmission tree or transmission network) is the fundamental structure which determines the statistical distributions relevant to source attribution. The nodes of this graph are infected individuals or aggregated sub-populations of individuals in which transmitted bacteria or viruses undergo clonal expansion, leading to a genetically heterogeneous population. Each edge of the graph represents a transmission event in which one or a small number of bacteria or virions infects another node thus increasing the size of the transmission network. Recombination and re-assortment events originate in nodes which are common to two distinct networks. In order to calculate the probability that one node was infected by another, given the observed genetic sequences of microbial isolates sampled from them, we require two fundamental probability distributions. The first is the probability of obtaining the observed mutational differences between two isolates given that they are separated by M steps in a transmission network. The second is the probability that two nodes sampled randomly from an outbreak transmission network are separated by M transmission events. We show how these distributions can be obtained from the genetic sequences of isolates obtained by sampling from past outbreaks combined with data from contact tracing studies. Realistic examples are drawn from the SARS outbreak of 2003, the FMDV outbreak in Great Britain in 2001, and HIV transmission cases. The likelihood estimators derived in this report, and the underlying probability distribution functions required to calculate them possess certain compelling general properties in the context of microbial forensics. These include the ability to quantify the significance of a sequence 'match' or &apos

  12. Quantifying meta-correlations in financial markets

    Science.gov (United States)

    Kenett, Dror Y.; Preis, Tobias; Gur-Gershgoren, Gitit; Ben-Jacob, Eshel

    2012-08-01

    Financial markets are modular multi-level systems, in which the relationships between the individual components are not constant in time. Sudden changes in these relationships significantly affect the stability of the entire system, and vice versa. Our analysis is based on historical daily closing prices of the 30 components of the Dow Jones Industrial Average (DJIA) from March 15th, 1939 until December 31st, 2010. We quantify the correlation among these components by determining Pearson correlation coefficients, to investigate whether mean correlation of the entire portfolio can be used as a precursor for changes in the index return. To this end, we quantify the meta-correlation - the correlation of mean correlation and index return. We find that changes in index returns are significantly correlated with changes in mean correlation. Furthermore, we study the relationship between the index return and correlation volatility - the standard deviation of correlations for a given time interval. This parameter provides further evidence of the effect of the index on market correlations and their fluctuations. Our empirical findings provide new information and quantification of the index leverage effect, and have implications to risk management, portfolio optimization, and to the increased stability of financial markets.

  13. Quantifying the synchronizability of externally driven oscillators.

    Science.gov (United States)

    Stefański, Andrzej

    2008-03-01

    This paper is focused on the problem of complete synchronization in arrays of externally driven identical or slightly different oscillators. These oscillators are coupled by common driving which makes an occurrence of generalized synchronization between a driving signal and response oscillators possible. Therefore, the phenomenon of generalized synchronization is also analyzed here. The research is concentrated on the cases of an irregular (chaotic or stochastic) driving signal acting on continuous-time (Duffing systems) and discrete-time (Henon maps) response oscillators. As a tool for quantifying the robustness of the synchronized state, response (conditional) Lyapunov exponents are applied. The most significant result presented in this paper is a novel method of estimation of the largest response Lyapunov exponent. This approach is based on the complete synchronization of two twin response subsystems via additional master-slave coupling between them. Examples of the method application and its comparison with the classical algorithm for calculation of Lyapunov exponents are widely demonstrated. Finally, the idea of effective response Lyapunov exponents, which allows us to quantify the synchronizability in case of slightly different response oscillators, is introduced.

  14. An optimised method for quantifying glenoid orientation

    Directory of Open Access Journals (Sweden)

    Amadi Hippolite

    2008-01-01

    Full Text Available A robust quantification method is essential for inter-subject glenoid comparison and planning of total shoulder arthroplasty. This study compared various scapular and glenoid axes with each other in order to optimally define the most appropriate method of quantifying glenoid version and inclination. Six glenoid and eight scapular axes were defined and quantified from identifiable landmarks of twenty-one scapular image scans. Pathology independency and insensitivity of each axis to inter-subject morphological variation within its region was tested. Glenoid version and inclination were calculated using the best axes from the two regions. The best glenoid axis was the normal to a least-square plane fit on the glenoid rim, directed approximately medio-laterally. The best scapular axis was the normal to a plane formed by the spine root and lateral border ridge. Glenoid inclination was 15.7° ± 5.1° superiorly and version was 4.9° ± 6.1°, retroversion. The choice of axes in the present technique makes it insensitive to pathology and scapular morphological variabilities. Its application would effectively improve inter-subject glenoid version comparison, surgical planning and design of prostheses for shoulder arthroplasty.

  15. Quantifying chemical reactions by using mixing analysis.

    Science.gov (United States)

    Jurado, Anna; Vázquez-Suñé, Enric; Carrera, Jesús; Tubau, Isabel; Pujades, Estanislao

    2015-01-01

    This work is motivated by a sound understanding of the chemical processes that affect the organic pollutants in an urban aquifer. We propose an approach to quantify such processes using mixing calculations. The methodology consists of the following steps: (1) identification of the recharge sources (end-members) and selection of the species (conservative and non-conservative) to be used, (2) identification of the chemical processes and (3) evaluation of mixing ratios including the chemical processes. This methodology has been applied in the Besòs River Delta (NE Barcelona, Spain), where the River Besòs is the main aquifer recharge source. A total number of 51 groundwater samples were collected from July 2007 to May 2010 during four field campaigns. Three river end-members were necessary to explain the temporal variability of the River Besòs: one river end-member is from the wet periods (W1) and two are from dry periods (D1 and D2). This methodology has proved to be useful not only to compute the mixing ratios but also to quantify processes such as calcite and magnesite dissolution, aerobic respiration and denitrification undergone at each observation point.

  16. Quantifying the efficiency of river regulation

    Directory of Open Access Journals (Sweden)

    R. Rödel

    2005-01-01

    Full Text Available Dam-affected hydrologic time series give rise to uncertainties when they are used for calibrating large-scale hydrologic models or for analysing runoff records. It is therefore necessary to identify and to quantify the impact of impoundments on runoff time series. Two different approaches were employed. The first, classic approach compares the volume of the dams that are located upstream from a station with the annual discharge. The catchment areas of the stations are calculated and then related to geo-referenced dam attributes. The paper introduces a data set of geo-referenced dams linked with 677 gauging stations in Europe. Second, the intensity of the impoundment impact on runoff times series can be quantified more exactly and directly when long-term runoff records are available. Dams cause a change in the variability of flow regimes. This effect can be measured using the model of linear single storage. The dam-caused storage change ΔS can be assessed through the volume of the emptying process between two flow regimes. As an example, the storage change ΔS is calculated for regulated long-term series of the Luleälven in northern Sweden.

  17. Quantifying Emergent Behavior of Autonomous Robots

    Directory of Open Access Journals (Sweden)

    Georg Martius

    2015-10-01

    Full Text Available Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.

  18. Quantifying lateral tissue heterogeneities in hadron therapy.

    Science.gov (United States)

    Pflugfelder, D; Wilkens, J J; Szymanowski, H; Oelfke, U

    2007-04-01

    In radiotherapy with scanned particle beams, tissue heterogeneities lateral to the beam direction are problematic in two ways: they pose a challenge to dose calculation algorithms, and they lead to a high sensitivity to setup errors. In order to quantify and avoid these problems, a heterogeneity number H(i) as a method to quantify lateral tissue heterogeneities of single beam spot i is introduced. To evaluate this new concept, two kinds of potential errors were investigated for single beam spots: First, the dose calculation error has been obtained by comparing the dose distribution computed by a simple pencil beam algorithm to more accurate Monte Carlo simulations. The resulting error is clearly correlated with H(i). Second, the analysis of the sensitivity to setup errors of single beam spots also showed a dependence on H(i). From this data it is concluded that H(i) can be used as a criterion to assess the risks of a compromised delivered dose due to lateral tissue heterogeneities. Furthermore, a method how to incorporate this information into the inverse planning process for intensity modulated proton therapy is presented. By suppressing beam spots with a high value of H(i), the unfavorable impact of lateral tissue heterogeneities can be reduced, leading to treatment plans which are more robust to dose calculation errors of the pencil beam algorithm. Additional possibilities to use the information of H(i) are outlined in the discussion.

  19. Computed tomography to quantify tooth abrasion

    Science.gov (United States)

    Kofmehl, Lukas; Schulz, Georg; Deyhle, Hans; Filippi, Andreas; Hotz, Gerhard; Berndt-Dagassan, Dorothea; Kramis, Simon; Beckmann, Felix; Müller, Bert

    2010-09-01

    Cone-beam computed tomography, also termed digital volume tomography, has become a standard technique in dentistry, allowing for fast 3D jaw imaging including denture at moderate spatial resolution. More detailed X-ray images of restricted volumes for post-mortem studies in dental anthropology are obtained by means of micro computed tomography. The present study evaluates the impact of the pipe smoking wear on teeth morphology comparing the abraded tooth with its contra-lateral counterpart. A set of 60 teeth, loose or anchored in the jaw, from 12 dentitions have been analyzed. After the two contra-lateral teeth were scanned, one dataset has been mirrored before the two datasets were registered using affine and rigid registration algorithms. Rigid registration provides three translational and three rotational parameters to maximize the overlap of two rigid bodies. For the affine registration, three scaling factors are incorporated. Within the present investigation, affine and rigid registrations yield comparable values. The restriction to the six parameters of the rigid registration is not a limitation. The differences in size and shape between the tooth and its contra-lateral counterpart generally exhibit only a few percent in the non-abraded volume, validating that the contralateral tooth is a reasonable approximation to quantify, for example, the volume loss as the result of long-term clay pipe smoking. Therefore, this approach allows quantifying the impact of the pipe abrasion on the internal tooth morphology including root canal, dentin, and enamel volumes.

  20. [Microbial geochemical calcium cycle].

    Science.gov (United States)

    Zavarzin, G A

    2002-01-01

    The participation of microorganisms in the geochemical calcium cycle is the most important factor maintaining neutral conditions on the Earth. This cycle has profound influence on the fate of inorganic carbon, and, thereby, on the removal of CO2 from the atmosphere. The major part of calcium deposits was formed in the Precambrian, when prokaryotic biosphere predominated. After that, calcium recycling based on biogenic deposition by skeletal organisms became the main process. Among prokaryotes, only a few representatives, e.g., cyanobacteria, exhibit a special calcium function. The geochemical calcium cycle is made possible by the universal features of bacteria involved in biologically mediated reactions and is determined by the activities of microbial communities. In the prokaryotic system, the calcium cycle begins with the leaching of igneous rock predominantly through the action of the community of organotrophic organisms. The release of carbon dioxide to the soil air by organotrophic aerobes leads to leaching with carbonic acid and soda salinization. Under anoxic conditions, of major importance is the organic acid production by primary anaerobes (fermentative microorganisms). Calcium carbonate is precipitated by secondary anaerobes (sulfate reducers) and to a smaller degree by methanogens. The role of the cyanobacterial community in carbonate deposition is exposed by stromatolites, which are the most common organo-sedimentary Precambrian structures. Deposition of carbonates in cyanobacterial mats as a consequence of photoassimilation of CO2 does not appear to be a significant process. It is argued that carbonates were deposited at the boundary between the "soda continent", which emerged as a result of subaerial leaching with carbonic acid, and the ocean containing Ca2+. Such ecotones provided favorable conditions for the development of the benthic cyanobacterial community, which was a precursor of stromatolites.

  1. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  2. Microbial formation of labile organic carbon in Antarctic glacial environments

    Science.gov (United States)

    Smith, H. J.; Foster, R. A.; McKnight, D. M.; Lisle, J. T.; Littmann, S.; Kuypers, M. M. M.; Foreman, C. M.

    2017-04-01

    Roughly six petagrams of organic carbon are stored within ice worldwide. This organic carbon is thought to be of old age and highly bioavailable. Along with storage of ancient and new atmospherically deposited organic carbon, microorganisms may contribute substantially to the glacial organic carbon pool. Models of glacial microbial carbon cycling vary from net respiration to net carbon fixation. Supraglacial streams have not been considered in models although they are amongst the largest ecosystems on most glaciers and are inhabited by diverse microbial communities. Here we investigate the biogeochemical sequence of organic carbon production and uptake in an Antarctic supraglacial stream in the McMurdo Dry Valleys using nanometre-scale secondary ion mass spectrometry, fluorescence spectroscopy, stable isotope analysis and incubation experiments. We find that heterotrophic production relies on highly labile organic carbon freshly derived from photosynthetic bacteria rather than legacy organic carbon. Exudates from primary production were utilized by heterotrophs within 24 h, and supported bacterial growth demands. The tight coupling of microbially released organic carbon and rapid uptake by heterotrophs suggests a dynamic local carbon cycle. Moreover, as temperatures increase there is the potential for positive feedback between glacial melt and microbial transformations of organic carbon.

  3. A simulation of microbial competition in the human colonic ecosystem.

    Science.gov (United States)

    Coleman, M E; Dreesen, D W; Wiegert, R G

    1996-10-01

    Many investigations of the interactions of microbial competitors in the gastrointestinal tract used continuous-flow anaerobic cultures. The simulation reported here was a deterministic 11-compartment model coded by using the C programming language and based on parameters from published in vitro studies and assumptions were data were unavailable. The resource compartments were glucose, lactose and sucrose, starch, sorbose, and serine. Six microbial competitors included indigenous nonpathogenic colonizers of the human gastrointestinal tract (Escherichia coli, Enterobacter aerogenes, Bacteroids ovatus, Fusobacterium varium, and Enterococcus faecalis) and the potential human enteropathogen Salmonella typhimurium. Flows of carbon from the resources to the microbes were modified by resource and space controls. Partitioning of resources to the competitors that could utilize them was calculated at each iteration on the basis of availability of all resources by feeding preference functions. Resources did not accumulate during iterations of the model. The results of the computer simulation of microbial competition model and for various modifications of the model. The results were based on few measured parameters but may be useful in the design of user-friendly software to aid researchers in defining and manipulating the microbial ecology of colonic ecosystems as relates to food-borne disease.

  4. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

    Directory of Open Access Journals (Sweden)

    Suzana Cláudia Silveira Martins

    2016-01-01

    Full Text Available There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation.

  5. Constructed Wetlands Revisited: Microbial Diversity in the -omics Era.

    Science.gov (United States)

    Sánchez, Olga

    2017-04-01

    Constructed wetlands (CWs) constitute an interesting alternative option to conventional systems for wastewater treatment. This technology is based on the utilization of the concerted activity of microorganisms for the removal of contaminants. Consequently, knowledge on the microbial assemblages dwelling CWs and the different environmental factors which can alter their activities is crucial for understanding their performance. In the last decades, the use of molecular techniques to characterize these communities and more recently, application of -omics tools, have broaden our view of microbial diversity and function in wastewater microbiology. In this manuscript, a review of the current knowledge on microbial diversity in CWs is offered, placing particular emphasis on the different molecular studies carried out in this field. The effect of environmental conditions, such as plant species, hydraulic design, water depth, organic carbon, temperature and substrate type on prokaryotic communities has been carefully revised, and the different studies highlight the importance of these factors in carbon, nitrogen and sulfur cycles. Overall, the novel -omics open a new horizon to study the diversity and ecophysiology of microbial assemblages and their interactions in CWs, particularly for those microorganisms belonging to the rare biosphere not detectable with conventional molecular techniques.

  6. Algal and microbial exopolysaccharides: new insights as biosurfactants and bioemulsifiers.

    Science.gov (United States)

    Paniagua-Michel, José de Jesús; Olmos-Soto, Jorge; Morales-Guerrero, Eduardo Roberto

    2014-01-01

    Currently, efforts are being made to utilize more natural biological systems as alternatives as a way to replace fossil forms of carbon. There is a growing concern at global level to have nontoxic, nonhazardous surface-active agents; contrary to synthetic surfactants, their biological counterparts or biosurfactants play a primary function, facilitating microbial presence in environments dominated by hydrophilic-hydrophobic interfaces. Algal and microbial biosurfactants/bioemulsifiers from marine and deep-sea environments are attracting major interest due to their structural and functional diversity as molecules actives of surface and an alternative biomass to replace fossil forms of carbon. Algal and microbial surfactants are lipid in nature and classified as glycolipids, phospholipids, lipopeptides, natural lipids, fatty acids, and lipopolysaccharides. These metabolic bioactive products are applicable in a number of industries and processes, viz., food processing, pharmacology, and bioremediation of oil-polluted environments. This chapter presents an update of the progress and potentialities of the principal producers of exopolysaccharide (EPS)-type biosurfactants and bioemulsifiers, viz., macro- and microalgae (cyanobacteria and diatoms) and bacteria from marine and extreme environments. Particular interest is centered into new sources and applications, viz., marine and deep-sea environments and promissory uses of these EPSs as biosurfactants/emulsifiers and other polymeric roles. The enormous benefits of these molecules encourage their discovery, exploitation, and development of new microbial EPSs that could possess novel industrial importance and corresponding innovations.

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

    Science.gov (United States)

    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

  8. Connecting Water Quality With Air Quality Through Microbial Aerosols

    Science.gov (United States)

    Dueker, M. Elias

    Aerosol production from surface waters results in the transfer of aquatic materials (including nutrients and bacteria) to air. These materials can then be transported by onshore winds to land, representing a biogeochemical connection between aquatic and terrestrial systems not normally considered. In urban waterfront environments, this transfer could result in emissions of pathogenic bacteria from contaminated waters. Despite the potential importance of this link, sources, near-shore deposition, identity and viability of microbial aerosols are largely uncharacterized. This dissertation focuses on the environmental and biological mechanisms that define this water-air connection, as a means to build our understanding of the biogeochemical, biogeographical, and public health implications of the transfer of surface water materials to the near-shore environment in both urban and non-urban environments. The effects of tidal height, wind speed and fog on coastal aerosols and microbial content were first quantified on a non-urban coast of Maine, USA. Culture-based, culture-independent, and molecular methods were used to simultaneously sample microbial aerosols while monitoring meteorological parameters. Aerosols at this site displayed clear marine influence and high concentrations of ecologically-relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height, onshore wind speed, and fog presence. Tidal height and fog presence did not significantly influence total microbial aerosol concentrations, but did have a significant effect on culturable microbial aerosol fallout. Molecular analyses of the microbes settling out of near-shore aerosols provided further evidence of local ocean to terrestrial transport of microbes. Aerosol and surface ocean bacterial communities shared species and in general were dominated by organisms previously sampled in marine environments. Fog presence strengthened the microbial connection between water and land through

  9. Methods for quantifying training in sprint kayak.

    Science.gov (United States)

    Borges, Thiago Oliveira; Bullock, Nicola; Duff, Christine; Coutts, Aaron J

    2014-02-01

    The aims of this study were to determine the validity of the session rating of perceived exertion (session-RPE) method by comparing 3 different scales of perceived exertion with common measures of training load (TL). A secondary aim was to verify the relationship between TLs, fitness, and performance in Sprint Kayak athletes. After laboratory assessment of maximal oxygen uptake (V[Combining Dot Above]O2peak) and lactate threshold, the athletes performed on water time trials over 200 and 1,000 m. Training load was quantified for external (distance and speed) and internal (session-RPE: 6-20, category ratio [CR]-10 and CR-100 scales, training impulse [TRIMP], and individual TRIMP). Ten (6 male, 4 female) well-trained junior Sprint Kayak athletes (age 17.1 ± 1.2 years; V[Combining Dot Above]O2peak 4.2 ± 0.7 L·min) were monitored over a 7-week period. There were large-to-very large within-individual correlations between the session distance and the various heart rate (HR) and RPE-based methods for quantifying TL (0.58-0.91). Correlations between the mean session speed and various HR- and RPE-based methods for quantifying TL were small to large (0.12-0.50). The within-individual relationships between the various objective and subjective methods of internal TL were large to very large (0.62-0.94). Moderate-to-large inverse relationships were found between mean session-RPE TL and various aerobic fitness variables (-0.58 to -0.37). Large-to-very large relationships were found between mean session-RPE TL and on water performance (0.57-0.75). In conclusion, session-RPE is a valid method for monitoring TL for junior Sprint Kayak athletes, regardless of the RPE scale used. The session-RPE TL relates to fitness and performance, supporting the use of session-RPE in Sprint Kayak training.

  10. Metabolic Engineering for Substrate Co-utilization

    Science.gov (United States)

    Gawand, Pratish

    mutant LMSE2, the mutant is subjected to targeted and whole genome sequencing. Finally, we use the mutant LMSE2 to produce D-ribose from a mixture of glucose and xylose by overexpressing an endogenous phosphatase. The methods developed in this thesis are anticipated to provide a novel approach to solve sugar co-utilization problem in industrial microorganisms, and provide insights into microbial response to forced co-utilization of sugars.

  11. Modeling microbial growth and dynamics.

    Science.gov (United States)

    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.

  12. MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

    Directory of Open Access Journals (Sweden)

    T. P. Pirog

    2015-08-01

    Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

  13. Microbial ecology: Fundamentals and applications

    Energy Technology Data Exchange (ETDEWEB)

    Atlas, R.M.; Bartha, R.

    1986-01-01

    Chapter 1 contains a short historical introduction. Chapter 2, represents an updated review of microbial diversity and systematics. It also provides essential information required for the understanding of the form, function, and systematic relationship of microorganisms. Chapter 3 is devoted to the formation and structure of microbial communities, and deals with this subject both in the evolutionary and successional senses. Chapter 4 describes the interactions between microorganisms, and Chapters 5 and 6 explore the interactions of microorganisms with plants and with animals, respectively. Chapter 7 discusses the quantitative measurement of numbers, biomass, and activity of microorganisms; Chapter 8 examines the influence and the measurement of their environmental determinants. Chapter 9 presents air, water, and soil as microbial habitats and describes the typical composition of their communities. Chapters 10 and 11 contain an expanded discussion of the biogeochemical cycling activities performed by microbial communities. Chapters 12-15 deal with applied aspects of microbial ecology evident in biodeterioration control, sanitation, soil conservation, pollution control, resource recovery, and biological control.

  14. Quantifying Stream Bed Gravel Mobility from Friction Angle Measurements

    Science.gov (United States)

    Meyers, M. A.; Dunne, T.

    2012-12-01

    A method to measure friction angles using force gauges was field tested to determine its utility at quantifying critical shear stress in a gravel bedded reach of the San Joaquin River in California. Predictions of mobility from friction angles were compared with observations of the movement of tagged particles from locations for which local shear stress was quantified with a validated 2-D flow model. The observations of movement, distance of travel, and location of the end of travel were made after extended flow releases from Friant dam. Determining the critical shear stress for gravel bed material transport currently depends upon bedload sampling or tracer studies. Often, such measurements can only be made during occasional and untimely flow events, and at limited, suboptimal locations. Yet, theoretical studies conclude that the friction angle is an important control on the critical shear stress for mobility of any grain size, and therefore of the excess shear stress which strongly influences bedload transport rate. The ability to predict bed mobility at ungauged and unmonitored locations is also an important requirement for planning of flow regimes and channel design. Therefore, a method to measure friction angles that can be performed quickly in low flow conditions would prove useful for river management and research. To investigate this promising method friction angle surveys were performed at two riffle sites where differences in bed material size and distribution, and channel slope were observed. The friction angle surveys are sensitive enough to detect differences between the sites as well as spatially and temporally within a single riffle. Low friction angles were observed along the inside of a long bend where sand content was greater (by ~20%) than other surveyed locations. Friction angles decreased slightly after a depositional event associated with transient large woody debris and bank erosion, and increased again after a 5 year return interval flow

  15. Targeted Proteomics Approaches To Monitor Microbial Activity In Basalt Aquifer

    Science.gov (United States)

    Paszczynski, A. J.; Paidisetti, R.

    2007-12-01

    communities to allow for better identification of specific proteins. This method not only identified the proteins of interest but also increased the peptide coverage and increased the number of proteins identified. We were able to identify methane monooxygenase proteins within TAN site microbial communities supporting the occurrence of co-metabolic oxidation of TCE in this aquifer. We correlated methane monooxygenase presence with the number of methanotrophs in the samples obtained through quantitative PCR and quantitative proteomic methods. Utilization of this extraction method in combination with UPLC/MS/MS resulted in successful extraction, identification, and quantification of MMO-derived biomarker peptides from both pure cultures and environmental samples. Along with MMO proteins, we identified proteins from non-methanotrophic organisms that may play major roles in macronutrients turnover and the attenuation of TCE in the TAN aquifer.

  16. Extensive microbial and functional diversity within the chicken cecal microbiome.

    Directory of Open Access Journals (Sweden)

    Martin J Sergeant

    Full Text Available Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs, the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.

  17. How to quantify conduits in wood?

    Directory of Open Access Journals (Sweden)

    Alexander eScholz

    2013-03-01

    Full Text Available Vessels and tracheids represent the most important xylem cells with respect to long distance water transport in plants. Wood anatomical studies frequently provide several quantitative details of these cells, such as vessel diameter, vessel density, vessel element length, and tracheid length, while important information on the three dimensional structure of the hydraulic network is not considered. This paper aims to provide an overview of various techniques, although there is no standard protocol to quantify conduits due to high anatomical variation and a wide range of techniques available. Despite recent progress in image analysis programs and automated methods for measuring cell dimensions, density, and spatial distribution, various characters remain time-consuming and tedious. Quantification of vessels and tracheids is not only important to better understand functional adaptations of tracheary elements to environment parameters, but will also be essential for linking wood anatomy with other fields such as wood development, xylem physiology, palaeobotany, and dendrochronology.

  18. Quantifying creativity: can measures span the spectrum?

    Science.gov (United States)

    Simonton, Dean Keith

    2012-01-01

    Because the cognitive neuroscientists have become increasingly interested in the phenomenon of creativity, the issue arises of how creativity is to be optimally measured. Unlike intelligence, which can be assessed across the full range of intellectual ability creativity measures tend to concentrate on different sections of the overall spectrum. After first defining creativity in terms of the three criteria of novelty, usefulness, and surprise, this article provides an overview of the available measures. Not only do these instruments vary according to whether they focus on the creative process, person, or product, but they differ regarding whether they tap into “little-c” versus “Big-C” creativity; only productivity and eminence measures reach into genius-level manifestations of the phenomenon. The article closes by discussing whether various alternative assessment techniques can be integrated into a single measure that quantifies creativity across the full spectrum. PMID:22577309

  19. Message passing for quantified Boolean formulas

    CERN Document Server

    Zhang, Pan; Zdeborová, Lenka; Zecchina, Riccardo

    2012-01-01

    We introduce two types of message passing algorithms for quantified Boolean formulas (QBF). The first type is a message passing based heuristics that can prove unsatisfiability of the QBF by assigning the universal variables in such a way that the remaining formula is unsatisfiable. In the second type, we use message passing to guide branching heuristics of a Davis-Putnam Logemann-Loveland (DPLL) complete solver. Numerical experiments show that on random QBFs our branching heuristics gives robust exponential efficiency gain with respect to the state-of-art solvers. We also manage to solve some previously unsolved benchmarks from the QBFLIB library. Apart from this our study sheds light on using message passing in small systems and as subroutines in complete solvers.

  20. Quantifying decoherence in continuous variable systems

    Energy Technology Data Exchange (ETDEWEB)

    Serafini, A [Dipartimento di Fisica ' ER Caianiello' , Universita di Salerno, INFM UdR Salerno, INFN Sezione Napoli, Gruppo Collegato Salerno, Via S Allende, 84081 Baronissi, SA (Italy); Paris, M G A [Dipartimento di Fisica and INFM, Universita di Milano, Milan (Italy); Illuminati, F [Dipartimento di Fisica ' ER Caianiello' , Universita di Salerno, INFM UdR Salerno, INFN Sezione Napoli, Gruppo Collegato Salerno, Via S Allende, 84081 Baronissi, SA (Italy); De Siena, S [Dipartimento di Fisica ' ER Caianiello' , Universita di Salerno, INFM UdR Salerno, INFN Sezione Napoli, Gruppo Collegato Salerno, Via S Allende, 84081 Baronissi, SA (Italy)

    2005-04-01

    We present a detailed report on the decoherence of quantum states of continuous variable systems under the action of a quantum optical master equation resulting from the interaction with general Gaussian uncorrelated environments. The rate of decoherence is quantified by relating it to the decay rates of various, complementary measures of the quantum nature of a state, such as the purity, some non-classicality indicators in phase space, and, for two-mode states, entanglement measures and total correlations between the modes. Different sets of physically relevant initial configurations are considered, including one- and two-mode Gaussian states, number states, and coherent superpositions. Our analysis shows that, generally, the use of initially squeezed configurations does not help to preserve the coherence of Gaussian states, whereas it can be effective in protecting coherent superpositions of both number states and Gaussian wavepackets. (review article)

  1. Quantifying truncation errors in effective field theory

    CERN Document Server

    Furnstahl, R J; Phillips, D R; Wesolowski, S

    2015-01-01

    Bayesian procedures designed to quantify truncation errors in perturbative calculations of quantum chromodynamics observables are adapted to expansions in effective field theory (EFT). In the Bayesian approach, such truncation errors are derived from degree-of-belief (DOB) intervals for EFT predictions. Computation of these intervals requires specification of prior probability distributions ("priors") for the expansion coefficients. By encoding expectations about the naturalness of these coefficients, this framework provides a statistical interpretation of the standard EFT procedure where truncation errors are estimated using the order-by-order convergence of the expansion. It also permits exploration of the ways in which such error bars are, and are not, sensitive to assumptions about EFT-coefficient naturalness. We first demonstrate the calculation of Bayesian probability distributions for the EFT truncation error in some representative examples, and then focus on the application of chiral EFT to neutron-pr...

  2. Quantifying interspecific coagulation efficiency of phytoplankton

    DEFF Research Database (Denmark)

    Hansen, J.L.S.; Kiørboe, Thomas

    1997-01-01

    Non-sticky latex beads and sticky diatoms were used as models to describe mutual coagulation between sticky and non-sticky particles. in mixed suspensions of beads and Thalassiosira nordenskjoeldii, both types of particles coagulated into mixed aggregates at specific rates, from which the intersp......Non-sticky latex beads and sticky diatoms were used as models to describe mutual coagulation between sticky and non-sticky particles. in mixed suspensions of beads and Thalassiosira nordenskjoeldii, both types of particles coagulated into mixed aggregates at specific rates, from which....... nordenskjoeldii. Mutual coagulation between Skeletonema costatum and the non-sticky cel:ls of Ditylum brightwellii also proceeded with hall the efficiency of S. costatum alone. The latex beads were suitable to be used as 'standard particles' to quantify the ability of phytoplankton to prime aggregation...

  3. Extraction of quantifiable information from complex systems

    CERN Document Server

    Dahmen, Wolfgang; Griebel, Michael; Hackbusch, Wolfgang; Ritter, Klaus; Schneider, Reinhold; Schwab, Christoph; Yserentant, Harry

    2014-01-01

    In April 2007, the  Deutsche Forschungsgemeinschaft (DFG) approved the  Priority Program 1324 “Mathematical Methods for Extracting Quantifiable Information from Complex Systems.” This volume presents a comprehensive overview of the most important results obtained over the course of the program.   Mathematical models of complex systems provide the foundation for further technological developments in science, engineering and computational finance.  Motivated by the trend toward steadily increasing computer power, ever more realistic models have been developed in recent years. These models have also become increasingly complex, and their numerical treatment poses serious challenges.   Recent developments in mathematics suggest that, in the long run, much more powerful numerical solution strategies could be derived if the interconnections between the different fields of research were systematically exploited at a conceptual level. Accordingly, a deeper understanding of the mathematical foundations as w...

  4. Quantifying Power Grid Risk from Geomagnetic Storms

    Science.gov (United States)

    Homeier, N.; Wei, L. H.; Gannon, J. L.

    2012-12-01

    We are creating a statistical model of the geophysical environment that can be used to quantify the geomagnetic storm hazard to power grid infrastructure. Our model is developed using a database of surface electric fields for the continental United States during a set of historical geomagnetic storms. These electric fields are derived from the SUPERMAG compilation of worldwide magnetometer data and surface impedances from the United States Geological Survey. This electric field data can be combined with a power grid model to determine GICs per node and reactive MVARs at each minute during a storm. Using publicly available substation locations, we derive relative risk maps by location by combining magnetic latitude and ground conductivity. We also estimate the surface electric fields during the August 1972 geomagnetic storm that caused a telephone cable outage across the middle of the United States. This event produced the largest surface electric fields in the continental U.S. in at least the past 40 years.

  5. A Simulation Platform for Quantifying Survival Bias

    DEFF Research Database (Denmark)

    Mayeda, Elizabeth Rose; Tchetgen Tchetgen, Eric J; Power, Melinda C

    2016-01-01

    Bias due to selective mortality is a potential concern in many studies and is especially relevant in cognitive aging research because cognitive impairment strongly predicts subsequent mortality. Biased estimation of the effect of an exposure on rate of cognitive decline can occur when mortality i......-mortality situations. This simulation platform provides a flexible tool for evaluating biases in studies with high mortality, as is common in cognitive aging research.......Bias due to selective mortality is a potential concern in many studies and is especially relevant in cognitive aging research because cognitive impairment strongly predicts subsequent mortality. Biased estimation of the effect of an exposure on rate of cognitive decline can occur when mortality...... platform with which to quantify the expected bias in longitudinal studies of determinants of cognitive decline. We evaluated potential survival bias in naive analyses under several selective survival scenarios, assuming that exposure had no effect on cognitive decline for anyone in the population. Compared...

  6. Quantifying the risk of extreme aviation accidents

    Science.gov (United States)

    Das, Kumer Pial; Dey, Asim Kumer

    2016-12-01

    Air travel is considered a safe means of transportation. But when aviation accidents do occur they often result in fatalities. Fortunately, the most extreme accidents occur rarely. However, 2014 was the deadliest year in the past decade causing 111 plane crashes, and among them worst four crashes cause 298, 239, 162 and 116 deaths. In this study, we want to assess the risk of the catastrophic aviation accidents by studying historical aviation accidents. Applying a generalized Pareto model we predict the maximum fatalities from an aviation accident in future. The fitted model is compared with some of its competitive models. The uncertainty in the inferences are quantified using simulated aviation accident series, generated by bootstrap resampling and Monte Carlo simulations.

  7. Historic Food Production Shocks: Quantifying the Extremes

    Directory of Open Access Journals (Sweden)

    Aled W. Jones

    2016-04-01

    Full Text Available Understanding global food production trends is vital for ensuring food security and to allow the world to develop appropriate policies to manage the food system. Over the past few years, there has been an increasing attention on the global food system, particularly after the extreme shocks seen in food prices after 2007. Several papers and working groups have explored the links between food production and various societal impacts however they often categorise production shocks in different ways even to the extent of identifying different levels, countries and timings for shocks. In this paper we present a simple method to quantify and categorise cereal production shocks at a country level. This method can be used as a baseline for other studies that examine the impact of these production shocks on the global food system.

  8. Quantifying the Anthropogenic Footprint in Eastern China

    Science.gov (United States)

    Meng, Chunlei; Dou, Youjun

    2016-04-01

    Urban heat island (UHI) is one of the most focuses in urban climate study. The parameterization of the anthropogenic heat (AH) is crucial important in UHI study, but universal method to parameterize the spatial pattern of the AH is lacking now. This paper uses the NOAA DMSP/OLS nighttime light data to parameterize the spatial pattern of the AH. Two experiments were designed and performed to quantify the influences of the AH to land surface temperature (LST) in eastern China and 24 big cities. The annual mean heating caused by AH is up to 1 K in eastern China. This paper uses the relative LST differences rather than the absolute LST differences between the control run and contrast run of common land model (CoLM) to find the drivers. The heating effect of the anthropogenic footprint has less influence on relatively warm and wet cities.

  9. Animal biometrics: quantifying and detecting phenotypic appearance.

    Science.gov (United States)

    Kühl, Hjalmar S; Burghardt, Tilo

    2013-07-01

    Animal biometrics is an emerging field that develops quantified approaches for representing and detecting the phenotypic appearance of species, individuals, behaviors, and morphological traits. It operates at the intersection between pattern recognition, ecology, and information sciences, producing computerized systems for phenotypic measurement and interpretation. Animal biometrics can benefit a wide range of disciplines, including biogeography, population ecology, and behavioral research. Currently, real-world applications are gaining momentum, augmenting the quantity and quality of ecological data collection and processing. However, to advance animal biometrics will require integration of methodologies among the scientific disciplines involved. Such efforts will be worthwhile because the great potential of this approach rests with the formal abstraction of phenomics, to create tractable interfaces between different organizational levels of life.

  10. Quantifying decoherence in continuous variable systems

    CERN Document Server

    Serafini, A; Illuminati, F; De Siena, S

    2005-01-01

    We present a detailed report on the decoherence of quantum states of continuous variable systems under the action of a quantum optical master equation resulting from the interaction with general Gaussian uncorrelated environments. The rate of decoherence is quantified by relating it to the decay rates of various, complementary measures of the quantum nature of a state, such as the purity, some nonclassicality indicators in phase space and, for two-mode states, entanglement measures and total correlations between the modes. Different sets of physically relevant initial configurations are considered, including one- and two-mode Gaussian states, number states, and coherent superpositions. Our analysis shows that, generally, the use of initially squeezed configurations does not help to preserve the coherence of Gaussian states, whereas it can be effective in protecting coherent superpositions of both number states and Gaussian wave packets.

  11. Another analytic view about quantifying social forces

    CERN Document Server

    Ausloos, Marcel

    2012-01-01

    Montroll had considered a Verhulst evolution approach for introducing a notion he called "social force", to describe a jump in some economic output when a new technology or product outcompetes a previous one. In fact, Montroll's adaptation of Verhulst equation is more like an economic field description than a "social force". The empirical Verhulst logistic function and the Gompertz double exponential law are used here in order to present an alternative view, within a similar mechanistic physics framework. As an example, a "social force" modifying the rate in the number of temples constructed by a religious movement, the Antoinist community, between 1910 and 1940 in Belgium is found and quantified. Practically, two temple inauguration regimes are seen to exist over different time spans, separated by a gap attributed to a specific "constraint", a taxation system, but allowing for a different, smooth, evolution rather than a jump. The impulse force duration is also emphasized as being better taken into account w...

  12. Quantifying the Cognitive Extent of Science

    CERN Document Server

    Milojević, Staša

    2015-01-01

    While the modern science is characterized by an exponential growth in scientific literature, the increase in publication volume clearly does not reflect the expansion of the cognitive boundaries of science. Nevertheless, most of the metrics for assessing the vitality of science or for making funding and policy decisions are based on productivity. Similarly, the increasing level of knowledge production by large science teams, whose results often enjoy greater visibility, does not necessarily mean that "big science" leads to cognitive expansion. Here we present a novel, big-data method to quantify the extents of cognitive domains of different bodies of scientific literature independently from publication volume, and apply it to 20 million articles published over 60-130 years in physics, astronomy, and biomedicine. The method is based on the lexical diversity of titles of fixed quotas of research articles. Owing to large size of quotas, the method overcomes the inherent stochasticity of article titles to achieve...

  13. How to quantify conduits in wood?

    Science.gov (United States)

    Scholz, Alexander; Klepsch, Matthias; Karimi, Zohreh; Jansen, Steven

    2013-01-01

    Vessels and tracheids represent the most important xylem cells with respect to long distance water transport in plants. Wood anatomical studies frequently provide several quantitative details of these cells, such as vessel diameter, vessel density, vessel element length, and tracheid length, while important information on the three dimensional structure of the hydraulic network is not considered. This paper aims to provide an overview of various techniques, although there is no standard protocol to quantify conduits due to high anatomical variation and a wide range of techniques available. Despite recent progress in image analysis programs and automated methods for measuring cell dimensions, density, and spatial distribution, various characters remain time-consuming and tedious. Quantification of vessels and tracheids is not only important to better understand functional adaptations of tracheary elements to environment parameters, but will also be essential for linking wood anatomy with other fields such as wood development, xylem physiology, palaeobotany, and dendrochronology.

  14. Quantifying capital goods for waste landfilling

    DEFF Research Database (Denmark)

    Brogaard, Line Kai-Sørensen; Stentsøe, Steen; Willumsen, Hans Christian

    2013-01-01

    Materials and energy used for construction of a hill-type landfill of 4 million m3 were quantified in detail. The landfill is engineered with a liner and leachate collections system, as well as a gas collection and control system. Gravel and clay were the most common materials used, amounting...... to approximately 260 kg per tonne of waste landfilled. The environmental burdens from the extraction and manufacturing of the materials used in the landfill, as well as from the construction of the landfill, were modelled as potential environmental impacts. For example, the potential impact on global warming was 2.......5 kg carbon dioxide (CO2) equivalents or 0.32 milli person equivalents per tonne of waste. The potential impacts from the use of materials and construction of the landfill are low-to-insignificant compared with data reported in the literature on impact potentials of landfills in operation...

  15. Quantifying capital goods for waste incineration

    DEFF Research Database (Denmark)

    Brogaard, Line Kai-Sørensen; Riber, C.; Christensen, Thomas Højlund

    2013-01-01

    Materials and energy used for the construction of modern waste incineration plants were quantified. The data was collected from five incineration plants (72,000–240,000tonnes per year) built in Scandinavia (Norway, Finland and Denmark) between 2006 and 2012. Concrete for the buildings was the main...... of producing the materials used in the construction, steel for the building and the machinery contributed the most. The material and energy used for the construction corresponded to the emission of 7–14kg CO2 per tonne of waste combusted throughout the lifetime of the incineration plant. The assessment showed...... material used amounting to 19,000–26,000tonnes per plant. The quantification further included six main materials, electronic systems, cables and all transportation. The energy used for the actual on-site construction of the incinerators was in the range 4000–5000MWh. In terms of the environmental burden...

  16. Quantifying creativity: can measures span the spectrum?

    Science.gov (United States)

    Simonton, Dean Keith

    2012-03-01

    Because the cognitive neuroscientists have become increasingly interested in the phenomenon of creativity, the issue arises of how creativity is to be optimally measured. Unlike intelligence, which can be assessed across the full range of intellectual ability creativity measures tend to concentrate on different sections of the overall spectrum. After first defining creativity in terms of the three criteria of novelty, usefulness, and surprise, this article provides an overview of the available measures. Not only do these instruments vary according to whether they focus on the creative process, person, or product, but they differ regarding whether they tap into "little-c" versus "Big-C" creativity; only productivity and eminence measures reach into genius-level manifestations of the phenomenon. The article closes by discussing whether various alternative assessment techniques can be integrated into a single measure that quantifies creativity across the full spectrum.

  17. Towards Quantifying a Wider Reality: Shannon Exonerata

    Directory of Open Access Journals (Sweden)

    Robert E. Ulanowicz

    2011-10-01

    Full Text Available In 1872 Ludwig von Boltzmann derived a statistical formula to represent the entropy (an apophasis of a highly simplistic system. In 1948 Claude Shannon independently formulated the same expression to capture the positivist essence of information. Such contradictory thrusts engendered decades of ambiguity concerning exactly what is conveyed by the expression. Resolution of widespread confusion is possible by invoking the third law of thermodynamics, which requires that entropy be treated in a relativistic fashion. Doing so parses the Boltzmann expression into separate terms that segregate apophatic entropy from positivist information. Possibly more importantly, the decomposition itself portrays a dialectic-like agonism between constraint and disorder that may provide a more appropriate description of the behavior of living systems than is possible using conventional dynamics. By quantifying the apophatic side of evolution, the Shannon approach to information achieves what no other treatment of the subject affords: It opens the window on a more encompassing perception of reality.

  18. Identification of Soil Microbes Capable of Utilizing Cellobiosan.

    Directory of Open Access Journals (Sweden)

    Jieni Lian

    Full Text Available Approximately 100 million tons of anhydrosugars, such as levoglucosan and cellobiosan, are produced through biomass burning every year. These sugars are also produced through fast pyrolysis, the controlled thermal depolymerization of biomass. While the microbial pathways associated with levoglucosan utilization have been characterized, there is little known about cellobiosan utilization. Here we describe the isolation and characterization of six cellobiosan-utilizing microbes from soil samples. Each of these organisms is capable of using both cellobiosan and levoglucosan as sole carbon source, though both minimal and rich media cellobiosan supported significantly higher biomass production than levoglucosan. Ribosomal sequencing was used to identify the closest reported match for these organisms: Sphingobacterium multivorum, Acinetobacter oleivorans JC3-1, Enterobacter sp SJZ-6, and Microbacterium sps FXJ8.207 and 203 and a fungal species Cryptococcus sp. The commercially-acquired Enterobacter cloacae DSM 16657 showed growth on levoglucosan and cellobiosan, supporting our isolate identification. Analysis of an existing database of 16S rRNA amplicons from Iowa soil samples confirmed the representation of our five bacterial isolates and four previously-reported levoglucosan-utilizing bacterial isolates in other soil samples and provided insight into their population distributions. Phylogenetic analysis of the 16S rRNA and 18S rRNA of strains previously reported to utilize levoglucosan and our newfound isolates showed that the organisms isolated in this study are distinct from previously described anhydrosugar-utilizing microbial species.

  19. Quantifying structural states of soft mudrocks

    Science.gov (United States)

    Li, B.; Wong, R. C. K.

    2016-05-01

    In this paper, a cm model is proposed to quantify structural states of soft mudrocks, which are dependent on clay fractions and porosities. Physical properties of natural and reconstituted soft mudrock samples are used to derive two parameters in the cm model. With the cm model, a simplified homogenization approach is proposed to estimate geomechanical properties and fabric orientation distributions of soft mudrocks based on the mixture theory. Soft mudrocks are treated as a mixture of nonclay minerals and clay-water composites. Nonclay minerals have a high stiffness and serve as a structural framework of mudrocks when they have a high volume fraction. Clay-water composites occupy the void space among nonclay minerals and serve as an in-fill matrix. With the increase of volume fraction of clay-water composites, there is a transition in the structural state from the state of framework supported to the state of matrix supported. The decreases in shear strength and pore size as well as increases in compressibility and anisotropy in fabric are quantitatively related to such transition. The new homogenization approach based on the proposed cm model yields better performance evaluation than common effective medium modeling approaches because the interactions among nonclay minerals and clay-water composites are considered. With wireline logging data, the cm model is applied to quantify the structural states of Colorado shale formations at different depths in the Cold Lake area, Alberta, Canada. Key geomechancial parameters are estimated based on the proposed homogenization approach and the critical intervals with low strength shale formations are identified.

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

    Science.gov (United States)

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

    2012-07-01

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

  1. Precambrian Skeletonized Microbial Eukaryotes

    Science.gov (United States)

    Lipps, Jere H.

    2017-04-01

    . Tintinnids first appear in the mid-Mesozoic, like other modern planktic groups, including planktic foraminifera, new types of radiolarians, and a host of skeletal micro-algae. Microbial eukaryotes track algal eukaryote and metazoan evolution—none or very few in the Precambrian, some in the early Paleozoic with radiations in the later Paleozoic, Mesozoic and Cenozoic, with extinctions ( 30) reducing their biodiversity at particular times in the fossil record—thus indicating strong environmental selection on all marine groups.

  2. Substituição do milho pela casca de café ou de soja em dietas para vacas leiteiras: comportamento ingestivo, concentração de nitrogênio uréico no plasma e no leite, balanço de compostos nitrogenados e produção de proteína microbiana Replacing corn with coffee hulls or soyhulls in diets of dairy cows: chewing activity, ruminal metabolism, nitrogen utilization and microbial protein synthesis

    Directory of Open Access Journals (Sweden)

    André Soares de Oliveira

    2007-02-01

    Full Text Available Objetivou-se avaliar o efeito da substituição do milho pela casca de café ou pela casca de soja em dietas à base de cana-de-açúcar, com 60% de concentrado, sobre o comportamento ingestivo, o pH e a concentração de amônia no líquido ruminal, a excreção de uréia na urina (EU, a concentração de N-uréia no plasma (NUP e no leite (NUL, o balanço de compostos nitrogenados e a síntese de proteína microbiana em vacas leiteiras, em comparação a uma dieta com silagem de milho. Foram utilizadas 12 vacas holandesas, puras e mestiças, distribuídas em três quadrados latinos 4 x 4. A dieta controle foi composta de silagem de milho e 40% de concentrado (SiMi, com base na MS. Foram utilizadas três dietas contendo cana-de-açúcar e 60% de concentrado, de modo que os percentuais de substituição do milho foram 0% (CMi, 25% com casca de café (CCC ou 50% com casca de soja (CCS, com base na MS total da dieta. O tempo total de mastigação foi menor para a dieta SiMi e não foi afetado pela inclusão de casca de café ou casca de soja. O pH ruminal não diferiu nos tempos 0 e 3 horas após a alimentação matinal. A dieta CCC resultou, três horas após alimentação, em menor concentração de amônia ruminal em relação às demais, com exceção da dieta CMi. Não foram observadas diferenças na EU e NUL, sendo registrados valores médios de 179,31 mg/kg de PV e 12,59 mg/dL, respectivamente. A substituição do milho pela casca de café ou de soja não promove melhora no ambiente ruminal. A síntese de compostos nitrogenados microbianos e a eficiência microbiana ruminal não são influenciadas pelas dietas e apresentam valores médios de 273 g/dia e 130,08 gPBmic/kg de NDT, respectivamente.Twelve purebred and crossbred Holstein cows were assigned to three replicated 4 x 4 Latin squares to evaluate the effects of replacing corn grain with coffee hulls or soyhulls on chewing activity, ruminal metabolism, nitrogen utilization, and

  3. Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

    Science.gov (United States)

    Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

    2012-12-01

    effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

  4. Pyrite oxidation by microbial consortia

    Science.gov (United States)

    Bostick, B. C.; Revill, K. L.; Doyle, C.; Kendelewicz, T.; Brown, G. E.; Spormann, A. M.; Fendorf, S.

    2003-12-01

    Acid mine drainage (AMD) is formed through pyrite oxidation, which produces acidity and releases toxic metals associated with pyrite and other sulfide minerals. Microbes accelerate pyrite oxidation markedly, thereby playing a major role in the production of AMD. Here, we probe pyrite oxidation by consortia of Thiobacillus ferrooxidans and thiooxidans using surface-sensitive photoelectron spectroscopy and X-ray absorption spectroscopy and compare them with surfaces oxidized through chemical and single species cultures. Microbial oxidation resulted in the formation of distinct oxidized surface species distributed non-uniformly over the pyrite surface; consortia produced a surface both more heterogeneous and more oxidized. In contrast, chemical oxidation proceeds without the build-up of passivating oxidation products. Surface morphology was not correlated with sites of nucleation or oxidation in any obvious manner. These results demonstrate that microbial oxidation occurs through a similar mechanism to chemical oxidation, but that the presence of complex microbial communities may impact the manner by which pyrite oxidation proceeds.

  5. Microbial metagenomics: beyond the genome.

    Science.gov (United States)

    Gilbert, Jack A; Dupont, Christopher L

    2011-01-01

    Metagenomics literally means "beyond the genome." Marine microbial metagenomic databases presently comprise approximately 400 billion base pairs of DNA, only approximately 3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

  6. Microbial Metagenomics: Beyond the Genome

    Science.gov (United States)

    Gilbert, Jack A.; Dupont, Christopher L.

    2011-01-01

    Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ˜400 billion base pairs of DNA, only ˜3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

  7. A Generalized Spatial Measure for Resilience of Microbial Systems

    Energy Technology Data Exchange (ETDEWEB)

    Renslow, Ryan S.; Lindemann, Stephen R.; Song, Hyun-Seob

    2016-04-07

    The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition, i.e., a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. As a limitation, however, this spatial metric of resilience is useful only for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (i.e., a sharp or smooth gradient). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat. PASMORE can help identify when a system, such as a microbial community, is on the verge of collapse or nearing an irreversible transition across a tipping point.

  8. Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates

    Directory of Open Access Journals (Sweden)

    AK Gregg

    2013-07-01

    Full Text Available Algae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA. BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community.

  9. Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

    Science.gov (United States)

    Radhakrishnan, Srinivasan; Varadharajan, Mohan

    2016-06-01

    Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems.

  10. Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates.

    Science.gov (United States)

    Gregg, Ak; Hatay, M; Haas, Af; Robinett, Nl; Barott, K; Vermeij, Mja; Marhaver, Kl; Meirelles, P; Thompson, F; Rohwer, F

    2013-01-01

    Algae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD) optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA). BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR) system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic) contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community.

  11. Universality of human microbial dynamics

    Science.gov (United States)

    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.

  12. Compound-specific 15N stable isotope probing of N assimilation by the soil microbial biomass: a new methodological paradigm in soil N cycling

    Science.gov (United States)

    Charteris, A. F.; Knowles, T. D. J.; Michaelides, K.; Evershed, R. P.

    2015-10-01

    A compound-specific nitrogen-15 stable isotope probing (15N-SIP) technique is described which allows investigation of the fate of inorganic- or organic-N amendments to soils. The technique uses gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) to determine the δ15N values of individual amino acids (AAs; determined as N-acetyl, O-isopropyl derivatives) as proxies of biomass protein production. The δ15N values are used together with AA concentrations to quantify N assimilation of 15N-labelled substrates by the soil microbial biomass. The utility of the approach is demonstrated through incubation experiments using inorganic 15N-labelled substrates ammonium (15NH4+) and nitrate (15NO3-) and an organic 15N-labelled substrate, glutamic acid (15N-Glu). Assimilation of all the applied substrates was undetectable based on bulk soil properties, i.e. % total N (% TN), bulk soil N isotope composition and AA concentrations, all of which remained relatively constant throughout the incubation experiments. In contrast, compound-specific AA δ15N values were highly sensitive to N assimilation, providing qualitative and quantitative insights into the cycling and fate of the applied 15N-labelled substrates. The utility of this 15N-AA-SIP technique is considered in relation to other currently available methods for investigating the microbially-mediated assimilation of nitrogenous substrates into the soil organic N pool. This approach will be generally applicable to the study of N cycling in any soil, or indeed, in any complex ecosystem.

  13. Functional Stability Of A Mixed Microbial Consortia Producing PHA From Waste Carbon Sources

    Energy Technology Data Exchange (ETDEWEB)

    David N. Thompson; Erik R. Coats; William A. Smith; Frank J. Loge; Michael P. Wolcott

    2006-04-01

    Polyhydroxyalkanoates (PHAs), naturally-occurring biological polyesters that are microbially synthesized from a myriad of carbon sources, can be utilized as biodegradable substitutes for petroleum-derived thermoplastics. However, current PHA commercialization schemes are limited by high feedstock costs, the requirement for aseptic reactors, and high separation and purification costs. Bacteria indigenous to municipal waste streams can accumulate large quantities of PHA under environmentally controlled conditions; hence, a potentially more environmentally-effective method of production would utilize these consortia to produce PHAs from inexpensive waste carbon sources. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing mixed microbial consortia from municipal activated sludge as inoculum, in cultures grown on real wastewaters. PHA production averaged 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. The PHA-producing microbial consortia were examined to explore the microbial community changes that occurred during reactor operations, employing denaturing gradient gel electrophoresis (DGGE) of 16S-rDNA from PCR-amplified DNA extracts. Distinctly different communities were observed both between and within wastewaters following enrichment. More importantly, stable functions were maintained despite the differing and contrasting microbial populations.

  14. [Seasonal variation of functional diversity of aquatic microbial community in Apostichopus japonicus cultural pond].

    Science.gov (United States)

    Yan, Fa-Jun; Tian, Xiang-Li; Dong, Shuang-Lin; Yang, Gang

    2014-05-01

    The functional diversity of aquatic microbial communities in sea cucumber (Apostichopus japonicus) cultural ponds was examined in this paper. The Biolog plate technique and redundancy analysis (RDA) method were used to evaluate seasonal changes and their relationships with environmental factors. The results showed that both total amount and types of carbon sources utilized by microbes in the sea cucumber cultural ponds varied seasonally, and were the highest in summer and lowest in winter, with polymers being the main type of carbon sources. Principal component analysis revealed that the carbon utilization diversity of the microbial communities varied significantly over the seasonal courses. A total of 10 categories of carbon sources were significantly related to the principal component 1, among which were polymers, carbohydrates, carboxylic acids, amino acids, and amines. Significant seasonal changes were detected for all carbon utilization diversity indices of the microbial communities, including Shannon, McIntosh, Simpson, and S-E. However, seasonal variations were different among the microbial diversity indices. RDA analysis revealed that TP, NO(3-)-N, TN, and PO4(3-)-P were the critical environmental factors influencing the seasonal changes in functional diversity of aquatic microbial community in sea cucumber cultural ponds.

  15. Recent progress in microbial cultivation techniques.

    Science.gov (United States)

    Park, Enoch Y

    2004-01-01

    Recent advances in the improvement of microbial cultivation are reviewed, with emphasis on biochemical engineering techniques as a means of obtaining high production rate of bioproduct. Possible uses of high cell density culture include their use in food industry as well as in the production of new medicines and in biotechnology. Concentration of microorganisms using a hollow fiber membrane or centrifuge, and increase in cell density by controlling the pH, dissolved oxygen, or carbon source concentrations of the culture broth with control algorithms are discussed. In a culture of filamentous microorganisms the mycelial morphology is hard to define and it is difficult to quantify its amount, and this is one of the bottlenecks hampering the improvement of production rate. Specific features of mycelial cultivation in the presence of highly pulpy mycelia and entangled-pellets are scrutinized by visual inspection through a microscope that is linked to a computer, and using software that can characterize the mycelial morphology. Image analysis technology for analyzing the mycelial image captured by a digital camera is a potential tool for morphological analysis, including analysis of the morphological development of filamentous microorganisms.

  16. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania.

    Directory of Open Access Journals (Sweden)

    Jay S Reti

    Full Text Available Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1 models the expected range of variation through large scale reduction experiments, 2 develops an algorithm to categorize archaeological flakes based on how they are produced, and 3 statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite and inefficiency in stone tool production for another raw material (basalt suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated

  17. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania.

    Science.gov (United States)

    Reti, Jay S

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  18. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy......Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...

  19. Diagnosing and managing microbial keratitis

    Directory of Open Access Journals (Sweden)

    Madan P Upadhyay

    2015-06-01

    Full Text Available Infections of the cornea can lead to corneal opacity and blindness if not identified quickly and managed appropriately. The terms ‘microbial keratitis’, ‘infective keratitis’ and ‘suppurative keratitis’ are all used to describe suppurative infections of the cornea. In this issue we use the term microbial keratitis. These infections are characterised by the presence of white or yellowish infiltrates in the corneal stroma, with or without an overlaying corneal epithelial defect, and associated with signs of inflammation.

  20. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  1. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping

    2004-01-01

    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  2. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAOGuo-ping

    2004-01-01

    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  3. Relationships between sediment microbial communities and pollutants in two California salt marshes.

    Science.gov (United States)

    Cao, Y; Cherr, G N; Córdova-Kreylos, A L; Fan, T W-M; Green, P G; Higashi, R M; Lamontagne, M G; Scow, K M; Vines, C A; Yuan, J; Holden, P A

    2006-11-01

    Salt marshes are important ecosystems whose plant and microbial communities can alter terrestrially derived pollutants prior to coastal water discharge. However, knowledge regarding relationships between anthropogenic pollutant levels and salt marsh microbial communities is limited, and salt marshes on the West Coast of the United States are rarely examined. In this study, we investigated the relationships between microbial community composition and 24 pollutants (20 metals and 4 organics) in two California salt marshes. Multivariate ordination techniques were used to assess how bacterial community composition, as determined by terminal restriction fragment length polymorphism and phospholipid fatty acid analyses, was related to pollution. Sea urchin embryo toxicity measurements and plant tissue metabolite profiles were considered two other biometrics of pollution. Spatial effects were strongly manifested across marshes and across channel elevations within marshes. Utilizing partial canonical correspondence analysis, an ordination technique new to microbial ecology, we found that several metals were strongly associated with microbial community composition after accounting for spatial effects. The major patterns in plant metabolite profiles were consistent with patterns across microbial community profiles, but sea urchin embryo assays, which are commonly used to evaluate ecological toxicity, had no identifiable relationships with pollution. Whereas salt marshes are generally dynamic and complex habitats, microbial communities in these marshes appear to be relatively sensitive indicators of toxic pollutants.

  4. Alterations in soil microbial community composition and biomass following agricultural land use change

    Science.gov (United States)

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

    2016-11-01

    The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

  5. Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

    Science.gov (United States)

    Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

    2016-09-01

    A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

  6. The importance of anabolism in microbial control over soil carbon storage

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

    2017-07-25

    Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolism and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.

  7. Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells.

    Science.gov (United States)

    Miyahara, Morio; Sakamoto, Akihiro; Kouzuma, Atsushi; Watanabe, Kazuya

    2016-12-01

    Laboratory microbial fuel cells were supplied with artificial wastewater and used to examine how supplementation with poly iron sulfate, an inorganic polymer flocculant widely used in wastewater-treatment plants, affects electricity generation and anode microbiomes. It is shown that poly iron sulfate substantially increases electric outputs from microbial fuel cells. Microbiological analyses show that iron and sulfate separately affect anode microbiomes, and the increase in power output is associated with the increases in bacteria affiliated with the families Geobacteraceae and/or Desulfuromonadaceae. We suggest that poly iron sulfate is an effective additive for increasing the electric output from microbial fuel cells. Other utilities of poly iron sulfate in microbial fuel cells are also discussed.

  8. Quantifier hierarchies over the first-Order definable tree languages

    Institute of Scientific and Technical Information of China (English)

    沈云付

    1996-01-01

    Using Boolean operations and concatenation product w.r.t special trees,quantifier hierarchies are given by way of alternate existential and universal quantifiers for the first-order definable tree languages.

  9. Spatial distribution of intact polar lipids in North Sea surface waters: Relationship with environmental conditions and microbial community composition

    NARCIS (Netherlands)

    Brandsma, J.; Hopmans, E.C.; Brussaard, C.P.D.; Witte, H.J.; Schouten, S.; Sinninghe Damsté, J.S.

    2012-01-01

    We characterized and quantified the intact polar lipid (IPL) composition of the surface waters of the North Sea and investigated its relationships with environmental conditions, microbial abundances, and community composition. The total IPL pool comprised at least 600 different IPL species in seven

  10. Microbial hydrogen production from sewage sludge bioaugmented with a constructed microbial consortium

    Energy Technology Data Exchange (ETDEWEB)

    Kotay, Shireen Meher; Das, Debabrata [Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

    2010-10-15

    A constructed microbial consortium was formulated from three facultative H{sub 2}-producing anaerobic bacteria, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1. This consortium was tested as the seed culture for H{sub 2} production. In the initial studies with defined medium (MYG), E. cloacae produced more H{sub 2} than the other two strains and it also was found to be the dominant member when consortium was used. On the other hand, B. coagulans as a pure culture gave better H{sub 2} yield (37.16 ml H{sub 2}/g COD{sub consumed}) than the other two strains using sewage sludge as substrate. The pretreatment of sludge included sterilization (15% v/v), dilution and supplementation with 0.5% w/v glucose, which was found to be essential to screen out the H{sub 2} consuming bacteria and ameliorate the H{sub 2} production. Considering (1:1:1) defined consortium as inoculum, COD reduction was higher and yield of H{sub 2} was recorded to be 41.23 ml H{sub 2}/g COD{sub reduced}. Microbial profiling of the spent sludge showed that B. coagulans was the dominant member in the constructed consortium contributing towards H{sub 2} production. Increase in H{sub 2} yield indicated that in consortium, the substrate utilization was significantly higher. The H{sub 2} yield from pretreated sludge (35.54 ml H{sub 2}/g sludge) was comparatively higher than that reported in literature (8.1-16.9 ml H{sub 2}/g sludge). Employing formulated microbial consortium for biohydrogen production is a successful attempt to augment the H{sub 2} yield from sewage sludge. (author)

  11. Microbial quality of a marine tidal pool

    CSIR Research Space (South Africa)

    Genthe, Bettina

    1995-01-01

    Full Text Available In this study the source of microbial pollution to a tidal pool was investigated. Both adjacent seawater which could contribute to possible faecal pollution and potential direct bather pollution were studied. The microbial quality of the marine...

  12. Microbially induced and microbially catalysed precipitation: two different carbonate factories

    Science.gov (United States)

    Meister, Patrick

    2016-04-01

    The landmark paper by Schlager (2003) has revealed three types of benthic carbonate production referred to as "carbonate factories", operative at different locations at different times in Earth history. The tropical or T-factory comprises the classical platforms and fringing reefs and is dominated by carbonate precipitation by autotrophic calcifying metazoans ("biotically controlled" precipitation). The cool or C-factory is also biotically controlled but via heterotrophic, calcifying metazoans in cold and deep waters at the continental margins. A further type is the mud-mound or M-factory, where carbonate precipitation is supported by microorganisms but not controlled by a specific enzymatic pathway ("biotically induced" precipitation). How exactly the microbes influence precipitation is still poorly understood. Based on recent experimental and field studies, the microbial influence on modern mud mound and microbialite growth includes two fundamentally different processes: (1) Metabolic activity of microbes may increase the saturation state with respect to a particular mineral phase, thereby indirectly driving the precipitation of the mineral phase: microbially induced precipitation. (2) In a situation, where a solution is already supersaturated but precipitation of the mineral is inhibited by a kinetic barrier, microbes may act as a catalyser, i.e. they lower the kinetic barrier: microbially catalysed precipitation. Such a catalytic effect can occur e.g. via secreted polymeric substances or specific chemical groups on the cell surface, at which the minerals nucleate or which facilitate mechanistically the bonding of new ions to the mineral surface. Based on these latest developments in microbialite formation, I propose to extend the scheme of benthic carbonate factories of Schlager et al. (2003) by introducing an additional branch distinguishing microbially induced from microbially catalysed precipitation. Although both mechanisms could be operative in a M

  13. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

  14. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into th

  15. Microbial keratitis: a community eye health approach

    Directory of Open Access Journals (Sweden)

    Kieran S O’Brien

    2015-06-01

    Full Text Available Microbial keratitis is an infection of the cornea. Corneal opacities, which are frequently due to microbial keratitis, remain among the top five causes of blindness worldwide. Microbial keratitis disproportionately affects low- and middle-income countries. Studies indicate that the incidence of microbial keratitis may be up to 10 times higher in countries like Nepal and India compared to the United States.

  16. Quantifying capital goods for biological treatment of organic waste

    DEFF Research Database (Denmark)

    Brogaard, Line Kai-Sørensen; Petersen, Per H.; Nielsen, Peter D.

    2015-01-01

    Materials and energy used for construction of anaerobic digestion (AD) and windrow composting plants were quantified in detail. The two technologies were quantified in collaboration with consultants and producers of the parts used to construct the plants. The composting plants were quantified bas...

  17. Using tangles to quantify topological mixing of fluids

    Science.gov (United States)

    Chen, Qianting; Sattari, Sulimon; Mitchell, Kevin

    2014-11-01

    Topological mixing is important in understanding complex fluid problems, ranging from oceanic transport to the design of micro-mixers. Typically, topological entropy (TE), the exponential growth rate of material lines, is used to quantify topological mixing. Computing TE from the direct stretching rate is computationally expensive and sheds little light on the source of the mixing. Previous work has focused on braiding by ``ghost rods'' (See, e.g. works by Boyland, Aref, Stremler, Tiffeault, and Finn). Following Grover et al. [Chaos 22, 043135 (2012)], we study topological mixing in a two-dimensional lid-driven cavity flow. For a certain parameter range, the TE is dominated by a period-3 braid. However, this braid alone cannot explain all the TE within this range, nor the TE outside the range of existence of the braid. By contrast, we explain TE through the topology of intersecting stable and unstable manifolds, i.e. heteroclinic tangles, using homotopic lobe dynamics (HLD). In the HLD approach, stirring originates from ``ghost rods'' placed on heteroclinic orbits. We demonstrate that these heteroclinic orbits generate excess TE not accounted for in Grover et al. Furthermore, in the limit of utilizing arbitrarily long manifolds, the HLD technique converges to the true TE. Supported by the US National Science Foundation under Grant PHY-0748828.

  18. Quantifying phase-amplitude coupling in neuronal network oscillations.

    Science.gov (United States)

    Onslow, Angela C E; Bogacz, Rafal; Jones, Matthew W

    2011-03-01

    Neuroscience time series data from a range of techniques and species reveal complex, non-linear interactions between different frequencies of neuronal network oscillations within and across brain regions. Here, we briefly review the evidence that these nested, cross-frequency interactions act in concert with linearly covariant (within-frequency) activity to dynamically coordinate functionally related neuronal ensembles during behaviour. Such studies depend upon reliable quantification of cross-frequency coordination, and we compare the properties of three techniques used to measure phase-amplitude coupling (PAC)--Envelope-to-Signal Correlation (ESC), the Modulation Index (MI) and Cross-Frequency Coherence (CFC)--by standardizing their filtering algorithms and systematically assessing their robustness to noise and signal amplitude using artificial signals. Importantly, we also introduce a freely-downloadable method for estimating statistical significance of PAC, a step overlooked in the majority of published studies. We find that varying data length and noise levels leads to the three measures differentially detecting false positives or correctly identifying frequency bands of interaction; these conditions should therefore be taken into careful consideration when selecting PAC analyses. Finally, we demonstrate the utility of the three measures in quantifying PAC in local field potential data simultaneously recorded from rat hippocampus and prefrontal cortex, revealing a novel finding of prefrontal cortical theta phase modulating hippocampal gamma power. Future adaptations that allow detection of time-variant PAC should prove essential in deciphering the roles of cross-frequency coupling in mediating or reflecting nervous system function.

  19. Microbial electricity generation in rice paddy fields: recent advances and perspectives in rhizosphere microbial fuel cells.

    Science.gov (United States)

    Kouzuma, Atsushi; Kaku, Nobuo; Watanabe, Kazuya

    2014-12-01

    Microbial fuel cells (MFCs) are devices that use living microbes for the conversion of organic matter into electricity. MFC systems can be applied to the generation of electricity at water/sediment interfaces in the environment, such as bay areas, wetlands, and rice paddy fields. Using these systems, electricity generation in paddy fields as high as ∼80 mW m(-2) (based on the projected anode area) has been demonstrated, and evidence suggests that rhizosphere microbes preferentially utilize organic exudates from rice roots for generating electricity. Phylogenetic and metagenomic analyses have been conducted to identify the microbial species and catabolic pathways that are involved in the conversion of root exudates into electricity, suggesting the importance of syntrophic interactions. In parallel, pot cultures of rice and other aquatic plants have been used for rhizosphere MFC experiments under controlled laboratory conditions. The findings from these studies have demonstrated the potential of electricity generation for mitigating methane emission from the rhizosphere. Notably, however, the presence of large amounts of organics in the rhizosphere drastically reduces the effect of electricity generation on methane production. Further studies are necessary to evaluate the potential of these systems for mitigating methane emission from rice paddy fields. We suggest that paddy-field MFCs represent a promising approach for harvesting latent energy of the natural world.

  20. Study on information utility

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Information has two aspects. One aspect is the objective one; another aspect is the subjective one. Shannon has discussed the objective aspect of information in information theory. But the subjective aspect of information has not been fully discussed. Someone use "Bayesian approaches" to evaluate the value of information. But in some cases it does not meet the information user's need. This paper is focus on the subjective aspect of objectively measurable information and gives formal definitions for information, information utility, and marginal information utility, normalized calculation of information utility. The information discussed in the paper has interdisciplinary nature. This work can be the foundation of many application areas.